{"id":652,"date":"2013-02-10T23:39:44","date_gmt":"2013-02-10T23:39:44","guid":{"rendered":"http:\/\/microbiologymatters.com\/?p=652"},"modified":"2013-02-10T23:42:27","modified_gmt":"2013-02-10T23:42:27","slug":"anti-microbial-resistance-testing-phenotype-genotype-and-proteotype","status":"publish","type":"post","link":"https:\/\/microbiologymatters.com\/?p=652","title":{"rendered":"&#8220;Anti-microbial Resistance Testing: Phenotype, Genotype and ?Proteotype&#8221;"},"content":{"rendered":"<p><span style=\"color: #0000ff;\">There has long been a debate over whether the\u00a0microbial\u00a0<span style=\"color: #ff0000;\">genotype<\/span> or <span style=\"color: #ff0000;\">phenotype<\/span> is a better determinant of clinical response when looking at antimicrobial resistance testing. The genotype\u00a0for antimicrobial susceptibility testing\u00a0identifies genes within the\u00a0microbe that have the potential to cause resistance.\u00a0However it does not provide information on whether the gene is &#8220;switched on&#8221;. The phenotype is how the microbe\u00a0responds to the antimicrobial in the laboratory setting, but would not pick up resistance potential, and in particular resistance genes that may\u00a0code for &#8220;inducible&#8221; resistance.\u00a0\u00a0There has been a trend in recent years for a move towards calling results from genotypic testing the &#8220;gold standard&#8221;. This is probably due to two factors:<\/span><\/p>\n<ul>\n<li><span style=\"color: #ff0000;\">Increased range of molecular assays for resistance determinants available.<\/span><\/li>\n<li><span style=\"color: #ff0000;\">Fear of not knowing the genotype and thus missing the potential for resistance.<\/span><\/li>\n<\/ul>\n<p><span style=\"color: #0000ff;\">My worry would be that genotypic resistance testing may well be <span style=\"color: #ff0000;\">over-calling anti-microbial resistance<\/span> in some cases, and thus pushing patients unnecessarily towards broader spectrum antibiotics, thus starting a <span style=\"color: #00ff00;\"><a title=\"Anti-microbial Stewardship in the Hospital Setting: \u201cThe Vicious Circles of Resistance\u201d\" href=\"http:\/\/microbiologymatters.com\/?p=609\"><span style=\"color: #00ff00;\">vicious circle of resistance<\/span><\/a><\/span>. This is not something however, that is often brought up in the anti-microbial stewardship committee setting.<\/span><\/p>\n<p><span style=\"color: #0000ff;\">In addition to this confused picture, <span style=\"color: #0000ff;\">if <span style=\"color: #00ff00;\"><a title=\"\u201cAntimicrobial Susceptibility Testing on MALDI-TOF: The Holy Grail\u201d\" href=\"http:\/\/microbiologymatters.com\/?p=522\"><span style=\"color: #00ff00;\">Maldi-tof techniques start reliably detecting resistance determinants<\/span><\/a><\/span><\/span>, then we will have another category to deal with. Maldi-tof in it&#8217;s current form in the diagnostic laboratory looks mainly at proteins, so we will therefore have the <span style=\"color: #ff0000;\">PROTEOTYPE<\/span>. This is different from both genotype and phenotype. Although it provides information on gene expression, it still does not necessarily\u00a0predict the phenotypic response.<\/span><\/p>\n<p><span style=\"color: #0000ff;\">Thus, as the process of anti-microbial susceptibility testing gets ever more complex, the number of people who fully understand it, (if anyone) diminishes further.<\/span><\/p>\n<p><span style=\"color: #0000ff;\">It may also be that as more and more genes are discovered that have the &#8220;potential&#8221; to cause resistance, the &#8220;gap&#8221; between the resistance genotype and phenotype, which is currently quite small, will continue to widen.<\/span><\/p>\n<p><span style=\"color: #0000ff;\">It&#8217;s an interesting topic, and I am sure debate on the above points will continue for generations yet.<\/span><\/p>\n<p><em>Michael<\/em><\/p>\n<p><em>p.s. I have downloaded some software which facilitates viewing of the website\u00a0on I-phones etc.<\/em><\/p>\n","protected":false},"excerpt":{"rendered":"<p>There has long been a debate over whether the\u00a0microbial\u00a0genotype or phenotype is a better determinant of clinical response when looking at antimicrobial resistance testing. The genotype\u00a0for antimicrobial susceptibility testing\u00a0identifies genes within the\u00a0microbe that have the potential to cause resistance.\u00a0However it does not provide information on whether the gene is &#8220;switched on&#8221;. The phenotype is how &hellip; <a href=\"https:\/\/microbiologymatters.com\/?p=652\" class=\"more-link\">Continue reading <span class=\"screen-reader-text\">&#8220;Anti-microbial Resistance Testing: Phenotype, Genotype and ?Proteotype&#8221;<\/span> <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"footnotes":"","jetpack_publicize_message":"","jetpack_publicize_feature_enabled":true,"jetpack_social_post_already_shared":true,"jetpack_social_options":{"image_generator_settings":{"template":"highway","enabled":false}}},"categories":[14,4],"tags":[36,50,35,49,51],"jetpack_publicize_connections":[],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"jetpack_shortlink":"https:\/\/wp.me\/p37jIp-aw","jetpack-related-posts":[{"id":3038,"url":"https:\/\/microbiologymatters.com\/?p=3038","url_meta":{"origin":652,"position":0},"title":"&#8220;The Transition&#8221;","author":"michael","date":"August 11, 2016","format":false,"excerpt":"At present, routine anti-microbial susceptibility testing is still dominated by phenotype, with genotypic testing occasionally getting a look in for MDROs. I doubt\u00a0this is likely to be the case forever... As our knowledge of genotypic resistance determinants increases, and the cost continues to decrease, I see a time when first\u2026","rel":"","context":"In &quot;Antimicrobial Resistance&quot;","block_context":{"text":"Antimicrobial Resistance","link":"https:\/\/microbiologymatters.com\/?cat=14"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":991,"url":"https:\/\/microbiologymatters.com\/?p=991","url_meta":{"origin":652,"position":1},"title":"&#8220;The Microbiology Lab in 2050&#8230;.&#8221;","author":"michael","date":"March 12, 2013","format":false,"excerpt":"What will you be doing in 2050? I will be 77. Fingers crossed I will still be alive.\u00a0If so,\u00a0I will probably still be working, as by then the retirement age will likely\u00a0have gone up to 80! Have you thought about how clinical microbiology laboratories in general\u00a0might look in 2050? Here\u2026","rel":"","context":"In &quot;Future of Microbiology&quot;","block_context":{"text":"Future of Microbiology","link":"https:\/\/microbiologymatters.com\/?cat=15"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":3640,"url":"https:\/\/microbiologymatters.com\/?p=3640","url_meta":{"origin":652,"position":2},"title":"&#8220;The dark art of antibiotic resistance surveillance&#8221;","author":"michael","date":"November 1, 2017","format":false,"excerpt":"This post is best read with a glass of wine... As a profession, I think we are really not very good at measuring antibiotic resistance\/antibiotic susceptibility patterns... We are very happy to proclaim at the start of presentations \"Antibiotic resistance is increasing\", or \"In the era of increasing antibiotic resistance.\"\u2026","rel":"","context":"In &quot;Antimicrobial Resistance&quot;","block_context":{"text":"Antimicrobial Resistance","link":"https:\/\/microbiologymatters.com\/?cat=14"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/microbiologymatters.com\/wp-content\/uploads\/2017\/11\/rough-day-wine-glass-300x251.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":3124,"url":"https:\/\/microbiologymatters.com\/?p=3124","url_meta":{"origin":652,"position":3},"title":"&#8220;Trending&#8230;&#8221;","author":"michael","date":"December 5, 2016","format":false,"excerpt":"I get the occasional\u00a0anxious phone call from clinicians concerned about the \"rising rates \" of trimethoprim resistance to E. coli... Not being entirely convinced, I did a (20 year) search for E. coli resistance to trimethoprim at my lab, analysing over 2 million isolates,\u00a0and came up with the following graph.\u2026","rel":"","context":"In &quot;Antimicrobial Resistance&quot;","block_context":{"text":"Antimicrobial Resistance","link":"https:\/\/microbiologymatters.com\/?cat=14"},"img":{"alt_text":"capture","src":"https:\/\/i0.wp.com\/microbiologymatters.com\/wp-content\/uploads\/2016\/12\/Capture.jpg?resize=350%2C200","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/microbiologymatters.com\/wp-content\/uploads\/2016\/12\/Capture.jpg?resize=350%2C200 1x, https:\/\/i0.wp.com\/microbiologymatters.com\/wp-content\/uploads\/2016\/12\/Capture.jpg?resize=525%2C300 1.5x, https:\/\/i0.wp.com\/microbiologymatters.com\/wp-content\/uploads\/2016\/12\/Capture.jpg?resize=700%2C400 2x"},"classes":[]},{"id":3836,"url":"https:\/\/microbiologymatters.com\/?p=3836","url_meta":{"origin":652,"position":4},"title":"&#8220;Cohort Bias&#8221;","author":"michael","date":"December 4, 2018","format":false,"excerpt":"At my laboratory we only test nasal Staphylococcus aureus susceptibility to mupirocin in the following two circumstances: Prior to joint replacement surgery as part of a Staphylococcal decolonisation bundle In patients where the clinical details state recurrent skin infections In the patients about to get their joints replaced, our nasal\u2026","rel":"","context":"In &quot;Data Interpretation&quot;","block_context":{"text":"Data Interpretation","link":"https:\/\/microbiologymatters.com\/?cat=207"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/microbiologymatters.com\/wp-content\/uploads\/2018\/12\/MUP.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":522,"url":"https:\/\/microbiologymatters.com\/?p=522","url_meta":{"origin":652,"position":5},"title":"&#8220;Antimicrobial Susceptibility Testing on MALDI-TOF: The Holy Grail&#8221;","author":"michael","date":"January 31, 2013","format":false,"excerpt":"We already know that Maldi-tof is a \"no brainer\" for most routine diagnostic microbiology labs. (Click here for a nice article on the realities of putting a Malditof instrument into a diagnostic laboratory) However if we could also\u00a0perform anti-microbial susceptibility testing on\u00a0Maldi-tof in addition to microbe identification, then it would\u2026","rel":"","context":"In &quot;Antimicrobial Resistance&quot;","block_context":{"text":"Antimicrobial Resistance","link":"https:\/\/microbiologymatters.com\/?cat=14"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]}],"_links":{"self":[{"href":"https:\/\/microbiologymatters.com\/index.php?rest_route=\/wp\/v2\/posts\/652"}],"collection":[{"href":"https:\/\/microbiologymatters.com\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/microbiologymatters.com\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/microbiologymatters.com\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/microbiologymatters.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=652"}],"version-history":[{"count":4,"href":"https:\/\/microbiologymatters.com\/index.php?rest_route=\/wp\/v2\/posts\/652\/revisions"}],"predecessor-version":[{"id":656,"href":"https:\/\/microbiologymatters.com\/index.php?rest_route=\/wp\/v2\/posts\/652\/revisions\/656"}],"wp:attachment":[{"href":"https:\/\/microbiologymatters.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=652"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/microbiologymatters.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=652"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/microbiologymatters.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=652"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}