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class="vector-toc-numb">4</span> <span>Conventional tests</span> </div> </a> <button aria-controls="toc-Conventional_tests-sublist" class="cdx-button cdx-button--weight-quiet cdx-button--icon-only vector-toc-toggle"> <span class="vector-icon mw-ui-icon-wikimedia-expand"></span> <span>Toggle Conventional tests subsection</span> </button> <ul id="toc-Conventional_tests-sublist" class="vector-toc-list"> <li id="toc-Antibody_detection" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Antibody_detection"> <div class="vector-toc-text"> <span class="vector-toc-numb">4.1</span> <span>Antibody detection</span> </div> </a> <ul id="toc-Antibody_detection-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Histological_detection_and_culture" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Histological_detection_and_culture"> <div class="vector-toc-text"> <span class="vector-toc-numb">4.2</span> <span>Histological detection and culture</span> </div> </a> <ul id="toc-Histological_detection_and_culture-sublist" class="vector-toc-list"> </ul> </li> </ul> </li> <li id="toc-Microscopy" class="vector-toc-list-item vector-toc-level-1"> <a class="vector-toc-link" href="#Microscopy"> <div class="vector-toc-text"> <span class="vector-toc-numb">5</span> <span>Microscopy</span> </div> </a> <button aria-controls="toc-Microscopy-sublist" class="cdx-button cdx-button--weight-quiet cdx-button--icon-only vector-toc-toggle"> <span class="vector-icon mw-ui-icon-wikimedia-expand"></span> <span>Toggle Microscopy subsection</span> </button> <ul id="toc-Microscopy-sublist" class="vector-toc-list"> <li id="toc-Staining" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Staining"> <div class="vector-toc-text"> <span class="vector-toc-numb">5.1</span> <span>Staining</span> </div> </a> <ul id="toc-Staining-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Wet_Prep" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Wet_Prep"> <div class="vector-toc-text"> <span class="vector-toc-numb">5.2</span> <span>Wet Prep</span> </div> </a> <ul id="toc-Wet_Prep-sublist" class="vector-toc-list"> </ul> </li> </ul> </li> <li id="toc-Rapid_antigen_tests" class="vector-toc-list-item vector-toc-level-1"> <a class="vector-toc-link" href="#Rapid_antigen_tests"> <div class="vector-toc-text"> <span class="vector-toc-numb">6</span> <span>Rapid antigen tests</span> </div> </a> <button aria-controls="toc-Rapid_antigen_tests-sublist" class="cdx-button cdx-button--weight-quiet cdx-button--icon-only vector-toc-toggle"> <span class="vector-icon mw-ui-icon-wikimedia-expand"></span> <span>Toggle Rapid antigen tests subsection</span> </button> <ul id="toc-Rapid_antigen_tests-sublist" class="vector-toc-list"> <li id="toc-Immunofluorescence" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Immunofluorescence"> <div class="vector-toc-text"> <span class="vector-toc-numb">6.1</span> <span>Immunofluorescence</span> </div> </a> <ul id="toc-Immunofluorescence-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Mass_spectrometry" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Mass_spectrometry"> <div class="vector-toc-text"> <span class="vector-toc-numb">6.2</span> <span>Mass spectrometry</span> </div> </a> <ul id="toc-Mass_spectrometry-sublist" class="vector-toc-list"> </ul> </li> </ul> </li> <li id="toc-Biochemical_Profile-based_Microbial_Identification_Systems" class="vector-toc-list-item vector-toc-level-1"> <a class="vector-toc-link" href="#Biochemical_Profile-based_Microbial_Identification_Systems"> <div class="vector-toc-text"> <span class="vector-toc-numb">7</span> <span>Biochemical Profile-based Microbial Identification Systems</span> </div> </a> <button aria-controls="toc-Biochemical_Profile-based_Microbial_Identification_Systems-sublist" class="cdx-button cdx-button--weight-quiet cdx-button--icon-only vector-toc-toggle"> <span class="vector-icon mw-ui-icon-wikimedia-expand"></span> <span>Toggle Biochemical Profile-based Microbial Identification Systems subsection</span> </button> <ul id="toc-Biochemical_Profile-based_Microbial_Identification_Systems-sublist" class="vector-toc-list"> <li id="toc-6.5%_salt_broth" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#6.5%_salt_broth"> <div class="vector-toc-text"> <span class="vector-toc-numb">7.1</span> <span>6.5% salt broth</span> </div> </a> <ul id="toc-6.5%_salt_broth-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Acetate_utilization" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Acetate_utilization"> <div class="vector-toc-text"> <span class="vector-toc-numb">7.2</span> <span>Acetate utilization</span> </div> </a> <ul id="toc-Acetate_utilization-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-ALA" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#ALA"> <div class="vector-toc-text"> <span class="vector-toc-numb">7.3</span> <span>ALA</span> </div> </a> <ul id="toc-ALA-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Aminopeptidase" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Aminopeptidase"> <div class="vector-toc-text"> <span class="vector-toc-numb">7.4</span> <span>Aminopeptidase</span> </div> </a> <ul id="toc-Aminopeptidase-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Analytical_profile_index" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Analytical_profile_index"> <div class="vector-toc-text"> <span class="vector-toc-numb">7.5</span> <span>Analytical profile index</span> </div> </a> <ul id="toc-Analytical_profile_index-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Antibiotic_disks" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Antibiotic_disks"> <div class="vector-toc-text"> <span class="vector-toc-numb">7.6</span> <span>Antibiotic disks</span> </div> </a> <ul id="toc-Antibiotic_disks-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Bile_esculin_agar" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Bile_esculin_agar"> <div class="vector-toc-text"> <span class="vector-toc-numb">7.7</span> <span>Bile esculin agar</span> </div> </a> <ul id="toc-Bile_esculin_agar-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Bile_solubility" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Bile_solubility"> <div class="vector-toc-text"> <span class="vector-toc-numb">7.8</span> <span>Bile solubility</span> </div> </a> <ul id="toc-Bile_solubility-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-CAMP" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#CAMP"> <div class="vector-toc-text"> <span class="vector-toc-numb">7.9</span> <span>CAMP</span> </div> </a> <ul id="toc-CAMP-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Catalase" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Catalase"> <div class="vector-toc-text"> <span class="vector-toc-numb">7.10</span> <span>Catalase</span> </div> </a> <ul id="toc-Catalase-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Cetrimide_agar" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Cetrimide_agar"> <div class="vector-toc-text"> <span class="vector-toc-numb">7.11</span> <span>Cetrimide agar</span> </div> </a> <ul id="toc-Cetrimide_agar-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-CLO_tests" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#CLO_tests"> <div class="vector-toc-text"> <span class="vector-toc-numb">7.12</span> <span>CLO tests</span> </div> </a> <ul id="toc-CLO_tests-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Coagulase" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Coagulase"> <div class="vector-toc-text"> <span class="vector-toc-numb">7.13</span> <span>Coagulase</span> </div> </a> <ul id="toc-Coagulase-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-DNA_hydrolysis" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#DNA_hydrolysis"> <div class="vector-toc-text"> <span class="vector-toc-numb">7.14</span> <span>DNA hydrolysis</span> </div> </a> <ul id="toc-DNA_hydrolysis-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Gelatin" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Gelatin"> <div class="vector-toc-text"> <span class="vector-toc-numb">7.15</span> <span>Gelatin</span> </div> </a> <ul id="toc-Gelatin-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Gonocheck_II" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Gonocheck_II"> <div class="vector-toc-text"> <span class="vector-toc-numb">7.16</span> <span>Gonocheck II</span> </div> </a> <ul id="toc-Gonocheck_II-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Hippurate" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Hippurate"> <div class="vector-toc-text"> <span class="vector-toc-numb">7.17</span> <span>Hippurate</span> </div> </a> <ul id="toc-Hippurate-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Indole_butyrate_disk" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Indole_butyrate_disk"> <div class="vector-toc-text"> <span class="vector-toc-numb">7.18</span> <span>Indole butyrate disk</span> </div> </a> <ul id="toc-Indole_butyrate_disk-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Lysine_iron_agar_slant" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Lysine_iron_agar_slant"> <div class="vector-toc-text"> <span class="vector-toc-numb">7.19</span> <span>Lysine iron agar slant</span> </div> </a> <ul id="toc-Lysine_iron_agar_slant-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Lysostaphin" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Lysostaphin"> <div class="vector-toc-text"> <span class="vector-toc-numb">7.20</span> <span>Lysostaphin</span> </div> </a> <ul id="toc-Lysostaphin-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Methyl_red_test" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Methyl_red_test"> <div class="vector-toc-text"> <span class="vector-toc-numb">7.21</span> <span>Methyl red test</span> </div> </a> <ul id="toc-Methyl_red_test-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Microdase" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Microdase"> <div class="vector-toc-text"> <span class="vector-toc-numb">7.22</span> <span>Microdase</span> </div> </a> <ul id="toc-Microdase-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Nitrite_test" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Nitrite_test"> <div class="vector-toc-text"> <span class="vector-toc-numb">7.23</span> <span>Nitrite test</span> </div> </a> <ul id="toc-Nitrite_test-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Oxidase" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Oxidase"> <div class="vector-toc-text"> <span class="vector-toc-numb">7.24</span> <span>Oxidase</span> </div> </a> <ul id="toc-Oxidase-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Phenylalanine_deaminase" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Phenylalanine_deaminase"> <div class="vector-toc-text"> <span class="vector-toc-numb">7.25</span> <span>Phenylalanine deaminase</span> </div> </a> <ul id="toc-Phenylalanine_deaminase-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-PYR" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#PYR"> <div class="vector-toc-text"> <span class="vector-toc-numb">7.26</span> <span>PYR</span> </div> </a> <ul id="toc-PYR-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Reverse_CAMP" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Reverse_CAMP"> <div class="vector-toc-text"> <span class="vector-toc-numb">7.27</span> <span>Reverse CAMP</span> </div> </a> <ul id="toc-Reverse_CAMP-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Simmons'_citrate_agar" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Simmons'_citrate_agar"> <div class="vector-toc-text"> <span class="vector-toc-numb">7.28</span> <span>Simmons' citrate agar</span> </div> </a> <ul id="toc-Simmons'_citrate_agar-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Spot_indole" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Spot_indole"> <div class="vector-toc-text"> <span class="vector-toc-numb">7.29</span> <span>Spot indole</span> </div> </a> <ul id="toc-Spot_indole-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Sulphide_indole_motility_medium" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Sulphide_indole_motility_medium"> <div class="vector-toc-text"> <span class="vector-toc-numb">7.30</span> <span>Sulphide indole motility medium</span> </div> </a> <ul id="toc-Sulphide_indole_motility_medium-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-TSI_slant" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#TSI_slant"> <div class="vector-toc-text"> <span class="vector-toc-numb">7.31</span> <span>TSI slant</span> </div> </a> <ul id="toc-TSI_slant-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Urea_agar_slant" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Urea_agar_slant"> <div class="vector-toc-text"> <span class="vector-toc-numb">7.32</span> <span>Urea agar slant</span> </div> </a> <ul id="toc-Urea_agar_slant-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Voges–Proskauer_test" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Voges–Proskauer_test"> <div class="vector-toc-text"> <span class="vector-toc-numb">7.33</span> <span>Voges–Proskauer test</span> </div> </a> <ul id="toc-Voges–Proskauer_test-sublist" class="vector-toc-list"> </ul> </li> </ul> </li> <li id="toc-Cellular_fatty_acid_based_identification" class="vector-toc-list-item vector-toc-level-1"> <a class="vector-toc-link" href="#Cellular_fatty_acid_based_identification"> <div class="vector-toc-text"> <span class="vector-toc-numb">8</span> <span>Cellular fatty acid based identification</span> </div> </a> <button aria-controls="toc-Cellular_fatty_acid_based_identification-sublist" class="cdx-button cdx-button--weight-quiet cdx-button--icon-only vector-toc-toggle"> <span class="vector-icon mw-ui-icon-wikimedia-expand"></span> <span>Toggle Cellular fatty acid based identification subsection</span> </button> <ul id="toc-Cellular_fatty_acid_based_identification-sublist" class="vector-toc-list"> <li id="toc-Mycolic_acid_analysis" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Mycolic_acid_analysis"> <div class="vector-toc-text"> <span class="vector-toc-numb">8.1</span> <span>Mycolic acid analysis</span> </div> </a> <ul id="toc-Mycolic_acid_analysis-sublist" class="vector-toc-list"> </ul> </li> </ul> </li> <li id="toc-Nucleic_acid_extraction_techniques" class="vector-toc-list-item vector-toc-level-1"> <a class="vector-toc-link" href="#Nucleic_acid_extraction_techniques"> <div class="vector-toc-text"> <span class="vector-toc-numb">9</span> <span>Nucleic acid extraction techniques</span> </div> </a> <button aria-controls="toc-Nucleic_acid_extraction_techniques-sublist" class="cdx-button cdx-button--weight-quiet cdx-button--icon-only vector-toc-toggle"> <span class="vector-icon mw-ui-icon-wikimedia-expand"></span> <span>Toggle Nucleic acid extraction techniques subsection</span> </button> <ul id="toc-Nucleic_acid_extraction_techniques-sublist" class="vector-toc-list"> <li id="toc-Cesium_chloride_/_Ethidium_bromide_density_gradient_centrifugation" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Cesium_chloride_/_Ethidium_bromide_density_gradient_centrifugation"> <div class="vector-toc-text"> <span class="vector-toc-numb">9.1</span> <span>Cesium chloride / Ethidium bromide density gradient centrifugation</span> </div> </a> <ul id="toc-Cesium_chloride_/_Ethidium_bromide_density_gradient_centrifugation-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Magnetic_bead_method" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Magnetic_bead_method"> <div class="vector-toc-text"> <span class="vector-toc-numb">9.2</span> <span>Magnetic bead method</span> </div> </a> <ul id="toc-Magnetic_bead_method-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Phenol–chloroform_extraction" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Phenol–chloroform_extraction"> <div class="vector-toc-text"> <span class="vector-toc-numb">9.3</span> <span>Phenol–chloroform extraction</span> </div> </a> <ul id="toc-Phenol–chloroform_extraction-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Solid_phase_extraction" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Solid_phase_extraction"> <div class="vector-toc-text"> <span class="vector-toc-numb">9.4</span> <span>Solid phase extraction</span> </div> </a> <ul id="toc-Solid_phase_extraction-sublist" class="vector-toc-list"> </ul> </li> </ul> </li> <li id="toc-Methods_with_electrophoretic_outputs" class="vector-toc-list-item vector-toc-level-1"> <a class="vector-toc-link" href="#Methods_with_electrophoretic_outputs"> <div class="vector-toc-text"> <span class="vector-toc-numb">10</span> <span>Methods with electrophoretic outputs</span> </div> </a> <ul id="toc-Methods_with_electrophoretic_outputs-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Restriction_enzyme_based" class="vector-toc-list-item vector-toc-level-1"> <a class="vector-toc-link" href="#Restriction_enzyme_based"> <div class="vector-toc-text"> <span class="vector-toc-numb">11</span> <span>Restriction enzyme based</span> </div> </a> <button aria-controls="toc-Restriction_enzyme_based-sublist" class="cdx-button cdx-button--weight-quiet cdx-button--icon-only vector-toc-toggle"> <span class="vector-icon mw-ui-icon-wikimedia-expand"></span> <span>Toggle Restriction enzyme based subsection</span> </button> <ul id="toc-Restriction_enzyme_based-sublist" class="vector-toc-list"> <li id="toc-Optical_mapping" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Optical_mapping"> <div class="vector-toc-text"> <span class="vector-toc-numb">11.1</span> <span>Optical mapping</span> </div> </a> <ul id="toc-Optical_mapping-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Pulsed-field_gel_electrophoresis" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Pulsed-field_gel_electrophoresis"> <div class="vector-toc-text"> <span class="vector-toc-numb">11.2</span> <span>Pulsed-field gel electrophoresis</span> </div> </a> <ul id="toc-Pulsed-field_gel_electrophoresis-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Restriction_enzymes_then_gel_electrophoresis" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Restriction_enzymes_then_gel_electrophoresis"> <div class="vector-toc-text"> <span class="vector-toc-numb">11.3</span> <span>Restriction enzymes then gel electrophoresis</span> </div> </a> <ul id="toc-Restriction_enzymes_then_gel_electrophoresis-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Ribotyping" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Ribotyping"> <div class="vector-toc-text"> <span class="vector-toc-numb">11.4</span> <span>Ribotyping</span> </div> </a> <ul id="toc-Ribotyping-sublist" class="vector-toc-list"> </ul> </li> </ul> </li> <li id="toc-PCR-based" class="vector-toc-list-item vector-toc-level-1"> <a class="vector-toc-link" href="#PCR-based"> <div class="vector-toc-text"> <span class="vector-toc-numb">12</span> <span>PCR-based</span> </div> </a> <button aria-controls="toc-PCR-based-sublist" class="cdx-button cdx-button--weight-quiet cdx-button--icon-only vector-toc-toggle"> <span class="vector-icon mw-ui-icon-wikimedia-expand"></span> <span>Toggle PCR-based subsection</span> </button> <ul id="toc-PCR-based-sublist" class="vector-toc-list"> <li id="toc-Multiple_loci_VNTR_analysis" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Multiple_loci_VNTR_analysis"> <div class="vector-toc-text"> <span class="vector-toc-numb">12.1</span> <span>Multiple loci VNTR analysis</span> </div> </a> <ul id="toc-Multiple_loci_VNTR_analysis-sublist" class="vector-toc-list"> </ul> </li> </ul> </li> <li id="toc-DNA_sequence-based_methods" class="vector-toc-list-item vector-toc-level-1"> <a class="vector-toc-link" href="#DNA_sequence-based_methods"> <div class="vector-toc-text"> <span class="vector-toc-numb">13</span> <span>DNA sequence-based methods</span> </div> </a> <button aria-controls="toc-DNA_sequence-based_methods-sublist" class="cdx-button cdx-button--weight-quiet cdx-button--icon-only vector-toc-toggle"> <span class="vector-icon mw-ui-icon-wikimedia-expand"></span> <span>Toggle DNA sequence-based methods subsection</span> </button> <ul 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class="vector-toc-numb">13.3</span> <span>Genotypic identifications</span> </div> </a> <ul id="toc-Genotypic_identifications-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Whole_genome_sequencing_(WGS)" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Whole_genome_sequencing_(WGS)"> <div class="vector-toc-text"> <span class="vector-toc-numb">13.4</span> <span>Whole genome sequencing (WGS)</span> </div> </a> <ul id="toc-Whole_genome_sequencing_(WGS)-sublist" class="vector-toc-list"> </ul> </li> </ul> </li> <li id="toc-References" class="vector-toc-list-item vector-toc-level-1"> <a class="vector-toc-link" href="#References"> <div class="vector-toc-text"> <span class="vector-toc-numb">14</span> <span>References</span> </div> </a> <ul id="toc-References-sublist" class="vector-toc-list"> </ul> </li> </ul> </div> </div> </nav> </div> </div> <div class="mw-content-container"> <main id="content" class="mw-body"> <header class="mw-body-header 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class="mw-body-content"><div class="mw-content-ltr mw-parser-output" lang="en" dir="ltr"><p><b>Diagnostic microbiology</b> is the study of microbial identification. Since the discovery of the <a href="/wiki/Germ_theory_of_disease" title="Germ theory of disease">germ theory of disease</a>, scientists have been finding ways to harvest specific organisms. Using methods such as <a href="/wiki/Differential_media" class="mw-redirect" title="Differential media">differential media</a> or <a href="/wiki/Whole_genome_sequencing" title="Whole genome sequencing">genome sequencing</a>, physicians and scientists can observe novel functions in organisms for more effective and accurate diagnosis of organisms. Methods used in diagnostic microbiology are often used to take advantage of a particular difference in organisms and attain information about what species it can be identified as, which is often through a reference of previous studies. New studies provide information that others can reference so that scientists can attain a basic understanding of the organism they are examining. </p> <style data-mw-deduplicate="TemplateStyles:r1044870489">@media all and (max-width:720px){body.skin-minerva .mw-parser-output .tocright{display:none}.mw-parser-output .tocright{width:100%!important}}@media all and (min-width:720px){.mw-parser-output .tocright{float:right;clear:right;width:auto;margin:0 0 0.5em 1em}.mw-parser-output .tocright-clear-left{clear:left}.mw-parser-output .tocright-clear-both{clear:both}.mw-parser-output .tocright-clear-none{clear:none}}</style><div class="tocright"><meta property="mw:PageProp/toc" /></div> <div class="mw-heading mw-heading2"><h2 id="Aerobic_vs_anaerobic">Aerobic vs anaerobic</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=1" title="Edit section: Aerobic vs anaerobic"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p><a href="/wiki/Anaerobic_organism" title="Anaerobic organism">Anaerobic organisms</a> require an oxygen-free environment. When culturing anaerobic microbes, broths are often flushed with nitrogen gas to extinguish oxygen present, and growth can also occur on media in a chamber without oxygen present.<sup id="cite_ref-1" class="reference"><a href="#cite_note-1"><span class="cite-bracket">[</span>1<span class="cite-bracket">]</span></a></sup> Sodium resazurin can be added to indicate <a href="/wiki/Redox" title="Redox">redox</a> potential.<sup id="cite_ref-2" class="reference"><a href="#cite_note-2"><span class="cite-bracket">[</span>2<span class="cite-bracket">]</span></a></sup> Cultures are to be incubated in an oxygen-free environment for 48 hours at 35 °C before growth is examined.<sup id="cite_ref-3" class="reference"><a href="#cite_note-3"><span class="cite-bracket">[</span>3<span class="cite-bracket">]</span></a></sup> </p> <figure class="mw-default-size" typeof="mw:File/Thumb"><a href="/wiki/File:Gas-Pak_jar.jpg" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/f/f1/Gas-Pak_jar.jpg/220px-Gas-Pak_jar.jpg" decoding="async" width="220" height="330" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/f/f1/Gas-Pak_jar.jpg 1.5x" data-file-width="320" data-file-height="480" /></a><figcaption>Gas-Pak jar</figcaption></figure> <p>Anaerobic bacteria collection can come from a variety of sources in patient samples, including blood, bile, bone marrow, <a href="/wiki/Cerebrospinal_fluid" title="Cerebrospinal fluid">cerebrospinal fluid</a>, direct lung aspirate, <a href="/wiki/Tissue_biopsies" class="mw-redirect" title="Tissue biopsies">tissue biopsies</a> from a normally sterile site, fluid from a normally sterile site (like a joint), dental, abscess, abdominal or pelvic abscess, knife, gunshot, or surgical wound, or severe burn.<sup id="cite_ref-4" class="reference"><a href="#cite_note-4"><span class="cite-bracket">[</span>4<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading2"><h2 id="Incubation_length">Incubation length</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=2" title="Edit section: Incubation length"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>Incubation times vary based upon the microbe that requires culturing. Traditional culturing techniques, for example, require less than 24 hours culture time for <i><a href="/wiki/Escherichia_coli" title="Escherichia coli">Escherichia coli</a></i> but 6–8 weeks for successful culturing of <i><a href="/wiki/Mycobacterium_tuberculosis" title="Mycobacterium tuberculosis">Mycobacterium tuberculosis</a></i> before definitive results are expressed.<sup id="cite_ref-:0_5-0" class="reference"><a href="#cite_note-:0-5"><span class="cite-bracket">[</span>5<span class="cite-bracket">]</span></a></sup> A benefit of non-culture tests is that physicians and microbiologists are not handicapped by waiting periods. </p><p>Incubation follows a growth curve variable for every microorganism. Cultures follow a lag, log, stationary, and finally death phase.<sup id="cite_ref-:1_6-0" class="reference"><a href="#cite_note-:1-6"><span class="cite-bracket">[</span>6<span class="cite-bracket">]</span></a></sup> The <a href="/wiki/Lag_phase" class="mw-redirect" title="Lag phase">lag phase</a> is not well known in microbiology, but it is speculated that this phase consists of the microorganism adjusting to its environment by synthesizing proteins specific for the surrounding habitat.<sup id="cite_ref-:1_6-1" class="reference"><a href="#cite_note-:1-6"><span class="cite-bracket">[</span>6<span class="cite-bracket">]</span></a></sup> The <a href="/wiki/Log_phase" class="mw-redirect" title="Log phase">log phase</a> is the period where a culture experiences logarithmic growth until nutrients become scarce. The stationary phase is when culture concentration is the highest and cells stop reproducing. When nutrients in the environment are depleting, organisms enter the death phase where toxic <a href="/wiki/Metabolite" title="Metabolite">metabolites</a> become abundant and nutrients are depleted to the point where cell death exceeds reproduction.<sup id="cite_ref-:0_5-1" class="reference"><a href="#cite_note-:0-5"><span class="cite-bracket">[</span>5<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading2"><h2 id="Rapid_identification_after_culture">Rapid identification after culture</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=3" title="Edit section: Rapid identification after culture"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <div class="mw-heading mw-heading3"><h3 id="Automated_culturing_systems">Automated culturing systems</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=4" title="Edit section: Automated culturing systems"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p><a href="/w/index.php?title=Automatic_cell_culturing_system&action=edit&redlink=1" class="new" title="Automatic cell culturing system (page does not exist)">Automatic cell culturing systems</a> are becoming popular because of their ability to maintain a sterile growth environment and remove strain on the laboratory staff involving repetitive experimentation.<sup id="cite_ref-7" class="reference"><a href="#cite_note-7"><span class="cite-bracket">[</span>7<span class="cite-bracket">]</span></a></sup> Laboratories can also set incubation times to adjust for the lag period involved in bacterial growth. </p> <div class="mw-heading mw-heading3"><h3 id="Blood_cultures">Blood cultures</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=5" title="Edit section: Blood cultures"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p><a href="/wiki/Blood_culture" title="Blood culture">Blood cultures</a> can allow for diagnostic results after culture. Recent development of DNA based <a href="/wiki/Polymerase_chain_reaction" title="Polymerase chain reaction">PCR</a> diagnostics have provided faster diagnostic results as opposed to overnight biochemical tests. DNA diagnostic test can diagnose with near the same specificity as biochemical test, resulting in the same diagnostic result in 90% of cases.<sup id="cite_ref-8" class="reference"><a href="#cite_note-8"><span class="cite-bracket">[</span>8<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading3"><h3 id="Breath_tests">Breath tests</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=6" title="Edit section: Breath tests"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p><a href="/wiki/Breath_test" title="Breath test">Breath test</a> for microbial diagnosis on patients has been used in a clinical setting for bacteria, including <i><a href="/wiki/Helicobacter_pylori" title="Helicobacter pylori">Helicobacter pylori</a></i>.<sup id="cite_ref-9" class="reference"><a href="#cite_note-9"><span class="cite-bracket">[</span>9<span class="cite-bracket">]</span></a></sup> Diagnostic test using the breath of patients look for metabolites excreted that were manufactured by the infectious microorganism. <i>H. pylori</i> is tested by testing patients for CO<sub>2</sub> concentration, increased because of the organism’s ability to convert urea into other derivatives.<sup id="cite_ref-10" class="reference"><a href="#cite_note-10"><span class="cite-bracket">[</span>10<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading2"><h2 id="Conventional_tests">Conventional tests</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=7" title="Edit section: Conventional tests"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <div class="mw-heading mw-heading3"><h3 id="Antibody_detection">Antibody detection</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=8" title="Edit section: Antibody detection"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>A benefit of antibody detection (<a href="/wiki/ELISA" title="ELISA">ELISA</a>) is that protein identification on a microorganism becomes faster than a <a href="/wiki/Western_blot" title="Western blot">western blot</a>. <a href="/wiki/Antibody" title="Antibody">Antibody</a> detection works by attaching an indicator to an antibody with a known specificity and observing whether the antibody attaches.<sup id="cite_ref-11" class="reference"><a href="#cite_note-11"><span class="cite-bracket">[</span>11<span class="cite-bracket">]</span></a></sup> ELISA can also indicate viral presence and is highly specific, having a detection specificity of 10<sup>−9</sup>-10<sup>−12</sup> moles per litre detection. By knowing the <a href="/wiki/Epitope" title="Epitope">epitope</a> sequence of the antibody, ELISA can also be used for antigen detection in a sample.<sup id="cite_ref-12" class="reference"><a href="#cite_note-12"><span class="cite-bracket">[</span>12<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading3"><h3 id="Histological_detection_and_culture">Histological detection and culture</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=9" title="Edit section: Histological detection and culture"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p><a href="/wiki/Histology" title="Histology">Histological</a> methods used for microbiology are useful because of their ability to quickly identify a disease present in a tissue <a href="/wiki/Biopsy" title="Biopsy">biopsy</a>. </p> <div class="mw-heading mw-heading2"><h2 id="Microscopy">Microscopy</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=10" title="Edit section: Microscopy"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <style data-mw-deduplicate="TemplateStyles:r1236090951">.mw-parser-output .hatnote{font-style:italic}.mw-parser-output div.hatnote{padding-left:1.6em;margin-bottom:0.5em}.mw-parser-output .hatnote i{font-style:normal}.mw-parser-output .hatnote+link+.hatnote{margin-top:-0.5em}@media print{body.ns-0 .mw-parser-output .hatnote{display:none!important}}</style><div role="note" class="hatnote navigation-not-searchable">Main article: <a href="/wiki/Microscopy" title="Microscopy">Microscopy</a></div> <div class="mw-heading mw-heading3"><h3 id="Staining">Staining</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=11" title="Edit section: Staining"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1236090951"><div role="note" class="hatnote navigation-not-searchable">Main article: <a href="/wiki/Staining" title="Staining">Staining</a></div> <p><a href="/wiki/Staining" title="Staining">Staining</a> used in microbiology identification include: <a href="/wiki/Gram_stain" title="Gram stain">Gram stain</a>, <a href="/wiki/Acid-fast_stain" class="mw-redirect" title="Acid-fast stain">Acid-fast stain</a>, <a href="/wiki/Giemsa_stain" title="Giemsa stain">Giemsa stain</a>, <a href="/wiki/India_ink_stain" class="mw-redirect" title="India ink stain">India ink stain</a>, <a href="/wiki/Ziehl%E2%80%93Neelsen_stain" title="Ziehl–Neelsen stain">Ziehl–Neelsen stain</a>. </p> <div class="mw-heading mw-heading3"><h3 id="Wet_Prep">Wet Prep</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=12" title="Edit section: Wet Prep"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1236090951"><div role="note" class="hatnote navigation-not-searchable">Main article: <a href="/wiki/Vaginal_wet_mount" title="Vaginal wet mount">Vaginal wet mount</a></div> <div class="mw-heading mw-heading2"><h2 id="Rapid_antigen_tests">Rapid antigen tests</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=13" title="Edit section: Rapid antigen tests"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <div class="mw-heading mw-heading3"><h3 id="Immunofluorescence">Immunofluorescence</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=14" title="Edit section: Immunofluorescence"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <figure class="mw-default-size" typeof="mw:File/Thumb"><a href="/wiki/File:ANCA_ETHANOL_AND_FORMALIN.JPEG" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/3/3f/ANCA_ETHANOL_AND_FORMALIN.JPEG/220px-ANCA_ETHANOL_AND_FORMALIN.JPEG" decoding="async" width="220" height="165" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/3/3f/ANCA_ETHANOL_AND_FORMALIN.JPEG/330px-ANCA_ETHANOL_AND_FORMALIN.JPEG 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/3/3f/ANCA_ETHANOL_AND_FORMALIN.JPEG/440px-ANCA_ETHANOL_AND_FORMALIN.JPEG 2x" data-file-width="2918" data-file-height="2189" /></a><figcaption>Immunofluorescence</figcaption></figure> <p><a href="/wiki/Immunofluorescence" title="Immunofluorescence">Immunofluorescence</a> is performed by the production of anti-antibodies with a fluorescent molecule attached, making it a <a href="/wiki/Chemiluminescence" title="Chemiluminescence">chemiluminescent</a> molecule, which provides a glow when subject to ultraviolet light.<sup id="cite_ref-13" class="reference"><a href="#cite_note-13"><span class="cite-bracket">[</span>13<span class="cite-bracket">]</span></a></sup> Antibodies are added to a bacterial solution, providing an antigen for the binding of fluorescent anti-antibody adherence. </p> <figure class="mw-default-size mw-halign-right" typeof="mw:File/Thumb"><a href="/wiki/File:Immunofluorescence.jpg" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/4/45/Immunofluorescence.jpg/220px-Immunofluorescence.jpg" decoding="async" width="220" height="116" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/4/45/Immunofluorescence.jpg/330px-Immunofluorescence.jpg 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/4/45/Immunofluorescence.jpg/440px-Immunofluorescence.jpg 2x" data-file-width="5532" data-file-height="2907" /></a><figcaption>Immunofluorescence</figcaption></figure> <div class="mw-heading mw-heading3"><h3 id="Mass_spectrometry">Mass spectrometry</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=15" title="Edit section: Mass spectrometry"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>MALDI-TOF (<a href="/wiki/Matrix-assisted_laser_desorption/ionization" title="Matrix-assisted laser desorption/ionization">Matrix-assisted laser desorption/ionization</a> - time of flight) is a specific type of <a href="/wiki/Mass_spectrometry" title="Mass spectrometry">mass spectrometry</a> that is able to identify microorganisms. A pure culture is isolated and spread directly on a stainless steel or disposable target. The cells are lysed and overlaid with a matrix, which forms protein complexes with the bacterial proteins. The MALDI fires a laser and ionizes the protein complexes, which break off and travel up the vacuum where they are detected based on mass and charge. The resulting protein spectra is compared to a known database of previously catalogued organisms, resulting in rapid diagnosis of microorganisms.<sup id="cite_ref-:2_14-0" class="reference"><a href="#cite_note-:2-14"><span class="cite-bracket">[</span>14<span class="cite-bracket">]</span></a></sup> Recent studies have suggested that these tests can become specific enough to diagnose down to the sub-species level by observing novel <a href="/wiki/Biomarker_(cell)" class="mw-redirect" title="Biomarker (cell)">biomarkers</a>.<sup id="cite_ref-:2_14-1" class="reference"><a href="#cite_note-:2-14"><span class="cite-bracket">[</span>14<span class="cite-bracket">]</span></a></sup> </p><p>The MALDI-TOF identification method requires pure cultures that are less than 72 hours old. This places the organism in log phase with an abundance of ribosomal proteins, which are the most common proteins detected in the spectra. Identifications with this technology can also be impacted if the culture is exposed to cold temperatures, as this would change the typical protein distribution. </p> <div class="mw-heading mw-heading2"><h2 id="Biochemical_Profile-based_Microbial_Identification_Systems">Biochemical Profile-based Microbial Identification Systems</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=16" title="Edit section: Biochemical Profile-based Microbial Identification Systems"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>Phenotypic tests are used to identify microbes based on metabolic and biochemical pathways present in those microbes.<sup id="cite_ref-15" class="reference"><a href="#cite_note-15"><span class="cite-bracket">[</span>15<span class="cite-bracket">]</span></a></sup> There are many automated and semi-automated commercial systems available. These methods can be very informative but are not as accurate as MALDI-TOF or genotypic methods. </p> <div class="mw-heading mw-heading3"><h3 id="6.5%_salt_broth"><span id="6.5.25_salt_broth"></span>6.5% salt broth</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=17" title="Edit section: 6.5% salt broth"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>The 6.5% <a href="/w/index.php?title=Salt_broth_test&action=edit&redlink=1" class="new" title="Salt broth test (page does not exist)">salt broth test</a> is used to analyze the tolerance level of various bacteria under halophilic conditions. This test is used because most organisms cannot survive in high salt concentrations while <i>Staphylococci</i>, <i>Enterococci</i>, and <a href="/wiki/Aerococcus" title="Aerococcus"><i>Aerococci</i></a> are all expected to tolerate 6.5% NaCl concentrations.<sup id="cite_ref-16" class="reference"><a href="#cite_note-16"><span class="cite-bracket">[</span>16<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading3"><h3 id="Acetate_utilization">Acetate utilization</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=18" title="Edit section: Acetate utilization"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>The <a href="/w/index.php?title=Acetate_utilization_test&action=edit&redlink=1" class="new" title="Acetate utilization test (page does not exist)">acetate utilization test</a> is used primarily to differentiate between <i>Escherichia coli </i>from members of the genus <i><a href="/wiki/Shigella" title="Shigella">Shigella</a></i>. Many of the <i>Escherichia coli </i>strains have the capability of the utilization of acetate for a sole carbon and energy source, while <i>Shigella</i> does not. Since acetate utilization results in an increase in pH, an indicator is added that changes color under conditions of acetate utilization. </p> <div class="mw-heading mw-heading3"><h3 id="ALA">ALA</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=19" title="Edit section: ALA"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>An ALA (<a href="/wiki/Delta-aminolevulinic_acid" class="mw-redirect" title="Delta-aminolevulinic acid">delta-aminolevulinic acid</a>) test is used to test for the presence of <a href="/wiki/Porphyrin" title="Porphyrin">porphyrin</a> and <a href="/wiki/Cytochrome" title="Cytochrome">cytochrome</a> compounds. Finding <a href="/wiki/Hemin" title="Hemin">hemin</a> synthesis indicates that the organism is likely <i><a href="/wiki/Haemophilus" title="Haemophilus">Haemophilus</a></i>.<sup id="cite_ref-17" class="reference"><a href="#cite_note-17"><span class="cite-bracket">[</span>17<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading3"><h3 id="Aminopeptidase">Aminopeptidase</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=20" title="Edit section: Aminopeptidase"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>The <a href="/w/index.php?title=Aminopeptidase_test&action=edit&redlink=1" class="new" title="Aminopeptidase test (page does not exist)">aminopeptidase test</a> analyzes bacteria for the production of the enzyme L-alanine-aminopeptidase, an enzyme found in many <a href="/wiki/Gram-negative_bacteria" title="Gram-negative bacteria">gram-negative bacteria</a>. Adding L-Alanine-4-nitroanilide hydrochloride to a bacterial culture works as an indicator, changing to a yellow color in the presence of L-alanine-aminopeptidase.<sup id="cite_ref-18" class="reference"><a href="#cite_note-18"><span class="cite-bracket">[</span>18<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading3"><h3 id="Analytical_profile_index">Analytical profile index</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=21" title="Edit section: Analytical profile index"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <figure class="mw-default-size" typeof="mw:File/Thumb"><a href="/wiki/File:Api20ne.jpg" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/9/99/Api20ne.jpg/220px-Api20ne.jpg" decoding="async" width="220" height="51" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/9/99/Api20ne.jpg/330px-Api20ne.jpg 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/9/99/Api20ne.jpg/440px-Api20ne.jpg 2x" data-file-width="1200" data-file-height="276" /></a><figcaption>API 20NE rapid test system, one day after sample application</figcaption></figure> <p>An <a href="/wiki/Analytical_profile_index" title="Analytical profile index">analytical profile index</a> is a fast identification system based on biochemical incubation tests. Usually, this test is used to quickly diagnose clinically relevant bacteria by allowing physicians to run about 20 tests at one time.<sup id="cite_ref-amrls.cvm.msu.edu_19-0" class="reference"><a href="#cite_note-amrls.cvm.msu.edu-19"><span class="cite-bracket">[</span>19<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading3"><h3 id="Antibiotic_disks">Antibiotic disks</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=22" title="Edit section: Antibiotic disks"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <figure typeof="mw:File/Thumb"><a href="/wiki/File:Antibiotic_suceptible_bacteria.jpg" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/1/1d/Antibiotic_suceptible_bacteria.jpg/320px-Antibiotic_suceptible_bacteria.jpg" decoding="async" width="320" height="192" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/1/1d/Antibiotic_suceptible_bacteria.jpg/480px-Antibiotic_suceptible_bacteria.jpg 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/1/1d/Antibiotic_suceptible_bacteria.jpg/640px-Antibiotic_suceptible_bacteria.jpg 2x" data-file-width="2592" data-file-height="1552" /></a><figcaption>Antibiotic susceptible bacteria</figcaption></figure> <p><a href="/w/index.php?title=Antibiotic_disk&action=edit&redlink=1" class="new" title="Antibiotic disk (page does not exist)">Antibiotic disks</a> are used to test the ability for an antibiotic to inhibit growth of a microorganism. This method, which is commonly used with <a href="/wiki/Mueller%E2%80%93Hinton_agar" title="Mueller–Hinton agar">Mueller–Hinton agar</a>, is used by evenly seeding bacteria over a petri dish and applying an antibiotic treated disk to the top of the agar. By observing the ring formed around the disk formed due to the lack of bacterial growth, the <a href="/wiki/Zone_of_inhibition" class="mw-redirect" title="Zone of inhibition">zone of inhibition</a> can be found, which is used to find the susceptibility of an organism to an antibiotic.<sup id="cite_ref-amrls.cvm.msu.edu_19-1" class="reference"><a href="#cite_note-amrls.cvm.msu.edu-19"><span class="cite-bracket">[</span>19<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading3"><h3 id="Bile_esculin_agar"><a href="/wiki/Bile_esculin_agar" title="Bile esculin agar">Bile esculin agar</a></h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=23" title="Edit section: Bile esculin agar"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>The <a href="/w/index.php?title=Bile_esculin_test&action=edit&redlink=1" class="new" title="Bile esculin test (page does not exist)">bile esculin test</a> is used to differentiate members of the genus <i>Enterococcus</i> from <i>Streptococcus</i>.<sup class="noprint Inline-Template Template-Fact" style="white-space:nowrap;">[<i><a href="/wiki/Wikipedia:Citation_needed" title="Wikipedia:Citation needed"><span title="This claim needs references to reliable sources. (April 2017)">citation needed</span></a></i>]</sup> </p> <div class="mw-heading mw-heading3"><h3 id="Bile_solubility">Bile solubility</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=24" title="Edit section: Bile solubility"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p><a href="/w/index.php?title=Bile_solubility&action=edit&redlink=1" class="new" title="Bile solubility (page does not exist)">Bile solubility</a> is used to test for <i>Streptococcus Pneumoniae</i> due to their unique ability to be lysed by <a href="/wiki/Sodium_deoxycholate" class="mw-redirect" title="Sodium deoxycholate">sodium deoxycholate</a>. Lysis indicates <i>S. Pneumoniae</i> while no lysis does not.<sup id="cite_ref-20" class="reference"><a href="#cite_note-20"><span class="cite-bracket">[</span>20<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading3"><h3 id="CAMP">CAMP</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=25" title="Edit section: CAMP"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <figure class="mw-default-size" typeof="mw:File/Thumb"><a href="/wiki/File:CAMP_test.JPG" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/d/d9/CAMP_test.JPG/220px-CAMP_test.JPG" decoding="async" width="220" height="164" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/d/d9/CAMP_test.JPG/330px-CAMP_test.JPG 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/d/d9/CAMP_test.JPG/440px-CAMP_test.JPG 2x" data-file-width="2592" data-file-height="1936" /></a><figcaption>A positive CAMP test with the characteristic arrowhead shaped zone of hemolysis</figcaption></figure> <p>A <a href="/wiki/CAMP_test" title="CAMP test">CAMP test</a> is used to differentiate between <i><a href="/wiki/Streptococcus_agalactiae" title="Streptococcus agalactiae">Streptococcus agalactiae</a></i> and other species of <a href="/wiki/Beta_hemolysis" class="mw-redirect" title="Beta hemolysis">beta-hemolytic</a> <i>Streptococcus.</i> This biochemical test uses the fact that <i>Streptococcus agalactiae</i> excretes a CAMP substance, making it slightly more hemolytic, which can be observed on blood agar media.<sup id="cite_ref-21" class="reference"><a href="#cite_note-21"><span class="cite-bracket">[</span>21<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading3"><h3 id="Catalase">Catalase</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=26" title="Edit section: Catalase"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>The catalase test tests whether a microbe produces the enzyme catalase, which catalyzes the breakdown of hydrogen peroxide. Smearing a colony sample onto a glass slide and adding a solution of hydrogen peroxide (3% H<sub>2</sub>O<sub>2</sub>) will indicate whether the enzyme is present or not. Bubbling is a positive test while nothing happening is a negative result.<sup id="cite_ref-:3_22-0" class="reference"><a href="#cite_note-:3-22"><span class="cite-bracket">[</span>22<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading3"><h3 id="Cetrimide_agar">Cetrimide agar</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=27" title="Edit section: Cetrimide agar"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p><a href="/wiki/Cetrimide_agar" title="Cetrimide agar">Cetrimide agar</a> slants is a selective agar used to isolate <i><a href="/wiki/Pseudomonas_aeruginosa" title="Pseudomonas aeruginosa">Pseudomonas aeruginosa</a></i>. </p> <div class="mw-heading mw-heading3"><h3 id="CLO_tests">CLO tests</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=28" title="Edit section: CLO tests"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>The <a href="/wiki/CLO_test" class="mw-redirect" title="CLO test">CLO test</a> is used to diagnose <i>H. Pylori</i> in patient biopsies. A sample of the biopsy is places in a medium containing <a href="/wiki/Urea" title="Urea">urea</a>, which <i>H. Pylori</i> can use in some of its biochemical pathways. Consumption of urea indicates a positive test result.<sup id="cite_ref-23" class="reference"><a href="#cite_note-23"><span class="cite-bracket">[</span>23<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading3"><h3 id="Coagulase">Coagulase</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=29" title="Edit section: Coagulase"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>The <a href="/wiki/Coagulase_test" class="mw-redirect" title="Coagulase test">coagulase test</a> determines whether an organism can produce the enzyme coagulase, which causes the <a href="/wiki/Fibrin" title="Fibrin">fibrin</a> to clot. Inoculating a plasma test tube with the microbe indicates whether coagulase is produced. A clot indicates the presence of coagulase, while no clot indicates the lack of coagulase.<sup id="cite_ref-24" class="reference"><a href="#cite_note-24"><span class="cite-bracket">[</span>24<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading3"><h3 id="DNA_hydrolysis">DNA hydrolysis</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=30" title="Edit section: DNA hydrolysis"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p><a href="/w/index.php?title=DNase_agar&action=edit&redlink=1" class="new" title="DNase agar (page does not exist)">DNase agar</a> is used to test whether a microbe can produce the <a href="/wiki/Exoenzyme" title="Exoenzyme">exoenzyme</a> <a href="/wiki/Deoxyribonuclease" title="Deoxyribonuclease">deoxyribonuclease</a> (DNase), which hydrolyzes DNA. <a href="/wiki/Methyl_green" title="Methyl green">Methyl green</a> is used as an indicator in the growth medium because it is a cation that provides an opaqueness to a medium with the presence of negatively charged DNA strands. When DNA is cleaved, the media becomes clear, showing the presence of DNase activity. DNA hydrolysis is tested by growing an organism on a DNase Test Agar plate (providing nutrients and DNA) and then checking the plate for hydrolysis. The agar plate has DNA-methyl green complex, and if the organism on the agar does hydrolyze DNA then the green color fades and the colony is surrounded by a colorless zone.<sup id="cite_ref-25" class="reference"><a href="#cite_note-25"><span class="cite-bracket">[</span>25<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading3"><h3 id="Gelatin">Gelatin</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=31" title="Edit section: Gelatin"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>The <a href="/w/index.php?title=Gelatin_test&action=edit&redlink=1" class="new" title="Gelatin test (page does not exist)">gelatin test</a> is used to analyze whether a microbe can hydrolyze gelatin with the enzyme <a href="/wiki/Gelatinase" title="Gelatinase">gelatinase</a>. The gelatin makes the agar solid, so if an organism can produce gelatinase and consume gelatin as an energy and carbon source, the agar will become liquid during growth.<sup id="cite_ref-26" class="reference"><a href="#cite_note-26"><span class="cite-bracket">[</span>26<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading3"><h3 id="Gonocheck_II">Gonocheck II</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=32" title="Edit section: Gonocheck II"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>The Gonochek II test, a commercial biochemical test, is used to differentiate between <i><a href="/wiki/Neisseria_lactamica" title="Neisseria lactamica">Neisseria lactamica</a></i>, <i><a href="/wiki/Neisseria_meningitidis" title="Neisseria meningitidis">Neisseria meningitidis</a></i>, <i>N. gonorrhoeae</i> and <i>Moraxella catarrhalis.</i> The principle behind this test is to use enzymes native to the organism to create a colored product in the presence of foreign molecules. The chemical 5-bromo-4-chloro-3-indolyl-beta-D-galactoside is used in the test because <i>N. lactamica</i> can hydrolyze it with the production of β-<a href="/wiki/Galactosidases" title="Galactosidases">galactosidase</a>, turning the solution into a blue color. Gamma-glutamyl-p-nitroanilide is added to the solution to indicate whether the bacteria is <i>N. meningitides,</i> which hydrolyzes the molecule with the enzyme gamma-glutamylaminopeptidase, producing a yellow end-product. Prolyl-4-methoxynaphthylamide is in the solution to identify <i>N. gonorrhoeae</i> because of its ability to hydrolyze the molecule with the enzyme hydroxyprolylaminopeptidase, creating a red-pink derivative. <i>M. catarrhalis</i> contains none of these enzymes, rendering the solution colorless. This process of identification takes approximately 30 minutes in total.<sup id="cite_ref-27" class="reference"><a href="#cite_note-27"><span class="cite-bracket">[</span>27<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading3"><h3 id="Hippurate">Hippurate</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=33" title="Edit section: Hippurate"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>The Hippurate diagnostic test is used to differentiate between <i><a href="/wiki/Gardnerella_vaginalis" title="Gardnerella vaginalis">Gardnerella vaginalis</a></i>, <i><a href="/wiki/Campylobacter_jejuni" title="Campylobacter jejuni">Campylobacter jejuni</a>,</i> <i><a href="/wiki/Listeria_monocytogenes" title="Listeria monocytogenes">Listeria monocytogenes</a></i> and group B streptococci using the chemical Hippurate. The Hippurate hydrolysis pathway, capable by organisms with the necessary enzymes, produces glycine as a byproduct. Using the indicator <a href="/wiki/Ninhydrin" title="Ninhydrin">ninhydrin</a>, which changes color in the presence of glycine, will display either a colorless product, a negative result, of a dark blue color, a positive result.<sup id="cite_ref-28" class="reference"><a href="#cite_note-28"><span class="cite-bracket">[</span>28<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading3"><h3 id="Indole_butyrate_disk">Indole butyrate disk</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=34" title="Edit section: Indole butyrate disk"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>An <a href="/w/index.php?title=Indole_butyrate_disc&action=edit&redlink=1" class="new" title="Indole butyrate disc (page does not exist)">indole butyrate disc</a> is used to differentiate between <i><a href="/wiki/Neisseria_gonorrhoeae" title="Neisseria gonorrhoeae">Neisseria gonorrhoeae</a></i> (negative result) and <i><a href="/wiki/Moraxella_catarrhalis" title="Moraxella catarrhalis">Moraxella catarrhalis</a></i> (positive result). This test involves a <a href="/wiki/Butyrate" class="mw-redirect" title="Butyrate">butyrate</a> disk, which when smeared with a culture, will change color for a positive result after 5 minutes of incubation. A blue color is the result of a positive test.<sup id="cite_ref-29" class="reference"><a href="#cite_note-29"><span class="cite-bracket">[</span>29<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading3"><h3 id="Lysine_iron_agar_slant">Lysine iron agar slant</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=35" title="Edit section: Lysine iron agar slant"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>The <a href="/wiki/Lysine_iron_agar_slant" class="mw-redirect" title="Lysine iron agar slant">lysine iron agar slant</a> test is used to tell whether an organism can <a href="/wiki/Decarboxylation" title="Decarboxylation">decarboxylate</a> <a href="/wiki/Lysine" title="Lysine">lysine</a> and/or produce <a href="/wiki/Hydrogen_sulfide" title="Hydrogen sulfide">hydrogen sulfide</a>. </p> <div class="mw-heading mw-heading3"><h3 id="Lysostaphin">Lysostaphin</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=36" title="Edit section: Lysostaphin"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>The <a href="/w/index.php?title=Lysostaphin_test&action=edit&redlink=1" class="new" title="Lysostaphin test (page does not exist)">lysostaphin test</a> is used to differentiate between <i>Staphylococcus</i> and <i>Micrococcus</i> bacteria. <a href="/wiki/Lysostaphin" title="Lysostaphin">Lysostaphin</a> can <a href="/wiki/Lysis" title="Lysis">lyse</a> <i>Staphylococcus,</i> but <i>Micrococcus</i> bacteria are resistant to the chemical.<sup id="cite_ref-30" class="reference"><a href="#cite_note-30"><span class="cite-bracket">[</span>30<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading3"><h3 id="Methyl_red_test">Methyl red test</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=37" title="Edit section: Methyl red test"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <figure typeof="mw:File/Thumb"><a href="/wiki/File:Color_transition_of_Methyl_red_solution_under_different_acid-base_conditions.jpg" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/e/e5/Color_transition_of_Methyl_red_solution_under_different_acid-base_conditions.jpg/319px-Color_transition_of_Methyl_red_solution_under_different_acid-base_conditions.jpg" decoding="async" width="319" height="126" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/e/e5/Color_transition_of_Methyl_red_solution_under_different_acid-base_conditions.jpg/479px-Color_transition_of_Methyl_red_solution_under_different_acid-base_conditions.jpg 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/e/e5/Color_transition_of_Methyl_red_solution_under_different_acid-base_conditions.jpg/638px-Color_transition_of_Methyl_red_solution_under_different_acid-base_conditions.jpg 2x" data-file-width="7980" data-file-height="3160" /></a><figcaption>Color transition of Methyl red solution under different acid-base conditions</figcaption></figure> <p>The <a href="/wiki/Methyl_red_test" class="mw-redirect" title="Methyl red test">methyl red test</a> is used to analyze whether a bacterium produces acids through sugar fermentation.<sup class="noprint Inline-Template Template-Fact" style="white-space:nowrap;">[<i><a href="/wiki/Wikipedia:Citation_needed" title="Wikipedia:Citation needed"><span title="This claim needs references to reliable sources. (April 2017)">citation needed</span></a></i>]</sup> </p> <div class="mw-heading mw-heading3"><h3 id="Microdase">Microdase</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=38" title="Edit section: Microdase"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p><a href="/w/index.php?title=Microdase&action=edit&redlink=1" class="new" title="Microdase (page does not exist)">Microdase</a> is a modified oxidase test used to differentiate <i><a href="/wiki/Micrococcus" title="Micrococcus">Micrococcus</a></i> from <i><a href="/wiki/Staphylococcus" title="Staphylococcus">Staphylococcus</a></i> by testing for the presence of <a href="/wiki/Cytochrome_c" title="Cytochrome c">cytochrome c</a>. A positive result produces a dark color around the inoculant while negative result produces no color change.<sup id="cite_ref-31" class="reference"><a href="#cite_note-31"><span class="cite-bracket">[</span>31<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading3"><h3 id="Nitrite_test">Nitrite test</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=39" title="Edit section: Nitrite test"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>The <a href="/wiki/Nitrite_test" title="Nitrite test">nitrite test</a> is commonly used to diagnose urinary tract infections by measuring the concentrations of nitrite in solution, indicating the presence of a gram-negative organism. A simple nitrite test can be performed by adding 4 M sulfuric acid to the sample until acidic, and then adding 0.1 M iron (II) sulfate to the solution. A positive test for nitrite is indicated by a dark brown solution, arising from the iron-nitric oxide complex ion. <sup class="noprint Inline-Template Template-Fact" style="white-space:nowrap;">[<i><a href="/wiki/Wikipedia:Citation_needed" title="Wikipedia:Citation needed"><span title="This claim needs references to reliable sources. (April 2017)">citation needed</span></a></i>]</sup> </p> <div class="mw-heading mw-heading3"><h3 id="Oxidase">Oxidase</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=40" title="Edit section: Oxidase"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>The oxidase test indicates whether a microbe is aerobic. By using the chemical <a href="/wiki/N,N,N,N-tetramethyl-1,4-phenylendiamin" class="mw-redirect" title="N,N,N,N-tetramethyl-1,4-phenylendiamin">N,N,N,N-tetramethyl-1,4-phenylendiamin</a>, an electron acceptor that changes color when oxidized by <a href="/wiki/Cytochrome_c_oxidase" title="Cytochrome c oxidase">cytochrome c oxidase</a>, one can deduce whether a microbe can perform aerobic respiration. A color change to purple indicates oxidative respiration while no color change provides evidence that the organism does not have cytochrome c oxidase.<sup id="cite_ref-:3_22-1" class="reference"><a href="#cite_note-:3-22"><span class="cite-bracket">[</span>22<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading3"><h3 id="Phenylalanine_deaminase">Phenylalanine deaminase</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=41" title="Edit section: Phenylalanine deaminase"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>The <a href="/wiki/Phenylalanine_deaminase" class="mw-redirect" title="Phenylalanine deaminase">phenylalanine deaminase</a> test is used to tell whether an organism can produce the enzyme deaminase. Deaminase is the enzyme that can deaminate the amino acid phenylalanine into the products ammonia and <a href="/wiki/Phenylpyruvic_acid" title="Phenylpyruvic acid">phenylpyruvic acid</a>. The test is performed by adding phenylalanine to the growth medium and allowing growth to occur. After incubation, 10% <a href="/wiki/Ferric_chloride" class="mw-redirect" title="Ferric chloride">ferric chloride</a> is added to the solution, which will react with phenylpyruvic acid in solution to make a dark green color, resulting in a positive test result.<sup id="cite_ref-32" class="reference"><a href="#cite_note-32"><span class="cite-bracket">[</span>32<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading3"><h3 id="PYR">PYR</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=42" title="Edit section: PYR"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>The PYR test is used to check if an organism has enzymes to <a href="/wiki/Hydrolysis" title="Hydrolysis">hydrolyze</a> L-pyrrolidonyl- β-napthylamide. A positive result indicates that the organism is either group A <i><a href="/wiki/Streptococcus" title="Streptococcus">streptococcus</a></i> and/or group D <i><a href="/wiki/Enterococcus" title="Enterococcus">enterococcus</a></i>.<sup id="cite_ref-33" class="reference"><a href="#cite_note-33"><span class="cite-bracket">[</span>33<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading3"><h3 id="Reverse_CAMP">Reverse CAMP</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=43" title="Edit section: Reverse CAMP"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>The <a href="/wiki/Reverse_CAMP_test" class="mw-redirect" title="Reverse CAMP test">reverse CAMP test</a> utilizes the synergetic hemolytic abilities of the CAMP factor produced by <i>Streptococcus agalactiae</i> with the α-toxin produced by <i><a href="/wiki/Clostridium_perfringens" title="Clostridium perfringens">Clostridium perfringens</a></i>. Streaking these two organisms perpendicular to each other on a blood agar plate will yield a “bow-tie” clearing of the blood agar by the hemolytic capabilities of the two organisms’ toxins. Incubation requires 24 hours at 37 °C.<sup id="cite_ref-34" class="reference"><a href="#cite_note-34"><span class="cite-bracket">[</span>34<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading3"><h3 id="Simmons'_citrate_agar"><span id="Simmons.27_citrate_agar"></span>Simmons' citrate agar</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=44" title="Edit section: Simmons' citrate agar"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p><a href="/wiki/Simmons%27_citrate_agar" title="Simmons' citrate agar">Simmons' citrate agar</a> is used to test whether an organism can utilize <a href="/wiki/Citrate" class="mw-redirect" title="Citrate">citrate</a> for its sole carbon source.<sup class="noprint Inline-Template Template-Fact" style="white-space:nowrap;">[<i><a href="/wiki/Wikipedia:Citation_needed" title="Wikipedia:Citation needed"><span title="This claim needs references to reliable sources. (April 2017)">citation needed</span></a></i>]</sup> </p> <div class="mw-heading mw-heading3"><h3 id="Spot_indole">Spot indole</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=45" title="Edit section: Spot indole"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <figure typeof="mw:File/Thumb"><a href="/wiki/File:Agar_tsi.JPG" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/e/ea/Agar_tsi.JPG/245px-Agar_tsi.JPG" decoding="async" width="245" height="176" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/e/ea/Agar_tsi.JPG/368px-Agar_tsi.JPG 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/e/ea/Agar_tsi.JPG/490px-Agar_tsi.JPG 2x" data-file-width="1021" data-file-height="734" /></a><figcaption>TSI Agar</figcaption></figure> <p>The spot indole test is used to determine if a microbe can <a href="/wiki/Deamination" title="Deamination">deaminate</a> <a href="/wiki/Tryptophan" title="Tryptophan">tryptophan</a> to produce <a href="/wiki/Indole" title="Indole">indole</a>. This test is performed by saturating a piece of filter paper with Indole Kovacs Reagent and scraping a portion of microbe onto the paper. A color to a pink-red color indicates a positive result while no color change indicates the lack of <a href="/wiki/Tryptophanase" title="Tryptophanase">tryptophanase</a>.<sup id="cite_ref-35" class="reference"><a href="#cite_note-35"><span class="cite-bracket">[</span>35<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading3"><h3 id="Sulphide_indole_motility_medium">Sulphide indole motility medium</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=46" title="Edit section: Sulphide indole motility medium"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>The <a href="/wiki/Sulfide_indole_motility_medium" class="mw-redirect" title="Sulfide indole motility medium">sulfide indole motility medium</a> is a three-part test for an organism’s ability to reduce sulfates, produce indoles, and motile ability.<sup class="noprint Inline-Template Template-Fact" style="white-space:nowrap;">[<i><a href="/wiki/Wikipedia:Citation_needed" title="Wikipedia:Citation needed"><span title="This claim needs references to reliable sources. (April 2017)">citation needed</span></a></i>]</sup> </p> <div class="mw-heading mw-heading3"><h3 id="TSI_slant">TSI slant</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=47" title="Edit section: TSI slant"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>The <a href="/wiki/TSI_slant" title="TSI slant">triple sugar iron (TSI) test</a> is a differential media used to tell whether an organism can ferment glucose, sucrose, and/or lactose and whether an organism can produce hydrogen sulfide gas.<sup id="cite_ref-36" class="reference"><a href="#cite_note-36"><span class="cite-bracket">[</span>36<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading3"><h3 id="Urea_agar_slant">Urea agar slant</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=48" title="Edit section: Urea agar slant"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <figure typeof="mw:File/Thumb"><a href="/wiki/File:Raoultella_planticola_on_urea_agar.jpg" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/a/a5/Raoultella_planticola_on_urea_agar.jpg/282px-Raoultella_planticola_on_urea_agar.jpg" decoding="async" width="282" height="282" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/a/a5/Raoultella_planticola_on_urea_agar.jpg/423px-Raoultella_planticola_on_urea_agar.jpg 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/a/a5/Raoultella_planticola_on_urea_agar.jpg/564px-Raoultella_planticola_on_urea_agar.jpg 2x" data-file-width="682" data-file-height="682" /></a><figcaption>Raoultella planticola on urea agar</figcaption></figure> <p>The urease agar slant is used to measure an organism’s ability to produce <a href="/wiki/Urease" title="Urease">urease</a>, an enzyme capable to digesting urea in carbon dioxide and ammonia through hydrolysis. Because ammonia is alkaline, the media contains phenol red, an indicator that changes from orange to pink when a pH increases above 8.1. When ammonia is increased to high enough concentrations, the media will change to a pink color, indicating the presence of urease production.<sup id="cite_ref-37" class="reference"><a href="#cite_note-37"><span class="cite-bracket">[</span>37<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading3"><h3 id="Voges–Proskauer_test"><span id="Voges.E2.80.93Proskauer_test"></span>Voges–Proskauer test</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=49" title="Edit section: Voges–Proskauer test"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>The <a href="/wiki/Voges-Proskauer_test" class="mw-redirect" title="Voges-Proskauer test">Voges-Proskauer test</a> detects whether a bacterium is producing the product <a href="/wiki/Acetoin" title="Acetoin">acetoin</a> from the digestion of glucose.<sup id="cite_ref-38" class="reference"><a href="#cite_note-38"><span class="cite-bracket">[</span>38<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading2"><h2 id="Cellular_fatty_acid_based_identification">Cellular fatty acid based identification</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=50" title="Edit section: Cellular fatty acid based identification"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <div class="mw-heading mw-heading3"><h3 id="Mycolic_acid_analysis">Mycolic acid analysis</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=51" title="Edit section: Mycolic acid analysis"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p><a href="/wiki/Mycolic_acid" title="Mycolic acid">Mycolic acid</a> analysis has been an evolving field of study for <a href="/wiki/Gas-liquid_chromatography" class="mw-redirect" title="Gas-liquid chromatography">gas-liquid chromatography</a>, as it offers a solution to slow growth rates in <i><a href="/wiki/Mycobacterium" title="Mycobacterium">Mycobacterium</a>.</i> Mycolic acid is a fatty acid found in the disease <a href="/wiki/Tuberculosis" title="Tuberculosis">tuberculosis</a>, offering a chemical target for diagnosticians to look for.<sup id="cite_ref-39" class="reference"><a href="#cite_note-39"><span class="cite-bracket">[</span>39<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading2"><h2 id="Nucleic_acid_extraction_techniques">Nucleic acid extraction techniques</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=52" title="Edit section: Nucleic acid extraction techniques"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <div class="mw-heading mw-heading3"><h3 id="Cesium_chloride_/_Ethidium_bromide_density_gradient_centrifugation"><span id="Cesium_chloride_.2F_Ethidium_bromide_density_gradient_centrifugation"></span>Cesium chloride / Ethidium bromide density gradient centrifugation</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=53" title="Edit section: Cesium chloride / Ethidium bromide density gradient centrifugation"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <figure class="mw-default-size" typeof="mw:File/Thumb"><a href="/wiki/File:Tabletop_centrifuge.jpg" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/0/0d/Tabletop_centrifuge.jpg/220px-Tabletop_centrifuge.jpg" decoding="async" width="220" height="293" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/0/0d/Tabletop_centrifuge.jpg/330px-Tabletop_centrifuge.jpg 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/0/0d/Tabletop_centrifuge.jpg/440px-Tabletop_centrifuge.jpg 2x" data-file-width="1704" data-file-height="2272" /></a><figcaption>Tabletop centrifuge</figcaption></figure> <p>With high speed <a href="/wiki/Buoyant_density_ultracentrifugation" class="mw-redirect" title="Buoyant density ultracentrifugation">buoyant density ultracentrifugation</a>, a density gradient is created with <a href="/wiki/Caesium_chloride" title="Caesium chloride">caesium chloride</a> in water. DNA will go to the density that reflects its own, and <a href="/wiki/Ethidium_bromide" title="Ethidium bromide">ethidium bromide</a> is then added to enhance the visuals the nucleic acid band provides.<sup id="cite_ref-40" class="reference"><a href="#cite_note-40"><span class="cite-bracket">[</span>40<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading3"><h3 id="Magnetic_bead_method">Magnetic bead method</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=54" title="Edit section: Magnetic bead method"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>New extraction techniques have been developed using <a href="/wiki/Magnetic_bead" class="mw-redirect" title="Magnetic bead">magnetic beads</a> for the purification of nucleic acids by taking advantage of the charged and polymeric nature of long strand of DNA. Beads are both uncoated to increase surface are and yield, while others are more selective by being coated with functional groups that interact with the <a href="/wiki/Polymer" title="Polymer">polymers</a> present in microbes.<sup id="cite_ref-41" class="reference"><a href="#cite_note-41"><span class="cite-bracket">[</span>41<span class="cite-bracket">]</span></a></sup> One common method is to use polyethylene glycol to drive DNA binding to the magnetic beads. The molecular weight and concentration of the PEG will control what molecular weight DNA binds. </p> <div class="mw-heading mw-heading3"><h3 id="Phenol–chloroform_extraction"><span id="Phenol.E2.80.93chloroform_extraction"></span>Phenol–chloroform extraction</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=55" title="Edit section: Phenol–chloroform extraction"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p><a href="/w/index.php?title=Phenol-Chloroform_extraction&action=edit&redlink=1" class="new" title="Phenol-Chloroform extraction (page does not exist)">Phenol-Chloroform extraction</a> is a liquid-liquid method used by biochemists to separate nucleic acids from proteins and lipids after cells have been lysed.<sup id="cite_ref-42" class="reference"><a href="#cite_note-42"><span class="cite-bracket">[</span>42<span class="cite-bracket">]</span></a></sup> <sup class="noprint Inline-Template Template-Fact" style="white-space:nowrap;">[<i><a href="/wiki/Wikipedia:Citation_needed" title="Wikipedia:Citation needed"><span title="This claim needs references to reliable sources. (April 2017)">citation needed</span></a></i>]</sup> This method has fallen out of favor with scientists and microbiologists as there are easier methods available which require less hazardous chemicals. </p> <div class="mw-heading mw-heading3"><h3 id="Solid_phase_extraction">Solid phase extraction</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=56" title="Edit section: Solid phase extraction"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p><a href="/wiki/Solid_phase_extraction" class="mw-redirect" title="Solid phase extraction">Solid phase extraction</a> which separates long polymers like DNA from other substances found in the cells. This is similar to magnetic beads, where the solid phase is fixed and selectively binds a cellular component, allowing for its isolation. </p> <div class="mw-heading mw-heading2"><h2 id="Methods_with_electrophoretic_outputs">Methods with electrophoretic outputs</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=57" title="Edit section: Methods with electrophoretic outputs"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p><a href="/wiki/Gel_electrophoresis" title="Gel electrophoresis">Gel electrophoresis</a> is a technique to separate <a href="/wiki/Macromolecule" title="Macromolecule">macromolecules</a> by taking advantage of the charge on many of the molecules found in nucleic acids and protein. This is also the key method for Sanger sequencing. Fluorescent-labeled DNA fragments move through a polymer and are separated with one base precision. A laser excites the fluorescent tag and is captured by a camera. The result is an electropherogram which reads the DNA sequence. </p> <div class="mw-heading mw-heading2"><h2 id="Restriction_enzyme_based">Restriction enzyme based</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=58" title="Edit section: Restriction enzyme based"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <div class="mw-heading mw-heading3"><h3 id="Optical_mapping">Optical mapping</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=59" title="Edit section: Optical mapping"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p><a href="/wiki/Optical_mapping" title="Optical mapping">Optical mapping</a> is a technique using multiple restriction enzymes to create a genomic “barcode” which can be referenced back to diagnose an unknown microbe. </p> <div class="mw-heading mw-heading3"><h3 id="Pulsed-field_gel_electrophoresis">Pulsed-field gel electrophoresis</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=60" title="Edit section: Pulsed-field gel electrophoresis"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p><a href="/wiki/Pulsed-field_gel_electrophoresis" title="Pulsed-field gel electrophoresis">Pulsed-field gel electrophoresis</a> is a technique used to separate large DNA in an electric field that periodically changes direction. By cutting segments of the DNA with <a href="/wiki/Restriction_enzyme" title="Restriction enzyme">restriction enzymes</a>, pulse-field can be used to separate out the segments of DNA. </p> <div class="mw-heading mw-heading3"><h3 id="Restriction_enzymes_then_gel_electrophoresis">Restriction enzymes then gel electrophoresis</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=61" title="Edit section: Restriction enzymes then gel electrophoresis"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>Restriction enzymes are first used to recognize and then cut specific nucleic acid sequences. These cut pieces of DNA can be run through a gel electrophoresis to allow diagnostics of the organism by referencing back to previous gel electrophoresis results. </p> <div class="mw-heading mw-heading3"><h3 id="Ribotyping">Ribotyping</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=62" title="Edit section: Ribotyping"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>Ribotyping is a rapid automated method for microbial diagnostics, testing for rRNA in bacteria using restriction enzyme digestion and Southern blot technology.<sup id="cite_ref-43" class="reference"><a href="#cite_note-43"><span class="cite-bracket">[</span>43<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading2"><h2 id="PCR-based">PCR-based</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=63" title="Edit section: PCR-based"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <div class="mw-heading mw-heading3"><h3 id="Multiple_loci_VNTR_analysis">Multiple loci VNTR analysis</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=64" title="Edit section: Multiple loci VNTR analysis"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p><a href="/wiki/Multiple-locus_VNTR_analysis" class="mw-redirect" title="Multiple-locus VNTR analysis">Multiple-locus VNTR analysis</a> is a test used to detect <a href="/wiki/Variable_number_tandem_repeats" class="mw-redirect" title="Variable number tandem repeats">variable number tandem repeats</a>, which act as a <a href="/wiki/DNA_fingerprint" class="mw-redirect" title="DNA fingerprint">DNA fingerprint</a> in microbial diagnostics.<sup id="cite_ref-44" class="reference"><a href="#cite_note-44"><span class="cite-bracket">[</span>44<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading2"><h2 id="DNA_sequence-based_methods">DNA sequence-based methods</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=65" title="Edit section: DNA sequence-based methods"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <div class="mw-heading mw-heading3"><h3 id="Multi-locus_sequence_typing">Multi-locus sequence typing</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=66" title="Edit section: Multi-locus sequence typing"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p><a href="/wiki/Multilocus_sequence_typing" title="Multilocus sequence typing">Multilocus sequence typing</a> (MLST) is the sequencing of numerous loci to diagnose an organism by comparing DNA sequences to a database of known organisms.<sup id="cite_ref-45" class="reference"><a href="#cite_note-45"><span class="cite-bracket">[</span>45<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-46" class="reference"><a href="#cite_note-46"><span class="cite-bracket">[</span>46<span class="cite-bracket">]</span></a></sup> This method is often used to compare isolates or strains of the same species to see if they are indistinguishable or different from each other. This is common for tracking food-borne illnesses and public health outbreaks. Most MLST assays are published in scientific journals so consistent methods are used worldwide. There are also public databases available for tracking and comparisons. </p> <div class="mw-heading mw-heading3"><h3 id="Single-locus_sequence_typing">Single-locus sequence typing</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=67" title="Edit section: Single-locus sequence typing"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p><a href="/w/index.php?title=Single-locus_sequence_typing&action=edit&redlink=1" class="new" title="Single-locus sequence typing (page does not exist)">Single-locus sequence typing</a> (SLST) is the sequencing of a single locus of an organism to produce data that can be used for strain-level comparisons between isolates of the same species.<sup id="cite_ref-47" class="reference"><a href="#cite_note-47"><span class="cite-bracket">[</span>47<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading3"><h3 id="Genotypic_identifications">Genotypic identifications</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=68" title="Edit section: Genotypic identifications"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>For bacterial identifications, microbiologists sequence the 16S rRNA gene and for fungal identifications, sequence the ITS regions. Both regions are part of the ribosomal operon so they are well-conserved but provide enough variation to allow for speciation. Accurate identifications require high quality sequence data, a robust data analysis, and a broad microbial database of known organisms. It is also useful to use a Neighbor Joining tree or some other phylogenetic approach to make the identification. </p> <div class="mw-heading mw-heading3"><h3 id="Whole_genome_sequencing_(WGS)"><span id="Whole_genome_sequencing_.28WGS.29"></span>Whole genome sequencing (WGS)</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=69" title="Edit section: Whole genome sequencing (WGS)"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p><a href="/wiki/Whole_genome_sequencing" title="Whole genome sequencing">Whole genome sequencing</a> and genomics applications can be used for large-scale alignment and comparative analysis with both bacteria and fungi. WGS can be used to diagnose, identify, or characterize an organism down to the individual base pairs by sequencing the entire genome.<sup id="cite_ref-48" class="reference"><a href="#cite_note-48"><span class="cite-bracket">[</span>48<span class="cite-bracket">]</span></a></sup> WGS can also be used to compare the genomes or average nucleotide identity (ANI) of the shared genes between two strains and can be a robust way to compare genetic relatedness and if often used for investigating organisms involved in foodborne illness and other outbreaks. </p> <div class="mw-heading mw-heading2"><h2 id="References">References</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Diagnostic_microbiology&action=edit&section=70" title="Edit section: References"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <style data-mw-deduplicate="TemplateStyles:r1239543626">.mw-parser-output .reflist{margin-bottom:0.5em;list-style-type:decimal}@media screen{.mw-parser-output .reflist{font-size:90%}}.mw-parser-output .reflist .references{font-size:100%;margin-bottom:0;list-style-type:inherit}.mw-parser-output .reflist-columns-2{column-width:30em}.mw-parser-output .reflist-columns-3{column-width:25em}.mw-parser-output .reflist-columns{margin-top:0.3em}.mw-parser-output .reflist-columns ol{margin-top:0}.mw-parser-output .reflist-columns li{page-break-inside:avoid;break-inside:avoid-column}.mw-parser-output .reflist-upper-alpha{list-style-type:upper-alpha}.mw-parser-output .reflist-upper-roman{list-style-type:upper-roman}.mw-parser-output .reflist-lower-alpha{list-style-type:lower-alpha}.mw-parser-output .reflist-lower-greek{list-style-type:lower-greek}.mw-parser-output .reflist-lower-roman{list-style-type:lower-roman}</style><div class="reflist reflist-columns references-column-width" style="column-width: 30em;"> <ol class="references"> <li id="cite_note-1"><span class="mw-cite-backlink"><b><a href="#cite_ref-1">^</a></b></span> <span class="reference-text"><style data-mw-deduplicate="TemplateStyles:r1238218222">.mw-parser-output cite.citation{font-style:inherit;word-wrap:break-word}.mw-parser-output .citation q{quotes:"\"""\"""'""'"}.mw-parser-output .citation:target{background-color:rgba(0,127,255,0.133)}.mw-parser-output .id-lock-free.id-lock-free a{background:url("//upload.wikimedia.org/wikipedia/commons/6/65/Lock-green.svg")right 0.1em center/9px no-repeat}.mw-parser-output .id-lock-limited.id-lock-limited a,.mw-parser-output .id-lock-registration.id-lock-registration a{background:url("//upload.wikimedia.org/wikipedia/commons/d/d6/Lock-gray-alt-2.svg")right 0.1em center/9px no-repeat}.mw-parser-output .id-lock-subscription.id-lock-subscription a{background:url("//upload.wikimedia.org/wikipedia/commons/a/aa/Lock-red-alt-2.svg")right 0.1em center/9px no-repeat}.mw-parser-output .cs1-ws-icon a{background:url("//upload.wikimedia.org/wikipedia/commons/4/4c/Wikisource-logo.svg")right 0.1em center/12px no-repeat}body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .id-lock-free a,body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .id-lock-limited a,body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .id-lock-registration a,body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .id-lock-subscription a,body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .cs1-ws-icon a{background-size:contain;padding:0 1em 0 0}.mw-parser-output .cs1-code{color:inherit;background:inherit;border:none;padding:inherit}.mw-parser-output .cs1-hidden-error{display:none;color:var(--color-error,#d33)}.mw-parser-output .cs1-visible-error{color:var(--color-error,#d33)}.mw-parser-output .cs1-maint{display:none;color:#085;margin-left:0.3em}.mw-parser-output .cs1-kern-left{padding-left:0.2em}.mw-parser-output .cs1-kern-right{padding-right:0.2em}.mw-parser-output .citation .mw-selflink{font-weight:inherit}@media screen{.mw-parser-output .cs1-format{font-size:95%}html.skin-theme-clientpref-night .mw-parser-output .cs1-maint{color:#18911f}}@media screen and (prefers-color-scheme:dark){html.skin-theme-clientpref-os .mw-parser-output .cs1-maint{color:#18911f}}</style><cite id="CITEREFStieglmeierWirthKminekMoissl-Eichinger2009" class="citation journal cs1">Stieglmeier, Michaela; 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href="/wiki/Clinical_microbiology" class="mw-redirect" title="Clinical microbiology">clinical microbiology</a></div></th></tr><tr><th scope="row" class="navbox-group" style="width:1%"><a href="/wiki/Isolation_(microbiology)" title="Isolation (microbiology)">Isolation</a><br />and <a href="/wiki/Culture_(microbiology)" class="mw-redirect" title="Culture (microbiology)">culture</a></th><td class="navbox-list-with-group navbox-list navbox-odd hlist" style="width:100%;padding:0"><div style="padding:0 0.25em"></div><table class="nowraplinks navbox-subgroup" style="border-spacing:0"><tbody><tr><th scope="row" class="navbox-group" style="width:1%">Isolation techniques</th><td class="navbox-list-with-group navbox-list navbox-odd" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Asepsis" title="Asepsis">Asepsis</a></li> <li><a href="/wiki/Streaking_(microbiology)" title="Streaking (microbiology)">Streak plate</a></li> <li><a href="/wiki/Selective_media" class="mw-redirect" title="Selective media">Selective media</a></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">Cultures by body site</th><td class="navbox-list-with-group navbox-list navbox-even" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Blood_culture" title="Blood culture">Blood culture</a></li> <li><a href="/w/index.php?title=Genital_culture&action=edit&redlink=1" class="new" title="Genital culture (page does not exist)">Genital culture</a></li> <li><a href="/wiki/Sputum_culture" title="Sputum culture">Sputum culture</a></li> <li><a href="/wiki/Throat_culture" title="Throat culture">Throat culture</a></li> <li><a href="/wiki/Urine_culture" class="mw-redirect" title="Urine culture">Urine culture</a></li> <li><a href="/wiki/Wound_culture" class="mw-redirect" title="Wound culture">Wound culture</a></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">Cultures by organism</th><td class="navbox-list-with-group navbox-list navbox-odd" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Bacterial_culture" class="mw-redirect" title="Bacterial culture">Bacterial culture</a></li> <li><a href="/w/index.php?title=Fungal_culture&action=edit&redlink=1" class="new" title="Fungal culture (page does not exist)">Fungal culture</a></li> <li><a href="/wiki/Viral_culture" title="Viral culture">Viral culture</a></li></ul> </div></td></tr></tbody></table><div></div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%"><a href="/wiki/Microbiological_identification" class="mw-redirect" title="Microbiological identification">Identification</a><br />and testing</th><td class="navbox-list-with-group navbox-list navbox-odd hlist" style="width:100%;padding:0"><div style="padding:0 0.25em"></div><table class="nowraplinks navbox-subgroup" style="border-spacing:0"><tbody><tr><th scope="row" class="navbox-group" style="width:1%">Manual testing: basic techniques</th><td class="navbox-list-with-group navbox-list navbox-even" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Colonial_morphology" title="Colonial morphology">Colonial morphology</a> <ul><li><a href="/wiki/Hemolysis_(microbiology)" title="Hemolysis (microbiology)">Hemolysis</a></li></ul></li> <li><a href="/wiki/Staining_(biology)" class="mw-redirect" title="Staining (biology)">Staining</a> <ul><li><a href="/wiki/Gram_stain" title="Gram stain">Gram stain</a></li> <li><a href="/wiki/Acid-fast_stain" class="mw-redirect" title="Acid-fast stain">Acid-fast stain</a></li> <li><a href="/wiki/Giemsa_stain" title="Giemsa stain">Giemsa stain</a></li> <li><a href="/wiki/India_ink_stain" class="mw-redirect" title="India ink stain">India ink stain</a></li> <li><a href="/wiki/Ziehl%E2%80%93Neelsen_stain" title="Ziehl–Neelsen stain">Ziehl–Neelsen stain</a></li></ul></li> <li><a href="/wiki/Wet_prep" class="mw-redirect" title="Wet prep">Wet prep</a></li> <li>Rapid tests <ul><li><a href="/wiki/Oxidase_test" title="Oxidase test">Oxidase</a></li> <li><a href="/wiki/Catalase_test" class="mw-redirect" title="Catalase test">Catalase</a></li> <li><a href="/wiki/Indole_test" title="Indole test">Indole</a></li> <li><a href="/wiki/PYR_test" class="mw-redirect" title="PYR test">PYR</a></li></ul></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">Manual testing:<br />biochemical and immunologic tests</th><td class="navbox-list-with-group navbox-list navbox-odd" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a class="mw-selflink-fragment" href="#ALA">ALA test</a></li> <li><a href="/w/index.php?title=Amino_acid_decarboxylase_test&action=edit&redlink=1" class="new" title="Amino acid decarboxylase test (page does not exist)">Amino acid decarboxylase test</a></li> <li><a href="/wiki/Bile_solubility_test" class="mw-redirect" title="Bile solubility test">Bile solubility test</a></li> <li><a href="/wiki/CAMP_test" title="CAMP test">CAMP test</a></li> <li><a href="/wiki/Citrate_test" title="Citrate test">Citrate test</a></li> <li><a href="/wiki/Coagulase_test" class="mw-redirect" title="Coagulase test">Coagulase test</a></li> <li><a class="mw-selflink-fragment" href="#DNA_hydrolysis">DNAse test</a></li> <li><a href="/wiki/IMViC" title="IMViC">IMViC</a></li> <li><a href="/wiki/KOH_test" title="KOH test">KOH test</a></li> <li><a href="/wiki/Methyl_red_test" class="mw-redirect" title="Methyl red test">Methyl red test</a></li> <li><a class="mw-selflink-fragment" href="#Nitrite_test">Nitrite test</a></li> <li><a href="/w/index.php?title=ONPG_test&action=edit&redlink=1" class="new" title="ONPG test (page does not exist)">ONPG test</a></li> <li><a href="/wiki/Oxidative/fermentation_glucose_test" title="Oxidative/fermentation glucose test">Oxidative/fermentation glucose test</a></li> <li><a href="/wiki/Phenylalanine_deaminase_test" class="mw-redirect" title="Phenylalanine deaminase test">Phenylalanine deaminase test</a></li> <li><a class="mw-selflink-fragment" href="#Reverse_CAMP_test">Reverse CAMP test</a></li> <li><a class="mw-selflink-fragment" href="#6.5%_salt_broth">Salt tolerance test</a></li> <li><a href="/wiki/Sulfide_indole_motility_test" class="mw-redirect" title="Sulfide indole motility test">Sulfide indole motility test</a></li> <li><a href="/wiki/Triple_sugar_iron_test" class="mw-redirect" title="Triple sugar iron test">Triple sugar iron test</a></li> <li><a href="/wiki/Urease#As_diagnostic_test" title="Urease">Urease test</a> <ul><li><a href="/wiki/Rapid_urease_test" title="Rapid urease test">rapid</a></li></ul></li> <li><a href="/wiki/Voges%E2%80%93Proskauer_test" title="Voges–Proskauer test">Voges–Proskauer test</a></li> <li><a href="/w/index.php?title=X_and_V_factor_test&action=edit&redlink=1" class="new" title="X and V factor test (page does not exist)">X and V factor test</a></li> <li><a href="/w/index.php?title=Bacitracin_susceptibility_test&action=edit&redlink=1" class="new" title="Bacitracin susceptibility test (page does not exist)">Bacitracin susceptibility test</a></li> <li><a href="/wiki/Optochin_susceptibility_test" class="mw-redirect" title="Optochin susceptibility test">Optochin susceptibility test</a></li> <li><a href="/wiki/Novobiocin_susceptibility_test" class="mw-redirect" title="Novobiocin susceptibility test">Novobiocin susceptibility test</a></li> <li><a href="/wiki/Lancefield_grouping" title="Lancefield grouping">Lancefield grouping</a></li> <li><a href="/wiki/RPR_test" class="mw-redirect" title="RPR test">RPR test</a></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">Automated and <a href="/wiki/Point-of-care_testing" title="Point-of-care testing">point-of-care testing</a></th><td class="navbox-list-with-group navbox-list navbox-even" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Analytical_profile_index" title="Analytical profile index">Analytical profile index</a></li> <li><a href="/wiki/MALDI-TOF" class="mw-redirect" title="MALDI-TOF">MALDI-TOF</a></li> <li><a href="/wiki/Polymerase_chain_reaction#Infectious_disease_applications" title="Polymerase chain reaction">Polymerase chain reaction</a></li> <li><a href="/wiki/VITEK" title="VITEK">VITEK</a></li> <li><a href="/wiki/Rapid_strep_test" title="Rapid strep test">Rapid strep test</a></li> <li><a href="/wiki/Monospot_test" class="mw-redirect" title="Monospot test">Monospot test</a></li></ul> </div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%"><a href="/wiki/Antibiotic_sensitivity" class="mw-redirect" title="Antibiotic sensitivity">Antibiotic susceptibility testing</a></th><td class="navbox-list-with-group navbox-list navbox-odd" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/w/index.php?title=Beta-lactamase_test&action=edit&redlink=1" class="new" title="Beta-lactamase test (page does not exist)">Beta-lactamase test</a></li> <li><a href="/wiki/Disk_diffusion_test" title="Disk diffusion test">Disk diffusion test</a></li> <li><a href="/wiki/Etest" title="Etest">Etest</a></li> <li><a href="/wiki/McFarland_standards" title="McFarland standards">McFarland standards</a></li> <li><a href="/wiki/Minimum_inhibitory_concentration" title="Minimum inhibitory concentration">Minimum inhibitory concentration</a></li></ul> </div></td></tr></tbody></table><div></div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%">Equipment</th><td class="navbox-list-with-group navbox-list navbox-even hlist" style="width:100%;padding:0"><div style="padding:0 0.25em"> <ul><li><a href="/wiki/Agar_plate" title="Agar plate">Agar plate</a> <ul><li><a href="/wiki/Growth_medium" title="Growth medium">Growth medium</a></li></ul></li> <li><a href="/wiki/McIntosh_and_Filde%27s_anaerobic_jar" class="mw-redirect" title="McIntosh and Filde's anaerobic jar">Anaerobic jar</a> <ul><li><a href="/wiki/Gas-pak" title="Gas-pak">Gas-pak</a></li></ul></li> <li><a href="/wiki/Durham_tube" title="Durham tube">Durham tube</a></li> <li><a href="/wiki/Biosafety_cabinet" title="Biosafety cabinet">Biosafety cabinet</a></li> <li><a href="/wiki/Incubator_(culture)" title="Incubator (culture)">Incubator</a></li> <li><a href="/wiki/Inoculation_loop" title="Inoculation loop">Inoculation loop</a></li> <li><a href="/wiki/Inoculation_needle" title="Inoculation needle">Inoculation needle</a></li></ul> </div></td></tr></tbody></table></div>    </div><noscript><img src="https://login.wikimedia.org/wiki/Special:CentralAutoLogin/start?type=1x1" alt="" width="1" height="1" style="border: none; position: absolute;"></noscript> <div class="printfooter" data-nosnippet="">Retrieved from "<a dir="ltr" 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