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Nomenclature and taxonomy of the genus Salmonella

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B J Tindall
B J Tindall
B J Tindall
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Patrick A Grimont at Institut Pasteur
Patrick A Grimont
George M Garrity at Michigan State University
George M Garrity
J P Euzéby
J P Euzéby
J P Euzéby
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Abstract

The nomenclature of the genus Salmonella has reached an unsatisfactory state of affairs, with two systems of nomenclature in circulation. One system, proposed in the 1980s by Le Minor and Popoff, has received wide acceptance, although it does not conform to the rules of the Bacteriological Code. The other system, which conforms to the rules of the Bacteriological Code, is being used by an ever-decreasing minority. As a result of a number of recent Requests for an Opinion, the Judicial Commission of the International Committee on the Systematics of Prokaryotes has issued an Opinion (Opinion 80) with the intention that it should solve these discrepancies. However, like all Opinions, it is limited to matters of nomenclature and does not help to interpret the taxonomic consequences. The Judicial Commission has therefore asked experts in the field of nomenclature and taxonomy to write a commentary on the nomenclatural and taxonomic consequences of Opinion 80. The present article explains the nomenclatural consequences of Opinion 80, together with a clear presentation of the taxonomy that results when applying the currently widely accepted interpretation that the genus Salmonella currently includes only two species.
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Taxonomic
Note
Nomenclature and taxonomy of the genus
Salmonella
B. J. Tindall,
1
P. A. D. Grimont,
2
G. M. Garrity
3
and J. P. Euze
´
by
4
Correspondence
B. J. Tindall
bti@dsmz.de
1
DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Mascheroder
Weg 1b, D-38124 Braunschweig, Germany
2
Unite
´
de Biodiversite
´
des Bacte
´
ries Pathoge
`
nes Emergentes, INSERM U389, Institut Pasteur,
F-75724 Paris Cedex 15, France
3
Bergey’s Manual Trust, Department of Microbiology and Molecular Genetics, 6162 Biomedical
Physical Sciences Bldg, Michigan State University, East Lansing, MI 48824-4320, USA
4
Socie
´
te
´
de Bacte
´
riologie Syste
´
matique et Ve
´
te
´
rinaire (SBSV) and Ecole Nationale Ve
´
te
´
rinaire
de Toulouse (ENVT), 23 Chemin des Capelles, BP 87614, F-31076 Toulouse Cedex 03,
France
The nomenclature of the genus Salmonella has reached an unsatisfactory state of affairs, with
two systems of nomenclature in circulation. One system, proposed in the 1980s by Le Minor
and Popoff, has received wide acceptance, although it does not conform to the rules of the
Bacteriological Code. The other system, which conforms to the rules of the Bacteriological Code,
is being used by an ever-decreasing minority. As a result of a number of recent Requests for an
Opinion, the Judicial Commission of the International Committee on the Systematics of Prokaryotes
has issued an Opinion (Opinion 80) with the intention that it should solve these discrepancies.
However, like all Opinions, it is limited to matters of nomenclature and does not help to interpret
the taxonomic consequences. The Judicial Commission has therefore asked experts in the field
of nomenclature and taxonomy to write a commentary on the nomenclatural and taxonomic
consequences of Opinion 80. The present article explains the nomenclatural consequences of
Opinion 80, together with a clear presentation of the taxonomy that results when applying the
currently widely accepted interpretation that the genus Salmonella currently includes only two
species.
The current taxonomy and nomenclature of the genus
Salmonella have been the subject of debate since Le Minor
& Popoff (1987) proposed changes in the 1980s. In their
Request for an Opinion, these authors not only proposed
changes in the nomenclature of the species of this genus,
but also requested that formal taxonomic interpretations
be taken into consideration. Their request to recognize a
single species could not be dealt with by the Judicial
Commission because the Commission may only act on
matters of nomenclature. Taxonomic opinion is not
governed by the Bacteriological Code (the Code).
The nomenclatural changes that were proposed dealt with
important human and animal pathogens. At the time, the
Judicial Commission could not predict whether these
changes would have severe consequences for the reporting
of disease caused by pathogens such as Salmonella typhi.
Following careful deliberations, the Judicial Commission
recommended that the authors reformulate their Request
for an Opinion to conform to the Code, but this did not
happen (Wayne, 1994). In the intervening years, the
nomenclature of Le Minor & Popoff (1987) has become
widely accepted in certain countries, despite the fact that
those names have not been validly published and have no
standing in nomenclature. In addition, their proposed
taxonomy is also now in common usage. Euze
´
by (1999),
Ezaki et al. (2000a, b) and Ezaki & Yabuuchi (2000) sub-
mitted proposals to deal with the problem of the serious
discrepancies between the nomenclature of Le Minor &
Popoff (1987) and that which is recognized under the
Code. The major problem at present is that two systems
of nomenclature are in use for members of the genus
Salmonella and that great care must be taken when attempts
are made to unify these systems. It was generally agreed
during the meeting of the Judicial Commission held in
2002 that a solution must be sought that provides a link
between the two nomenclatural systems while causing as
little confusion as possible. Recognizing that the average
microbiologist was not familiar with the Code, the com-
missioners believed that it would be necessary to deal
with the nomenclatural problem and to provide a guide as
to how the taxonomic consequences could be illustrated.
In publishing Opinion 80, the Judicial Commission (2005)
has sought to provide a solution to the problem of
63580
G
2005 IUMS Printed in Great Britain 521
International Journal of Systematic and Evolutionary Microbiology (2005), 55, 521–524 DOI 10.1099/ijs.0.63580-0
nomenclature in this genus. However, the Judicial Com-
mission does not have the power to rule on how these
nomenclatural changes will affect the taxonomy of this
group. In order to avoid confusion, it is the purpose of
the present article to provide a clear interpretation of the
nomenclature and taxonomy of members of the genus
Salmonella.
Prior to the publication of Opinion 80, the Code recognized
the following names as being validly published within the
genus Salmonella:
Salmonella choleraesuis (Smith 1894) Weldin 1927 (type
species of the genus), type strain ATCC 13312 =CIP 55.133
=NCTC 5735 =DSM 14846 =JCM 1651 (serovar
Choleraesuis),
Salmonella bongori (Le Minor et al. 1985) Reeves et al. 1989,
type strain ATCC 43975 =CCUG 30042 =CIP 82.33
=DSM 13772 =NCTC 12419,
Salmonella choleraesuis subsp. bongori Le Minor et al. 1985,
type strain ATCC 43975 =CCUG 30042 =CIP 82.33
=DSM 13772 =NCTC 12419,
Salmonella enteritidis (Gaertner 1888) Castellani and
Chalmers 1919, type strain ATCC 13076 =NCTC 12694,
Salmonella paratyphi (ex Kayser 1902) Ezaki et al. 2000, type
strain NCTC 5702 =KI 1015,
Salmonella typhi (Schroeter 1886) Warren and Scott 1930,
type strain ATCC 19430 =CUETM 79.394 =HAMBI 1306
=NCTC 8385,
Salmonella typhimurium (Loeffler 1892) Castellani and
Chalmers 1919, type strain ATCC 13311 =NCTC 74 =CIP
58.58 =JCM 1652 (serovar Typhimurium),
Salmonella choleraesuis subsp. choleraesuis (Smith 1894)
Weldin 1927, type strain ATCC 13312 =CIP 55.133 =NCTC
5735 =DSM 14846 =JCM 1651 (serovar Choleraesuis),
Salmonella arizonae (Borman 1957) Kauffmann 1964, type
strain ATCC 13314 =CCUG 6322 =CIP 82.30 =DSM
9386=NCTC 8297,
Salmonella choleraesuis subsp. arizonae (Borman 1957) Le
Minor et al. 1985, type strain ATCC 13314 =CCUG 6322
=CIP 82.30 =DSM 9386 =NCTC 8297,
Salmonella choleraesuis subsp. diarizonae Le Minor et al.
1985, type strain ATCC 43973 =CCUG 30040 =CIP 82.31
=NCTC 10060 =DSM 14847,
Salmonella choleraesuis subsp. houtenae Le Minor et al.
1985, type strain ATCC 43974 =CCUG 30041 =CIP 82.32
=DSM 9221 =NCTC 12418,
Salmonella choleraesuis subsp. indica Le Minor et al. 1987,
type strain K1240 =ATCC 43976 =CCUG 30038 = CIP
102501 =NCTC 12420 = DSM 14848, and
Salmonella choleraesuis subsp. salamae Le Minor et al.
1985, type strain ATCC 43972 =CCUG 30039 =CIP 8229
=DSM 9220 =NCTC 5773.
Le Minor & Popoff (1987) proposed that the type species
of the genus Salmonella should be changed to Salmonella
enterica, with the type strain of that species being strain LT2.
The authors did not exclude the fact that other authors
may wish to retain other names that were validly published:
‘Since we recognize the right of other bacteriologists to
believe that the genus Salmonella should be composed of
several species, including S. choleraesuis, we shall refrain
from requesting the rejection of that name.’
In reacting to the Requests for an Opinion by Ezaki et al.
(2000a, b) and Euze
´
by (1999), the Judicial Commission
has also taken the request of Le Minor & Popoff (1987)
into consideration and decided that Salmonella enterica
becomes the type species of the genus, replacing Salmonella
choleraesuis (Judicial Commission, 2005). The type strain
of Salmonella enterica is CIP 60.62 =NCIMB 11450 =
LT2 =ATCC 43971 =NCTC 12416. Furthermore, to avoid
any ambiguities in interpreting the Code, the epithet enterica
in Salmonella enterica is conserved over all earlier epithets
that may be applied to this species. The Judicial Commission
has also ruled that the subspecies combinations proposed
by these authors should also be considered to be validly
published, with the dates and authorship being assigned to
these authors. In proposing these subspecies, Salmonella
enterica subsp. enterica is automatically created (Rule 40d/
46). The circumscription of Salmonella enterica is given by
Le Minor & Popoff (1987) and also applies to Salmonella
enterica subsp. enterica. However, this also means that the
following names are validly published:
Salmonella enterica Le Minor and Popoff 1987 (type species
of the genus), type strain CIP 60.62 =NCIMB 11450 =LT2
=ATCC 43971 =NCTC 12416 (serovar Typhimurium),
Salmonella bongori (Le Minor et al. 1985) Reeves et al.
1989, type strain ATCC 43975 =CCUG 30042 =CIP 82.33
=DSM 13772 =NCTC 12419,
Salmonella enterica subsp. bongori (Le Minor et al. 1985) Le
Minor and Popoff 1987, type strain ATCC 43975 =CCUG
30042 =CIP 82.33 =DSM 13772 =NCTC 12419,
Salmonella choleraesuis subsp. bongori Le Minor et al. 1985,
type strain ATCC 43975 =CCUG 30042 =CIP 82.33
=DSM 13772 =NCTC 12419,
Salmonella enterica subsp. enterica Le Minor and Popoff
1987, type strain CIP 60.62 =NCIMB 11450 =LT2
=ATCC 43971 =NCTC 12416 (serovar Typhimurium),
Salmonella enteritidis (Gaertner 1888) Castellani and
Chalmers 1919, type strain ATCC 13076 =NCTC 12694,
Salmonella paratyphi (ex Kayser 1902) Ezaki et al. 2000,
type strain NCTC 5702 =KI 1015,
522 International Journal of Systematic and Evolutionary Microbiology 55
B. J. Tindall and others
Salmonella typhi (Schroeter 1886) Warren and Scott 1930,
type strain ATCC 19430 =CUETM 79.394 =HAMBI 1306
=NCTC 8385,
Salmonella typhimurium (Loeffler 1892) Castellani and
Chalmers 1919 (type strain ATCC 13311 =NCTC 74 =CIP
58.58 =JCM 1652 (serovar Typhimurium),
Salmonella choleraesuis (Smith 1894) Weldin 1927, type
strain ATCC 13312 =CIP 55.133 =NCTC 5735 =DSM
14846 =JCM 1651 (serovar Choleraesuis),
Salmonella choleraesuis subsp. choleraesuis (Smith 1894)
Weldin 1927, type strain ATCC 13312 =CIP 55.133 =NCTC
5735 =DSM 14846 =JCM 1651 (serovar Choleraesuis),
Salmonella enterica subsp. arizonae (Borman 1957) Le
Minor and Popoff 1987, type strain ATCC 13314 =CCUG
6322 =CIP 82.30 =DSM 9386 =NCTC 8297,
Salmonella arizonae (Borman 1957) Kauffmann 1964, type
strain ATCC 13314 =CCUG 6322 =CIP 82.30 =DSM
9386 =NCTC 8297,
Salmonella choleraesuis subsp. arizonae (Borman 1957) Le
Minor et al. 1985, type strain ATCC 13314 =CCUG 6322
=CIP 82.30 =DSM 9386 =NCTC 8297,
Salmonella enterica subsp. diarizonae (Le Minor et al. 1985)
Le Minor and Popoff 1987 1985, type strain ATCC 43973
=CCUG 30040 =CIP 82.31 =NCTC 10060 =DSM
14847,
Salmonella choleraesuis subsp. diarizonae Le Minor et al.
1985, type strain ATCC 43973 =CCUG 30040 =CIP 82.31
=NCTC 10060 =DSM 14847,
Salmonella enterica subsp. houtenae (Le Minor et al. 1985)
Le Minor and Popoff 1987, type strain ATCC 43974
=CCUG 30041 =CIP 82.32 = DSM 9221 =NCTC 12418,
Salmonella choleraesuis subsp. houtenae Le Minor et al.
1985, type strain ATCC 43974 =CCUG 30041 =CIP 82.32
=DSM 9221 =NCTC 12418,
Salmonella enterica subsp. indica (Le Minor et al . 1987)
Le Minor and Popoff 1987, type strain K1240 =ATCC
43976 =CCUG 30038 =CIP 102501 =NCTC 12420 =DSM
14848,
Salmonella choleraesuis subsp. indica Le Minor et al. 1987,
type strain K1240 =ATCC 43976 =CCUG 30038 = CIP
102501 =NCTC 12420 = DSM 14848,
Salmonella enterica subsp. salamae (Le Minor et al. 1985)
Le Minor and Popoff 1987 1985, type strain ATCC 43972
=CCUG 30039 =CIP 8229 =DSM 9220 =NCTC 5773,
and
Salmonella choleraesuis subsp. salamae Le Minor et al. 1985,
type strain ATCC 43972=CCUG 30039=CIP 8229=DSM
9220=NCTC 5773.
However, this does not appear to solve the current problems
of nomenclature, nor the different taxonomic interpreta-
tions. This is primarily due to the fact that the Judicial
Commission is not empowered by the Code as a taxonomic
arbiter [see Principle 1 (4)]. However, it is evident that, if
the taxonomic proposals of Le Minor & Popoff (1987) and
Reeves et al. (1989) are followed, only two species are to be
recognized. The Judicial Commission (2005) has ruled that
the type species of the genus Salmonella Lignieres 1900 is
Salmonella enterica Le Minor and Popoff 1987 and that the
epithet enterica be conserved over all earlier epithets that
may be applied to this species. At the same time, Le Minor &
Popoff (1987) also recognized that the species Salmonella
enterica be divided into several subspecies. Thus, by applying
the recent ruling of the Judicial Commission (2005) together
with the taxonomic interpretation of Le Minor & Popoff
(1987) and Reeves et al. (1989), the taxonomy and resulting
nomenclature that should be followed are listed below.
Those names that are to be used within the resulting
taxonomy are underlined.
Salmonella enterica (ex Kauffmann and Edwards 1952)
Le Minor and Popoff 1987 (type species of the genus),
type strain CIP 60.62 =NCIMB 11450 =LT2 =ATCC
43971 =NCTC 12416 (serovar Typhimurium),
=Salmonella choleraesuis (Smith 1894) Weldin 1927
(heterotypic synonym), type strain ATCC 13312 =CIP
55.133 =NCTC 5735 =DSM 14846 =JCM 1651 (serovar
Choleraesuis),
Salmonella bongori (Le Minor et al. 1985) Reeves et al. 1989,
=Salmonella enterica subsp. bongori (Le Minor et al. 1985)
Le Minor and Popoff 1987 (homotypic synonym)
=Salmonella choleraesuis subsp. bongori Le Minor et al.
1985 (homotypic synonym), type strain ATCC 43975 =
CCUG 30042 =CIP 82.33 =DSM 13772 =NCTC 12419,
Salmonella enterica subsp. enteri ca (ex Kauffmann and
Edwards 1952) Le Minor and Popoff 1987, type strain CIP
60.62 =NCIMB 11450 =LT2 =ATCC 43971 =NCTC
12416 (serovar Typhimurium),
=Salmonella enteritidis (Gaertner 1888) Castellani and
Chalmers 1919 (heterotypic synonym), type strain ATCC
13076 =NCTC 12694,
=Salmonella paratyphi (ex Kayser 1902) Ezaki et al. 2000
(heterotypic synonym), type strain NCTC 5702=KI 1015,
=Salmonella typhi (Schroeter 1886) Warren and Scott 1930
(heterotypic synonym), type strain ATCC 19430 =CUETM
79.394=HAMBI 1306 =NCTC 8385,
=Salmonella typhimurium (Loeffler 1892) Castellani and
Chalmers 1919 (heterotypic synonym), type strain ATCC
13311 =NCTC 74 =CIP 58.58 =JCM 1652 (serovar
Typhimurium),
http://ijs.sgmjournals.org 523
Taxonomy and nomenclature of the genus Salmonella
=Salmonella choleraesuis subsp. choleraesuis (Smith 1894)
Weldin 1927 (heterotypic synonym), type strain ATCC
13312 =CIP 55.133 =NCTC 5735 =DSM 14846 =JCM
1651 (serovar Choleraesuis),
Salmonella enterica subsp. arizonae (Borman 1957) Le
Minor and Popoff 1987,
=Salmonella arizonae (Borman 1957) Kauffmann 1964
(homotypic synonym) =Salmonella choleraesuis subsp.
arizonae (Borman 1957) Le Minor et al. 1985 (homotypic
synonym), type strain ATCC 13314 =CCUG 6322 =CIP
82.30 =DSM 9386 =NCTC 8297,
Salmonella enterica subsp. diarizonae (Le Minor et al. 1985)
Le Minor and Popoff 1987,
=Salmonella choleraesuis subsp. diarizonae Le Minor et al.
1985 (homotypic synonym), type strain ATCC 43973
=CCUG 30040 =CIP 82.31 =NCTC 10060 =DSM 14847,
Salmonella enterica subsp. houtenae (Le Minor et al. 1985) Le
Minor and Popoff 1987,
=Salmonella choleraesuis subsp. houtenae Le Minor et al.
1985 (homotypic synonym), type strain ATCC 43974
=CCUG 30041 =CIP 82.32 = DSM 9221 =NCTC 12418,
Salmonella enterica subsp. indica (Le Minor et al. 1987) Le
Minor and Popoff 1987,
=Salmonella choleraesuis subsp. indica Le Minor et al.
1987 (homotypic synonym), type strain K1240 =ATCC
43976 =CCUG 30038 =CIP 102501 =NCTC 12420
=DSM 14848, and
Salmonella enterica subsp. salamae (Le Minor et al. 1985) Le
Minor and Popoff 1987,
=Salmonella choleraesuis subsp. salamae Le Minor et al.
1985 (homotypic synonym), type strain ATCC 43972
=CCUG 30039 = CIP 8229 =DSM 9220 =NCTC 5773.
It is hoped that the recent actions of the Judicial Com-
mission (2005) have allowed the nomenclatural changes
envisaged by Le Minor & Popoff (1987) to take effect. In
addition, the taxonomic opinion of Le Minor et al. (1982),
Le Minor & Popoff (1987) and Reeves et al. (1989), that the
genus Salmonella should currently comprise two species
and that the type species Salmonella enterica should be
divided into six subspecies, results in the taxonomy and
nomenclature currently in use by the WHO and other
organizations. It is now hoped that the resulting taxonomy
and nomenclature will find widespread usage.
References
Euze
´
by, J. P. (1999). Revised Salmonella nomenclature: designation
of Salmonella enterica (ex Kauffmann and Edwards 1952) Le Minor
and Popoff 1987 sp. nov., nom. rev. as the neotype species of the
genus Salmonella Lignieres 1900 (Approved Lists 1980), rejection
of the name Salmonella choleraesuis (Smith 1894) Weldin 1927
(Approved Lists 1980), and conservation of the name Salmonella
typhi (Schroeter 1886) Warren and Scott 1930 (Approved Lists
1980). Request for an Opinion. Int J Syst Bacteriol 49, 927–930.
Ezaki, T., Amano, M., Kawamura, Y. & Yabuuchi, E. (2000a).
Proposal of Salmonella paratyphi sp. nov., nom. rev. and Request for
an Opinion to conserve the specific epithet paratyphi in the binary
combination Salmonella paratyphi as nomen epitheton conservandum.
Int J Syst Evol Microbiol 50, 941–944.
Ezaki, T., Kawamura, Y. & Yabuuchi, E. (2000b). Recognition of
nomenclatural standing of Salmonella typhi (Approved Lists 1980),
Salmonella enteritidis (Approved Lists 1980) and Salmonella
typhimurium (Approved Lists 1980), and conservation of specific
epithets enteritidis and typhimurium. Request for an Opinion. Int
J Syst Evol Microbiol 50, 945–947.
Judicial Commission (2005). The type species of the genus
Salmonella Lignieres 1900 is Salmonella enterica (ex Kauffmann
and Edwards 1952) Le Minor and Popoff 1987, with the type strain
LT2
T
, and conservation of the epithet enterica in Salmonella enterica
over all earlier epithets that may be applied to this species. Opinion
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ation of Salmonella enterica sp. nov., nom. rev., as the type and only
species of the genus Salmonella. Int J Syst Bacteriol 37, 465–468.
Le Minor, L., Ve
´
ron, M. & Popoff, M. Y. (1982). Proposition pour
une nomenclature des Salmonella. Ann Microbiol Paris 133B, 245–
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ron, M. & Popoff, M. Y. (1985). Salmonella cholerae-
suis subsp. arizonae comb. nov. etc. In Validation of the Publication of
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J. J., III (1989).
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Wayne, L. G. (1994). Actions of the Judicial Commission of the
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524 International Journal of Systematic and Evolutionary Microbiology 55
B. J. Tindall and others
... Salmonella is a Gram negative, rod-shaped, and non-spore forming bacterium with facultative respiratory metabolism and made up of two species, Salmonella bongori and Salmonella enterica (Tindall et al., 2005;Su and Chui, 2007). Among the six subspecies of Salmonella enterica, subspecies enterica is responsible for 99% of salmonellosis in humans and warm-blooded animals (Issenhuth-Jeanjean et al., 2014;Lamas et al., 2018). ...
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  • Apr 2024
  • INFLAMM BOWEL DIS
Background Despite the known association between microorganisms and development of inflammatory bowel disease (IBD), the role of nontyphoidal Salmonella (NTS) in IBD is not adequately addressed. We aimed at elucidating the relationship between NTS infection and the risk of IBD. Methods Based on the National Health Insurance Research Database in Taiwan, this retrospective cohort study enrolled patients with NTS infection (exposure group; n = 4651) and those without NTS infection (comparator group; n = 4651) who were propensity score matched (1:1) by demographic data, medications, comorbidities, and index date. All patients were followed until IBD onset, individual mortality, or December 31, 2018. Cox proportional hazards regression analysis was performed to determine the hazard ratios and 95% confidence intervals (CIs). Sensitivity analyses were used for cross-validation. Results The NTS group demonstrated an increased risk of IBD compared with the non-NTS groups (adjusted hazard ratio [aHR], 2.12; 95% CI, 1.62-2.78) with a higher risk of developing ulcerative colitis in the former (aHR, 2.27; 95% CI, 1.69-3.04). Nevertheless, the small sample size may contribute to lack of significant difference in Crohn’s disease. Consistent findings were noted after excluding IBD diagnosed within 6 months of NTS infection (aHR, 2.28; 95% CI, 1.71-3.03), excluding those with enteritis/colitis before index date (aHR, 1.85; 95% CI, 1.28-2.68), excluding those using antibiotics for 1 month in the year before IBD onset (aHR, 1.81; 95% CI, 1.34-2.45), inverse probability of treatment weighting (aHR, 1.64; 95% CI, 1.31-2.04), and inclusion of individuals regardless of age (n = 10 431; aHR, 1.83; 95% CI, 1.53-2.19). Conclusions Patients with NTS were associated with an increased risk of developing IBD, especially ulcerative colitis.
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Structure classification of the proteins from Salmonella enterica pangenome revealed novel potential pathogenicity islands
Preprint
Full-text available
  • Feb 2024
Salmonella enterica is a pathogenic bacterium known for causing severe typhoid fever in humans, making it important to study due to its potential health risks and significant impact on public health. This study provides evolutionary classification of proteins from Salmonella enterica pangenome. We classified 17,238 domains from 13,147 proteins from 79,758 Salmonella enterica strains and studied in detail domains of 272 proteins from fourteen characterized Salmonella pathogenicity islands (SPIs). Among SPIs-related proteins, 90 proteins function in the secretion machinery. 41% domains of SPI proteins have no previous sequence annotation. By comparing clinical and environmental isolates, we identified 3682 proteins that are overrepresented in clinical group that we consider as potentially pathogenic. 69 of them overlap with SPI proteins. Among domains of potentially pathogenic proteins only 50% domains were annotated by sequence methods previously. Moreover, 36% (1330 out of 3682) of potentially pathogenic proteins cannot be classified into Evolutionary Classification of Protein Domains database (ECOD). Among classified domains of potentially pathogenic proteins the most populated homology groups include helix-turn-helix (HTH), Immunoglobulin-related, and P-loop domains-related. Functional analysis revealed overrepresentation of these protein in biological processes related to viral entry into host cell, antibiotic biosynthesis, DNA metabolism and conformation change, and underrepresentation in translational processes. Analysis of the potentially pathogenic proteins indicates that they form 119 clusters (islands) within the Salmonella genome, suggesting their potential contribution to the bacterium's virulence. Overall, our analysis revealed that identified potentially pathogenic proteins are poorly studied. ECOD hierarchy of classified Salmonella enterica domains is available online: http://prodata.swmed.edu/ecod/index_salm.php
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Prevalence of Non-Typhoidal Salmonella and Aerobic Bacteria Causing Bacteraemia among HIV/AIDS Seropositive Patients Attending Aminu Kano Teaching Hospital, Kano State
Article
  • Dec 2023
The study aimed at determining the prevalence of non-typhoidal Salmonella and aerobic bacteria causing bacteraemia among HIV/AIDS seropositive patients attending Aminu Kano Teaching Hospital, Kano, the relationship between the CD4 cell counts and prevalence of these bacterial infections among the study population. Two hundred and sixty (260) HIV patients of 77 (29.6%) males and 183 (70.4%) females of 22-75 years were enrolled for the study. Socio-demographic and clinical history were obtained. The CD4 cell counts were enumerated using Cytoflometer. Bacteriological blood culture, isolation, identification and characterization of isolates were carried out using standard microbiological methods. The Salmonella isolates identified were further subjected to biochemical reactions using Enterosystem 18R test kits. Data were analysed using Chi-squared method. P-value < 0.05 was taken as the level of significance. The overall prevalence of Non-typhoidal Salmonella (NTS) was 5.7% (n=2) with male and female having the same prevalence of 1 (2.9%) each. Other bacteria isolated were Staphylococcus aureus 19 (54.1%), Klebsiella spp 6(17.1%), Escherichia coli 3(8.6%), Pseudomonas aeruginosa 3(8.6%), Salmonella typhi 2(5.7%). Staphylococcus aureus had good sensitivities to vancomycin, chloramphenicol, ciprofloxacin and amikacin but were resistant mainly erythromycin (68%). The Gram-negative organisms isolated also showed 100% resistance to ampicillin, chloramphenicol, colistin and trimethoprim sulfamethoxazole while being highly sensitive to meropenem, amikacin, and ciprofloxacin .Though the association of NTS and bacteraemia among HIV infected patients was low in this study (13.5%), there is need for increased public enlightenment on the subject-matter to limit the spread of this infectious agents to reduce associated morbidity and mortality.
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Isolation, Identification of Bacteria and Fungi and FTIR and Proximate Analysis of Cassava Flakes (Garri) in Dutsin-Ma Markets
Article
Full-text available
  • Dec 2023
Garri is a staple food made from cassava tuber that is consumed in many homes across Nigeria and other West Africa countries. This study isolated, identified bacteria and fungi and Furrier Transformed Infrared Spectrometer (FTIR) and proximate analysis of garri in Dutsin-Ma markets. Nine garri samples (smooth white garri, yellow graveled garri and yellow garri) were obtained in Dutsin-Ma Town, from three different markets: Wednesday, Abuja Road and Tsamiya markets respectively. The microbial load of the samples was determined using pour plate technique and the isolates were identified using conventional method. The bacteria colony count was done and the bacteria were identified using gram staining and biochemical test. Three bacteria species were isolated; Klebsiella pneumonia (44.4%), Staphylococcus aureus (88.9%) and Bacillus spp (11.1%) and Twelve Fungi: Aspergillus spp (33.3%), Colletotrichum coccoides (11.1%), Histoplasma capsulatum (11.1%), Trichophyton schenlenii (11.1%) Trichomonas equinum (11.1%), Trichophyton equinum (11.1%), Balassezia baillon (11.1%), Coniochaeta haffmannii (11.1%), Cryptococcus spp (11.1%), Microsporidium (11.1%) and Rhizopus spp (11.1%) in all the samples. The FTIR of Smooth white garri (Sample A) shows five (5) peaks, Yellow gravel (Sample B) show five (5) peaks and the yellow garri (Sample C) show eight (8) peaks indicate indicating different wave number, intensity and compound The proximate analysis result shows the compositions for garri. The Moisture content recorded showed higher content in yellow garri (7.31%) while white garri is (5.98%). The presence of these bacteria and fungi in all the garri samples indicate a serious threat to the health of consumers.
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Antimicrobial Resistance in Salmonella : Its Mechanisms in Comparison to Other Microbes, and The Reversal Effects of Traditional Chinese Medicine on Its Resistance
Chapter
Full-text available
  • Nov 2023
Salmonella is one of the most notable pathogens leading to the outbreak of foodborne diseases worldwide. Antimicrobial chemotherapy with 3rd-generation cephalosporins or fluoroquinolones is often used for severe infections caused by Salmonella. Therefore, antibiotic or antimicrobial resistance (AMR) of Salmonella is a serious threat to human and animal health in China and worldwide. In order to better understand the current situation and development status of AMR in Salmonella isolates, this chapter will provide an overview of the following: 1. The history and development trend of AMR in Salmonella, and a comparison of its AMR with that of other major pathogenic bacteria in animals. 2. The AMR mechanisms of Salmonella to various antibiotics, with a particular focus on the commonly used antibiotics. 3. The mechanisms of the spread of AMR in Salmonella, including the AMR genes or mobile genetic elements carrying AMR genes among microbes, and among people, animal-derived foods, and the environment. 4. The elimination or reversal of AMR in Salmonella by using traditional Chinese medicine or the active ingredients in traditional Chinese medicine. 5. The development of detection technology for Salmonella serotypes, virulence, and AMR, and the improvement from conventional detection methods to more advanced biological detection methods and bioinformatics technology.
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The type species of the genus Salmonella Lignieres 1900 is Salmonella enterica (ex Kauffmann and Edwards 1952) Le Minor and Popoff 1987, with the type strain LT2(T) and conservation of the epithet enterica in Salmonella enterica over all earlier epithets that may be applied to this species. Opinion 80
Article
  • Jan 2005
The Judicial Commission of the International Committee for Systematics of Prokaryotes has decided that the type species of the genus Salmonella Lignieres 1900 is Salmonella enterica (ex Kauffmann and Edwards 1952) Le Minor and Popoff 1987 and that the type strain of this conserved over species is strain LT2(T). In addition, the epithet enterica in Salmonella enterica is all earlier epithets that may be applied to this species.
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Actions of the Judicial Commission of the International Committee on Systematic Bacteriology on Requests for Opinions Published Between January 1985 and July 1993
Article
  • Jan 1994
Eleven requests were published between January 1985 and July 1993. Four of these requests were granted and have been published as Opinion 64, replacing and recognizing type strains of Methanobacterium formicicum and Methanobacterium bryantii, respectively; Opinion 65, replacing the type strain of Selenomonas sputigena; Opinion 66, replacing the type strain of Streptococcus mitis; and Opinion 67, rejecting Citrobacter diversum. Six requests were denied, including requests for conservation or recognition of 'Rhodococcus lentifragmentus,' 'Pediococcus acidilactici,' and 'Salmonella enterica,' rejection of Erwinia carnegieana, Pectobacterium carnegieana, and Lactobacillus paracasei, and transfer of the type strain of Methanosaeta concilii to Methanothrix soehngenii. A request based on a proposal for reinterpretation of the position of Xanthomonas maltophilia was not considered by the Judicial Commission because it represented a substantive taxonomic issue rather than a nomenclatural question governed by the Bacteriological Code.
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Actions of the Judicial Commission of the International Committee on Systematic Bacteriology on Requests for Opinions Published in
Article
  • Apr 1984
The statutes of the International Committee on Systematic Bacteriology, which are published in the International Code of Nomenclature of Bacteria (7), provide for formal publi- cation of opinions that have been issued by the Judicial Commission of the International Committee. However, there is no provision for formal publication of denials of opinions that have been requested, other than as minutes of the meetings of the Judicial Commission. To minimize uncertainty in the scientific community in the period be- tween resolution of some questions by mail ballot of the Judicial Commission and the appearance of the decision in minutes of the quadrennial meetings, we have established the practice of publishing interim reports of decisions. This is such a report on the resolution of seven requests for opinions upon which votes were taken 12 months or more after publication of the requests. Replacement of the type strain of Acetobacter aceti subsp.
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Designation of Salmonella enterica sp. nov., nom. rev., as the type and only species of the genus Salmonella
Article
  • Oct 1987
Since the publication of the Approved Lists of Bacterial Names, the type species of the genus Salmonella has been S. choleraesuis. At the time of publication of the Approved Lists, five Salmonella species had standing in the nomenclature, and the description of S. choleraesuis was the same as that of the serotype of that name. Several studies have shown that the genus Salmonella consists of only one species, and the strict application of the Bacteriological Code would recognize S. choleraesuis (the type species) as the single Salmonella species. This can lead to confusion and hazards since the specific epithet is also the name of a serovar (serovar Choleraesuis). This confusion is increased by the common practice of using serovar names as if they represented species names (e.g., S. typhi, S. choleraesuis, and S. typhimurium). Some serovars (e.g., Salmonella choleraesuis subsp. choleraesuis serovar Typhi) are highly pathogenic and cause a disease different from that caused by other serovars (e.g. S. choleraesuis subsp. choleraesuis serovar Choleraesuis). To avoid further confusion, it is proposed to use for the single Salmonella species a name which has not been used earlier for a serotype. It is thus requested that the type species of the genus Salmonella be Salmonella enterica sp. nov., nom. rev. with strain CIP 60.62 (a H2S-producing clone of strain LT2) as the type strain. Since the name S. choleraesuis is not proposed for rejection, bacteriologists who do not accept the single species concept of the genus Salmonella will be free to use the name S. choleraesuis as a synonym of Salmonella enterica subsp. enterica serotype C holeraesuis. The species concept in the genus Salmonella has evolved in four overlapping phases. Each of these phases relied on available methodology and knowledge stressing (i) clinical evidence, (ii) antigenic specificities, (iii) biochemical proper- ties and (iv) deoxyribonucleic acid (DNA) relatedness. Taxonomy based on the clinical role of Salmonella strains. Strains were considered different species when isolated from different clinical conditions (e.g., "Eberthella typhosa" or S. typhi and S. enteritidis) or different hosts ("S. abortusovis," "S. gallinarum-pullorum," and S. cholerae- suis). It was soon realized that a number of these so-called species were ubiquitous, and emphasis shifted to antigenic properties. Taxonomy based on antigenic specificities. Serological anal- ysis of 0 and H antigens initiated by White (36) and continued and extended by Kauffmann (17) resulted in the description of a great number of serovars. In 1961, Kauff- mann (16) defined the species as "a group of related sero- fermentative phage types," with the result that each Salmo- nella serovar was considered as a species. This "one serovar-one species" concept is untenable. It should be noted that more than 2,100 serovars have been described. Since some names inferring a host specificity happened to be bad choices, epithets of the new serovars were later derived from the geographic location where the first strain was isolated (e.g., "S. panama" and "S. montevideo"). Taxonomy based on biochemical properties. Most serovars cannot be separated by biochemical tests, and several au- thors have made proposals aimed at reducing the number of species. In 1944, Borman et al. (2) proposed that only three
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Clonal nature of Salmonella typhi and its genetic relatedness to other salmonellae as shown by multilocus enzyme electrophoresis, and proposal of Salmonella bongori comb. nov
Article
  • Mar 1989
Crude cell extracts of 26 isolates of Salmonella serotype typhi (S. typhi) and 48 other Salmonella isolates representing 28 serotypes and seven DNA hybridization subgroups were analyzed for electrophoretic variants of 24 metabolic enzymes by starch gel electrophoresis. All strains of S. typhi had identical isoenzyme patterns, indicating that they were a single clone. All of the enzymes detected in the remaining strains were polymorphic, and the degree of genetic variation was quite high. The average number of alleles per enzyme locus was 4.7, and the mean genetic diversity per locus was 0.556. Thirty-two distinct allele profiles, or electrophoretic types (ETs), were found in these 48 strains of Salmonella serotypes other than S. typhi. Analysis of the genetic relationships of the ETs to each other showed that, with one exception, the ETs formed subgroups that were consistent with the subgroupings based on DNA hybridization studies. ET profiles were not always linked to specific serologic patterns. These data show that multilocus enzyme electrophoresis has a potential application in epidemiologic and taxonomic studies of salmonellae, although it is not differential for S. typhi. We also propose a new species, Salmonella bongori comb. nov., a new combination base on the elevation of Salmonella choleraesuis subsp. bongori to the level of species.
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A proposal for Salmonella nomenclature
Article
  • Sep 1982
A single species, composed of six subspecies, was found in the genus Salmonella following a numerical taxonomy and a study of the DNA relatedness (see p. 223, Le Minor et al.). The Salmonella nomenclature is herein updated to take into account modern taxonomic knowledge. The single Salmonella species is S. choleraesuis (type species). Six subspecies are proposed: (1) S. choleraesuis subsp. choleraesuis subsp. nov. is composed of all Salmonella strains formerly assigned to the subgenus I; (2) S. choleraesuis subsp. salamae subsp. nov. corresponds to the former subgenus II; (3) S. choleraesuis subsp. arizonae comb. nov. is composed of monophasic serovars of the former subgenus III ("Arizona"); (4) S. choleraesuis subsp. diarizonae subsp. nov. is composed of diphasic serovars of the former subgenus III ("Arizona"); (5) S. choleraesuis subsp. houtenae subsp. nov. corresponds to the former subgenus IV; and (6) S. choleraesuis subsp. bongori subsp. nov. is composed of strains positive for dulcitol fermentation, ONPG, and KCN tests. Type strains are proposed for each subspecies. The name of S. choleraesuis subsp. choleraesuis serotypes (e.g. typhimurium) should be used without italicization or underlining (e.g. S. choleraeusis subsp. choleraesuis ser. typhimurium). A practical and unofficial use of non-italicized serotype names is discussed.
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Revised Salmonella nomenclature: designation of Salmonella enterica (ex Kauffmann and Edwards 1952) Le Minor and Popoff 1987 sp. nov. nom. rev. as the neotype species of the genus Salmonella Lignieres 1900 (Approv Lists 1980), rejection of the name Salmonella choleraesuis (Smith 1894) Weldin 1927 (Approved Lists 1980), and conservation of the name Salmonella typhi (Schroeter 1886) Warren and Scott 1930 (Approved Lists 1980). Request for an Opinion
Article
  • May 1999
The Request for an Opinion by Le Minor and Popoff 1987, proposing designation of 'Salmonella enterica' (ex Kauffman and Edwards 1952) Le Minor and Popoff 1987 as the type and only species of the genus Salmonella Lignieres 1900 (Approved Lists 1980), has not been positively decided upon by the Judicial Commission. However, many bacteriologists use the name 'Salmonella enterica'. To avoid further confusion, it is requested to reject the name Salmonella choleraesuis (Smith 1894) Weldin 1927 (Approved Lists 1980), to recognize the species Salmonella enterica, to conserve the name Salmonella typhi (Schroeter 1886) Warren and Scott 1930 (Approved Lists 1980), and to emend the genus Salmonella with the establishment of a neotype species, Salmonella enterica.
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Recognition of nomenclatural standing of Salmonella typhi (Approved Lists 1980), Salmonella enteritidis (Approved Lists 1980) and Salmonella typhimurium (Approved Lists 1980), and conservation of the specific epithets enteritidis and typhimurium. Request for an Opinion
Article
  • Apr 2000
In 1994, the Judicial Commission of the ICSB announced that Le Minor and Popoff's Request for an Opinion in 1987 to designate Salmonella enterica sp. nov., nom. rev. as the type and only species of the genus Salmonella was denied. Thus, the current species of the genus Salmonella are Salmonella typhimurium, Salmonella enteritidis, Salmonella typhi, Salmonella choleraesuis (including six subspecies) and Salmonella bongori, with the type species, S. choleraesuis (Smith 1894) Weldin 1927 (Approved Lists 1980). Because the decision of the Judicial Commission about the request by Le Minor in 1987 was suspended for 7 years, the non-validated name 'S. enterica' has been used among microbiologists and has caused confusion in the nomenclature of Salmonella. In order to overcome such confusion, and because of their importance as human pathogens, we herein propose to recognize the nomenclatural status of S. typhi, S. enteritidis and S. typhimurium as species and request to issue an Opinion to conserve the specific epithets enteritidis and typhimurium in the species names Salmonella enteritidis and Salmonella typhimurium.
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Proposal of Salmonella paratyphi sp. nov., nom. rev. and Request for an Opinion to conserve the specific epithet paratyphi in the binary combination Salmonella paratyphi as nomen epitheton conservandum
Article
  • Apr 2000
We propose Salmonella paratyphi sp. nov., nom. rev., by raising Salmonella choleraesuis subsp. choleraesuis serovar Paratyphi A to species status and request an Opinion to include the specific epithet paratyphi in the binary combination of Salmonella paratyphi in the list of epitheta specifica conservanda.
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