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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?

• 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

Bacterial Taxonomy for Clinical Microbiologists

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

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Description of a New Species [Idealized]

NEW SPECIES

Bios

16S

DDH, ANI

TypeStrain

Chemo

Morpho&

Physio

Some Requirements for a Valid Species

• 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

• G+C mol%

• Full 16S rRNA gene sequence, DDH, and/or ANI

Proposed New Species

Published in IJSEM

Automatically

Validated

Not Published in IJSEM (AVL)

Subsequent Publication on Validation List in IJSEM

Validated Species

Pathways to Species Validation

C. malonaticussp. nov.

Enterobacter sakazakii

(Farmer, 1980)

C. turicensissp. nov.

C. muytjensiisp. nov.

C. dublinensissp. nov.

Cronobactersakazakii

(Iversen, 2008)

Classification

Nomenclature

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 1995 – 2010 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)

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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 58:1737-1745)

– International Code of Nomenclature

(2018) IJSEM (in press)

• List of Prokaryotic Names with

Standing in Nomenclature

http://www.bacterio.net/index.html

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 - 2018

Group Proposal Basis

M. africanum, M. bovis, M. caprae, M. microti, etc (N)

Heterotypic synonyms of Mycobacterium tuberculosis

WGS, dDDH

Enterobacteriaceae (C) Reclassification of species into 6 or 7 different families or subfamilies

WGS, MLSA, 16S, 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 Atlantibacter

MLSA

Escherichia vulneris (C) Proposed reclassification to genus Pseudescherichia

Modern Bacterial Taxonomy –Pluses, Perils, and Pitfalls

1970 1980 1990 20101960

Miniaturized

Automated

MALDI-TOF

Conventional

2000

PCR

WGS

16SImportant Changes in Bacterial Taxonomy

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Changing Face of Bacterial Species Identification “Have Sequencer, Will Travel”

Evolution of Bacterial Species Species Proliferation

0

200

400

600

800

1000

1200

1980 1985 1990 1995 2000 2005 2010 2015

LPSN

Genus Species

New Species Described in 2016 – 2017 in New Microbes and New Infections

Well , here's another nice mess you've gotten me into

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Problems for the Bench Microbiologist with Modern Day Bacterial Taxonomy

• Species proposals often based upon a single type strain

• 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

New Bacterial Species (2016)One of the Problems

Journal No. Species Described

(est.)

From Clinical Samples (%)

Clinically Important

(%, est.)

Int J Systematic Evolutionary Microbiology

719 21 (2.9%) <10%

Antonie van Leeuwenhoek 80 4 (5%) <25%

New Microbes & New Infections 67 65 (97%) 0%

Archives of Microbiology 26 0 (0%) NA

Current Microbiology 25 1 (4%) 0%

Systematic & Applied Microbiology

24 1 (4) 100%

“Localimania”

• Laribacter honkongensis (2001)

• Actinomyces hongkongensis (2003)

• Eggerthella hongkongensis (2004)

• Sedimentibacter hongkongensis (2004)

• Anaerospora hongkongensis (2005)

• Alkanindiges hongkongensis (2005)

• Catabacter hongkongensis (2007)

“Salami Slicing”

• 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”

• 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

Remedial Solutions for the Patient

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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).

• Have one or more staff periodically review potential taxonomic updates or changes; discuss these updates at lab meetings when appropriate

• You cannot completely ignore modern day taxonomy. Some proposals can have important consequences.

Elizabethkingia anophelis

2010 2012 2014 20162006

Two outbreaks of E. anophelis bloodstream

infections, USA

1st retrospective case of E. anophelis infection

identified, Central African Republic

E. anophelis sp. nov.from mosquito

1st reported case of E. anophelismeningitis

1st reported outbreak with E. anophelis (ICU)

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 (https://www.ncbi.nlm.nih.gov/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)

• Systematic and Applied Microbiology (SAM)

• Antonie van Leeuwenhoek (AEM)

• New Microbes and New Infections (NMNI)

• Current Microbiology

Diagnostic Microbiology & Infectious Disease Updates

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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