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Update on Modern Bacterial Taxonomy for Bench Microbiologists

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Update on Modern Bacterial Taxonomy for Bench Microbiologists 11/5/2018 Update on Modern Bacterial Taxonomy for Bench Microbiologists J. Michael Janda Kern County Public Health Laboratory Bakersfield CA The “Name Game” Which Ones Different? Bacterial Taxonomy for Why is Taxonomy Important? Clinical Microbiologists • Think of it as a “LABEL” NOMENCLATURE CLASSIFICATION • We communicate with colleagues around the world regarding • Correct naming and use of • Determines where specific infectious diseases using a standardized communication bacterial names species or groups reside system, microbial taxonomy • Codified compared to others • Basic rules are in • Determines • We describe new diseases, disease outbreaks, epidemics, or pandemics, and emerging syndromes using a binomial name the “Red Book” phylogenetic • to indicate the infectious agent(s) Unlike classification, position relatively stable • Not codified • A lack of a standardized communication system can lead to: but subject to • Can change rapidly – Misidentifications change • What is accepted is – Inappropriate therapeutic decisions based upon common – Inability to determine disease prognosis, treatment and pathogenicity usage and acceptance by the – Identify important outbreaks and epidemics scientific community 1 11/5/2018 Description of a New Species [Idealized] Some Requirements for a Valid Species • Type strain must be identified and defined (etymology); deposited Bios in at least two recognized international culture collections Morpho & 16S • Properties of the taxon, including phenotypic characteristics must Physio NEW be described and compared to closest neighbors on both a phylogenetic as swell as phenotypic basis SPECIES – Cell shape, motility, color, Gram stain DDH, Chemo ANI – Physiologic properties: pH, temperature range Type • Strain G+C mol% • Full 16S rRNA gene sequence, DDH, and/or ANI Classification Pathways to Species Validation Enterobacter Cronobacter Proposed New sakazakii sakazakii Species (Farmer, 1980) (Iversen, 2008) C. malonaticus Published in Not Published in sp. nov. IJSEM IJSEM (AVL) C. turicensis Subsequent sp. nov. Nomenclature Automatically Publication on Validated Validation List in IJSEM C. muytjensii sp. nov. Validated Species C. dublinensis sp. nov. A Nomenclature Issue A Nomenclature Issue (cont.) • The type species of the genus Shewanella is Sh. putrefaciens • Retrospective investigations between 1995 – 2010 found that (Lee et al., 1981), previously Pseudomonas putrefaciens most strains previously identified from clinical specimens as [Classification issue] Sh. putrefaciens were actually Sh. algae (Janda and Abbott, 2014) • Essentially all clinical isolates of this genus were identified as • Sh. haliotis was proposed by Kim et al. in 2007 Sh. putrefaciens • Sh. haliotis has been associated with septicemia and soft • Sh. algae was proposed by Simidu et al. in 1990; the species tissue infections was soon found in clinical material; can be biochemically distinguished from Sh. putrefaciens • WGS indicates Sh. haliotis is a later heterotypic synonym of Sh. algae (Szeinbaum et al., 2018) 2 11/5/2018 Sources You Need to be Aware of There are Exceptions to the Rules of (whether you use them or not) Nomenclature • The “Red Book” International Code of Nomenclature of Bacteria • Escherichia coli = Shigella species (1990 Revision) – 2008 Revision (IJSEM 58:1737-1745) – International Code of Nomenclature • Yersinia pestis = Yersinia pseudotuberculosis (2018) IJSEM (in press) • List of Prokaryotic Names with • Bacillus anthracis = Bacillus cereus Standing in Nomenclature http://www.bacterio.net/index.html Some Proposed Nomenclature and Modern Bacterial Taxonomy – Classification Changes or Issues - 2018 Pluses, Perils, and Pitfalls Group Proposal Basis M. africanum, M. bovis, M. Heterotypic synonyms of WGS, dDDH caprae, M. microti, etc (N) Mycobacterium tuberculosis Enterobacteriaceae (C) Reclassification of species into 6 or 7 WGS, MLSA, 16S, different families or subfamilies AAI Borrelia (C) Proposal not to subdivide genus into two distinct genera Klebsiella aerogenes (N) Klebsiella mobilis and Enterobacter aerogenes are homotypic synonyms Escherichia hermannii (C) Proposed reclassification to genus MLSA Atlantibacter Escherichia vulneris (C) Proposed reclassification to genus Pseudescherichia WGS MALDI-TOF Important Changes in Bacterial Taxonomy 16S PCR Automated Miniaturized Conventional 1960 1970 1980 1990 2000 2010 3 11/5/2018 Changing Face of Bacterial Species Identification “Have Sequencer, Will Travel” Evolution of Bacterial Species Species Proliferation LPSN 1200 1000 800 600 400 200 0 1980 1985 1990 1995 2000 2005 2010 2015 Genus Species New Species Described in 2016 – 2017 Well , here's another nice mess you've in New Microbes and New Infections gotten me into 4 11/5/2018 Problems for the Bench Microbiologist with Modern Day Bacterial Taxonomy New Bacterial Species (2016) One of the Problems • Species proposals often based upon a single type strain • Many species described but not validated Journal No. Species From Clinical Clinically Described Samples (%) Important (est.) (%, est.) • Limited phenotypic data provided, especially on non-validly IntJ Systematic Evolutionary 719 21 (2.9%) <10% Microbiology published species Antonie van Leeuwenhoek 80 4 (5%) <25% New Microbes & New Infections 67 65 (97%) 0% • Species often cannot be separated from nearest neighbors on Archives of Microbiology 26 0 (0%) NA a biochemical basis Current Microbiology 25 1 (4%) 0% Systematic& Applied 24 1 (4) 100% • Nomenclature often confusing Microbiology “Localimania” “Salami Slicing” • Laribacter honkongensis (2001) • Based upon the “least publishable unit” • Actinomyces hongkongensis (2003) • Eggerthella hongkongensis (2004) • Data gathered in one research project are • Sedimentibacter hongkongensis (2004) reported in a number of short, very similar • Anaerospora hongkongensis (2005) papers, each describing a new species • Alkanindiges hongkongensis (2005) • • Catabacter hongkongensis (2007) `One Colony – One Species – One Article’ descriptions “Descriptopenia” Remedial Solutions for the Patient • Typically <5 clinical strains in proposed species • Little or no clinical information on significance • Frequency of taxon – unknown • Antimicrobial susceptibility data – missing • Phenotypic data useful in identifying taxon with commercial systems – missing • Pathogenicity - unknown 5 11/5/2018 Step 1: Some Suggestions Elizabethkingia anophelis • Don’t panic! Most (>99%) of newly proposed species are of little or no clinical or public health importance when first published (2018). 1st reported outbreak with E. anophelis (ICU) E. anophelis sp. nov. from mosquito Two outbreaks of E. • Have one or more staff periodically review potential 1st retrospective case of 1st reported case of anophelis bloodstream E. anophelis infection E. anophelis infections, USA identified, Central meningitis taxonomic updates or changes; discuss these African Republic updates at lab meetings when appropriate • You cannot completely ignore modern day taxonomy. 2006 2010 2012 2014 2016 Some proposals can have important consequences. Some Suggestions (cont.) Step 2: Sources for Taxonomic Updates • Periodically check taxonomic journals for newly • Classification changes can also be important. Follow the described species of clinical origin literature to see if they are generally accepted or not. • Check LPSN website for updates • Unless you are a researcher, state reference laboratory , or major medical center, do not attempt to periodically • Database searches such as PubMed (https://www.ncbi.nlm.nih.gov/pubmed) update identification schemes (e.g., MALDI-TOF) with recently proposed taxa unless warranted. Use final identifications such as [below] when appropriate: • Check journals that publish taxonomic updates of • Aeromonas species possible clinical or public health importance • Cronobacter sakazakii complex or group – Diagnostic Microbiology & Infectious Diseases (since 2015) • Coagulase-negative Staphylococcus species (not S. saprophyticus) – Journal of Clinical Microbiology (since 2017) Diagnostic Microbiology & Infectious Disease Journals to Watch for New Species Proposals Updates • International Journal of Systematic and Evolutionary Microbiology (IJSEM) • Systematic and Applied Microbiology (SAM) • Antonie van Leeuwenhoek (AEM) • New Microbes and New Infections (NMNI) • Current Microbiology 6 11/5/2018 The “Bench Microbiologists” Taxonomic Creed • A new species proposal of clinical origin is just that, IT’S JUST A PROPOSAL, IT MAY OR MAY NOT BE CORRECT AND VALID • WALK SLOWLY, DON’T RUSH to make proposed taxonomic changes unless the medical and scientific data is overwhelming • When you do decide to make changes, notify key medical staff in advance of those proposed changes; see if your identification systems are up-to-date (VITEK, MicroScan, Phoenix, MALDI-TOF, 16S) • For classification changes, always put the old name in parenthesis for a minimum of 6 months to make sure medical staff understand it is the same organism 7.
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