ArticlePDF Available

Campylobacter ornithocola sp. nov., a new member of the Campylobacter lari group isolated from wild bird faecal samples

Authors:

Abstract and Figures

During a study on the prevalence and diversity of campylobacteria in wild birds faecal samples in the city of Valdivia (South of Chile) 17 Gram-negative, curved rod isolates, were initially identified as Campylobacter lari by PCR-RFLP. Further identification by 16S rRNA sequence analysis revealed that they formed a distinct group in the genus Campylobacter. This unique position was confirmed by rpoB, atpA and cpn60 gene sequence analysis. The average nucleotide identity between the representative strain WBE38T and the type strain of the closest taxon Campylobacter lari subsp. concheus (LMG 11760) was 90.8%. The oxidase and urease activity of the novel isolates enabled them to be phenotypically differentiated from recognized Campylobacter species. Therefore, on the basis of phenotypic, genetic and genomic characterizations, this study clearly shows that these strains represent a novel species within the genus Campylobacter, for which the name Campylobacter ornithocola sp. nov. is proposed, with the type strain WBE38T (=CECT 9147T =LMG 29815T).
Content may be subject to copyright.
Downloaded from www.microbiologyresearch.org by
IP: 193.62.202.242
On: Fri, 30 Jun 2017 09:35:38
Campylobacter ornithocola sp. nov., a novel member of the
Campylobacter lari group isolated from wild bird faecal samples
Alberto C
aceres,
1
Ivo Muñoz,
1
Gregorio Iraola,
2
Florencia Díaz-Viraqu
e
3
and Luis Collado
1,
*
Abstract
During a study on the prevalence and diversity of campylobacteria in wild birds faecal samples from the city of Valdivia
(southern Chile) 17 Gram-stain-negative, curved-rod-shaped isolates, were initially identified as Campylobacter lari by PCR
RFLP. Further identification by 16S rRNA sequence analysis revealed that they formed a distinct group in the genus
Campylobacter. This unique position was confirmed by the results of analysis of rpoB,atpA and cpn60 gene sequences. The
average nucleotide identity between the representative strain WBE38
T
and the type strain of the most closely related taxon C.
lari subsp. concheus (LMG 11760) was 90.8 %. The oxidase and urease activity of the novel isolates enabled them to be
phenotypically differentiated from species of the genus Campylobacter with validly published names. Therefore, on the basis
of phenotypic, genetic and genomic characterizations, the results of this study clearly indicate that these strains represent a
novel species within the genus Campylobacter, for which the name Campylobacter ornithocola sp. nov. is proposed, with the
type strain WBE38
T
(=CECT 9147
T
=LMG 29815
T
).
The genus Campylobacter was proposed by Sebald and
Veron [1], to accommodate the species Vibrio fetus (now
Campylobacter fetus, the type species of the genus). Since
then the number of species of the genus Campylobacter has
greatly increased and, at the time of writing (September
2016), this genus encompassed 28 species and 9 subspecies
with validly published names [24]. Infection with members
of the genus Campylobacter is the leading cause of food-
borne bacterial gastroenteritis in the developed world,
where infection is principally the result of consumption of
contaminated meat and poultry. The most common symp-
toms of campylobacteriosis include severe diarrhoea, with a
proportion of patients developing chronic sequelae such as
GuillainBarr
e syndrome, reactive arthritis and irritable
bowel syndrome [5]. Campylobacter jejuni and Campylobac-
ter coli are by far the most isolated and studied species, while
the epidemiology and the clinical role of the other less com-
mon species in human and animal diseases is far less under-
stood [5, 6].
In the present study, 17 novel isolates of members of the
genus Campylobacter recovered from wild bird faecal sam-
ples were subjected to a polyphasic approach including
molecular identification by PCRRFLP, genotyping by
enterobacterial repetitive intergenic consensus PCR
(ERICPCR), phylogenetic analysis using the 16S rRNA,
rpoB,atpA and cpn60 genes and phenotypic characteriza-
tion, in order to determine their taxonomic positions.
Additionally, the whole genome of WBE38
T
was
sequenced, since it was selected as the type strain. On the
basis of our results, we propose and describe these strains
as representing a novel species within the genus
Campylobacter.
Over the period between January 2013 and October 2015, a
study was conducted to evaluate the prevalence and diver-
sity of campylobacteria in wild bird faecal samples from the
city of Valdivia, in the south of Chile, where a collection of
isolates of members of the genus Campylobacter was
obtained (L. Collado, paper in preparation). The samples
corresponded to birds faecal droppings excreted in public
urban parks. Although the specific type of bird correspond-
ing to each specimen remains unidentified, at the time of
sampling black-faced ibis (Theristicus melanopis), southern
lapwing (Vanellus chilensis) and chimango caracara (Mil-
vago chimango) were the main species observed at these
sites. Faecal samples were collected using sterile cotton-
tipped swabs that were immediately placed into 8 ml Bolton
broth (Oxoid). Incubation was performed at 37 C for 48 h
under micro-aerobic conditions (CampyGen, Oxoid). After
Author affiliations:
1
Institute of Biochemistry and Microbiology, Faculty of Sciences, Universidad Austral de Chile, Valdivia, Chile;
2
Bioinformatics Unit,
Institut Pasteur Montevideo, Montevideo, Uruguay;
3
Molecular Biology Unit, Institut Pasteur Montevideo, Montevideo, Uruguay.
*Correspondence: Luis Collado, luiscollado@uach.cl
Keywords: wild bird; Campylobacter; Valdivia; Chile.
Abbreviation: ERIC, enterobacterial repetitive intergenic consensus.
The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA, rpoB,atpA,cpn60 genes and the draft genome of the strain WBE38
T
are KX467974,
KX467989, KX467979, KX467985 and LXSU00000000, respectively.
Three supplementary figures are available with the online Supplementary Material.
TAXONOMIC DESCRIPTION
C
aceres et al., Int J Syst Evol Microbiol
DOI 10.1099/ijsem.0.001822
001822 ã2017 IUMS
1
Downloaded from www.microbiologyresearch.org by
IP: 193.62.202.242
On: Fri, 30 Jun 2017 09:35:38
enrichment, an aliquot (400 µl) was transferred onto the
surface of a 0.45 µm membrane filter (Millipore) which was
placed on a Petri dish containing Blood Agar Base (Merck)
supplemented with 5 % defibrinated sheep blood (Quad
Five) and it was allowed to filter passively under
room temperature conditions for 30 min. After filtration,
the filters were removed with sterile forceps and discarded.
The inoculated plates were incubated under the aforemen-
tioned conditions [7]. The 17 novel isolates described here
were initially identified as Campylobacter lari by the PCR
RFLP described by Marshall et al. [8] showing the C1 and
C1b restriction patterns with the endonucleases DdeI and
BsrI, respectively (data not shown). However, recently this
species has been divided into two subspecies (C. lari subsp.
lari and C. lari subsp. concheus) [9]. Additionally, several
C. lari-like novel species have been described, i.e.,
Campylobacter insulaenigrae [10], Campylobacter peloridis
[9], C. subantarcticus [11] and Campylobacter volucris [12],
that collectively have been referred to as the Campylobacter
lari group [13]. Since no available PCR method could differ-
entiate these highly related taxa, all isolates we identified as
C. lari by PCRRFLP were further analyzed by a polyphasic
taxonomic approach.
The 17 isolates were first analysed by means of the ERIC
PCR technique using the protocol of Houf et al. [14], in
order to avoid further analysis of strains with the same
genotype. The electrophoretic patterns were analysed using
the Jaccard index and a dendrogram was reconstructed by
using the unweighted pair group linkage analysis (UPGMA)
method with the Phoretix 1d Pro software (Totallab). As
shown in Fig. 1, all the isolates belonged to different ERIC
PCR types and, consequently, were considered to represent
different strains. Nearly complete 16S rRNA gene sequences
(1350 bp) of five selected strains (WBE38
T
, WBE186,
WBE206, WBE215 and WBE241), were amplified as
described by Vandamme et al. [15]. Additionally, the rpoB,
atpA and cpn60 genes were also evaluated with the protocols
described by Korczak et al. [16], Miller et al. [17] and Hill
et al. [18], respectively. Due to the high number of strains,
only the analysis of rpoB gene sequences included all 17
strains. Both DNA strands of the PCR products were
directly sequenced with an ABI 3730 XL automatic DNA
WBE258
WBE212
WBE241
WBE215
WBE225
WBE249
WBE210
WBE206
WBE201
WBE193
WBE187
WBE38
WBE186
WBE188
WBE195
WBE196
WBE189
0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00
Fig. 1. Cluster analysis based on the patterns obtained by ERICPCR from the Campylobacter ornithocola sp. nov. strains.
C
aceres et al., Int J Syst Evol Microbiol
2
Downloaded from www.microbiologyresearch.org by
IP: 193.62.202.242
On: Fri, 30 Jun 2017 09:35:38
sequencer (ABI) by a commercial sequencing facility (Mac-
rogen, Seoul, Korea). Alignment of the sequences was per-
formed with the CLUSTAL W program [19]. Phylogenetic trees
were reconstructed with the MEGA 6 software [20], by using
the neighbour-joining method [21] with Kimuras two-
parameter substitution model [22] and the stability of the
groupings, estimated by bootstrap analysis (500 replica-
tions). Similarity values between the 16S rRNA gene
sequence of WBE38
T
and those of the type strains of all
members of the genus Campylobacter with validly published
names were calculated with the EzTaxon-e server [23]
obtaining a similarity range of 99.590.7 %. The 16S rDNA
phylogenetic tree (Fig. 2) clearly indicated that the five
strains represented a single species within the genus Cam-
pylobacter, most closely related to C. subantarcticus (99.5 %
similarity) and C. lari subsp. concheus (99.4 % similarity).
The taxonomic position of the novel strains within the Cam-
pylobacter lari group and the demonstration that they
C. ornithocola WBE 215 (KX467977)
C. ornithocola WBE 241 (KX467978)
C. ornithocola WBE 206 (KX467976)
C. ornithocola WBE 186 (KX467975)
C. ornithocola WBE 38T (KX467974)
C. lari UPTC NCTC 11845 (CP007775)
C. lari subsp. concheus LMG 21009T (AM922330)
C. subantarcticus LMG 24377T (AM933371)
C. volucris LMG 24380T (FM883694)
Campylobacter sp. RM16704 (CP007769)
C. lari subsp. lari ATCC 35221T (AY621114)
C. peloridis LMG 23910T (AM922331)
C. hepaticus NCTC 13823T (KU886019)
C. insulaenigrae NCTC 12927T (AJ620504)
C. jejuni subsp. doylei LMG 8843T (DQ174144)
C. jejuni subsp. jejuni NCTC 11351T (AF372091)
C. coli LMG 6440T (AF372092)
C. cuniculorum LMG 24588T (DQ400345)
C. helveticus ATCC 51209T (U03022)
C. avium LMG 24591T (EU623473)
C. upsaliensis CCUG 14913T (DQ174157)
C. canadensis LMG 24001T (EF621894)
C. hyointestinalis subsp. lawsonii LMG 14432T (AF097685)
C. lanienae NCTC 13004T (AF043425)
C. iguaniorum LMG 28143T (KF425533)
C. hyointestinalis subsp. hyointestinalis NCTC 11608T (AF097689)
C. fetus subsp. testudinum LMG 27499T (CP006833)
C. fetus subsp. fetus ATCC 27374T (DQ174127)
C. fetus subsp. venerealis NCTC 10354T (DQ174131)
C. corcagiensis CIT045T (KF745861)
C. ureolyticus ATCC 33387T (L04321)
C. mucosalis ATCC 43264T (DQ174173)
C. concisus ATCC 33237T (L04322)
C. sputorum biovar paraureolyticus LMG 17590 (AF022768)
C. sputorum biovar sputorum LMG 7795 (X67775)
C. sputorum biovar fecalis LMG 6617 (AF550637)
C. curvus ATCC 35224T (DQ174165)
C. hominis NCTC 13146T (AJ251584)
C. gracilis ATCC 33236T (DQ174168)
C. rectus ATCC 33238T (L04317)
C. showae CCUG 30254T (DQ174155)
100
99
99
100
100
98
91
93
89
94
92
79
88
94
100
92
90
80
98
0.01
Fig. 2. Neighbour-joining tree based on 16S rRNA sequences showing the phylogentic position of Campylobacter ornithocola sp. nov.
within the genus Campylobacter. Bootstrap values>70 %, generated from 500 replicates, are shown at the nodes. Bar, 0.01 substitutions
per site.
C
aceres et al., Int J Syst Evol Microbiol
3
Downloaded from www.microbiologyresearch.org by
IP: 193.62.202.242
On: Fri, 30 Jun 2017 09:35:38
represent a novel lineage were confirmed by the rpoB,atpA
and cpn60 phylogenetic trees (Figs S1, S2 and S3 available in
the online Supplementary Material).
For the whole-genome sequencing of WBE38
T
, genomic
libraries were prepared with the Nextera XT DNA Sample
Preparation Kit (Illumina) and then sequenced using a
MiSeq Illumina platform, which produced 5 250 728 pair-
end reads (2150 cycles). After an initial quality check,
reads were assembled with SPAdes [24] and annotated with
Prokka [25], producing 160 contigs that were deposited in
the GenBank under the accession number LXSU00000000.
The version described in this paper is version
LXSU01000000. The average nucleotide identity (ANI) was
used as an alternative to DNADNA hybridization [26].
The ANIb (based on BLAST) values of WBE38
T
compared
with the sequenced type strains of all other species of the C.
lari group were calculated using JSpecies v1.2.1 [27] and
were below the 95 % species cut-off (Table 1) [26]. The
genomic DNA G+C content of WBE38
T
was calculated
using in-house R scripts and was 29.5 mol%, which is within
the range reported for the genus Campylobacter (2947 mol
%) [28].
For the physiological and biochemical characterizations of all
the novel strains, phenotypic testing was performed as
described previously [2932]. Growth of strains was deter-
mined on nutrient broth no. 2 (Oxoid) supplemented with
5 % defibrinated sheep blood (Quad Five) and 2% agar
(Merck). Micro-aerobic growth (using CampyGen, Oxoid)
was evaluated at 25 C, 37 and 42 C for 48 to 72 h. Aerobic
and anaerobic growth (using AnaeroGen, Oxoid) were evalu-
ated at 37 C for 72 h. Catalase activity was evaluated by add-
ing a 3 % H
2
O
2
solution and observing the reaction within
5 s. Oxidase activity was determined with Bactident Oxidase
strips (Merck). Indoxyl acetate hydrolysis was determined as
described by Mills and Gherna [33]. In addition to this, a set
of additional phenotypic tests (reduction of nitrates, esterase
activity, hydrolysis of hippurate, g-glutamyl transferase activ-
ity, reduction of triphenyltetrazolium chloride (TTC),
alkaline phosphatase activity, production of H
2
S, assimilation
of glucose and pyrrolidonyl arylamidase, L-arginine arylami-
dase and L-aspartate arylamidase activities) were evaluated by
using the API Campy identification system (bioM
erieux)
according to the manufacturers instructions. All tests were
performed at least twice with Campylobacter jejuni (DSM
4688
T
), Campylobacter coli (DSM 4689
T
), C. lari (DSM
11375
T
), C. subantarcticus (LMG 24377
T
), C. insulaenigrae
(LMG 22716
T
), C. volucris (LMG 24380
T
) and Escherichia
coli (ATCC 25922) used as controls. The novel isolates were
biochemically different from most of the species of the genus
Campylobacter with validly published names because oxidase
activity was not detected. This test is positive in all species
except Campylobacter gracilis and sporadic isolates of
Campylobacter concisus and Campylobacter showae [34].
However, the novel isolates could be differentiated from oxi-
dase-negative members of the genus Campylobacter by the
urease test. Table 2 shows the most important phenotypic
characteristics differentiating the novel strains from the other
species of the genus Campylobacter. Bacterial cell shape was
observed using a scanning electron microscope (LEO 420;
Zeiss) following the protocol described by Kawamura et al.
[35]. The organism exhibits a curved shape and cells became
spherical or coccoid after 72 h of incubation (Fig. 3).
In conclusion, the results from this taxonomic study clearly
demonstrate that the isolates recovered from wild birds fae-
cal samples comprise a novel species distinct from other
currently known species of the genus Campylobacter, based
on 16S rRNA, housekeeping genes, sequence comparison of
eight whole genomes, morphological, physiological and bio-
chemical properties. The name Campylobacter ornithocola
sp. nov. is proposed, with WBE38
T
(=CECT 9147
T
=LMG
29815
T
) as the type strain.
DESCRIPTION OF CAMPYLOBACTER
ORNITHOCOLA SP. NOV.
Campylobacter ornithocola [or.ni.tho¢co.la. Gr. n. ornis, -
ithos bird; L. suff. -cola (from L. n. incola) dweller; N.L. n.
ornithocola bird dweller].
Cells are Gram-negative curved rods, non-encapsulated,
non-spore-forming and are 0.30.5 µm wide and 1.23 µm
long. After incubation on Columbia agar (5 % sheep blood)
in a microaerobic atmosphere at 37 C for 48 h, colonies are
glossy, slightly convex, round with smooth margins. Coc-
coid cells were observed in old cultures. Swarming on solid
media was noted. Pigments are not produced. Grows on
blood agar at 37 C and at 42 C under micro-aerobic culture
conditions (does not require atmospheric hydrogen) and at
37 C in anaerobic conditions. No growth was observed at
37 C on aerobiosis and at 25 C under micro-aerobic condi-
tions. No haemolysis is seen on blood agar. Catalase and
urease activity is present but no oxidase. Esterase activity
and reduction of triphenyltetrazolium chloride (TTC)
are variable.
Table 1. Average nucleotide identity based on BLAST (ANIb) values (in
percentages) for C. ornithocola sp. nov. and the most closely related
members of the genus Campylobacter
Strains: 1, C. ornithocola sp. nov. WBE38
T
; 2, C. lari subsp. concheus
LMG 11760; 3, C. lari subsp. lari RM 2100; 4, C. subantarcticus LMG
24377
T
; 5, C. peloridis LMG 23910
T
; 6, C. volucris LMG 24379; 7, C. insu-
laenigrae NCTC 12927.
Strains 1 2 3 4 5 6 7
1
290.8
389.5 92.8
488.4 89.7 88.8
586.0 86.2 86.1 85.3
682.0 82.3 83.1 81.8 82.4
780.9 81.0 81.2 80.2 81.1 82.9
C
aceres et al., Int J Syst Evol Microbiol
4
Downloaded from www.microbiologyresearch.org by
IP: 193.62.202.242
On: Fri, 30 Jun 2017 09:35:38
Table 2. Phenotypic characteristics that differentiate Campylobacter ornithocola sp. nov. from other species of the genus Campylobacter
Species: 1, C. ornithocola sp. nov (n=17); 2, C. avium; 3, C. canadensis; 4, C. coli; 5, C. concisus; 6, C. corcagiensis; 7, C. cuniculorum; 8, C. curvus; 9, C. fetus subsp. fetus; 10, C. fetus subsp. testudinum;
11, C. fetus subsp. venerealis; 12, C. geochelonis; 13, C. gracilis; 14, C. helveticus; 15, C. hepaticus; 16, C. hominis; 17, C. hyointestinalis subsp. hyointestinalis; 18, C. hyointestinalis subsp. lawsonii; 19. C.
iguaniorum; 20, C. insulaenigrae; 21, C. jejuni subsp. doylei; 22, C. jejuni subsp. jejuni; 23, C. lanienae; 24, C. lari subsp. concheus; 25, C. lari subsp. lari; 26, C. mucosalis; 27, C. peloridis; 28, C. rectus;
29, C. showae; 30, C. sputorum; 31, C. subantarcticus; 32, C. upsaliensis; 33, C. ureolyticus; 34, C. volucris. Data for reference taxa were taken from [3, 4, 912, 28, 36] . +, 100 % of strains positive; ,
100 % of strains negative; (+), 8094 % of strains positive; V, 4266 % of strains positive; (), 733 % of strains positive; ND, not determined.
Characteristic 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34
Oxidase * + + + V+ + + + + + + + + + + + + + + + + + + + + + V+ + + + +
Catalase + V V ++ + + + (+) V V ++ + + + V+ + + + + () + V+V+
Urease + V +        ND  
+
Alkaline phosphatase     V+VND   ND ()ND   + (+) ND   ND  
Reduction of
Nitrate V+V+ () (+) + + + + (+) + (+) + V+ + + + + + + + ()ND + + (+) ++ + +
2,3,5,Triphenyltetra-
zolium
chloride (TTC)
()ND +  V V +   ND   ND ND V +ND + + ND   ND V  
Hydrolysis of
Hippurate +  ()  +  (+)   + +      
Indoxyl acetate ++V+V  V+ +   + + ND +V +V
H
2
S production (TSI)   V +()    + + +  
+ND V+   
a-Haemolysis () ()+ ()ND V +  V V ND + + + ND +ND + + + + + V ND
Growth at/in/on
25 C (microaerobic)     ND   + + +     +     
37 C (microaerobic) + + + + + + + V+ + + + + + + + + + + + + + + + + + V+ + + + +
42 C (microaerobic) + + + + (+) + (+) V(+) V  V+ + () + + + + + + + + + ()V+ + + V+
37 C (anaerobic) + ++ + + () + V+ + ++ +   +ND +ND + + + + V+
37 C (aerobic)   V      
Glycine 1% + V(+) (+) + + + + () + + V+ + V+ + () + (+) + V+ + V+ (+) + +
H
2
requirement V  + +  + +V V ND ND +ND + + ND
DNA G+C content
(mol%)
29.5 35 ND 31 37
41
31.9 32.4 45
46
33
35
ND 33
34
33.6 44
46
34 27.9 32.5 35
36
31
33
36 ND 31 30
31
36 30 29
30
36
38
29 45
46
44
46
29
33
30 32
36
28
30
29
* Oxidase negative test allows differentiation of the novel species from urease-positive thermophilic Campylobacter (UPTC) strains.
This test was determined for the corresponding type strain, in this study.
We obtained a different result from that published by Debruyne et al. [12], when we evaluated the nitrate test with the API Campy (nitrate reduction negative for LMG 24377
T
).
C
aceres et al., Int J Syst Evol Microbiol
5
Downloaded from www.microbiologyresearch.org by
IP: 193.62.202.242
On: Fri, 30 Jun 2017 09:35:38
Pathogenicity is unknown; strains have been recovered
from faecal samples of wild birds. The type strain is
WBE38
T
(=CECT 9147
T
=LMG 29815
T
) which was isolated
from a faecal sample in Valdivia, Chile.
Funding information
This work was supported by the Comisión Nacional de Investigación
Científica y Tecnológica (CONICYTChile) under the project FONDECYT
N11130402.
Acknowledgements
We thank Bernhard Schink (University of Konstanz, Konstanz, Ger-
many) for his help with the specific etymology and nomenclature. We
also thank Ricardo Silva (Universidad Austral de Chile) for his help
with SEM.
Conflicts of interest
The authors declare that there are no conflicts of interest.
Ethical statement
No experiments with humans or animals were carried out.
References
1. Sebald M, Veron M. Base DNA content and classification of vib-
rios. Ann Inst Pasteur 1963;105:897910.
2. List of prokaryotic names with standing in nomenclature (LPSN).
2016. http://www.bacterio.cict.fr/c/campylobacter.html [accessed
17 September 2016].
3. Piccirillo A, Niero G, Calleros L, P
erez R, Naya H et al. Campylo-
bacter geochelonis sp. nov. isolated from the western Hermanns
tortoise (Testudo hermanni hermanni). Int J Syst Evol Microbiol
2016;66:34683476.
4. Van TTH, Elshagmani E, Gor MC, Scott PC, Moore RJ. Campylobac-
ter hepaticus sp. nov., isolated from chickens with spotty liver dis-
ease. Int J Syst Evol Microbiol 2016;66:45184524.
5. Man SM. The clinical importance of emerging Campylobacter spe-
cies. Nat Rev Gastroenterol Hepatol 2011;8:669685.
6. Iraola G, P
erez R, Naya H, Paolicchi F, Pastor E et al. Genomic
evidence for the emergence and evolution of pathogenicity and
niche preferences in the genus Campylobacter.Genome Biol Evol
2014;6:23922405.
7. Collado L, Jara R, Gonz
alez S. Description of Helicobacter valdi-
viensis sp. nov., an Epsilonproteobacteria isolated from wild bird
faecal samples. Int J Syst Evol Microbiol 2014;64:19131919.
8. Marshall SM, Melito PL, Woodward DL, Johnson WM, Rodgers FG
et al. Rapid identification of Campylobacter,Arcobacter, and Helico-
bacter isolates by PCRrestriction fragment length polymorphism
analysis of the 16S rRNA gene. J Clin Microbiol 1999;37:4158
4160.
9. Debruyne L, On SLW, de Brandt E, Vandamme P. Novel Campylo-
bacter lari-like bacteria from humans and molluscs: description of
Campylobacter peloridis sp. nov., Campylobacter lari subsp. con-
cheus subsp. nov. and Campylobacter lari subsp. lari subsp. nov.
Int J Syst Evol Microbiol 2009;59:11261132.
10. Foster G, Holmes B, Steigerwalt AG, Lawson PA, Thorne P et al.
Campylobacter insulaenigrae sp. nov., isolated from marine mam-
mals. Int J Syst Evol Microbiol 2004;54:23692373.
11. Debruyne L, Broman T, Bergström S, Olsen B, On SLW et al.
Campylobacter subantarcticus sp. nov., isolated from birds in
the sub-Antarctic region. Int J Syst Evol Microbiol 2010;60:815
819.
12. Debruyne L, Broman T, Bergström S, Olsen B, On SLW et al. Cam-
pylobacter volucris sp. nov., isolated from black-headed gulls
(Larus ridibundus). Int J Syst Evol Microbiol 2010;60:18701875.
13. Miller WG, Yee E, Chapman MH, Smith TP, Bono JL et al. Compar-
ative genomics of the Campylobacter lari group. Genome Biol Evol
2014;6:32523266.
14. Houf K, de Zutter L, van Hoof J, Vandamme P. Assessment of the
genetic diversity among arcobacters isolated from poultry prod-
ucts by using two PCR-based typing methods. Appl Environ
Microbiol 2002;68:21722178.
15. Vandamme P, Holmes B, Bercovier H, Coenye T. Classification of
centers for disease control group eugonic fermenter (EF)-4a and
EF-4b as Neisseria animaloris sp. nov. and Neisseria zoodegmatis
sp. nov., respectively. Int J Syst Evol Microbiol 2006;56:18011805.
16. Korczak BM, Stieber R, Emler S, Burnens AP, Frey J et al. Genetic
relatedness within the genus Campylobacter inferred from rpoB
sequences. Int J Syst Evol Microbiol 2006;56:937945.
17. Miller WG, Yee E, Jolley KA, Chapman MH. Use of an improved
atpA amplification and sequencing method to identify members of
the Campylobacteraceae and Helicobacteraceae.Lett Appl Microbiol
2014;58:582590.
18. Hill JE, Paccagnella A, Law K, Melito PL, Woodward DL et al.
Identification of Campylobacter spp. and discrimination from Heli-
cobacter and Arcobacter spp. by direct sequencing of PCR-ampli-
fied cpn60 sequences and comparison to cpnDB, a chaperonin
reference sequence database. J Med Microbiol 2006;55:393399.
19. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the
sensitivity of progressive multiple sequence alignment through
sequence weighting, position-specific gap penalties and weight
matrix choice. Nucleic Acids Res 1994;22:46734680.
20. Tamura K, Peterson D, Peterson N, Stecher G, Nei M et al.
MEGA5: molecular evolutionary genetics analysis using maximum
likelihood, evolutionary distance, and maximum parsimony meth-
ods. Mol Biol Evol 2011;28:27312739.
21. Saitou N, Nei M. The neighbor-joining method: a new method for
reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406425.
22. Kimura M. A simple method for estimating evolutionary rates of
base substitutions through comparative studies of nucleotide
sequences. J Mol Evol 1980;16:111120.
23. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M et al. Introducing
EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with
phylotypes that represent uncultured species. Int J Syst Evol
Microbiol 2012;62:716721.
24. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al.
SPAdes: a new genome assembly algorithm and its applications to
single-cell sequencing. J Comput Biol 2012;19:455477.
25. Seemann T. Prokka: rapid prokaryotic genome annotation.
Bioinformatics 2014;30:20682069.
Fig. 3. Images of cells of WBE38
T
as observed with scanning electron
microscopy. The organism exhibits a curved shape while spherical or
coccoid forms can also be observed. Bar, 3 µm.
C
aceres et al., Int J Syst Evol Microbiol
6
Downloaded from www.microbiologyresearch.org by
IP: 193.62.202.242
On: Fri, 30 Jun 2017 09:35:38
26. Konstantinidis KT, Tiedje JM. Genomic insights that advance the
species definition for prokaryotes. Proc Natl Acad Sci USA 2005;
102:25672572.
27. Richter M, Rosselló-Móra R. Shifting the genomic gold standard
for the prokaryotic species definition. Proc Natl Acad Sci USA
2009;106:1912619131.
28. Debruyne L, Gevers D, Vandamme P. Taxonomy of the family
Campylobacteraceae. In: Nachamkin I, Szymanski CM and Blaser
MJ (editors). Campylobacter. Washington, DC: American Society for
Microbiology; 2008. pp. 326.
29. On SL, Holmes B. Effect of inoculum size on the phenotypic char-
acterization of Campylobacter species. J Clin Microbiol 1991;29:
923926.
30. On SL, Holmes B. Reproducibility of tolerance tests that are useful
in the identification of campylobacteria. J Clin Microbiol 1991;29:
17851788.
31. On SL, Holmes B. Assessment of enzyme detection tests useful
in identification of campylobacteria. J Clin Microbiol 1992;30:
746749.
32. Ursing JB, Lior H, Owen RJ. Proposal of minimal standards for
describing new species of the family Campylobacteraceae.Int J
Syst Bacteriol 1994;44:842845.
33. Mills CK, Gherna RL. Hydrolysis of indoxyl acetate by Campylobac-
ter species. J Clin Microbiol 1987;25:15601561.
34. Vandamme P, Dewhirst FE, Paster BJ, On SLW. Genus I. Campylo-
bacter Sebald and V
eron 1963, 907,
AL
emend. Vandamme, Falsen,
Rossau, Hoste, Segers, Tytgat and De Ley 1991a, 98. In: Brenner
DJ, Kreig NP, Staley JT and Garrity GM (editors). Bergeys Manual
of Systematic Bacteriology, 2nd ed, vol. 2. New York: Springer;
2005. pp. 11471160.
35. Kawamura Y, Kuwabara S, Kania SA, Kato H, Hamagishi M et al.
Porphyromonas pogonae sp. nov., an anaerobic but low concentra-
tion oxygen adapted coccobacillus isolated from lizards (Pogona
vitticeps) or human clinical specimens, and emended description
of the genus Porphyromonas Shah and Collins 1988. Syst Appl
Microbiol 2015;38:104109.
36. Matsuda M, Moore JE. Urease-positive thermophilic Campylobac-
ter species. Appl Environ Microbiol 2004;70:44154418.
C
aceres et al., Int J Syst Evol Microbiol
7
Five reasons to publish your next article with a Microbiology Society journal
1. The Microbiology Society is a not-for-profit organization.
2. We offer fast and rigorous peer review average time to first decision is 46 weeks.
3. Our journals have a global readership with subscriptions held in research institutions around
the world.
4. 80% of our authors rate our submission process as excellentor very good.
5. Your article will be published on an interactive journal platform with advanced metrics.
Find out more and submit your article at microbiologyresearch.org.
... lari (27), C. lari subsp. concheus (27), C. mucosalis (28), C. ornithocola (29), C. peloridis (27), C. pinnipediorum subsp. pinnipediorum (30), C. pinnipediorum subsp. ...
... A more comprehensive inspection of these variants using molecular typing methods resulted in the taxonomic revision and reclassification of several strains as novel taxa, such as C. peloridis (27) and C. volucris (38). Additionally, other C. lari-like species have recently been described, including C. insulaenigrae (24), C. subantarcticus (34), and C. ornithocola (29). Currently, C. lari is divided into two subspecies: C. lari subsp. ...
Article
Full-text available
Campylobacter is among the four main causes of gastroenteritis worldwide and has increased in both developed and developing countries over the last 10 years. The vast majority of reported Campylobacter infections are caused by Campylobacter jejuni and, to a lesser extent, C. coli; however, the increasing recognition of other emerging Campylobacter pathogens is urgently demanding a better understanding of how these underestimated species cause disease, transmit, and evolve. In parallel to the enhanced clinical awareness of campylobacteriosis due to improved diagnostic protocols, the application of high-throughput sequencing has augmented the availability of whole-genome sequences of dozens of strains of many emerging campylobacters. This has allowed for comprehensive comparative pathogenomic analyses for several species, such as C. fetus and C. concisus. These studies have started to reveal the evolutionary forces shaping their genomes and have brought to light many genomic features related to pathogenicity in these neglected species, promoting the development of new tools and approaches relevant for clinical microbiology. Despite the need for additional characterization of genomic diversity in emerging campylobacters, the increasing body of literature describing pathogenomic studies on these species deserves to be discussed from an integrative perspective. This review compiles the current knowledge and highlights future work toward deepening our understanding about genome dynamics and the mechanisms governing the evolution of pathogenicity in emerging Campylobacter species, which is urgently needed to develop strategies to prevent or control the spread of these pathogens.
... Campylobacter have been isolated from the faeces of cats, dogs (Rahimi et al., 2012;Koene et al., 2009), and also from sheep, goats and cattle (Moriarty et al., 2011;Hanlon et al., 2018;Dong et al., 2016;. Also, Non confirmed disease association Campylobacter species have been reported by Data from (Lastovica et al., 2014), from (Silva et al., 2020), from (Boukerb et al., 2019), from (Gilbert et al., 2018), from (Cáceres et al., 2017), from and from (Piccirillo et al., 2016) (Table 1.5). ...
Article
Full-text available
Infection with Campylobacter is considered to be the most common bacterial cause of human gastroenteritis worldwide. In light of the dramatic increase of antibiotic resistant bacteria, alternative solutions including biological controls such as bacteriophage therapy and bacteriophage biosanitization are being considered. One way in which campylobacters enter the human food chain is through consumption of contaminated raw milk. An updated study of the ability of campylobacters to survive in milk, including species other than C. jejuni, was carried out. Isolation of bacteriophages from bovine slurry, with potential for biocontrol and therapeutic purposes was attempted using conventional methods. Campylobacter and Arcobacter hosts were isolated and characterised, including genome sequencing, from the same environment. The method used for this purpose was proven efficacious for porcine slurry; however, no lytic phage were isolated from bovine samples. During the isolation experiments unusual plaques were formed on the lawn of the C. hyointestinalis S12 host strain. The causative agent of this lytic activity was found to be due to a new predatory bacterium, which was characterised with respect host range and genome sequence. Phylogenetic analysis placed the new bacterium in the family Oceanospirillaceae and the name Venatorbacter cucullus gen. nov. sp. nov proposed.
... accessed 18.03.2018). C. ornithocola [33], C. pinnipediorum subsp. caledonicus, C. pinnipediorum subsp. ...
... nov. se describió como una nueva especie aislada de aves urbanas en Chile 60 . La información sobre el papel de las aves silvestres en la transmisión de Campylobacter a las aves de corral y los seres humanos en Chile es actualmente inexistente. ...
Article
Full-text available
Conflictos de interes: ninguno que declarar Financiamiento: Proyecto FONDECYT 1170972 Recibido (segunda versión): 15 de noviembre de 2019 / Aceptado: 17 de julio de 2020 Resumen El conocimiento acerca de agentes patógenos presentes en aves silvestres es crucial para la apropiada prevención de eventos de transmisión que puedan afectar a la salud pública y animal. Esta revisión sistemática organiza toda la información disponible acerca de los patógenos virales y bacterianos de las aves silvestres chilenas, determina qué patógenos y órdenes de aves han recibido atención reciente por parte de la comunidad científica local, evalúa cambios en la frecuencia de publicación de artículos e identifica brechas en el conocimiento respecto a estos patógenos. Un total de 35 artículos revisados por pares han sido publicados desde enero de 1941 hasta abril de 2019. Agentes virales fueron evaluados en 11 estudios, mientras que 24 concernieron a bacterias. Los artículos científicos se han publicado mayormente de forma discontinua en años previos al 2006. Salmonella spp. e influenza aviar han sido los patógenos más estudiados con 10 y 8 estudios, respectivamente. Las regiones de Los Ríos y Valparaíso concentran el mayor número de estudios y no se ha realizado investigación en las regiones de O'Higgins, Maule y Aysén. En general, la información acerca de patógenos en aves silvestres es escasa, por lo que es necesario incrementar los esfuerzos para identificar patógenos portados por reservorios aviares y evaluar el riesgo potencial que pueden representar para la conservación de fauna silvestre, producción animal y el sistema de salud pública en Chile. Abstract Knowledge about pathogenic agents present in wild birds is pivotal to properly prevent transmission events that might threaten public and animal health. This systematic review organizes all information available about viral and bacterial pathogens of Chilean wild birds, determines which pathogens and avian orders have received attention from the local scientific community, evaluates changes in the frequency of article publication, and identifies gaps in knowledge regarding these pathogens. A total of 35 peer-reviewed publications have been published from January 1941 through April 2019. Viral agents were evaluated in 11 studies, while 24 involved bacteria. Article publication has been mostly discontinuous in years prior to 2006. Salmonella spp. and avian influenza have been the most studied pathogens with 10 and 8 studies, respectively. Los Ríos and Valparaíso regions concentrate the highest number of studies and no research has been carried out in O'Higgins, Maule, and Aysén regions. Overall, information about pathogens in wild birds is scarce, highlighting the need for increased effort to identify pathogens being carried by avian reservoirs and evaluate the potential threat that they might pose for wildlife conservation, animal production, and the public health system in Chile.
... ornithocola. Data for reference taxa were obtained from previous species descriptions [7][8][9]33,[35][36][37][38][39][40][41][42][43][44][45][46][47]. + 90-100%; (+) 75-89%; v 26-74%; (-) 11-25%; -0-10%; nd-not determined; w-weakly positive. ...
Article
Full-text available
A new species of the Campylobacter genus is described, isolated from the preputial mucosa of bulls (Bos taurus). The five isolates obtained exhibit characteristics of Campylobacter, being Gram-negative non-motile straight rods, oxidase positive, catalase negative and microaerophilic. Phenotypic characteristics and nucleotide sequence analysis of 16S rRNA and hsp60 genes demonstrated that these isolates belong to a novel species within the genus Campylobacter. Based on hsp60 gene phylogenetic analysis, the most related species are C. ureolyticus, C. blaseri and C. corcagiensis. The whole genome sequence analysis of isolate FMV-PI01 revealed that the average nucleotide identity with other Campylobacter species was less than 75%, which is far below the cut-off for isolates of the same species. However, whole genome sequence analysis identified coding sequences highly homologous with other Campylobacter spp. These included several virulence factor coding genes related with host cell adhesion and invasion, transporters involved in resistance to antimicrobials, and a type IV secretion system (T4SS), containing virB2-virB11/virD4 genes, highly homologous to the C. fetus subsp. venerealis. The genomic G+C content of isolate FMV-PI01 was 28.3%, which is one of the lowest values reported for species of the genus Campylobacter. For this species the name Campylobacter portucalensis sp. nov. is proposed, with FMV-PI01 (= LMG 31504, = CCUG 73856) as the type strain.
... The genus Campylobacter now comprises twenty-eight member species and nine subspecies, most of which are microaerophilic, i.e. grow preferentially in low oxygen concentrations (Caceres et al., 2017). The majority of cases of acute campylobacteriosis are caused by two species: C. jejuni and the closely related C. coli, while C. lari and C. concisus may also play a role in enteritis (Kaakoush and Mitchell, 2012). ...
Article
Full-text available
Enteritis campylobacterialis has an increasing trend in Serbia. Human illness usually appears as sporadic case, most commonly in children with obvious seasonality. In registered outbreaks, incriminated food was most frequently poultry meat. Campylobacter is one of the most important food borne pathogens, commonly underreported, mostly because isolation of this bacteria requires specific equipment. Since 1 January 2019, monitoring of Campylobacter in poultry carcasses is mandatory when it comes to poultry production fa­cilities in Serbia. The aim of this paper was to analyze data from Autonomous Province of Vojvodina about the prevalence of Campylobacter spp. in poultry meat and risk for human illness. Our results indicate high prevalence of Campylobacter spp. in whole food chain: poultry farms, slaughterhouses, retail and, correspondingly, high risk for consumers in Vojvodina. Measures for risk reduction of disease incidence include better bio security measures on the farm level as a main source of pathogen but also introduction of Campylo­bacter diagnostic equipment in all human diagnostic and food control laboratories. [Project of the Serbian Ministry of Education, Science and Technological Development, Grant no. TR 31084]
... Of the most recently added species, few have been associated with disease in the host. Most have been incidental findings in surveys of primates, sea mammals, captive reptiles or wild birds (Caceres, Munoz, Iraola, Diaz-Viraque, & Collado, 2017;Debruyne et al., 2010;Gilbert, Kik, Miller, Duim, & Wagenaar, 2015;Gilbert et al., 2018;Kaur et al., 2011;Koziel et al., 2014;Piccirillo et al., 2016). In contrast, C. hepaticus was isolated from clinical disease (SLD) in laying hens and has been confirmed Time for visible growth on first isolation 3 days 3-7 days Colony morphology Discrete yellow or colour- less smooth colonies or grey confluent film Discrete cream, tan or dirty yellow smooth colonies or a thin spread- ing TA B L E 1 Consensus biochemistry and culture characteristics for the agent of AVH (Fletcher & Plastridge, 1964;Hofstad et al., 1958;Peckham, 1958Peckham, , 1972Whenham et al., 1961) and Campylobacter hepaticus (Crawshaw et al., 2015;Gregory et al., 2018;Van et al., 2016) ...
Article
In 2015 a novel thermophilic Campylobacter, was isolated from cases of spotty liver disease in laying hens in the UK. In 2016 it was isolated from laying hens in Australia where it was formally named Campylobacter hepaticus and confirmed as the cause of spotty liver disease. It has also been isolated from laying hens in America. It is fastidious, grows slowly on first isolation and does not grow on media used to routinely isolate Campylobacter. Spotty liver disease is an acute, randomly distributed, focal, necrotic hepatitis causing mortality in up to 10% of a flock and a 10 to 15% fall in egg production. It occurs mainly in free range hens or hens reared on the ground at around the time of peak lay. The incidence of the disease has increased in countries where there is an increase in keeping free range laying hens. It is similar to the condition avian vibrionic hepatitis which was reported in America, Europe and Australasia in the 1950s to 1970s and the agent isolated from cases of avian vibrionic hepatitis and C. hepaticus appear to be very similar. It is not known if C. hepaticus is zoonotic but whole genome sequencing shows it is most closely related to the known zoonotic campylobacters Campylobacter jejuni and Campylobacter coli. Human exposure to C. hepaticus is likely through similar exposure routes. Analysis of the whole genome showed a reduction in the genes for iron metabolism compared to C. jejuni. A requirement for iron was confirmed as it showed reduced growth in an iron depletion assay and this may explain its tissue tropism. With a move towards free range egg production in many countries the incidence of C. hepaticus hepatitis is likely to increase but the identification of the causal agent will provide opportunities for the development of control methods. This article is protected by copyright. All rights reserved.
Article
During a sampling of wild red foxes (Vulpes vulpes) for the detection of Epsilonproteobacteria, 14 strains were isolated from the caecal contents of 14 epidemiologically-unrelated animals. A genus-specific PCR indicated that the isolates belonged to the genus Campylobacter. Based on the results of a species-specific PCR, the isolates were initially identified as C. upsaliensis. However, multi-locus sequence typing (MLST) revealed that the isolates were significantly different from the C. upsaliensis present in the MLST database. A polyphasic study, including conventional biochemical and tolerance characteristics, morphology by transmission electron microscopy (TEM), MALDI-TOF analysis, and genetic comparisons based on partial 16S rDNA and atpA gene sequences, was undertaken. Finally, the complete genome sequence of the type strain 251/13T and the draft genome sequences of the other isolates were determined. Average nucleotide identity, average amino acid identity and in silico DNA-DNA hybridization analyses confirmed that the isolates represent a novel taxon for which the name Campylobacter vulpis sp. nov. is proposed, with isolate 251/13T (= CCUG 70587T = LMG 30110T) as the type strain. In order to allow a rapid discrimination of C. vulpis from the closely-related C. upsaliensis, a specific PCR test was designed, based on atpA gene sequences.
Article
Knowledge about pathogenic agents present in wild birds is pivotal to properly prevent transmission events that might threaten public and animal health. This systematic review organizes all information available about viral and bacterial pathogens of Chilean wild birds, determines which pathogens and avian orders have received attention from the local scientific community, evaluates changes in the frequency of article publication, and identifies gaps in knowledge regarding these pathogens. A total of 35 peer-reviewed publications have been published from January 1941 through April 2019. Viral agents were evaluated in 11 studies, while 24 involved bacteria. Article publication has been mostly discontinuous in years prior to 2006. Salmonella spp. and avian influenza have been the most studied pathogens with 10 and 8 studies, respectively. Los Ríos and Valparaíso regions concentrate the highest number of studies and no research has been carried out in O'Higgins, Maule, and Aysén regions. Overall, information about pathogens in wild birds is scarce, highlighting the need for increased effort to identify pathogens being carried by avian reservoirs and evaluate the potential threat that they might pose for wildlife conservation, animal production, and the public health system in Chile.
Article
Full-text available
Milk and milk products have been utilized by humans for many thousands of years. With the advent of metagenomic studies, our knowledge on the microbiota of milk and milk products, especially as affected by the environment, production, and storage parameters, has increased. Milk quality depends on chemical parameters (fat and protein content and absence of inhibitory substances), as well as microbial and somatic cells counts, and affects the price of milk. The effects of hygiene and effective cooling on the spoilage microbiota have shown that proteolytic and lipolytic bacteria such as Pseudomonas or Acinetobacter spp. predominate the spoilage bacterial populations. These bacteria can produce heat‐stable proteases and lipases, which remain active after pasteurization and thus can spoil the milk during prolonged storage. Additionally, milk can become contaminated after pasteurization and therefore there is still a high demand on developing better cleaning and sanitation regimes and equipment, as well as test systems to (quantitatively) detect relevant pathogenic or spoilage microorganisms. Raw milk and raw milk cheese consumption is also increasing worldwide with the growing demand of minimally processed, sustainable, healthy, and local foods. In this context, emerging and re‐emerging pathogens once again represent a major food safety challenge. As a result of global warming, it is conceivable that not only microbiological risks but also chemical risks relating to presence of mycotoxins or plant toxins in milk will increase. Herein, we provide an overview of the major microbial hazards occurring in the 21st century.
Article
Full-text available
During a screening study to determine the presence of Campylobacter spp. in reptiles, three putative strains (RC7, RC11, and RC20) were isolated from different individuals of the western Hermann's tortoise (Testudo hermanni hermanni). Initially, these isolates were characterized as C. fetus subsp. fetus by multiplex PCR and partial 16S rRNA gene sequence analysis. Further whole genome characterization revealed considerable differences compared to other Campylobacter species. A polyphasic study was then undertaken to determine the exact taxonomic position of the isolates. The three strains were characterized by conventional phenotypic tests and whole-genome sequencing. We generated robust phylogenies that showed a distinct clade containing only these strains using the 16S rRNA and atpA genes and a set of 40 universal proteins. Our phylogenetic analysis demonstrates their designation as a new species and this was further confirmed using whole genome average nucleotide identity within the Campylobacter genus (~80%). Compared to most Campylobacter species, these strains hydrolysed hippurate, grew well at 25 °C but not at 42 °C. Phenotypic and genetic analyses demonstrate that the three Campylobacter strains isolated from the western Hermann's tortoise represent a novel species within the Campylobacter genus, for which the name Campylobacter geochelonis sp. nov. is proposed, with RC20T (=DSM 102159T =LMG 29375T) as the type strain.
Article
Full-text available
The genus Campylobacter includes some of the most relevant pathogens for human and animal health; the continuous effort in their characterization has also revealed new species putatively involved in different kind of infections. Nowadays, the available genomic data for the genus comprise a wide variety of species with different pathogenic potential and niche preferences. In this work we contribute to enlarge this available information presenting the first genome for the species Campylobacter sputorum bv. sputorum and use this and the already sequenced organisms to analyze the emergence and evolution of pathogenicity and niche preferences among Campylobacter species. We found that campylobacters can be unequivocally distinguished in established and putative pathogens depending on their repertory of virulence genes, which have been horizontally acquired from other bacteria since the non-pathogenic Campylobacter ancestor emerged, and posteriorly inter-changed between some members of the genus. Additionally, we demonstrated the role of both horizontal gene transfers and diversifying evolution in niche preferences, being able to distinguish genetic features associated to the tropism for oral, genital and gastrointestinal tissues. In particular, we highlight the role of non-synonymous evolution of DSB (disulphide bond) proteins, the invasion antigen B (CiaB) and other secreted proteins in the determination of niche preferences. Our results arise from assessing the previously unmet goal of considering the whole available Campylobacter diversity for genome comparisons, unveiling notorious genetic features that could explain particular phenotypes and set the basis for future research in Campylobacter biology.
Article
Full-text available
The multiplex capability and high yield of current day DNA sequencing instruments has made bacterial whole genome sequencing a routine affair. The subsequent de novo assembly of reads into contigs has been well addressed. The final step of annotating all relevant genomic features on those contig can be achieved slowly using existing web and email-based systems, but these are not applicable for sensitive data or integrating into computational pipelines. Here we introduce Prokka, a command line software tool to fully annotate a draft bacterial genome in about ten minutes on a typical desktop computer. It produces standards-compliant output files for further analysis or viewing in genome browsers. Prokka is implemented in Perl and is freely available under an open source GPLv2 license from http://vicbioinformatics.com/. torsten.seemann@monash.edu.
Article
Full-text available
Two Gram negative, gently curved rod-shaped isolates (WBE14T and WBE19), recovered from wild bird faecal samples in the city of Valdivia (Southern Chile) were subjected to a polyphasic taxonomic study. A genus-specific PCR indicated that these isolates belong to the genus Helicobacter. This was further confirmed by a phylogenetic analyses based on the 16S rRNA, 60 kDa heat shock protein (cpn60) and gyrase subunit B (gyrB) genes, where both strains formed a new phylogenetic line within this genus. The 16S rRNA gene sequence similarity of strain WBE14T to the type strains of all other Helicobacter species ranged from 89.4 to 97.0%, being Helicobacter brantae and Helicobacter pametensis the most closely related species. However, on the basis of the protein-coding genes Helicobacter pullorum and Helicobacter canadiensis are the most closely related helicobacters. These data, together with their different morphological and biochemical characteristics, revealed that these strains represent a new species, for which the name Helicobacter valdiviensis sp. nov. is proposed, with the type strain WBE14T (= CECT 8410T = LMG 27920T).
Article
Ten strains of an unknown Campylobacter species were isolated from the livers of spotty liver disease affected birds in Australia. They are Gram negative, microaerobic, catalase and oxidase positive and urease negative. Unlike most other species of the genus Campylobacter, most of the tested strains of this novel species hydrolyse hippurate and half of them could not reduce nitrate. All strains showed resistance, or intermediate resistance, to nalidixic acid and most of them were resistant to cephalothin. Examination of negatively stained cells under transmission electron microscopy revealed that they were S-shaped, with bipolar unsheathed flagella. Phylogenetic analyses based on the 16S rRNA gene and the heat shock protein 60 (hsp60) gene sequences indicated that the strains formed a robust clade that was clearly distinct from recognised Campylobacter species. Unusually, they have a mol% G+C of 27.9 %; lower than any previously described Campylobacter species and have less than 84% average nucleotide identity to the nearest sequenced species. Taken together, these data indicate that the strains belong to a novel Campylobacter species for which the name Campylobacter hepaticus sp. nov. is proposed, with the type strain NCTC 13823T (=CIP111092T).
Article
A new method called the neighbor-joining method is proposed for reconstructing phylogenetic trees from evolutionary distance data. The principle of this method is to find pairs of operational taxonomic units (OTUs [= neighbors]) that minimize the total branch length at each stage of clustering of OTUs starting with a starlike tree. The branch lengths as well as the topology of a parsimonious tree can quickly be obtained by using this method. Using computer simulation, we studied the efficiency of this method in obtaining the correct unrooted tree in comparison with that of five other tree-making methods: the unweighted pair group method of analysis, Farris's method, Sattath and Tversky's method, Li's method, and Tateno et al.'s modified Farris method. The new, neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods.
Article
This chapter presents an overview of the biological diversity of Campylobacter species and Arcobacter species and also addresses the taxonomic information that has become available through whole-genome sequence analysis. Classical biochemical tests routinely used for the identification of clinical bacteria often yielded negative or variable results within Campylobacter species. This poor biochemical reactivity and lack of clear-cut differential characters led to the wide application of vernacular names for many groups of Campylobacter-like organisms (CLOs). Some of the CLO groups were later classified as novel species, but several were identified as biochemical variants of well-known species. The first isolated Campylobacter was almost certainly Campylobacter fetus. In 1914, a researcher observed a vibrio, later classified as Vibrio sputorum, in sputum of a patient with bronchitis. Similar bacteria isolated from the bovine vagina and semen were classified as V. bubulus. During a study of the bacterial flora of the cloacae of whooping cranes, 10 atypical Campylobacter isolates were recovered on two separate occasions and were classified as C. canadensis. Strain NP4, isolated from groundwater with high arsenic concentrations, is classified as a Sulfurospirillum species on the basis of 16S rRNA gene sequence analysis, and it differs from the other Sulfurospirillum isolates in its carbon source and electron acceptor usage profiles. Representative strains of Bacteroides ureolyticus species were included in a polyphasic taxonomic study to elucidate their taxonomic status. Strains have been isolated from superficial ulcers and soft tissue infections, urethritis, vaginosis, and periodontal disease.
Article
During the process of identifying a Gram-negative coccobacillus isolated from a human clinical specimen, we found that the isolate's 16S rRNA gene had very close sequence identity with that of a variant Porphyromonas isolated from polymicrobial infections in the central bearded dragon, a species of lizard [2]. The 16S rRNA gene sequences of the human isolate and of six isolates from lizards were nearly identical (99.9-100%). Phylogenetic analysis placed all of these isolates in a single phylogenetic cluster well separated from other species in the genus Porphyromonas. The closest species was Porphyromonas catoniae with 90.7-90.9% sequence identity, although there was less than 6% DNA similarity between the P. catoniae type strain and our representative isolates from lizards (PAGU 1787(T)) and human (PAGU 1776). These isolates could grow under anaerobic or microaerobic conditions (6% O2 atmosphere). The isolates were positive for catalase and very strong β-hemolytic activity, but did not show black or brown pigmentation. Biochemically, the isolates could be differentiated from closely related species by pyroglutamic acid arylamidase and glycine arylamidase activity, and some others. The fermentation products mainly included succinic acid and propionic acid. The major fatty acids detected in cells of the isolates were iso-C15:0, anteiso-C15:0, and 3OH-iso-C17:0. The G+C content was 43.0±0.62mol%. The species name Porphyromonas pogonae sp. nov. is proposed for these isolates with the type strain of PAGU 1787(T) (=MI 10-1288(T)=JCM 19732(T)=ATCC BAA-2643(T)). Copyright © 2014 Elsevier GmbH. All rights reserved.
Article
The Campylobacter lari group is a phylogenetic clade within the epsilon subdivision of the Proteobacteria and is part of the thermotolerant Campylobacter spp., a division within the genus that includes the human pathogen Campylobacter jejuni. The C. lari group is currently composed of five species (C. lari, C. insulaenigrae, C. volucris, C. subantarcticus and C. peloridis), as well as a group of strains termed the urease-positive thermophilic Campylobacter (UPTC) and other C. lari-like strains. Here we present the complete genome sequences of 11 C. lari group strains, including the five C. lari group species, four UPTC strains and a lari-like strain isolated in this study. The genome of C. lari subsp. lari strain RM2100 was described previously. Analysis of the C. lari group genomes indicates that this group is highly related at the genome level. Furthermore, these genomes are strongly syntenic with minor rearrangements occurring only in four of the twelve genomes studied. The C. lari group can be bifurcated, based on the flagella and flagellar modification genes. Genomic analysis of the UPTC strains indicated that these organisms are variable but highly-similar, closely related to but distinct from C. lari. Additionally, the C. lari group contains multiple genes encoding hemagglutination domain proteins, which are either contingency genes or linked to conserved contingency genes. Many of the features identified in strain RM2100, such as major deficiencies in amino acid biosynthesis and energy metabolism, are conserved across all 12 genomes, suggesting that these common features may play a role in the association of the C. lari group with coastal environments and watersheds.