Genomic epidemiology of Campylobacter jejuni associated with asymptomatic pediatric infection in the Peruvian Amazon

Pascoe, Ben; Schiaffino, Francesca; Murray, Susan F.; Méric, Guillaume; Bayliss, Sion C.; Hitchings, Matthew D.; Mourkas, Evangelos; Calland, Jessica K.; Burga, Rosa; Yori, Pablo Peñataro; Jolley, Keith A.; Cooper, Kerry K.; Parker, Craig T.; Olórtegui, Maribel Paredes; Kosek, Margaret; Sheppard, Samuel K.

doi:10.1371/journal.pntd.0008533

Cited by 24 publications

(38 citation statements)

References 101 publications

(185 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Pascoe et al ., sequenced and analyzed the genomes of 62 C . jejuni strains of a longitudinal cohort study of a semi-rural community near Iquitos in the Peruvian Amazon [ 6 ]. They found distinct locally disseminated genotypes and evidence of poultry as an important cause of transmission.…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Genomic analysis of the diversity, antimicrobial resistance and virulence potential of clinical Campylobacter jejuni and Campylobacter coli strains from Chile

et al. 2021

View full text Add to dashboard Cite

Campylobacter jejuni and Campylobacter coli are the leading cause of human gastroenteritis in the industrialized world and an emerging threat in developing countries. The incidence of campylobacteriosis in South America is greatly underestimated, mostly due to the lack of adequate diagnostic methods. Accordingly, there is limited genomic and epidemiological data from this region. In the present study, we performed a genome-wide analysis of the genetic diversity, virulence, and antimicrobial resistance of the largest collection of clinical C. jejuni and C. coli strains from Chile available to date (n = 81), collected in 2017–2019 in Santiago, Chile. This culture collection accounts for more than one third of the available genome sequences from South American clinical strains. cgMLST analysis identified high genetic diversity as well as 13 novel STs and alleles in both C. jejuni and C. coli. Pangenome and virulome analyses showed a differential distribution of virulence factors, including both plasmid and chromosomally encoded T6SSs and T4SSs. Resistome analysis predicted widespread resistance to fluoroquinolones, but low rates of erythromycin resistance. This study provides valuable genomic and epidemiological data and highlights the need for further genomic epidemiology studies in Chile and other South American countries to better understand molecular epidemiology and antimicrobial resistance of this emerging intestinal pathogen.

show abstract

Section: Discussionmentioning

confidence: 99%

“…jejuni and C . coli in comparison to other enteric bacterial pathogens [ 1 , 5 , 6 ]. In Chile, the National Laboratory Surveillance Program of the Public Health Institute has reported an incidence rate of campylobacteriosis of 0.1 to 0.6 cases per 100,000 persons [ 7 ].…”

Section: Introductionmentioning

confidence: 99%

Genomic analysis of the diversity, antimicrobial resistance and virulence potential of clinical Campylobacter jejuni and Campylobacter coli strains from Chile

et al. 2021

View full text Add to dashboard Cite

show abstract

“…Notably, two recent genomic epidemiology studies have added valuable data from both Peru and Brazil. Pascoe et al ., sequenced and analyzed the genomes of 62 C. jejuni strains of a longitudinal cohort study of a semi-rural community near Iquitos in the Peruvian Amazon [6]. They found distinct locally disseminated genotypes and evidence of poultry as an important cause of transmission.…”

Section: Discussionmentioning

confidence: 99%

“…In South America, there is limited data available on the prevalence of C. jejuni and C. coli in comparison to other enteric bacterial pathogens [1,5,6]. In Chile, the National Laboratory Surveillance Program of the Public Health Institute has reported an incidence rate of campylobacteriosis of 0.1 to 0.6 cases per 100,000 persons [7].…”

Section: Introductionmentioning

confidence: 99%

Genomic analysis of the diversity, antimicrobial resistance and virulence potential of clinical Campylobacter jejuni and Campylobacter coli strains from Chile

Bravo

Katz

Porte

et al. 2020

Preprint

View full text Add to dashboard Cite

ABSTRACTCampylobacter jejuni and Campylobacter coli are the leading causes of human gastroenteritis in the developed world and an emerging threat in developing countries. There is increasing evidence that the incidence of campylobacteriosis in Chile and other South American countries is greatly underestimated, mostly due to the lack of adequate diagnostic methods. Accordingly, there is limited genomic and epidemiological data from these countries, leaving an important knowledge gap in our understanding of the population structure, virulence potential, and antimicrobial resistance profiles of clinical Campylobacter strains. We recently published the whole-genome sequences of a collection of 68 C. jejuni and 12 C. coli strains isolated from patients with enteric infections during a 2-year period (2017-2019) attending Clinica Alemana in Santiago, Chile. In the present study, we sequenced an additional C. jejuni genome and performed a genome-wide analysis of the genetic diversity, virulence, and antimicrobial resistance potential of these 81 strains. cgMLST analysis identified a high genetic diversity of C. jejuni as well as 13 novel STs and alleles in both C. jejuni and C. coli. Pangenome and virulome analyses showed a differential distribution of virulence factors, including both plasmid and chromosomally encoded T6SSs and T4SSs. Resistome analysis predicted widespread resistance to fluoroquinolones, but a low rate of erythromycin resistance. This study provides valuable genomic and epidemiological data and highlights the need for larger genomic epidemiology studies to better understand the genetic diversity, virulence potential and antimicrobial resistance of human clinical Campylobacter strains in South America.DATA SUMMARYGenome sequences and assemblies of all C. jejuni and C. coli used in this study have been deposited in public databases (Table S1) and most strains have also been published as genome resource announcements [1,2].Bacterial draft genome sequence reannotations and nucleotide sequence fasta files used for virulome and plasmid screening analysis are available as a supplementary dataset on Zenodo (DOI: 10.5281/zenodo.3925206) https://doi.org/10.5281/zenodo.3925206.The reconstructed phylogenetic trees and associated metadata of clinical strains from Chile in the global context of C. jejuni and C. coli sequenced strains can be interactively visualized on Microreact at https://microreact.org/project/VbEQsZtQD.

show abstract

“…All novel genome sequences (n=475) generated for use in this study are available on NCBI BioProjects PRJNA689604 and PRJEB11972. These were augmented with 498 previously published genomes and accession numbers for all genomes can be found in Supplementary Data 3 16,24,29,47,56,[58][59][60][61] .…”

Section: Genomic Context and Physiological Role Of Epistatically Linkmentioning

confidence: 99%

A two-hit epistasis model prevents core genome disharmony in recombining bacteria

Taylor

Yahara

Pascoe

et al. 2021

Preprint

Self Cite

View full text Add to dashboard Cite

The lateral transfer of genes among bacterial strains and species has opposing effects, conferring potentially beneficial adaptations whilst introducing disharmony in coadapted genomes. The prevailing outcome will depend upon the fitness cost of disrupting established epistatic interactions between genes. It is challenging to understand this in nature because it requires population-scale analysis of recombination and genomic coadaptation, and laboratory confirmation of the functional significance of genotype variation. By assigning the ancestry of DNA in the genomes of two species of the world's most common enteric bacterial pathogen, we show that up to 28% of the Campylobacter coli genome has been recently introgressed from Campylobacter jejuni. Then, by quantifying covariation across the genome we show that >83% of putative epistatic links are between introgressed C. jejuni genes in divergent genomic positions (>20kb apart), consistent with independent acquisition. Much of this covariation is between 16 genes, with just 5 genes accounting for 99% of epistatic SNP pairs. Laboratory mutagenesis and complementation cloning assays demonstrated functional links between these genes, specifically related to formate dehydrogenase (FDH) activity. These findings suggest that the genetic confederations that define genomic species may be transient. Even for complex traits such as central metabolism in the bacterial cell, conditions can arise where epistatic genes can be decoupled, transferred and reinstated in a new genetic background.

show abstract

Genomic epidemiology of Campylobacter jejuni associated with asymptomatic pediatric infection in the Peruvian Amazon

Cited by 24 publications

References 101 publications

Genomic analysis of the diversity, antimicrobial resistance and virulence potential of clinical Campylobacter jejuni and Campylobacter coli strains from Chile

Genomic analysis of the diversity, antimicrobial resistance and virulence potential of clinical Campylobacter jejuni and Campylobacter coli strains from Chile

Genomic analysis of the diversity, antimicrobial resistance and virulence potential of clinical Campylobacter jejuni and Campylobacter coli strains from Chile

A two-hit epistasis model prevents core genome disharmony in recombining bacteria

Contact Info

Product

Resources

About