11/5/2018. Update on Modern Bacterial Taxonomy for Bench Microbiologists. Why is Taxonomy Important? Bacterial Taxonomy for Clinical Microbiologists

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1 Update on Modern Bacterial Taxonomy for Bench Microbiologists J. Michael Janda Kern County Public Health Laboratory Bakersfield CA The Name Game Which Ones Different? Why is Taxonomy Important? Bacterial Taxonomy for Clinical Microbiologists Think of it as a LABEL We communicate with colleagues around the world regarding infectious diseases using a standardized communication system, microbial taxonomy We describe new diseases, disease outbreaks, epidemics, or pandemics, and emerging syndromes using a binomial name to indicate the infectious agent(s) A lack of a standardized communication system can lead to: Misidentifications Inappropriate therapeutic decisions Inability to determine disease prognosis, treatment and pathogenicity Identify important outbreaks and epidemics NOMENCLATURE Correct naming and use of bacterial names Codified Basic rules are in the Red Book Unlike classification, relatively stable but subject to change CLASSIFICATION Determines where specific species or groups reside compared to others Determines phylogenetic position Not codified Can change rapidly What is accepted is based upon common usage and acceptance by the scientific community 1

2 Description of a New Species [Idealized] Some Requirements for a Valid Species Morpho & Physio Chemo Bios NEW SPECIES 16S DDH, ANI Type strain must be identified and defined (etymology); deposited in at least two recognized international culture collections Properties of the taxon, including phenotypic characteristics must be described and compared to closest neighbors on both a phylogenetic as swell as phenotypic basis Cell shape, motility, color, Gram stain Physiologic properties: ph, temperature range Type Strain G+C mol% Full 16S rrna gene sequence, DDH, and/or ANI Pathways to Species Validation Classification Proposed New Species Enterobacter sakazakii (Farmer, 1980) Cronobacter sakazakii (Iversen, 2008) Published in IJSEM Not Published in IJSEM (AVL) C. malonaticus Automatically Validated Subsequent Publication on Validation List in IJSEM C. turicensis C. muytjensii Nomenclature Validated Species C. dublinensis A Nomenclature Issue The type species of the genus Shewanella is Sh. putrefaciens (Lee et al., 1981), previously Pseudomonas putrefaciens [Classification issue] Essentially all clinical isolates of this genus were identified as Sh. putrefaciens Sh. algae was proposed by Simidu et al. in 1990; the species was soon found in clinical material; can be biochemically distinguished from Sh. putrefaciens A Nomenclature Issue (cont.) Retrospective investigations between found that most strains previously identified from clinical specimens as Sh. putrefaciens were actually Sh. algae (Janda and Abbott, 2014) Sh. haliotis was proposed by Kim et al. in 2007 Sh. haliotis has been associated with septicemia and soft tissue infections WGS indicates Sh. haliotis is a later heterotypic synonym of Sh. algae (Szeinbaum et al., 2018) 2

3 Sources You Need to be Aware of (whether you use them or not) The Red Book International Code of Nomenclature of Bacteria (1990 Revision) 2008 Revision (IJSEM 58: ) International Code of Nomenclature (2018) IJSEM (in press) List of Prokaryotic Names with Standing in Nomenclature There are Exceptions to the Rules of Nomenclature Escherichia coli = Shigella species Yersinia pestis = Yersinia pseudotuberculosis Bacillus anthracis = Bacillus cereus Some Proposed Nomenclature and Classification Changes or Issues Group Proposal Basis M. africanum, M. bovis, M. caprae, M. microti, etc (N) Heterotypic synonyms of Mycobacterium tuberculosis Enterobacteriaceae (C) Reclassification of species into 6 or 7 different families or subfamilies Borrelia (C) Klebsiella aerogenes (N) Escherichia hermannii (C) Escherichia vulneris (C) Proposal not to subdivide genus into two distinct genera Klebsiella mobilis and Enterobacter aerogenes are homotypic synonyms Proposed reclassification to genus Atlantibacter Proposed reclassification to genus Pseudescherichia WGS, dddh WGS, MLSA, 16S, AAI MLSA Modern Bacterial Taxonomy Pluses, Perils, and Pitfalls 16S MALDI-TOF WGS Important Changes in Bacterial Taxonomy PCR Automated Miniaturized Conventional

4 Changing Face of Bacterial Species Identification Have Sequencer, Will Travel Evolution of Bacterial Species Species Proliferation 1200 LPSN Genus Species New Species Described in in New Microbes and New Infections Well, here's another nice mess you've gotten me into 4

5 Problems for the Bench Microbiologist with Modern Day Bacterial Taxonomy Species proposals often based upon a single type strain New Bacterial Species (2016) One of the Problems Many species described but not validated Limited phenotypic data provided, especially on non-validly published species Species often cannot be separated from nearest neighbors on a biochemical basis Nomenclature often confusing Journal IntJ Systematic Evolutionary Microbiology No. Species Described (est.) From Clinical Samples (%) Clinically Important (%, est.) (2.9%) <10% Antonie van Leeuwenhoek 80 4 (5%) <25% New Microbes & New Infections (97%) 0% Archives of Microbiology 26 0 (0%) NA Current Microbiology 25 1 (4%) 0% Systematic & Applied Microbiology 24 1 (4) 100% Localimania Salami Slicing Laribacter honkongensis (2001) Actinomyces hongkongensis (2003) Eggerthella hongkongensis (2004) Sedimentibacter hongkongensis (2004) Anaerospora hongkongensis (2005) Alkanindiges hongkongensis (2005) Catabacter hongkongensis (2007) Based upon the least publishable unit Data gathered in one research project are reported in a number of short, very similar papers, each describing a new species `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

6 Step 1: Some Suggestions Don t panic! Most (>99%) of newly proposed species are of little or no clinical or public health importance when first published (2018). Elizabethkingia anophelis 1 st reported outbreak with E. anophelis (ICU) Have one or more staff periodically review potential taxonomic updates or changes; discuss these updates at lab meetings when appropriate 1 st retrospective case of E. anophelis infection identified, Central African Republic E. anophelis from mosquito 1 st reported case of E. anophelis meningitis Two outbreaks of E. anophelis bloodstream infections, USA You cannot completely ignore modern day taxonomy. Some proposals can have important consequences Some Suggestions (cont.) Classification changes can also be important. Follow the literature to see if they are generally accepted or not. Unless you are a researcher, state reference laboratory, or major medical center, do not attempt to periodically update identification schemes (e.g., MALDI-TOF) with recently proposed taxa unless warranted. Use final identifications such as [below] when appropriate: Aeromonas species Cronobacter sakazakii complex or group Coagulase-negative Staphylococcus species (not S. saprophyticus) Step 2: Sources for Taxonomic Updates Periodically check taxonomic journals for newly described species of clinical origin Check LPSN website for updates Database searches such as PubMed ( Check journals that publish taxonomic updates of possible clinical or public health importance Diagnostic Microbiology & Infectious Diseases (since 2015) Journal of Clinical Microbiology (since 2017) Journals to Watch for New Species Proposals International Journal of Systematic and Evolutionary Microbiology (IJSEM) Diagnostic Microbiology & Infectious Disease Updates Systematic and Applied Microbiology (SAM) Antonie van Leeuwenhoek (AEM) New Microbes and New Infections (NMNI) Current Microbiology 6

7 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