MINIREVIEW

crossm

An Update on the Novel Genera and Species and Revised

Taxonomic Status of Bacterial Organisms Described in 2016
and 2017
Erik Munson,a Karen C. Carrollb

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a
College of Health Sciences, Marquette University, Milwaukee, Wisconsin, USA
b Division of Medical Microbiology, Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA

ABSTRACT Recognition and acknowledgment of novel bacterial taxonomy and no-

menclature revisions can impact clinical practice, disease epidemiology, and routine
clinical microbiology laboratory operations. The Journal of Clinical Microbiology (JCM)
herein presents its biannual report summarizing such changes published in the years
2016 and 2017, as published and added by the International Journal of Systematic
and Evolutionary Microbiology. Noteworthy discussion centers around descriptions of
novel Corynebacteriaceae and an anaerobic mycolic acid-producing bacterium in the
suborder Corynebacterineae; revisions within the Propionibacterium, Clostridium, Bor-
relia, and Enterobacter genera; and a major reorganization of the family Enterobacte-
riaceae. JCM intends to sustain this series of reports as advancements in molecular
genetics, whole-genome sequencing, and studies of the human microbiome con-
tinue to produce novel taxa and clearer understandings of bacterial relatedness.

KEYWORDS bacteria, nomenclature, phylogenetics, taxonomy

I n 2017, the Journal of Clinical Microbiology (JCM) published its first series of minire-
views summarizing newly published novel microbial taxa and revisions to taxonomic
nomenclature within the disciplines of bacteriology (1), parasitology (2), virology (3),
mycology (4), and mycobacteriology (5). With respect to bacteriology, this itemization
and discussion of novel taxa and changes to taxonomy are particularly relevant because
these are often the by-products of human microbiome investigations and/or advance-
ments in molecular genetics and genomic sequencing strategies. Applications of
taxonomic changes can be broad ranging. The impact on clinical care includes appro-
priate utilization of antimicrobial susceptibility testing standards in terms of test
procurement and data interpretation (6) and a broader understanding of the patho-
genesis and epidemiology of emerging pathogens (7, 8). In addition, nomenclature
changes can directly impact a given clinical microbiology laboratory from an adminis-
trative standpoint (conformity to accreditation checklist standards [9]). In a recent Citation Munson E, Carroll KC. 2019. An update
on the novel genera and species and revised
survey on the impact of taxonomic changes on clinical care sent to the American taxonomic status of bacterial organisms
Society for Microbiology ClinMicroNet listserv, several respondents mentioned the described in 2016 and 2017. J Clin Microbiol
challenge of trying to know when changes are made and how to efficiently implement 57:e01181-18. https://doi.org/10.1128/JCM
.01181-18.
and communicate their relevance to both the laboratory and clinicians (K. Carroll,
Editor Colleen Suzanne Kraft, Emory University
unpublished data). Copyright © 2019 American Society for
As such, we add to the comprehensive capstone previously established (1, 10) by Microbiology. All Rights Reserved.
providing a (second) biannual update of novel prokaryotic taxa and bacterial nomen- Address correspondence to Karen C. Carroll,
clature revisions published in the years 2016 and 2017. Unless otherwise indicated, the kcarrol7@jhmi.edu.
Accepted manuscript posted online 26
presented organisms were derived from human clinical material and nomenclature
September 2018
designations have been published or added by the International Journal of Systematic Published 30 January 2019
and Evolutionary Microbiology (IJSEM).

February 2019 Volume 57 Issue 2 e01181-18 Journal of Clinical Microbiology jcm.asm.org 1

Minireview Journal of Clinical Microbiology

METHODS
Validly published novel and revised taxa pertinent to prokaryotic species must meet
one of two requirements: (i) they must be described in an original investigation
published in IJSEM, or (ii) they must be described in a study published in an alternative
journal with later inclusion on an approved list in IJSEM. Journals that have published
studies providing an effective description of validly named new taxa which may be
relevant to the practice of clinical microbiology include Anaerobe; Antonie Van Leeu-
wenhoek; APMIS; Clinical Microbiology and Infection; Current Microbiology; Diagnostic
Microbiology and Infectious Disease; Emerging Microbes and Infections; Frontiers in Ge-
netics; Frontiers in Microbiology; Infection, Genetics and Evolution; Journal of Antimicrobial
Chemotherapy; JCM; Journal of General and Applied Microbiology; Microbiology and
Immunology; Microbiologyopen; New Microbes and New Infections; Research in Microbi-
ology; Standards in Genomic Sciences; and Systematic and Applied Microbiology. Six times

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per year, IJSEM publishes papers entitled “List of new names and new combinations
previously effectively, but not validly, published” (an example is provided in reference
11). To be considered for inclusion on this approved list, authors must submit a copy
of the published article to the editorial office of IJSEM for confirmation that all elements
necessary for valid publication have been met. In addition, type strains are to be
deposited into recognized culture collections in two separate countries. Taxa on these
approved lists may be subject to reclassification on the basis of a synonym designation
or transfer to another genus. Within this article, taxa that were previously and effec-
tively described in journals outside of IJSEM are footnoted in such fashion.
All issues of IJSEM published from January 2016 through December 2017 were
searched for original articles describing new species taxonomy or accepted changes in
taxonomic nomenclature. This audit was further filtered by organisms recovered from
human sources. When an initial organism reservoir could not be ascertained, PubMed
primary literature searches (U.S. National Library of Medicine and the National Institutes
of Health) of the novel or revised taxon attempted to index subsequent case reports for
further investigation; several of these case reports are referenced throughout this
article. A number of IJSEM publications simply identified isolates as being derived from
a specific specimen source (including sterile body sites) but did not provide contextual
clinical data. Therefore, in these scenarios (including for a number of novel taxa derived
from blood culture), the clinical significance of these taxa was interpreted as “not
established” (examples are provided in references 12 to 21). (By way of PubMed primary
literature searches, attempts were also made to investigate the uncertain clinical
significance of previously reported novel and revised taxa [1]). Additional studies may
be necessary to characterize the ultimate clinical significance of novel taxa (22).
Twice per year, IJSEM publishes papers entitled “Notification of changes in taxo-
nomic opinion previously published outside the IJSEM.” The journal publicizes these
changes in taxonomic opinion simply as a service to bacteriology, rather than state-
ments of validly published or approved taxonomy. No such reports pertaining to
isolates derived from human sources were found in searches of IJSEM literature from
2016 and 2017; two such publications from 2014 and 2015 (23, 24) were noted in the
previous minireview (1). Future JCM taxonomy compendia will report pertinent findings
from such publications in an effort to subsequently ascertain either the true clinical
significance of isolates or determine if official taxonomic status has been granted.

RESULTS AND DISCUSSION

Table 1 is a compilation of novel taxa recovered from human sources stratified by
Gram reaction, cellular morphology, and oxygen requirement for growth. Table 2 lists
taxonomic revisions for organisms recovered from human sources. Finally, Table 3, on
the basis of recent peer-reviewed publications, attempts to retrospectively ascribe
clinical significance to a number of organisms whose clinical significance was not
established in the previous taxonomy compendium or to add new knowledge for
organisms recovered from clinical infections (1). Those findings warranting emphasis
are discussed below.

February 2019 Volume 57 Issue 2 e01181-18 jcm.asm.org 2

 TABLE 1 New bacterial species recovered from human clinical material reported from January 2016 through December 2017
Scientific name Family Source Clinical relevance Growth characteristics Reference(s)
Gram-positive cocci
Minireview

Streptococcus halichoeri subsp.
hominis subsp. nov.
Auricoccus indicus gen. nov.,
sp. nov.
Streptococcaceae Blood, empyema, sinus At least one patient had sepsis Gram-positive cocci occurring in pairs or chains; non-spore forming; hydrolyzes bile esculin; 25–27
colony description is similar to the species description provided in reference 25; colonies
are white, nonhemolytic, and umbonate; Lancefield group B
Staphylococcaceae Skin Isolated from the external ear of a Gram-positive aerobic cocci, nonmotile, non-spore forming; positive for catalase and 28
healthy human oxidase; grows between 20 and 40°C, with optimum growth at 35°C

Gram-positive bacilli
Tsukamurella hongkongensis
sp. nov.
Tsukamurella sinensis sp. nov.
Tsukamurellaceae Corneal scraping; blood culture Isolated from a patient who had
keratitis and a second patient
with catheter-related
bacteremia; both patients were
from Hong Kong
Tsukamurellaceae Conjunctival swab Isolated from a patient in Hong
Kong with conjunctivitis
Aerobic, Gram-positive, nonmotile, non-spore-forming bacillus; catalase positive; grows best 29
on Columbia agar with 5% defibrinated sheep blood agar; colonies are orange to red,
dry, and rough after 48 h of incubation at 37°C
Aerobic, Gram-positive, nonmotile, non-spore-forming rod; catalase positive; grows best on 29
Columbia agar with 5% defibrinated sheep blood agar; colonies are white, dry, and

February 2019 Volume 57 Issue 2 e01181-18

Dermabacter vaginalis sp. nov.
Dermabacter jinjuensis sp. nov.
Corynebacterium lowii sp. nov.
Corynebacterium oculi sp. nov.
Lawsonella clevelandensis gen.
nov., sp. nov.
Nocardia shinanonensis sp.
nov.
Gordonia hongkongensis sp.
nov.
Corynebacterium gottingense
sp. nov.
Paenibacillus ihumii sp. nov.
rough after 48 h of incubation at 37°C
Dermabacteraceae Vaginal fluid Not established; isolated from Facultative anaerobic, Gram-positive, short bacillus; non-spore forming, nonmotile, catalase 30
vaginal fluid of a Korean positive, oxidase negative; creamy white colonies that grow optimally at 37°C
female
Dermabacteraceae Pus from a finger wound Patient in a hospital in Jinju, Cells are Gram-positive coryneform-like coccobacilli; on sheep blood agar, colonies are 31
South Korea, with finger gray-white, round, and 0.5–1 mm; growth is optimum at 30–40°C; cells grow under
necrosis anaerobic conditions and can tolerate NaCl up to 6%; pyrrolidonyl arylamidase positive;
acid is produced from a variety of carbohydrates
Corynebacteriaceae Eye Associated with ocular infections Short to medium-length Gram-positive bacilli that occur singly or in palisades, pairs, or V 32
shapes; colonies are slow growing (72 h), convex smooth gray-white or light beige,
nonhemolytic; grows in air, in 5% CO2, and under anaerobic conditions at 37°C or 42°C
but not at 25°C; catalase positive, oxidase negative, nonmotile, lipophilic, urease
positive, nitrate negative
Corynebacteriaceae Eye Associated with ocular infections Short to medium-length Gram-positive bacilli that occur singly or in palisades, pairs, or V 32
shapes; colonies are slow growing (72 h), convex smooth gray-white or light beige,
nonhemolytic; grows in air, in 5% CO2, and under anaerobic conditions at 37°C and 42°C
but not at 25°C; catalase positive, oxidase negative, nonmotile, lipophilic, urease
positive, nitrate negative
Suborder Abscesses Associated with a variety of Pleomorphic Gram-positive cocci and bacilli; partially acid fast; forms pinpoint, waxy 33–35
Corynebacterineae; human abscesses in the breast, colonies on CDC anaerobic blood agar after 5–7 days of incubation; optimal growth at
no family liver, spine, peritoneum 35°C in an environment of ⱕ1.0% oxygen
assignment
Nocardiaceae Eye Isolated from the aqueous humor Aerobic Gram-positive partially acid fast, nonmotile; forms white aerial mycelium; grows at 36
from a patient with 25, 35, and 45°C
endophthalmitis
Nocardiaceae Blood Recovered from two patients: in Gram-positive modified acid-fast, nonsporulating bacilli; grows on Columbia agar with 5% 12
one from a blood culture and defibrinated sheep blood aerobically as pink to orange nonhemolytic colonies; catalase
in the other from peritoneal positive; oxidase negative
dialysis effluent
Corynebacteriaceae Blood Isolated from the blood of a Gram-positive, bacillus-shaped bacteria that show typical palisade arrangements of the 13
patient with bacteremia of cells; non-spore forming, catalase positive, oxidase negative; forms white-cream circular
unknown origin in Göttingen, colonies on Columbia blood agar
Germany
Paenibacillaceaea Feces Not established; the isolate was Motile, spore-forming, Gram-positive bacillus (frequently overdecolorizes in Gram stain); 37b
from a female in France prior optimal growth at 37°C; capable of growth under microaerophilic and anaerobic
to bariatric surgery conditions; 1- to 2-mm-diameter gray colonies on blood-enriched Columbia agar;
catalase and urease negative; utilization of several carbohydrates

Gram-negative cocci
Neisseria dumasiana sp. nov.
Neisseriaceae Sputum (n ⫽ 2) Not established; clinical isolates
submitted to a U.S. reference
laboratory in 2009 and 2012
Facultative anaerobic, nonmotile, oxidase-positive Gram-negative coccus or coccobacillus; 38
optimal growth at 37°C; gray-pigmented 1.9- to 2.8-mm-diameter colonies cultivated on
chocolate agar plates supplemented with 10% horse blood in 5% CO2; catalase and
proline isomerase positive; reduces nitrate to nitrite; acid production from D-glucose but
not from maltose or sucrose
(Continued on next page)

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Journal of Clinical Microbiology

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 TABLE 1 (Continued)
Scientific name
Gram-negative bacilli
Enterobacter bugandensis sp.
nov.
Alkanindiges hongkongensis
sp. nov.
Microvirga massiliensis sp. nov.
February 2019 Volume 57 Issue 2 e01181-18
Oblitimonas alkaliphila gen.
nov., sp. nov
Burkholderia concitans
Burkholderia turbans
Achromobacter deleyi sp. nov.
Acinetobacter dijkshoorniae sp.
nov.
Vibrio cidicii sp. nov.
Enterobacter hormaechei
subsp. hormaechei subsp.
nov.
Enterobacter hormaechei
subsp. oharae subsp. nov.
Enterobacter hormaechei
subsp. steigerwaltii subsp.
nov.
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Family Source
Enterobacteriaceae Blood (17)
Moraxellaceae Parotid abscess incision and
drainage
Methylobacteriaceae Feces
Pseudomonadaceae Urine (n ⫽ 3), leg tissue (n ⫽
2), liver, lung tissue, and
foot wound specimens
Burkholderiaceae Lung tissue, blood
Burkholderiaceae Pleural fluid
Alcaligeneaceae Prostatic secretion, pharyngeal
swab
Moraxellaceae Clinical strains, including those
from wound (n ⫽ 3),
sputum (n ⫽ 2), blood,
urine, catheter, and
nephrology drain specimens
Vibrionaceae Blood (n ⫽ 3)
Enterobacteriaceae Sputum (n ⫽ 2), throat, blood,
groin, and fecal samples, as
described in reference 17
Enterobacteriaceae Blood (n ⫽ 2), trachea (n ⫽ 2),
bronchoalveolar lavage fluid
(n ⫽ 2), throat (n ⫽ 2),
feces, ear, sputum, mouth,
urine, and abscess
specimens, as described
previously (17)
Enterobacteriaceae Wound (n ⫽ 6), urine (n ⫽ 5),
blood (n ⫽ 3), trachea (n ⫽
2), bronchoalveolar lavage
fluid, sputum, lung biopsy,
throat, vaginal, and central
line specimens, as described
previously (17)
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Clinical relevance
Isolates from a neonatal
septicemia outbreak in
Tanzania; possessed the CTX-
M-15 resistance gene; resistant
to fluoroquinolone,
aminoglycoside, and
tetracycline antimicrobials
Infected Warthin’s tumor resulting
in parotid gland abscess and
peripheral leukocytosis; the
patient responded to drainage
and amoxicillin-clavulanate
Not established; possesses the
largest genome (9.2
megabases) of any human
isolate
Not established; clinical isolates
submitted to a U.S. reference
laboratory from 1969 to 1979
Not established
Not established
Not established; pharyngeal
isolate from a U.S. cystic
fibrosis patient
Not established
Not established
Not established
Not established
Not established
Growth characteristics Reference(s)
Minireview
Colonial growth consistent with that of other Enterobacter spp.; lactose fermentation 39
observed only after 24 h of incubation; citrate, arginine dihydrolase, and ornithine
decarboxylase positive; lysine decarboxylase, urease, and Voges-Proskauer negative
Aerobic, nonmotile, oxidase-negative Gram-negative coccobacillus; 0.5-mm-diameter 40c
(nonhemolytic) colonies on blood and MacConkey agars at 37°C; general failure to
ferment or oxidize carbohydrates
Aerobic, nonmotile, non-spore-forming, oxidase-negative Gram-negative bacillus; colonies 41d
propagated on modified 7H10 medium supplemented with sheep blood; optimal
growth at 37°C; leucine arylamidase, nitrate reductase, and cysteine arylamidase
positive; alkaline phosphatase negative
Microaerophilic, nonmotile, oxidase-positive Gram-negative bacillus; growth on routine 42
bacteriologic media (including blood agar and MacConkey agar); optimal growth at 20–
35°C; urea, gelatin, and esculin hydrolysis negative; leucine arylamidase and glucose
oxidation positive; lactose and sucrose utilization negative
Nonmotile, oxidase-positive Gram-negative bacillus; less than 1-mm-diameter colonies 14e
cultivated on tryptic soy and MacConkey agars at 15–28°C; positive for Tween 60
hydrolysis, negative for Tween 80 hydrolysis; urease, esculin hydrolysis, ␤-galactosidase,
and caprate assimilation negative; subsequent taxonomic revision described in Table 2
Nonmotile, oxidase-positive Gram-negative bacillus; less than 1-mm-diameter colonies 14e
cultivated on tryptic soy and MacConkey agars at 15–37°C; positive for Tween 60
hydrolysis, negative for Tween 80 hydrolysis; glucose and caprate assimilation positive;
urease, esculin hydrolysis, and ␤-galactosidase negative; subsequent taxonomic revision
is described in Table 2
Motile, oxidase-positive Gram-negative bacillus; nonpigmented 1.0- to 1.5-mm-diameter 43
colonies cultivated on tryptic soy agar at 28°C; growth of selected strains on cetrimide
agar in the presence of 3.0% and 4.5% NaCl; nitrite reduction and denitrification
negative; caprate assimilation and alkaline phosphatase positive
Aerobic, nonmotile, oxidase-negative Gram-negative coccobacillus; 1- to 2-mm-diameter 15
nonhemolytic colonies cultivated on tryptic soy agar at 30°C; gelatin hydrolysis and
citraconate negative; produces acid from D-glucose; 53% of strains utilize tryptamine
Curved, motile, oxidase-positive Gram-negative bacillus; sucrose-fermentative colonies 16
cultivated on thiosulfate-citrate-bile salts-sucrose agar; growth observed in tryptic soy
broth at 30°C with NaCl concentrations up to 8% for most isolates; utilizes L-rhamnose
as the sole carbon source; most isolates do not utilize sodium citrate
Gram-negative bacillus exhibiting general characteristics of Enterobacter cloacae complex; 17f
dulcitol positive; adonitol, D-arabitol, D-sorbitol, and D-melibiose negative
Gram-negative bacillus exhibiting general characteristics of the Enterobacter cloacae 17f
complex; AmpC hyperproduction in 25% of strains characterized in reference 17;
D-sorbitol and D-melibiose positive; adonitol, D-arabitol, and dulcitol negative
Gram-negative bacillus exhibiting general characteristics of Enterobacter cloacae complex; 17f
AmpC hyperproduction in 42% of strains characterized in reference 17; positive adonitol,
D-arabitol, D-sorbitol, and D-melibiose test results; negative dulcitol test result
(Continued on next page)
Journal of Clinical Microbiology
 TABLE 1 (Continued)
Scientific name
Citrobacter europaeus sp. nov.
Sphingobacterium cellulitidis
sp. nov.
Haemophilus massiliensis sp.
nov.
Weeksella massiliensis sp. nov.
February 2019 Volume 57 Issue 2 e01181-18
Ehrlichia muris subsp.
eauclairensis subsp. nov.
Kingella negevensis sp. nov.
Psychrobacter pasteurii sp.
nov.
Psychrobacter piechaudii sp.
nov.
Burkholderia singularis sp. nov.
Shewanella carassii sp. nov.
Gram-positive anaerobes
Sellimonas intestinalis gen.
nov., sp. nov.
Peptoniphilus catoniae sp. nov.
Propionibacterium namnetense
sp. nov.
Agathobaculum
butyriciproducens gen.
nov., sp. nov.
Butyricicoccus faecihominis sp.
nov.
jcm.asm.org 5
Family Source Clinical relevance
Enterobacteriaceae Feces Not established; isolate from a
U.S. patient with diarrhea
Sphingobacteriaceae Toe Purulent discharge from a Kuwaiti
cellulitis patient; nucleic acid
homology demonstrated with
previously unnamed Singapore
environmental isolate
Pasteurellaceae Peritoneal fluid Isolate from a Senegalese female
with pelvic peritonitis
complicating a ruptured
ovarian abscess
Flavobacteriaceae Urine Isolate from a Senegalese male
with acute cystitis
Anaplasmataceae Whole blood Isolate from a febrile Wisconsin
(USA) patient with a history of
tick exposure in 2009
Neisseriaceae Oropharynx (n ⫽ 21) Not established; isolates from
healthy Israeli and Swiss
children
Moraxellaceae Human origin (n ⫽ 2); not Not established; isolates
otherwise specified submitted to a French
collection bank in 1972
Moraxellaceae Human origin (n ⫽ 4); not Not established; isolates
otherwise specified submitted to a French
collection bank in 1972
Burkholderiaceae Respiratory (n ⫽ 4) Not established; isolates from
cystic fibrosis patients in
Canada and Germany
Shewanellaceae Feces Not established; isolate from a
Chinese infant with diarrhea
Lachnospiraceae Feces Not established; isolated from a
fecal sample from a healthy
Korean woman
Peptoniphilaceae Feces Not established; isolated from a
human fecal sample in
southern Peru
Propionibacteriaceae Bone Infected tibial fracture
Ruminococcaceae Feces Not established; recovered from
the feces of a healthy 23-year-
old Korean woman
Clostridiaceae Feces Not established; recovered from
the feces of a healthy human
adult
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Growth characteristics Reference(s)
Gram-negative bacillus exhibiting general characteristics of Citrobacter spp.; growth 44
Minireview
observed from 20 to 50°C; H2S, inositol, and salicin positive; arginine dihydrolase, citrate,
sucrose, and starch negative
Aerobic, nonmotile, non-spore-forming, oxidase-positive Gram-negative bacillus; 0.5-mm- 45
diameter pale yellow colonies cultivated on nutrient, tryptic soy, and MacConkey agars
after 48 h of incubation at 28–37°C; catalase, Voges-Proskauer, tryptophan deaminase,
and ␤-galactosidase positive; urease, decarboxylases, citrate, and nitrate negative
Facultative, nonmotile, non-spore-forming, oxidase-positive Gram-negative bacillus; 0.5- to 46b
1-mm-diameter nonhemolytic colonies on blood-enriched Columbia agar; optimal
growth at 37°C; alkaline phosphatase, leucine arylamidase, and D-glucose utilization
positive; indole and D-mannose utilization negative
Aerobic, nonmotile, non-spore-forming, oxidase-positive Gram-negative bacillus; light 47b
yellow, 2-mm-diameter, smooth, nonhemolytic colonies on blood-enriched Columbia
agar; alkaline phosphatase, leucine arylamidase, and D-xylose utilization positive; trypsin,
indole, urease, ␤-galactosidase, and D-glucose utilization negative
Morphologic and cultural similarities to E. muris subsp. muris subsp. nov. (Table 2); 48
however, E. muris subsp. euclairensis subsp. nov. is localized to the United States; the
sole vector is Ixodes scapularis, and it causes human disease
Nonmotile, non-spore-forming, oxidase-positive Gram-negative coccobacillus that exhibits 49
capnophilic growth; pale yellow, beta-hemolytic 0.5- to 1-mm-diameter colonies on
blood-enriched Columbia agar; optimal growth at 37°C; leucine arylamidase positive;
urease, catalase, indole, ornithine decarboxylase, and proline arylamidase negative
Aerobic, nonmotile, non-spore-forming, oxidase-positive Gram-negative coccobacillus; 50
optimal growth at 30°C; translucent, bright, 1- to 2-mm-diameter colonies observed on
blood agar; catalase, urease, and lipase positive; reduces nitrate to nitrite; originally
identified as a member of the Moraxella genus
Aerobic, nonmotile, non-spore-forming, oxidase-positive Gram-negative coccobacillus; 50
optimal growth at 30°C; translucent, bright, 1- to 2-mm-diameter colonies observed on
blood agar; catalase positive; urease and lipase activity is variable; unable to reduce
nitrate to nitrite; originally identified as a member of the Moraxella genus
Aerobic, non-spore-forming Gram-negative bacillus; motility variable; growth on Columbia 51g
sheep blood agar (mucoid, nonhemolytic colonies), Burkholderia cepacia agar, yeast
extract mannitol agar, and MacConkey agar at 42°C; slow oxidase activity; acidification
of glucose, maltose, lactose, and xylose but not sucrose; nitrate reduction, lysine
decarboxylase, and ornithine decarboxylase negative
Facultative, motile, oxidase-positive Gram-negative bacillus; growth on LB agar and blood 52
agar (hemolytic), with optimal growth at 35°C; poor growth on MacConkey agar;
colonies on LB agar are pink-orange with a 2- to 3-mm diameter; catalase, H2S, nitrate
reduction, and L-proline arylamidase positive; urease and ornithine decarboxylase
negative; does not grow in 10% NaCl
Gram-positive diplococcus-shaped, obligate anaerobe, non-spore-forming; forms ivory 53
yellow colonies; growth occurs at 25–45°C; the optimal growth temperature is 37°C;
motile; H2S, indole, urease, and esculin hydrolysis negative; acid production from a
variety of carbohydrates
Gram-positive, non-spore-forming coccus; obligate anaerobe; colonies on blood agar are 54
needle point in size, beige, and circular with a smooth surface; optimal growth at 37°C;
catalase, urease, indole, and nitrate negative
Gram-positive, non-spore-forming, nonmotile, pleomorphic bacilli; anaerobic; after 6 days of 55
incubation colonies are circular, dome shaped, and from pale cream to orange-salmon;
optimal growth at 35°C
Gram-positive, non-spore-forming strict anaerobe; grows optimally at 37°C in the presence 56
of 0.5% NaCl, pH 7; nonmotile; catalase and oxidase negative; butyrate producing
Gram-positive coccoid-shaped organisms; nonmotile without spores; obligately anaerobic; 57
colonies may appear waxy and yellowish after growth at 37°C for 72 h; indole positive
(Continued on next page)
Journal of Clinical Microbiology
 TABLE 1 (Continued)
Scientific name
Faecalimonas umbilicata gen.
nov., sp. nov.
Merdimonas faecis gen. nov.,
sp. nov.
Monoglobus pectinilyticus gen.
nov., sp. nov.
Gram-negative anaerobes
Anaerospora hongkongensis
gen. nov., sp. nov.
February 2019 Volume 57 Issue 2 e01181-18
Megasphaera massiliensis sp.
nov.
Sedimentibacter hongkongensis
sp. nov.
Dielma fastidiosa gen. nov.,
sp. nov.
Prevotella colorans sp. nov.
Ruthenibacterium
lactatiformans gen. nov.,
sp. nov.
Gabonibacter massiliensis gen.
nov., sp. nov.
Fournierella massiliensis gen.
nov., sp. nov.
Alistipes ihumii sp. nov.
Bacteroides koreensis sp. nov.
Bacteroides kribbi sp. nov.
jcm.asm.org 6
Family Source Clinical relevance Growth characteristics Reference(s)
Lachnospiraceae Feces Not established; recovered from Gram-positive bacilli in pairs or chains; obligate anaerobe; nonmotile; nonpigmented; may 58
Minireview
the feces of a healthy human form spores; colonies have a depressed center (umbilicate); H2S produced; indole,
adult catalase, and urease negative
Lachnospiraceae Feces Not established; recovered from Gram-positive strictly anaerobic; non-spore forming; catalase, indole, and oxidase negative; 59
the feces of a healthy human colonies are ivory colored and grow optimally at 37°C
adult
Ruminococcaceae Feces Not established; recovered from Gram-positive cocci that are strictly anaerobic; catalase positive; oxidase negative; indole 60
the feces of a 27-year-old negative; ferments pectin; optimum growth between 30 and 40°C
healthy woman living in New
Zealand
Veillonellaceae Blood Not established; isolates from an Obligate anaerobic, slightly curved, multiple-spore-forming, Gram-negative bacillus (up to 18c
asymptomatic intravenous drug 14 ␮m in length); yields pinpoint, catalase-negative, nonhemolytic colonies on blood
abuser agar following 48 h of incubation at 37°C; relatively inert biochemically
Veillonellaceae Feces Not established; isolate from an Obligate anaerobic, non-spore-forming, nonmotile Gram-negative coccobacillus; yields 61c
HIV-positive patient catalase-negative, 0.5- to 1.0-mm-diameter colonies on blood-enriched Columbia agar;
optimal growth at 37°C; acid production from sorbitol and arabitol
Peptostreptococcaceaeh Blood Isolated from a patient with septic Obligate anaerobic, slightly curved, motile, terminal-spore-forming Gram-negative bacillus; 62c
shock and multiorgan failure yields pinpoint colonies on buffered charcoal yeast extract agar following 72 h of
secondary to colon carcinoma incubation at 37°C; growth on agar utilizing Bactec anaerobic blood culture broth under
anaerobic conditions; no growth on brucella agar, brain heart infusion medium, or
cooked meat medium; catalase and indole positive; nitrate reduction negative
Erysipelotrichaceae Feces Not established Obligate anaerobic, motile, non-spore-forming Gram-negative bacillus; 0.5- to 1.0-mm- 63d
diameter colonies on blood-enriched Columbia agar; optimal growth at 30°C; esculin
hydrolysis and acid arylamidase positive; mannose, sucrose, and D-glucose utilization
negative
Prevotellaceae Wound Isolated in the context of a Obligate anaerobic, nonmotile, non-spore-forming, short and pleomorphic Gram-negative 64
polymicrobial infection bacillus; after 2–5 days of incubation at 35–37°C, 1-mm-diameter colonies have weak
greyish brown pigment; colonies develop toffee brown pigment after extended
incubation; glucose, sucrose, and lactose fermentation positive; catalase (15% H2O2) and
indole negative
Ruminococcaceae Feces Not established; isolate from a Obligate anaerobic, nonmotile, non-spore-forming Gram-negative bacillus; nonhemolytic, 65
healthy Russian male 0.15- to 0.40-mm-diameter colonies after 96 h of incubation on EG agar at 37°C; bile
tolerant; growth can be stimulated by 5 mg hemin, 0.5% maltose, and 2–3% Oxgall;
esculin and starch hydrolysis positive
Porphyromonadaceae Feces Not established; isolate from a Obligate anaerobic, motile Gram-negative coccobacillus; 2-mm-diameter white colonies 66i
healthy Gabonese male after incubation on sheep blood-enriched Columbia agar at 37°C; indole, esterase,
esterase lipase, and acid phosphatase positive; catalase, oxidase, alkaline phosphatase,
and lipase negative
Ruminococcaceae Feces Not established; isolate from a Obligate anaerobic, nonmotile, non-spore-forming Gram-negative bacillus; optimal growth 67
healthy French male at 37°C; 1-mm-diameter colonies exhibit white pigment; catalase, oxidase, and indole
negative; nitrate reductase, D-mannose, and maltose positive; the major short-chain
fatty acid is acetic acid
Rikenellaceae Feces Isolate from a French female with Obligate anaerobic, non-spore-forming, nonmotile Gram-negative bacillus; optimal growth 68b
anorexia nervosa; clinical at 37°C; translucent 0.2-mm-diameter colonies on blood-enriched Columbia agar; leucyl
significance not established glycine arylamidase, raffinose, and mannose positive; urease, indole, catalase, and nitrate
reductase negative
Bacteroidaceae Feces Not established; isolate from a Obligate anaerobic, nonmotile, non-spore-forming Gram-negative bacillus; optimal growth 69
healthy adult at 37°C; smooth, creamy, 1-mm-diameter colonies on reinforced clostridial medium;
grows in the presence of bile; similar biochemical and fatty acid profile as Bacteroides
kribbi sp. nov., with the exception of negative reactions for ␤-glucosidase and glutamic
acid decarboxylase
Bacteroidaceae Feces Not established; isolate from a Obligate anaerobic, nonmotile, non-spore-forming Gram-negative bacillus; optimal growth 69
healthy adult at 37°C; smooth, creamy, 1-mm-diameter colonies on reinforced clostridial medium;
grows in the presence of bile; similar biochemical and fatty acid profile as Bacteroides
koreensis sp. nov., with the exception of positive reactions for ␤-glucosidase and
glutamic acid decarboxylase
(Continued on next page)
Journal of Clinical Microbiology
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 Minireview

TABLE 1 (Continued)
Scientific name
Spirochetes
Haematospirillum jordaniae
gen. nov., sp. nov.
Family Source Clinical relevance Growth characteristics Reference(s)
Rhodospirillaceae Blood (n ⫽ 14) Clinical diagnoses of septicemia Motile, helical Gram-negative bacterium with dimensions of 1.6 ␮m by 0.1–0.25 ␮m; 1-mm- 70, 71e
(n ⫽ 3) and bacteremia (n ⫽ 1) diameter colonies with slight alpha-hemolysis cultivated on heart infusion agar
provided in select instances supplemented with 5% rabbit blood after 48 h of incubation at 35°C; catalase, oxidase,
and hydrogen sulfide positive; urease, nitrate reduction, and indole negative

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Borrelia mayonii sp. nov. Spirochaetaceae Blood (n ⫽ 5), synovial fluid Clinical significance is described in Motile spirochetes cultivated from blood specimens utilizing Barbour-Stoenner-Kelly 73
reference 72 medium in a 34°C microaerophilic environment; B. mayonii-specific nucleic acid detected
by PCR from Ixodes scapularis ticks collected in Wisconsin and Minnesota (USA)
aOther members of the Paenibacillaceae have been reported to be Gram positive, Gram negative, or Gram variable.
bTaxonomic designation subsequently added in validation list no. 176 (74).
cTaxonomic designation subsequently added in validation list no. 168 (11).

dTaxonomic designation subsequently added in validation list no. 170 (75).

eTaxonomic designation subsequently added in validation list no. 171 (76).

fTaxonomic designation subsequently added in validation list no. 172 (77).

gTaxonomic designation subsequently added in validation list no. 178 (78).

hGenera of Peptostreptococcaceae are typically Gram-positive organisms.

iTaxonomic designation subsequently added in validation list no. 173 (79).

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TABLE 2 Revised bacterial taxa from January 2016 through December 2017
Former name Revised name Other information Reference(s)
Gram-positive cocci
Streptococcus oralis The main characteristics are those provided in references 80 and 81, with the 82
emended addition that some strains hydrolyze arginine
description
Streptococcus oralis Closely related species to S. oralis in the mitis S. oralis subsp. oralis was created; all strains produce IgA1 protease and 82
subsp. oralis group have been reclassified as subspecies of extracellular polysaccharide; they do not hydrolyze arginine
subsp. nov. S. oralis
Streptococcus Streptococcus oralis subsp. dentisani comb. nov. The description is the same as that provided in reference 83, with the 82
dentisani addition that it does not produce IgA1 protease or extracellular
polysaccharide; most strains possess ␣-galactosidase; strains have been
isolated from the dorsum of the tongue and human caries-free tooth
surfaces
Streptococcus Streptococcus oralis subsp. tigurinus comb. nov. The description is the same as that provided in reference 84, with the 82
tigurinus addition that most strains possess the enzyme ␣-galactosidase and all
possess the gene for N-acetyl-␤-glucosaminidase; strains have been

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isolated from human blood

Gram-positive bacilli
Brevibacterium Brevibacterium ravenspurgense emended The previous taxonomic status of B. massiliense is described in reference 85; 86
massiliense organism originally isolated from ankle discharge
Arthrobacter Haematomicrobium sanguinus gen. nov., comb. Original isolation from blood culture is described in reference 87; it has also 89
sanguinus nov. caused peritonitis in a dialysis patient (88)

Gram-negative bacilli
Achromobacter Achromobacter marplatensis Taxonomy revision related to previous erroneous report of sequence data; 92
spiritinus the previous taxonomy of A. spiritinus is described in references 1, 90, and
91; clinical relevance in humans is not established
Acinetobacter Acinetobacter courvalinii sp. nov. Human strains include those isolated from skin and soft tissue (n ⫽ 3), blood 19
genomic (n ⫽ 1), urine (n ⫽ 1), conjunctiva (n ⫽ 1), and tracheal aspirate
species 14BJ (n ⫽ 1) specimens; the previous designation is described in references 93
and 94; the clinical relevance of all isolates could not be ascertained
Acinetobacter Acinetobacter dispersus sp. nov. Human strains include those isolated from skin and soft tissue specimens 19
genomic (n ⫽ 3) and an unknown source (n ⫽ 1); the previous designation is
species 17 described in reference 93; the clinical relevance of all isolates could not be
ascertained
Acinetobacter Acinetobacter modestus sp. nov. Human strains include those isolated from blood (n ⫽ 2), throat (n ⫽ 1), 19
taxon 18 urine (n ⫽ 1), and skin and soft tissue (n ⫽ 1) specimens; the previous
designation is described in references 94 to 96; the clinical relevance of all
isolates could not be ascertained
Acinetobacter Acinetobacter proteolyticus sp. nov. Human isolates from skin and soft tissue (n ⫽ 4), blood (n ⫽ 1), and ear 19
taxon 19 (n ⫽ 1) specimens; the previous designation is described in reference 93;
the clinical relevance of all isolates could not be ascertained
Acinetobacter Acinetobacter vivianii sp. nov. Human strains include those isolated from blood (n ⫽ 2) and skin and soft 19
taxon 20 tissue (n ⫽ 1) specimens and an unknown source (n ⫽ 1); the previous
designation is described in references 93 and 94; the clinical relevance of
all isolates could not be ascertained
Klebsiella alba Klebsiella quasipneumoniae subsp. K. alba was originally isolated from a polluted soil sample in China, with the 100
similipneumoniae taxonomy previously published (97) and added (98); the taxonomic status
and clinical significance of K. quasipneumoniae subsp. similipneumoniae
human isolates are discussed elsewhere (1, 99)
Capnocytophaga Capnocytophaga canis sp. nov. Subset of less virulent C. canimorsus strains not isolated from human 101a
canimorsus infections has been given a novel species designation; the C. canimorsus
(selected designation is reserved for species including human pathogens
strains)
Paraburkholderia Caballeronia zhejiangensis comb. nov. The initial designation of Burkholderia zhejiangensis was published in 20
zhejiangensis reference to a wastewater isolate (102) and augmented by three clinical
isolates (blood, respiratory secretions) (103); the intermediate taxonomic
status of P. zhejiangensis was previously published (104) and added (105)
Helicobacter Helicobacter canicola sp. nov. Subset of H. cinaedi strains not isolated from human infections has been 106b
cinaedi given a novel species designation
(selected
strains)
Rhizobium pusense Agrobacterium pusense comb. nov. The initial designation of R. pusense was published in reference to a 21b
rhizosphere isolate (107); the pathogenicity of R. pusense (and the previous
reclassification of other Agrobacterium spp. as R. pusense) in human
infections is described in reference 108
Agrobacterium sp. Agrobacterium pusense comb. nov. Isolated from human blood 21b,c
genomovar G2
Elizabethkingia Elizabethkingia anophelis Clinical relevance not established in humans; the previous designation of E. 110
endophytica endophytica is described in reference 109; E. endophytica is no longer
considered a separate species of the genus Elizabethkingia
Rahnella Rahnella variigena sp. nov. Taxonomic status previously discussed in reference 1 111d
genomospecies
2
Enterobacter Klebsiella aerogenes comb. nov. Taxonomic status previously discussed in reference 112 113
aerogenes
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TABLE 2 (Continued)
Former name Revised name Other information Reference(s)
Herbaspirillum Noviherbaspirillum massiliense comb. nov. Isolation from feces of a healthy Senegal patient, with the initial taxonomic 116, 117
massiliense status previously described in references 1, 114, and 115
[Pasteurella] Rodentibacter pneumotropicus comb. nov. Official 16S rRNA-based taxonomic designation granted for (misclassified) [P.] 119
pneumotropica pneumotropica; human respiratory tract isolates are described in reference
118
Ehrlichia muris Ehrlichia muris subsp. muris subsp. nov. Clinical significance in humans not definitively established; serologic evidence 48
of human infection in Japan (120)
Acinetobacter Acinetobacter colistiniresistens sp. nov. Isolation previously described in reference 93 121
genospecies 13
Acinetobacter DNA Acinetobacter colistiniresistens sp. nov. Isolation previously described in reference 122 121
group 14
Burkholderia Caballeronia concitans comb. nov. Isolation and proposed taxonomic status previously published (14) and 123
concitans added (76)
Burkholderia Caballeronia turbans comb. nov. Isolation and proposed taxonomic status previously described (14) and 123
turbans added (76)

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Enterobacter Metakosakonia massiliensis comb. nov. Previous taxonomic status of E. massiliensis described in references 1 and 124 125e
massiliensis
Escherichia vulneris Pseudescherichia vulneris comb. nov. Previous taxonomic status of E. vulneris described in reference 126 125e

Gram-positive
anaerobes
Propionibacterium Cutibacterium acnes comb. nov. The description is the same as that provided in reference 127 128, 129
acnes
Propionibacterium Cutibacterium avidum comb. nov. The description is the same as that provided in reference 127
avidum
Propionibacterium Cutibacterium granulosum comb. nov. The description is the same as that provided in reference 127
granulosum
Propionibacterium Pseudopropionibacterium propionicum comb. nov. The description is the same as that provided in reference 127; the species 128
propionicum has been associated with abscesses at a variety of different sites (psoas,
brain)
Clostridium difficile Clostridioides difficile gen. nov., comb. nov. The description is identical to that for Clostridium difficile (130) 131
Clostridium Clostridioides mangenotii comb. nov. The description of Clostridioides mangenotii is identical to that provided in
mangenotii reference 132
Eubacterium Faecalicatena contorta gen. nov., comb. nov. A previous description of Eubacterium contorta can be found in reference 58
contortum 133; Faecalicatena spp. are obligately anaerobic Gram-positive bacilli found
in chains or pairs; nonmotile; may or may not form spores; F. contorta
grows optimally at 37°C
aTaxonomic designation subsequently added in validation list no. 170 (75).
bTaxonomic designation subsequently added in validation list no. 172 (77).
cX. Nesme, personal communication.

dTaxonomic designation subsequently added in validation list no. 174 (134).

eTaxonomic designation subsequently added in validation list no. 178 (78).

Novel taxa. Of the two novel genera that fall into the “Gram-positive cocci” group
in Table 1, the most interesting is Streptococcus halichoeri subsp. hominis. Streptococcus
halichoeri was originally isolated from gray seals (Halichoerus grypus) in 2004 in the
United Kingdom (25). Subsequent to the description of this organism, isolates that were
associated with infections in humans (four from blood and one from a sinus) and that
were sent to the Centers for Disease Control and Prevention (CDC) were found to be
phenotypically similar to S. halichoeri (26). In 2014, an additional isolate was recovered
from a man with empyema in Singapore (27). None of these patients were believed to
have an association with seals or ocean water; the average age of the patients was
63 years, and they were from different geographic locations (26). In a comprehensive
investigation of the human isolates of S. halichoeri, the six isolates were characterized
by Shewmaker et al. (26) using whole-genome and targeted gene sequencing and a
variety of phenotypic methods. The six human isolates were genetically and pheno-
typically identical and most closely related to S. halichoeri. They can be distinguished
from the type strain recovered from a seal as follows: positive for bile esculin and
esculin hydrolysis, positive for acid production from sucrose, and positive for
␤-glucosidase, ␤-glucuronidase, and acid production from methyl-␤-D-glucopyranoside
(Rapid ID32 test system [bioMérieux, Inc., Durham, NC]) (26). On the basis of both
phenotypic and genotypic differences from the seal type strain, the human isolates are
believed to be a subspecies of S. halichoeri and are referred to as S. halichoeri subsp.
hominis. Strains from marine animals are referred to as S. halichoeri subsp. halichoeri.
Two new Gram-positive aerobic bacilli associated with ocular infections have been
added to the genus Corynebacterium. Corynebacterium lowii and Corynebacterium oculi

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TABLE 3 Update on clinical relevance for selected new taxonomy described previously in JCM in 2017
Source previously reported in
Organism JCM (1) Updated clinical relevance Reference
Streptococcus dentisani Caries-free human tooth surfaces Infective endocarditis; refer to Table 2 for current taxonomic status 135
Staphylococcus argenteus Lymph node drainage Purulent lymphadenitis in a Japanese boy 136
Gemella taiwanensis Blood Infective endocarditis in a woman with dental caries 137
Nocardia kroppenstedtii Brain abscess, blood Immunocompromised patient who presented with central nervous 138
system symptoms; the patient was found to have brain
abscesses and endocarditis
Achromobacter animicus Sputum Multidrug-resistant organism implicated in wound infection in 139
Tanzania
Burkholderia Sputum Bacteremia (not otherwise specified) 140
pseudomultivorans
Klebsiella quasipneumoniae Type strain derived from blood Biliary tract infection 141
subsp. quasipneumoniae

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Liver abscess 142
Urinary tract infection (n ⫽ 2) 143
Klebsiella quasipneumoniae Type strain derived from blood Extended-spectrum ␤-lactamase-producing urine culture isolate 144
subsp. similipneumoniae
Sepsis (necrotizing fasciitis source) 145
Clinical isolates from Malaysia (not otherwise specified) harboring 146
CTX-M, TEM, and NDM resistance determinants
Odontogenic infection 147
Nosocomial infection isolates from Brazil (not otherwise specified) 148
harboring KPC-2 and OKP-B-6 resistance determinants
Acinetobacter variabilis Urine, feces, ocular, blood, leg, Neonatal sepsis in India 149
peritoneal dialysis fluid, toe
Sputum from cystic fibrosis patients in Brazil 150
Acinetobacter seifertii Blood, ulcer, respiratory Catheter-related bloodstream infection 151
Sputum from cystic fibrosis patients in Brazil 150
Ten isolates characterized, including urine culture isolate from 152
elderly female with dizziness
Catheter-related sepsis in pediatric patient; pressure ulcer; intra- 153
abdominal abscess
Archived tracheal aspirate and nasal secretion isolates from 1993 154
and 1997 harboring OXA-58 resistance determinant
Christensenella minuta Feces Coisolated with Desulfovibrio desulfuricans from blood of patient 155
with acute appendicitis
Eisenbergiella tayi Blood Canadian study of eight blood culture isolates and one appendix 156
tissue culture isolate (also with positive blood culture)
Klebsiella michiganensis Toothbrush holder Isolate harboring KPC-2, NDM-1, and NDM-5 resistance 157
determinants recovered from immunocompromised Chinese
patient with acute diarrhea
Actinotignum spp. Blood Bacteremia among elderly patients 158

were recovered primarily from patients in Japan at the time of ocular surgery and/or
from patients with conjunctivitis (32). At the time of recovery from clinical material, they
were described as high-level fluoroquinolone-resistant isolates distinguishable from
Corynebacterium macginleyi (32). Additional characterization found them to be novel
species.
Another noteworthy novel genus and species listed with the aerobic Gram-positive
bacilli is Lawsonella clevelandensis gen nov., sp. nov. This is a very unusual organism, in
that it grows best anaerobically, requiring prolonged incubation, yet it is modified
acid-fast positive and beaded and branching on Gram stain and by sequencing is most
closely related to members of the genus Dietzia (33, 34). In the original paper describing
these infections, patients from Cleveland, Ohio, Winnipeg, Manitoba, Canada, and New
York City had significant abscess collections of the spine (hardware associated), breast,
and liver, respectively (34). Three of the patients were immunocompromised, and
diabetes was a significant comorbid factor. Because of the fastidious nature of the
organism growth, susceptibility testing could not be performed. Two of the patients
responded to a combination of abscess drainage and amoxicillin-clavulanate; the other
patients received regimens that included trimethoprim-sulfamethoxazole (34). Two

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additional cases of infection caused by L. clevelandensis have been reported. The first
occurred in a patient with ulcerative colitis and a right lower quadrant intra-abdominal
abscess (35). Because of the acid-fast nature of the organism, the patient was initially
thought to have intra-abdominal tuberculosis. However, subsequent 16S rRNA gene
sequencing performed on the abscess fluid identified the organism as L. clevelandensis,
and the patient responded well to amoxicillin-clavulanate and drainage of the abscess
(35). A very recent case report involved a 29-year-old woman who had a breast nodule
that yielded a Gram-positive filamentous organism identified by molecular methods as
L. clevelandensis (159).
With respect to Gram-negative organisms, three valid subspecies of Enterobacter
hormaechei (namely, Enterobacter hormaechei subsp. hormaechei subsp. nov., Entero-
bacter hormaechei subsp. oharae subsp. nov., and Enterobacter hormaechei subsp.
steigerwaltii subsp. nov.) have been officially added by IJSEM (17, 77), though clinical

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data were not provided to ascribe true clinical relevance. A novel Enterobacter spp.,
Enterobacter bugandensis sp. nov. (39), was isolated from 17 neonates in a Tanzanian
sepsis outbreak. These isolates tested resistant to fluoroquinolones, aminoglycosides,
and tetracycline and harbored the CTX-M-15 resistance determinant. A pair of faculta-
tive Gram-negative bacilli, Citrobacter europaeus sp. nov. (44) and Shewanella carassii sp.
nov. (52), have been isolated from individuals with diarrhea.
The nonmotile coccobacillus Alkanindiges hongkongensis sp. nov. was isolated from
a Chinese patient with an infected Warthin’s tumor that resulted in a parotid gland
abscess and peripheral leukocytosis (11, 40). The patient responded well to surgical
drainage of the abscess and a course of amoxicillin-clavulanate. Organism growth was
significantly enhanced by Tween 80 supplementation. The oxidase-positive, Gram-
negative bacillus Sphingobacterium cellulitidis sp. nov. (45) was isolated from a patient
with cellulitis in Kuwait. The erythematous and purulent infection resolved following a
1-week amoxicillin-clavulanate regimen. During genetic characterization of the clinical
isolate, homology with a previously unnamed activated sludge isolate derived from
Singapore was demonstrated.
A novel member of the Anaplasmataceae, Ehrlichia muris subsp. eauclairensis subsp.
nov. (48), was isolated from an upper midwestern United States febrile patient with
previous Ixodes scapularis tick exposure. This subspecies is now delineated from
Ehrlichia muris subsp. muris subsp. nov. (Table 2), in that the latter has been recovered
from multiple genera of ticks, involves multiple natural reservoir hosts, and has distri-
bution in Eastern Europe and Japan. Furthermore, human clinical disease with an E.
muris subsp. muris subsp. nov. etiology has not been definitively established, though
serologic evidence of a human immune response has been reported from Japan (120).
Only one of the new species listed under the Gram-positive anaerobes category in
Table 1 was recovered from a clinical infection. Propionibacterium namnetense sp. nov.
was isolated from a patient who had an infected tibial fracture (55). The remaining
novel genera and species were recovered from the feces of otherwise healthy humans
in many cases during the study of intestinal microbiomes. Similarly, many of the novel
anaerobic Gram-negative agents have not had clinical significance established, though
Megasphaera massiliensis sp. nov. (11, 61) was isolated from an HIV-positive patient and
Sedimentibacter hongkongensis sp. nov. (11, 62) was recovered from a patient with
septic shock and multiorgan failure.
With respect to spirochetes, the valid name of Haematospirillum jordaniae gen. nov.,
sp. nov. (70, 71), was added by IJSEM in 2016 (76). The type strain was derived from
human blood and referred to CDC in 2010. During a brief interval in 2012, 3 isolates
with identical 16S rRNA sequences matching those of both the type strain and 10
previously characterized (but unnamed) isolates were forwarded to CDC. All isolates
were derived from men (mean age, 60 years), and the clinical diagnoses ranged from
septicemia to tularemia. Limited clinical data were available (70), though two patients
reported headache, fever, chills, diarrhea, and swelling in the lower extremities.
Routine Borrelia burgdorferi sensu lato oppA1 PCR testing performed at an upper
midwestern United States reference laboratory revealed six clinical specimens (five

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blood specimens and one synovial fluid specimen from six patients) with atypical
melting curve profiles (72). Subsequent sequencing of amplified 16S rRNA, in part,
resulted in the characterization of the novel taxon Borrelia mayonii sp. nov. (73). Field
surveys in Wisconsin and Minnesota recovered I. scapularis ticks from which B. mayonii
sp. nov. DNA was detected by PCR. This form of spirochetal disease differed from typical
Lyme borreliosis paradigms in several facets (72). In the limited data set, the novel
agent was detected more frequently from blood specimens than from synovial fluid
specimens. To an extent, these data were corroborated by higher median oppA1 copy
numbers and profound spirochetemia (as observed by microscopy) compared to those
in infections caused by B. burgdorferi sensu stricto. Finally, clinical presentations in-
cluded findings of diffuse macular rash not consistent with erythema migrans, nausea
and vomiting, and high-grade fever. Several symptoms more closely resembled those

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associated with relapsing fever borrelial disease (160).
Taxonomic revisions. In the previous taxonomic update in this journal published in
2017, a novel Streptococcus species, Streptococcus tigurinus, was highlighted (1). Zbin-
den et al. (84) described this organism as causing serious and invasive infections,
including bacteremia and endocarditis. In 2016, this organism was reclassified as a
subspecies of Streptococcus oralis (Table 2) (82). Streptococcus oralis now has three
subspecies: S. oralis subsp. oralis, S. oralis subsp. dentisani, and S. oralis subsp. tigurinus
(82). S. oralis subsp. dentisani comb. nov. has been reported as a cause of infective
endocarditis (Table 3) (135).
In 1971, Bascomb et al. (161) characterized a subset of Enterobacter aerogenes strains
that more closely resembled Klebsiella spp. from a phenotypic perspective. At that time,
taxonomic transfer to Klebsiella aerogenes was not possible and the taxon Klebsiella
mobilis was utilized for naming this species. It was subsequently determined by
taxonomists (113) that this nomenclature convention was illegitimate. Moreover, by
way of adherence to contemporary nomenclature code (162), it was determined that
the name Klebsiella aerogenes was available for use. Thus, E. aerogenes has now been
transferred to Klebsiella aerogenes comb. nov. (Table 2) (113) and K. mobilis is a
homotypic synonym of Klebsiella aerogenes comb. nov. The clinical utility of this
taxonomic revision remains to be seen, particularly with respect to salient differences
in the predicted antimicrobial susceptibility profiles of the Klebsiella and Enterobacter
genera in general (particularly relevant to cephamycins, first-generation cephems, and
␤-lactam–␤-lactamase inhibitor combinations, such as ampicillin-sulbactam [163]) and
the confusion that this may present to clinicians.
In a publication not included in Table 2, Adeolu et al. (164) used comparative
genomic analyses based on greater than 1,500 core proteins, 53 ribosomal proteins,
and 4 multilocus sequence analysis proteins to reorganize families and genera within
what is now known as Enterobacteriales ord. nov. Essentially, six new families have been
created from the family Enterobacteriaceae. These new families and the inclusive genera
are Erwiniaceae fam. nov. (containing the genera Erwinia, Buchnera, Pantoea, Phaseoli-
bacter, Tatumella, and Wigglesworthia), Pectobacteriaceae fam. nov. (containing the
genera Pectobacterium, Brenneria, Dickeya, Lonsdalea, and Sodalis), Yersiniaceae fam.
nov. (containing the genera Yersinia, Chania, Ewingella, Rahnella, Rouxiella, Samsonia,
and Serratia), Hafniaceae fam. nov. (containing the genera Hafnia, Edwardsiella, and
Obesumbacterium), Morganellaceae fam. nov. (containing the genera Morganella, Ar-
senophonus, Cosenzaea, Moellerella, Photorhabdus, Proteus, Providencia, and Xenorhab-
dus), and Budviciaceae fam. nov. (containing the genera Budvicia, Leminorella, and
Pragia). The remaining Enterobacteriales genera remain in an emended description of
the family Enterobacteriaceae (164).
Perhaps the most clinically impactful changes have been among the genera Clos-
tridium and Propionibacterium. The group of propionibacteria associated with the skin
biome of human hosts constitutes a distinct clade in the genus Propionibacterium.
Whole-genome sequencing and more sophisticated phylogenetic analyses support
placing the species associated with human skin into a new genus, Cutibacterium. The

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novel Cutibacterium genus includes the species Cutibacterium acnes, C. avidum, and C.
granulosum previously assigned to the Propionibacterium genus (Table 2) (128). The
novel genus Pseudopropionibacterium now contains the species formerly called Propi-
onibacterium propionicum (Table 2) (128). Several of the propionibacteria associated
with dairy sources, such as matured cheeses, have been placed into the genus
Acidipropionibacterium gen. nov. (refer to reference 128 for more details about dairy
strains). As also inferred with the Klebsiella aerogenes (Enterobacter aerogenes) para-
digm, the clinical microbiologist may wish to consult with clinical practitioner col-
leagues regarding the optimal manner to report the identification of organisms af-
fected by taxonomic revisions. With respect to the former Propionibacterium acnes,
possibilities may include “Cutibacterium acnes (formerly Propionibacterium acnes)” or
“Cutibacterium acnes (formerly P. acnes).”

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The genus Clostridium is also undergoing substantial changes. Application of mo-
lecular methods, including complete sequencing of the 16S rRNA gene and other
methods, emphasizes the phylogenetic diversity of this group of organisms and has led
to the decision to reserve the genus designation of Clostridium sensu stricto to rRNA
cluster I, which includes the type species Clostridium butyricum (131, 165). Conse-
quently, the majority of Clostridium species which are not consistent with the genus
Clostridium description, as emended by Lawson and Rainey (165), will be assigned to
other genera. Clostridium difficile is phylogenetically distant from cluster I and is located
in cluster XI (131). Phylogenetic studies have shown that the type strain of C. difficile
belongs in the family Peptostreptococcaceae. In 2013, Yutin and Galperin (166) proposed
creating a new genus, Peptoclostridium, to accommodate the Clostridium species reas-
signed to the family Peptostreptococcaceae. This proposal, which would have placed
many diverse species into a single genus (including C. difficile), was rejected as being
too simplistic (167). Subsequently, with the recognition that the proposed name
Peptoclostridium difficile would change the monikers of C. difficile or C diff already
ingrained in commercial products, packaging, computer systems, and clinical labora-
tories and to avoid tremendous confusion among clinicians, Lawson and colleagues
(131) proposed a compromise with the new designation of Clostridioides difficile,
thereby retaining the abbreviation commonly used for C. difficile. It is hoped that this
designation will mitigate the time and cost associated with the required reclassification,
as oftentimes only the abbreviation is used. The only other species in this new genus
is Clostridioides mangenotii. Changes to other genera not highlighted here have been
made or are forthcoming. Many of these new genera contain species not associated
with human infections. In the 2017 minireview, we highlighted the reassignment of
Clostridium hathewayi into the new genus Hungatella as Hungatella hathewayi gen.
nov., comb. nov., in 2014 (1). A resident of the human intestinal tract, this organism has
been associated with surgical site infections and bacteremia (reviewed in reference
168). Like other clostridia, it may stain Gram negative.
One major paradigm of bacterial taxonomy revision was, unfortunately, overlooked
in our first compendium. Adeolu and Gupta (169) proposed a reclassification of Borrelia
sp. spirochetes in 2014. Agents responsible for Lyme disease (formerly residing in the
Borrelia burgdorferi sensu lato complex) were transferred to Borreliella gen. nov., while
spirochetal agents largely responsible for relapsing fever retained the Borrelia genus
designation (type species, Borrelia anserina). Per Adeolu and Gupta (169), specific
agents within Borreliella gen. nov. include Borreliella burgdorferi comb. nov. (the type
species of Borreliella), B. afzelii comb. nov., B. americana comb. nov., B. bavariensis comb.
nov., B. carolinensis comb. nov., B. garinii comb. nov., B. japonica comb. nov., B.
kurtenbachii comb. nov., B. lusitaniae comb. nov., B. sinica comb. nov., B. spielmanii
comb. nov., B. tanukii comb. nov., B. turdi comb. nov., and B. valaisiana comb. nov. Valid
names of B. bavariensis, B. burgdorferi, B. carolinensis, B. garinii, B. japonica, B. kurten-
bachii, B. sinica, and B. spielmanii have been added by IJSEM (170), yet this topic remains
the subject of controversy and discussion (171, 172). To our knowledge, the nomen-
clature of the novel taxon Borrelia mayonii sp. nov. (Table 1) has not been revised.

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Minireview Journal of Clinical Microbiology

Recently ascribed clinical significance. New literature on novel Gram-positive taxa

highlighted in the original series (1) is summarized here and in Table 3. A case of
purulent lymphadenitis attributed to Staphylococcus argenteus was reported in a
Japanese child (136). The authors highlight the observations that this organism is often
misidentified as nonpigmented S. aureus. Up to this time, most human cases have been
found in northeastern Thailand (136). The first case report of infective endocarditis
caused by Gemella taiwanensis was published by Hikone et al. (137). In contrast to the
cases mentioned in the initial description of this organism (173), this patient was not
immunocompromised, and it is believed that her native valve endocarditis occurred
after extensive treatment for dental caries (137). The first reported case of disseminated
Nocardia kroppenstedtii was reported by Majeed et al. (138). This patient was an
immunocompromised gentleman (mantle cell lymphoma) who presented with new

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central nervous system symptoms. He was found to have brain abscesses as well as a
mitral valve mass. Blood cultures and a brain biopsy specimen were positive for N.
kroppenstedtii (138). Finally, with respect to the Gram-positive anaerobes, much new
literature on Actinotignum schaalii can be found via PubMed primary literature
searches, and the interested reader is directed there for those papers. A comprehensive
review highlighting the clinical and microbiological features of Actinotignum spp. is
referenced (158), with the authors noting that Actinotignum bacteremia affects elderly
persons with comorbidities and is associated with high mortality.
Particular clinical significance can be ascribed to several taxa listed in Table 3 on the
basis of multidrug resistance (139, 144, 146, 148, 149, 154, 157). One of these genus/
species designations, Klebsiella quasipneumoniae, is frequently misidentified by the
clinical microbiology laboratory as Klebsiella pneumoniae (174), yet it has the potential
to harbor similar resistance determinants and virulence factors as K. pneumoniae. Elliott
et al. (175) published the whole-genome sequence of the commonly utilized quality
control strain ATCC 700603, identifying it as K. quasipneumoniae subsp. similipneu-
moniae. K. quasipneumoniae subsp. quasipneumoniae has been recovered in clinical
specimens from patients with biliary tract infection (141), liver abscess (142), and
urinary tract infection (143), while K. quasipneumoniae subsp. similipneumoniae has
been implicated in urinary tract infection (144), sepsis (with antecedent necrotizing
fasciitis) (145), odontogenic infection (147), and nosocomial infection (148). In addition
to recent reports of Acinetobacter variabilis isolation in the context of neonatal sepsis
(149) and cystic fibrosis (150), organism-specific nucleic acid has been isolated from
Pediculus humanus capitis organisms collected from schoolchildren and homeless
individuals in northern Africa (176, 177). The authors raise the possibility of human
body lice potentially serving as vectors/reservoirs of a range of pathogens broader than
previously appreciated.
Other novel agents of interest. One taxon briefly described in the first bacterial
taxonomy compendium (1) was Klebsiella michiganensis, an isolate of which was
originally recovered from a toothbrush holder. In 2018, Zheng et al. (157) reported a
case of acute diarrhea from a patient after hematopoietic stem cell transplantation in
which a K. michiganensis isolate harboring the resistance determinants KPC-2, NDM-1,
and NDM-5 was recovered from a stool culture (Table 3). While not included within the
formal tables of this minireview, the following paragraphs describe examples of new
taxa that possess the potential to progress into the realm of human clinical disease.
Although they have yet to be associated with human clinical specimens, several new
taxa have been cultivated from known disease vector agents. These include the
rickettsial agents Rickettsia asembonensis sp. nov., Rickettsia amblyommatis sp. nov.,
Rickettsia gravesii sp. nov., and Occidentia massiliensis gen. nov., sp. nov., recovered
from fleas (178) or ticks (179–181); Borrelia bissettiae sp. nov., Borrelia californiensis sp.
nov., and Borrelia lanei sp. nov. from Ixodes pacificus ticks (182, 183); three novel
Anaplasmataceae from ticks (184, 185); and the Gram-negative bacillus Coetzeea brasil-
iensis gen. nov., sp. nov., from mosquito larvae (186). The valid O. massiliensis gen. nov.,
sp. nov., designation was subsequently added by IJSEM (74).

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Minireview Journal of Clinical Microbiology

Other agents have been associated with ingestible or inhalable material. Serratia
aquatilis sp. nov. and Ampullimonas aquatilis gen. nov., sp. nov., have recently been
isolated from drinking (187) and bottled mineral (188) water, respectively. Agents
recovered from raw cow’s milk include Pseudomonas helleri sp. nov., Pseudomonas
weihenstephanensis sp. nov. (189), Pseudomonas lactis sp. nov., and Pseudomonas
paralactis sp. nov. (190). Rooney et al. (191) reported the isolation of Acinetobacter
lactucae sp. nov. from iceberg lettuce. Examples of novel agents recovered from
seafood include Halomonas garicola sp. nov. (192), Proteus cibarius sp. nov. (193), and
Thalassotalea crassostreae sp. nov. (194). Finally, several nonfermentative Gram-
negative bacilli have been isolated from air-conditioning systems (195–199).
In summary, studies of the human microbiome and advancements in molecular
characterization modalities have largely been responsible for the identification of novel
bacterial agents from human sources. Newer and improved tools have also contributed

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to the assessment of closely related pathogens and, in many instances, have resulted
in revisions to previously accepted taxonomy. We have attempted to summarize these
changes for 2016 and 2017 (as relevant to humans) and to provide insight into the
clinical relevance of these agents. Additional changes to the Clostridiales are anticipated
in the next few years. As a result, this project will be sustainable into the near future,
while retrospectively attempting to ascertain the clinical significance of agents that are
currently believed to have uncertain or commensal status.

ACKNOWLEDGMENT
This report was not subject to influence from any funding agency in the public,
commercial, or not-for-profit sectors.

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