scholarly journals Comparative Analysis of New Zealand Campylobacter Isolates Using MLST, PFGE and flaA PCR RFLP Genotyping

2021 ◽  
Author(s):  
◽  
Sharla McTavish
Keyword(s):  
New Zealand ◽  
Bacterial Species ◽  
Housekeeping Genes ◽  
Species Boundaries ◽  
Campylobacter Coli ◽  
Closely Related Species ◽  
Pcr Rflp ◽  
Population Structures ◽  
Human Campylobacteriosis ◽  
Dominant Genotype

<p>Campylobacter jejuni and Campylobacter coli are the most commonly identified sources of campylobacteriosis in New Zealand, yet little is known about the distribution of genotypes within the respective population structures. Using multi-locus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE) and flaA genotyping, the current study identified the distribution of genotypes within New Zealand C. jejuni and C. coli isolates from an outbreak situation, as well as isolates present in the ESR Campylobacter collection. Although the most commonly identified MLST genotypes were similar to international genotypes, a number of internationally rare, or unique to New Zealand genotypes were observed. One rare dominant genotype, ST-474, arising from a point source outbreak, was found to cause a large proportion of human campylobacteriosis cases in New Zealand. A unique cluster of New Zealand genotypes were isolated only from river water, identifying a potentially water adapted C. jejuni strain. Frequent homologous recombination and horizontal gene transfer events were identified within the seven housekeeping genes characterised in the New Zealand sample and the MLST C. jejuni/C. coli database. The identified genetic instability within the current study questions the legitimacy of bacterial species boundaries, especially when examining closely related species such as C. jejuni and C. coli.</p>

scholarly journals Comparative Analysis of New Zealand Campylobacter Isolates Using MLST, PFGE and flaA PCR RFLP Genotyping

2021 ◽  
Author(s):  
◽  
Sharla McTavish
Keyword(s):  
New Zealand ◽  
Bacterial Species ◽  
Housekeeping Genes ◽  
Species Boundaries ◽  
Campylobacter Coli ◽  
Closely Related Species ◽  
Pcr Rflp ◽  
Population Structures ◽  
Human Campylobacteriosis ◽  
Dominant Genotype

<p>Campylobacter jejuni and Campylobacter coli are the most commonly identified sources of campylobacteriosis in New Zealand, yet little is known about the distribution of genotypes within the respective population structures. Using multi-locus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE) and flaA genotyping, the current study identified the distribution of genotypes within New Zealand C. jejuni and C. coli isolates from an outbreak situation, as well as isolates present in the ESR Campylobacter collection. Although the most commonly identified MLST genotypes were similar to international genotypes, a number of internationally rare, or unique to New Zealand genotypes were observed. One rare dominant genotype, ST-474, arising from a point source outbreak, was found to cause a large proportion of human campylobacteriosis cases in New Zealand. A unique cluster of New Zealand genotypes were isolated only from river water, identifying a potentially water adapted C. jejuni strain. Frequent homologous recombination and horizontal gene transfer events were identified within the seven housekeeping genes characterised in the New Zealand sample and the MLST C. jejuni/C. coli database. The identified genetic instability within the current study questions the legitimacy of bacterial species boundaries, especially when examining closely related species such as C. jejuni and C. coli.</p>

scholarly journals MLSTar: automatic multilocus and core genome sequence typing in R

2018 ◽  
Author(s):  
Ignacio Ferrés ◽  
Gregorio Iraola
Keyword(s):  
Core Genome ◽  
Bacterial Species ◽  
Housekeeping Genes ◽  
R Package ◽  
Great Accuracy ◽  
Campylobacter Coli ◽  
Gene Sets ◽  
Standard Tool ◽  
Comparable Performance ◽  
Sequence Types

Multilocus sequence typing (MLST) is a standard tool in population genetics and bacterial epidemiology that assesses the genetic variation present in a reduced number of housekeeping genes (typically seven) along the genome. This methodology assigns arbitrary integer identifiers to genetic variations at these loci allowing to efficiently compare bacterial isolates using allele-based methods. Now, the increasing availability of whole-genome sequences for hundreds to thousands of strains from the same bacterial species has motivated to upgrade the resolution of traditional MLST schemes using larger gene sets or even the core genome (cgMLST). The PubMLST database is the most comprehensive resource of described MLST and cgMLST schemes available for a wide variety of species. Here we present MLSTar as the first R package that allows to i) connect with the PubMLST database to select a target scheme, ii) screen a desired set of genomes to assign alleles and sequence types and iii) interact with other widely used R packages to analyze and produce graphical representations of the data. We applied MLSTar to analyze a set of 400 Campylobacter coli genomes, showing great accuracy and comparable performance with previously published command-line tools. MLSTar can be freely downloaded from http://github.com/iferres/MLSTar.

scholarly journals MLSTar: automatic multilocus and core genome sequence typing in R

2018 ◽  
Author(s):  
Ignacio Ferrés ◽  
Gregorio Iraola
Keyword(s):  
Core Genome ◽  
Bacterial Species ◽  
Housekeeping Genes ◽  
R Package ◽  
Great Accuracy ◽  
Campylobacter Coli ◽  
Gene Sets ◽  
Standard Tool ◽  
Comparable Performance ◽  
Sequence Types

Multilocus sequence typing (MLST) is a standard tool in population genetics and bacterial epidemiology that assesses the genetic variation present in a reduced number of housekeeping genes (typically seven) along the genome. This methodology assigns arbitrary integer identifiers to genetic variations at these loci allowing to efficiently compare bacterial isolates using allele-based methods. Now, the increasing availability of whole-genome sequences for hundreds to thousands of strains from the same bacterial species has motivated to upgrade the resolution of traditional MLST schemes using larger gene sets or even the core genome (cgMLST). The PubMLST database is the most comprehensive resource of described MLST and cgMLST schemes available for a wide variety of species. Here we present MLSTar as the first R package that allows to i) connect with the PubMLST database to select a target scheme, ii) screen a desired set of genomes to assign alleles and sequence types and iii) interact with other widely used R packages to analyze and produce graphical representations of the data. We applied MLSTar to analyze a set of 400 Campylobacter coli genomes, showing great accuracy and comparable performance with previously published command-line tools. MLSTar can be freely downloaded from http://github.com/iferres/MLSTar.

scholarly journals MLSTar: automatic multilocus and core genome sequence typing in R

2018 ◽  
Author(s):  
Ignacio Ferrés ◽  
Gregorio Iraola
Keyword(s):  
Core Genome ◽  
Bacterial Species ◽  
Housekeeping Genes ◽  
R Package ◽  
Great Accuracy ◽  
Campylobacter Coli ◽  
Gene Sets ◽  
Standard Tool ◽  
Comparable Performance ◽  
Sequence Types

Multilocus sequence typing (MLST) is a standard tool in population genetics and bacterial epidemiology that assesses the genetic variation present in a reduced number of housekeeping genes (typically seven) along the genome. This methodology assigns arbitrary integer identifiers to genetic variations at these loci allowing to efficiently compare bacterial isolates using allele-based methods. Now, the increasing availability of whole-genome sequences for hundreds to thousands of strains from the same bacterial species has motivated to upgrade the resolution of traditional MLST schemes using larger gene sets or even the core genome (cgMLST). The PubMLST database is the most comprehensive resource of described MLST and cgMLST schemes available for a wide variety of species. Here we present MLSTar as the first R package that allows to i) connect with the PubMLST database to select a target scheme, ii) screen a desired set of genomes to assign alleles and sequence types and iii) interact with other widely used R packages to analyze and produce graphical representations of the data. We applied MLSTar to analyze a set of 400 Campylobacter coli genomes, showing great accuracy and comparable performance with previously published command-line tools. MLSTar can be freely downloaded from http://github.org/iferres/MLSTar.

scholarly journals Genomic Insights into the Convergence and Pathogenicity Factors of Campylobacter jejuni and Campylobacter coli Species

2009 ◽  
Vol 191 (18) ◽  
pp. 5824-5831 ◽  
Author(s):  
Alejandro Caro-Quintero ◽  
Gina P. Rodriguez-Castaño ◽  
Konstantinos T. Konstantinidis
Keyword(s):  
Spatial Distribution ◽  
Gene Flow ◽  
Campylobacter Jejuni ◽  
Ecological Niche ◽  
Bacterial Species ◽  
Distinct Species ◽  
Species Boundaries ◽  
Campylobacter Coli ◽  
Cellular Functions ◽  
Convergence Hypothesis

ABSTRACT Whether or not bacteria form coherent evolutionary groups via means of genetic exchange and, hence, elicit distinct species boundaries remains an unsettled issue. A recent report implied that not only may the former be true but also, in fact, the clearly distinct Campylobacter jejuni and Campylobacter coli species may be converging as a consequence of increased interspecies gene flow fostered, presumably, by the recent invasion of an overlapping ecological niche (S. K. Sheppard, N. D. McCarthy, D. Falush, and M. C. Maiden, Science 320:237-239, 2008). We have reanalyzed the Campylobacter multilocus sequence typing database used in the previous study and found that the number of interspecies gene transfer events may actually be too infrequent to account, unequivocally, for species convergence. For instance, only 1 to 2% of the 4,507 Campylobacter isolates examined appeared to have imported gene alleles from another Campylobacter species. Furthermore, by analyzing the available Campylobacter genomic sequences, we show that although there seems to be a slightly higher number of exchanged genes between C. jejuni and C. coli relative to other comparable species (∼10% versus 2 to 3% of the total genes in the genome, respectively), the function and spatial distribution in the genome of the exchanged genes are far from random, and hence, inconsistent with the species convergence hypothesis. In fact, the exchanged genes appear to be limited to a few environmentally selected cellular functions. Accordingly, these genes may represent important pathogenic determinants of pathogenic Campylobacter, and convergence of (any) two bacterial species remains to be seen.

scholarly journals Molecular data analysis of selected housekeeping and informational genes from nineteen Campylobacter jejuni genomes

F1000Research ◽  
2013 ◽  
Vol 2 ◽  
pp. 87 ◽  
Author(s):  
Vathsala Mohan ◽  
Mark Stevenson
Keyword(s):  
Information Processing ◽  
Campylobacter Jejuni ◽  
Genetic Recombination ◽  
Bacterial Species ◽  
Housekeeping Genes ◽  
Housekeeping Gene ◽  
Molecular Data ◽  
Sequence Type ◽  
Molecular Characteristics ◽  
Research Article

Campylobacter jejuni (C. jejuni) is a rapidly evolving bacterial species with massive genetic recombination potential to generate niche specific genotypes. Generally the housekeeping gene lineage has been evidenced to undergo lateral gene transfer and recombination fairly frequently compared to the information processing gene lineage. During such exchanges, gene amelioration takes place over time acquiring the host genomes’ molecular characteristics. In this study fifty genes that comprised twenty five housekeeping lineage genes and twenty five information processing lineage genes from nineteen C. jejuni genomes were studied. These nineteen genomes included seven C. jejuni isolates that belonged to the same genotype or multilocus sequence type ST-474. The genes from both lineages were tested for recombination and the guanine-cytosine (GC) variation. This paper details about the data collected and the analyses performed in the corresponding research article entitled ”Campylobacter jejuni genomes exhibit notable GC variation within housekeeping genes”. Further, this paper provides details on the results that are not included in the research paper to provide completeness to the study conducted. The gene sequences from the seven C. jejuni ST-474 isolates were submitted to the GenBank and the corresponding gene IDs are provided for referencing purposes.

scholarly journals The first report on Campylobacter coli family outbreak detected in Poland in 2006

2008 ◽  
Vol 13 (9) ◽  
pp. 5-6
Author(s):  
S Wardak ◽  
J Szych ◽  
M Sadkowska-Todys
Keyword(s):  
General Practitioners ◽  
Bloody Diarrhea ◽  
Outbreak Investigation ◽  
Campylobacter Coli ◽  
The South ◽  
First Report ◽  
Source Of Infection ◽  
Pcr Rflp ◽  
Family Outbreak

A family outbreak of gastroenteritis caused by Campylobacter coli occurred in May 2006 in Bielsko-Biala, in the south of Poland. Four members of a family had non-bloody diarrhea and abdominal cramps. C. coli were isolated in three of the four patients. PFGE and PCR-RFLP-flaA patterns confirmed the link between cases, showing the usefulness of these methods in outbreak investigation. At the same time, the epidemiological and environmental investigations of this outbreak were very limited and did not provide enough evidence to identify the source of infection, and thus to support the hypothesis formulated by the local epidemiologist. It is necessary to improve surveillance of campylobacteriosis mainly by multidisciplinary training of epidemiologists, microbiologists and general practitioners.

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