Local genes for local bacteria: evidence of allopatry in the genomes of transatlantic <i>Campylobacter </i>populations

Pascoe, Ben; Méric, Guillaume; Yahara, Koji; Wimalarathna, Helen; Murray, Susan F.; Hitchings, Matthew D.; Sproston, E. L.; Carrillo, Catherine D.; Taboada, Eduardo; Cooper, Kerry K.; Huynh, Steven; Cody, Alison J.; Jolley, Keith A.; Maiden, Martin C. J.; McCarthy, Noel D.; Didelot, Xavier; Parker, Craig T.; Sheppard, Samuel K.

doi:10.7287/peerj.preprints.2638v2

Cited by 6 publications

(9 citation statements)

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“…jejuni isolated from chicken, ruminant, environmental water and wild birds from different countries and published in previous studies (Fig. 4 ) 85 – 88 . This gave a total of 859 C .…”

Section: Methodsmentioning

confidence: 76%

Ruminant and chicken: important sources of campylobacteriosis in France despite a variation of source attribution in 2009 and 2015

Thépault

Rose

Quesne

et al. 2018

Sci Rep

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Pathogen source attribution studies are a useful tool for identifying reservoirs of human infection. Based on Multilocus Sequence Typing (MLST) data, such studies have identified chicken as a major source of C. jejuni human infection. The use of whole genome sequence-based typing methods offers potential to improve the precision of attribution beyond that which is possible from 7 MLST loci. Using published data and 156 novel C. jejuni genomes sequenced in this study, we performed probabilistic host source attribution of clinical C. jejuni isolates from France using three types of genotype data: comparative genomic fingerprints; MLST genes; 15 host segregating genes previously identified by whole genome sequencing. Consistent with previous studies, chicken was an important source of campylobacteriosis in France (31–63% of clinical isolates assigned). There was also evidence that ruminants are a source (22–55% of clinical isolates assigned), suggesting that further investigation of potential transmission routes from ruminants to human would be useful. Additionally, we found evidence of environmental and pet sources. However, the relative importance as sources varied according to the year of isolation and the genotyping technique used. Annual variations in attribution emphasize the dynamic nature of zoonotic transmission and the need to perform source attribution regularly.

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“…jejuni isolated from chicken, ruminant, environmental water and wild birds from different countries and published in previous studies (Fig. 4 ) 85 – 88 . This gave a total of 859 C .…”

Section: Methodsmentioning

confidence: 76%

Ruminant and chicken: important sources of campylobacteriosis in France despite a variation of source attribution in 2009 and 2015

Thépault

Rose

Quesne

et al. 2018

Sci Rep

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“…Furthermore, C. coli from clinical and animal samples have displayed resistance to macrolides including erythromycin and the aminoglycoside streptomycin (Food and Authority, ). More worryingly, there is an apparent trend towards multidrug resistance (MDR), particularly among C. coli that regularly harbour different AMR genes simultaneously within the genome of a single isolate (Luangtongkum et al ., ; Pascoe et al ., ; Food and Authority, ).…”

Section: Introductionmentioning

confidence: 99%

Gene pool transmission of multidrug resistance among Campylobacter from livestock, sewage and human disease

Mourkas

Florez‐Cuadrado

Pascoe

et al. 2019

Environmental Microbiology

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Summary The use of antimicrobials in human and veterinary medicine has coincided with a rise in antimicrobial resistance (AMR) in the food‐borne pathogens Campylobacter jejuni and Campylobacter coli. Faecal contamination from the main reservoir hosts (livestock, especially poultry) is the principal route of human infection but little is known about the spread of AMR among source and sink populations. In particular, questions remain about how Campylobacter resistomes interact between species and hosts, and the potential role of sewage as a conduit for the spread of AMR. Here, we investigate the genomic variation associated with AMR in 168 C. jejuni and 92 C. coli strains isolated from humans, livestock and urban effluents in Spain. AMR was tested in vitro and isolate genomes were sequenced and screened for putative AMR genes and alleles. Genes associated with resistance to multiple drug classes were observed in both species and were commonly present in multidrug‐resistant genomic islands (GIs), often located on plasmids or mobile elements. In many cases, these loci had alleles that were shared among C. jejuni and C. coli consistent with horizontal transfer. Our results suggest that specific antibiotic resistance genes have spread among Campylobacter isolated from humans, animals and the environment.

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“…Technical advances in high-throughput genome sequencing and analysis methods continue to improve understanding of C. jejuni from bottom-up studies that test the function of specific genes or operons, often with insertion or deletion mutants [55, 97], to top-down comparative genomic approaches in which isolates are clustered by phenotype and associated genomic variations are identified in large genome collections [50, 64, 100]. Early genome typing using DNA microarrays hinted at the level of diversity among C.…”

Section: Resultsmentioning

confidence: 99%

“…Early genome typing using DNA microarrays hinted at the level of diversity among C. jejuni isolates [27, 101], and comparisons of large isolate genome collections are now linking strain variation to differences in ecology [65, 102–105], epidemiology and evolution [63, 100, 106–110]. Advances in sequencing technology are helping us to study genome variation in greater depth, and long read sequencing of isolate 2 identified large inversions (>90 000 bp) compared to the original finished genome (Table S1).…”

Section: Resultsmentioning

confidence: 99%

Domestication of Campylobacter jejuni NCTC 11168

et al. 2019

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Reference and type strains of well-known bacteria have been a cornerstone of microbiology research for decades. The sharing of well-characterized isolates among laboratories has run in parallel with research efforts and enhanced the reproducibility of experiments, leading to a wealth of knowledge about trait variation in different species and the underlying genetics. Campylobacter jejuni strain NCTC 11168, deposited at the National Collection of Type Cultures in 1977, has been adopted widely as a reference strain by researchers worldwide and was the first Campylobacter for which the complete genome was published (in 2000). In this study, we collected 23 C . jejuni NCTC 11168 reference isolates from laboratories across the UK and compared variation in simple laboratory phenotypes with genetic variation in sequenced genomes. Putatively identical isolates, identified previously to have aberrant phenotypes, varied by up to 281 SNPs (in 15 genes) compared to the most recent reference strain. Isolates also display considerable phenotype variation in motility, morphology, growth at 37 °C, invasion of chicken and human cell lines, and susceptibility to ampicillin. This study provides evidence of ongoing evolutionary change among C. jejuni isolates as they are cultured in different laboratories and highlights the need for careful consideration of genetic variation within laboratory reference strains. This article contains data hosted by Microreact.

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Local genes for local bacteria: evidence of allopatry in the genomes of transatlantic Campylobacter populations

Cited by 6 publications

References 0 publications

Ruminant and chicken: important sources of campylobacteriosis in France despite a variation of source attribution in 2009 and 2015

Ruminant and chicken: important sources of campylobacteriosis in France despite a variation of source attribution in 2009 and 2015

Gene pool transmission of multidrug resistance among Campylobacter from livestock, sewage and human disease

Domestication of Campylobacter jejuni NCTC 11168

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