Variation in Campylobacter Multilocus Sequence Typing Subtypes from Chickens as Detected on Three Plating Media

2016 ◽  
Vol 79 (11) ◽  
pp. 1986-1989 ◽  
Author(s):  
M. E. BERRANG ◽  
S. R. LADELY ◽  
R. J. MEINERSMANN ◽  
J. E. LINE ◽  
B. B OAKLEY ◽  
...  
Keyword(s):  
Campylobacter Jejuni ◽  
Multilocus Sequence Typing ◽  
Clonal Complex ◽  
Sequence Type ◽  
Campylobacter Coli ◽  
Processing Plant ◽  
Full Genome Sequencing ◽  
Multiple Sequence ◽  
Commercial Broiler ◽  
Sequence Types

ABSTRACT The objective of this study was to compare subtypes of Campylobacter jejuni and Campylobacter coli detected on three selective Campylobacter plating media to determine whether each medium selected for different subtypes. Fifty ceca and 50 carcasses (representing 50 flocks) were collected from the evisceration line in a commercial broiler processing plant. Campylobacter was cultured and isolated from cecal contents and carcass rinses on Campy-Cefex, Campy Line, and RF Campylobacter jejuni/coli agars. When a positive result was obtained with all three media, one colony of the most prevalent morphology on each medium was selected for further analysis by full genome sequencing and multilocus sequence typing. Sequence types were assigned according to PubMLST. A total of 49 samples were positive for Campylobacter on all three media. Forty samples contained only C. jejuni, three had only C. coli, and both species were detected in six samples. From 71% of samples, Campylobacter isolates of the same sequence type were recovered on all three media. From 81.6% of samples, isolates were all from the same clonal complex. From significantly fewer samples (26%, P < 0.01), one medium recovered an isolate with a sequence type different from the type recovered on the other two media. When multiple sequence types were detected, six times the medium with the odd sequence type was Campy-Cefex, four times it was Campy-Line, and six times it was RF Campylobacter jejuni/coli. From one sample, three sequence types were detected. In most cases, all three plating media allowed detection of the same type of Campylobacter from complex naturally contaminated chicken samples.

scholarly journals Molecular Epidemiologic Investigation of Campylobacter coli in Swine Production Systems, Using Multilocus Sequence Typing

2006 ◽  
Vol 72 (8) ◽  
pp. 5666-5669 ◽  
Author(s):  
Siddhartha Thakur ◽  
W. E. Morgan Morrow ◽  
Julie A. Funk ◽  
Peter B. Bahnson ◽  
Wondwossen A. Gebreyes
Keyword(s):  
Multilocus Sequence Typing ◽  
Clonal Complex ◽  
Production Systems ◽  
Genotypic Diversity ◽  
Sequence Type ◽  
Campylobacter Coli ◽  
Swine Production ◽  
Epidemiologic Investigation ◽  
Resistant Strains

ABSTRACT Multilocus sequence typing of 151 Campylobacter coli isolates from swine reared in conventional (n = 74) and antimicrobial-free (n = 77) production systems revealed high genotypic diversity. Sequence type (ST) 1413 was predominant and observed among ciprofloxacin-resistant strains. We identified a C. coli ST 828 clonal complex consisting of isolates from both production systems.

scholarly journals Genetic Diversity of Campylobacter jejuni Isolates from Farm Animals and the Farm Environment

2003 ◽  
Vol 69 (12) ◽  
pp. 7409-7413 ◽  
Author(s):  
F. M. Colles ◽  
K. Jones ◽  
R. M. Harding ◽  
M. C. J. Maiden
Keyword(s):  
Genetic Diversity ◽  
Campylobacter Jejuni ◽  
Human Disease ◽  
Clonal Complex ◽  
Food Samples ◽  
Complex Model ◽  
Farm Animals ◽  
Significant Genetic Differentiation ◽  
Sequence Types ◽  
Retail Food

ABSTRACT The genetic diversity of Campylobacter jejuni isolates from farm animals and their environment was investigated by multilocus sequence typing (MLST). A total of 30 genotypes, defined by allelic profiles (assigned to sequence types [STs]), were found in 112 C. jejuni isolates originating in poultry, cattle, sheep, starlings, and slurry. All but two of these genotypes belonged to one of nine C. jejuni clonal complexes previously identified in isolates from human disease and retail food samples and one clonal complex previously associated with an environmental source. There was some evidence for the association of certain clonal complexes with particular farm animals: isolates belonging to the ST-45 complex predominated among poultry isolates but were absent among sheep isolates, while isolates belonging to the ST-61 and ST-42 complexes were predominant among sheep isolates but were absent from the poultry isolates. In contrast, ST-21 complex isolates were distributed among the different isolation sources. Comparison with MLST data from 91 human disease isolates showed small but significant genetic differentiation between the farm and human isolates; however, representatives of six clonal complexes were found in both samples. These data demonstrate that MLST and the clonal complex model can be used to identify and compare the genotypes of C. jejuni isolates from farm animals and the environment with those from retail food and human disease.

scholarly journals Population Genetics and Characterization ofCampylobacter jejuniIsolates from Western Jackdaws and Game Birds in Finland

2018 ◽  
Vol 85 (4) ◽  
Author(s):  
Sara Kovanen ◽  
Mirko Rossi ◽  
Mari Pohja-Mykrä ◽  
Timo Nieminen ◽  
Mirja Raunio-Saarnisto ◽  
...  
Keyword(s):  
Host Specificity ◽  
Campylobacter Jejuni ◽  
Multilocus Sequence Typing ◽  
Wild Birds ◽  
Whole Genome ◽  
Mallard Duck ◽  
Content Type ◽  
Game Birds ◽  
Hygienic Measures ◽  
Sequence Types

ABSTRACTPoultry are considered a major reservoir and source of human campylobacteriosis, but the roles of environmental reservoirs, including wild birds, have not been assessed in depth. In this study, we isolated and characterizedCampylobacter jejunifrom western jackdaws (n= 91, 43%), mallard ducks (n= 82, 76%), and pheasants (n= 9, 9%). Most of the western jackdaw and mallard duckC. jejuniisolates represented multilocus sequence typing (MLST) sequence types (STs) that diverged from those previously isolated from human patients and various animal species, whereas all pheasant isolates represented ST-19, a common ST among human patients and other hosts worldwide. Whole-genome MLST revealed that mallard duck ST-2314 and pheasant ST-19 isolates represented bacterial clones that were genetically highly similar to human isolates detected previously. Further analyses revealed that in addition to a divergent ClonalFrame genealogy, certain genomic characteristics of the western jackdawC. jejuniisolates, e.g., a novelcdtABCgene cluster and the type VI secretion system (T6SS), may affect their host specificity and virulence. Game birds may thus pose a risk for acquiring campylobacteriosis; therefore, hygienic measures during slaughter and meat handling warrant special attention.IMPORTANCEThe roles of environmental reservoirs, including wild birds, in the molecular epidemiology ofCampylobacter jejunihave not been assessed in depth. Our results showed that game birds may pose a risk for acquiring campylobacteriosis, because they hadC. jejunigenomotypes highly similar to human isolates detected previously. Therefore, hygienic measures during slaughter and meat handling warrant special attention. On the contrary, a unique phylogeny was revealed for the western jackdaw isolates, and certain genomic characteristics identified among these isolates are hypothesized to affect their host specificity and virulence. Comparative genomics within sequence types (STs), using whole-genome multilocus sequence typing (wgMLST), and phylogenomics are efficient methods to analyze the genomic relationships ofC. jejuniisolates.

scholarly journals Wide spread of OXA-48-producing Enterobacteriaceae in Algerian hospitals: A four years’ study

2018 ◽  
Vol 12 (11) ◽  
pp. 1039-1044
Author(s):  
Nadjet Aggoune ◽  
Hassiba Tali Maamar ◽  
Farida Assaous ◽  
Badia Guettou ◽  
Rym Laliam ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Multilocus Sequence Typing ◽  
Genetic Relationships ◽  
Wide Distribution ◽  
Multi Locus Sequence Typing ◽  
Wide Spread ◽  
Multiple Sequence ◽  
Sequence Types ◽  
Susceptibility Patterns ◽  
Urgent Action

Introduction: The aim of this study was to investigate the presence of carbapenemase-producing Enterobacteriaceae (CPE) in Algerian hospitals and to characterize the molecular types of carbapenemases found. Methodology: During a four years study lasting between 2012 and 2015, 81 strains of Enterobacteriaceae with reduced susceptibility to carbapenems were collected from different hospitals. Carbapenemase genes were detected by PCR. Multi locus sequence typing was used to study genetic relationships between carbapenemase- producing Klebsiella pneumoniae isolates. Results: Among 56 confirmed CPE, blaOXA-48 was detected in 98.21% of isolates. Two isolates co-expressed NDM, and a single one was only an NDM producer. The strains displayed various susceptibility patterns to antibiotics with variable levels of resistance to carbapenems. Multilocus sequence typing (MLST) revealed the presence of multiple sequence types in circulation. Conclusions: This report highlights the wide distribution of several clones of OXA-48-producing Enterobacteriaceae in Algeria. Urgent action should be taken to avoid epidemic situations.

scholarly journals Evidence for Phenotypic Plasticity among Multihost Campylobacter jejuni and C. coli Lineages, Obtained Using Ribosomal Multilocus Sequence Typing and Raman Spectroscopy

2012 ◽  
Vol 79 (3) ◽  
pp. 965-973 ◽  
Author(s):  
Daniel S. Read ◽  
Dan J. Woodcock ◽  
Norval J. C. Strachan ◽  
Kenneth J. Forbes ◽  
Frances M. Colles ◽  
...  
Keyword(s):  
Raman Spectroscopy ◽  
Raman Spectra ◽  
Campylobacter Jejuni ◽  
Multilocus Sequence Typing ◽  
Clonal Complex ◽  
Phenotypic Characterization ◽  
Spectrometric Analysis ◽  
Content Type ◽  
Automatic Relevance Determination ◽  
Clonal Origin

ABSTRACTClosely related bacterial isolates can display divergent phenotypes. This can limit the usefulness of phylogenetic studies for understanding bacterial ecology and evolution. Here, we compare phenotyping based on Raman spectrometric analysis of cellular composition to phylogenetic classification by ribosomal multilocus sequence typing (rMLST) in 108 isolates of the zoonotic pathogensCampylobacter jejuniandC. coli. Automatic relevance determination (ARD) was used to identify informative peaks in the Raman spectra that could be used to distinguish strains in taxonomic and host source groups (species, clade, clonal complex, and isolate source/host). Phenotypic characterization based on Raman spectra showed a degree of agreement with genotypic classification using rMLST, with segregation accuracy between species (83.95%), clade (inC. coli, 98.41%), and, to some extent, clonal complex (86.89%C. jejuniST-21 and ST-45 complexes) being achieved. This confirmed the utility of Raman spectroscopy for lineage classification and the correlation between genotypic and phenotypic classification. In parallel analysis, relatively distantly related isolates (different clonal complexes) were assigned the correct host origin irrespective of the clonal origin (74.07 to 96.97% accuracy) based upon different Raman peaks. This suggests that the phenotypic characteristics, from which the phenotypic signal is derived, are not fixed by clonal descent but are influenced by the host environment and change as strains move between hosts.

scholarly journals Multilocus sequence typing of Campylobacter jejuni and Campylobacter coli to identify potential sources of colonization in commercial turkey farms

2018 ◽  
Vol 47 (5) ◽  
pp. 455-466
Author(s):  
Alessandra Piccirillo ◽  
Martina Giacomelli ◽  
Giulia Niero ◽  
Carlotta De Luca ◽  
Lisa Carraro ◽  
...  
Keyword(s):  
Campylobacter Jejuni ◽  
Multilocus Sequence Typing ◽  
Campylobacter Coli ◽  
Potential Sources ◽  
Commercial Turkey

scholarly journals Comparison of Molecular Subtyping and Antimicrobial Resistance Detection Methods Used in a Large Multistate Outbreak of Extensively Drug-Resistant Campylobacter jejuni Infections Linked to Pet Store Puppies

2020 ◽  
Vol 58 (10) ◽  
Author(s):  
Lavin A. Joseph ◽  
Louise K. Francois Watkins ◽  
Jessica Chen ◽  
Kaitlin A. Tagg ◽  
Christy Bennett ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Campylobacter Jejuni ◽  
Multilocus Sequence Typing ◽  
The United States ◽  
Sequence Type ◽  
Outbreak Detection ◽  
Detection Methods ◽  
Drug Resistant ◽  
Molecular Subtyping ◽  
Content Type

ABSTRACT Campylobacter jejuni is a leading cause of enteric bacterial illness in the United States. Traditional molecular subtyping methods, such as pulsed-field gel electrophoresis (PFGE) and 7-gene multilocus sequence typing (MLST), provided limited resolution to adequately identify C. jejuni outbreaks and separate out sporadic isolates during outbreak investigations. Whole-genome sequencing (WGS) has emerged as a powerful tool for C. jejuni outbreak detection. In this investigation, 45 human and 11 puppy isolates obtained during a 2016–2018 outbreak linked to pet store puppies were sequenced. Core genome multilocus sequence typing (cgMLST) and high-quality single nucleotide polymorphism (hqSNP) analysis of the sequence data separated the isolates into the same two clades containing minor within-clade differences; however, cgMLST analysis does not require selection of an appropriate reference genome, making the method preferable to hqSNP analysis for Campylobacter surveillance and cluster detection. The isolates were classified as sequence type 2109 (ST2109)—a rarely seen MLST sequence type. PFGE was performed on 38 human and 10 puppy isolates; PFGE patterns did not reliably predict clustering by cgMLST analysis. Genetic detection of antimicrobial resistance determinants predicted that all outbreak-associated isolates would be resistant to six drug classes. Traditional antimicrobial susceptibility testing (AST) confirmed a high correlation between genotypic and phenotypic antimicrobial resistance determinations. WGS analysis linked C. jejuni isolates in humans and pet store puppies even when canine exposure information was unknown, aiding the epidemiological investigation during the outbreak. WGS data were also used to quickly identify the highly drug-resistant profile of these outbreak-associated C. jejuni isolates.

scholarly journals Distribution of epidemic antibiotic-resistant pneumococcal clones in Scottish pneumococcal isolates analysed by multilocus sequence typing

Microbiology ◽  
2006 ◽  
Vol 152 (2) ◽  
pp. 361-365 ◽  
Author(s):  
A. J. Smith ◽  
J. Jefferies ◽  
S. C. Clarke ◽  
C. Dowson ◽  
G. F. S. Edwards ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Molecular Epidemiology ◽  
Multilocus Sequence Typing ◽  
Type Strain ◽  
Sequence Type ◽  
Reference Laboratory ◽  
Antibiotic Resistant ◽  
Clone Sequence ◽  
Sequence Types ◽  
Type Strains

Sequence types of pneumococci isolated in Scotland between 1996 and 2003 were compared with those of globally prevalent antibiotic-resistant clones. Multilocus sequence typing was performed on 252 invasive pneumococcal isolates referred to the Scottish Meningococcus and Pneumococcus Reference Laboratory. Isolates were not preselected for antimicrobial resistance, patient age or disease caused. Sequence types were compared with globally significant antimicrobial-resistant clones identified by the Pneumococcal Molecular Epidemiology Network (PMEN). Sequence types identical with three of the 26 PMEN clones were present in the Scottish collection; the clones were the Spain9V-3 clone (sequence type 156, seven isolates), the England14-9 clone (sequence type 9, eight isolates) and the Utah35B-24 clone (sequence type 377, one isolate). Many Scottish isolates related to PMEN clones had lower antimicrobial MICs than those described for the corresponding PMEN type strain. A number of single- (SLVs) and double-locus variants (DLVs) were present. Fifteen SLVs related to PMEN sequence types 37, 67, 90, 81, 156, 236 and 377 were detected. The collection contained 10 DLVs related to PMEN sequence types 37, 156, 173 and 338. The majority of SLVs and DLVs were penicillin- or erythromycin-sensitive variants of the resistant PMEN type strains. Capsule switching in isolates related to the PMEN clones was also detected. The highest levels of penicillin resistance were detected in sequence type 320 (serotype 19F), which is not a PMEN clone. These data suggest that PMEN clones are not widely distributed in disease-causing isolates in Scotland.

scholarly journals Genetic Diversity and Quinolone Resistance in Campylobacter jejuni Isolates from Poultry in Senegal

2006 ◽  
Vol 72 (5) ◽  
pp. 3309-3313 ◽  
Author(s):  
Alfred Dieudonn� Kinana ◽  
Eric Cardinale ◽  
Fatou Tall ◽  
Ibrahim Bahsoun ◽  
Jean-Marie Sire ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Campylobacter Jejuni ◽  
Human Disease ◽  
Multilocus Sequence Typing ◽  
Sequence Type ◽  
Quinolone Resistance ◽  
Resistance Phenotype ◽  
Mechanism Of Resistance ◽  
Unique Clone

ABSTRACT We used the multilocus sequence typing (MLST) method to evaluate the genetic diversity of 46 Campylobacter jejuni isolates from chickens and to determine the link between quinolone resistance and sequence type (ST). There were a total of 16 ST genotypes, and the majority of them belonged to seven clonal complexes previously identified by using isolates from human disease. The ST-353 complex was the most common complex, whereas the ST-21, ST-42, ST-52, and ST-257 complexes were less well represented. The resistance phenotype varied for each ST, and the Thr-86-Ile substitution in the GyrA protein was the predominant mechanism of resistance to quinolone. Nine of the 14 isolates having the Thr-86-Ile substitution belonged to the ST-353 complex. MLST showed that the emergence of quinolone resistance is not related to the diffusion of a unique clone and that there is no link between ST genotype and quinolone resistance. Based on silent mutations, different variants of the gyrA gene were shown to exist for the same ST. These data provide useful information for understanding the epidemiology of C. jejuni in Senegal.

scholarly journals First Insights into the Evolution of Streptococcus uberis: a Multilocus Sequence Typing Scheme That Enables Investigation of Its Population Biology

2006 ◽  
Vol 72 (2) ◽  
pp. 1420-1428 ◽  
Author(s):  
Tracey J. Coffey ◽  
Gillian D. Pullinger ◽  
Rachel Urwin ◽  
Keith A. Jolley ◽  
Stephen M. Wilson ◽  
...  
Keyword(s):  
Multilocus Sequence Typing ◽  
Population Biology ◽  
Clonal Complex ◽  
Bovine Mastitis ◽  
Housekeeping Gene ◽  
Global Scale ◽  
Streptococcus Uberis ◽  
Capsule Production ◽  
Sequence Types ◽  
Better Than

ABSTRACT Intramammary infection with Streptococcus uberis is a common cause of bovine mastitis throughout the world. Several procedures to differentiate S. uberis isolates have been proposed. However, all are prone to interlaboratory variation, and none is suitable for the description of the population structure. We describe here the development of a multilocus sequence typing (MLST) scheme for S. uberis to help address these issues. The sequences of seven housekeeping gene fragments from each of 160 United Kingdom milk isolates of S. uberis were determined. Between 5 and 17 alleles were obtained per locus, giving the potential to discriminate between 1.3 × 107 sequence types. In this study, 57 sequence types (STs) were identified. Statistical comparisons between the maximum-likelihood trees constructed by using the seven housekeeping gene fragments showed that the congruence was no better than that between each tree and trees of random topology, indicating there had been significant recombination within these loci. The population contained one major lineage (designated the ST-5 complex). This dominated the population, containing 24 STs and representing 112 isolates. The other 33 STs were not assigned to any clonal complex. All of the isolates in the ST-5 lineage carried hasA, a gene that is essential for capsule production. There was no clear association between ST or clonal complex and disease. The S. uberis MLST system offers researchers a valuable tool that allows further investigation of the population biology of this organism and insights into the epidemiology of this disease on a global scale.

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