Complete Genome Sequences of 17 Clinical Campylobacter jejuni Strains from Chile

Bravo, Verónica; Porte, Lorena; Weitzel, Thomas; Varela, Carmen; Blondel, Carlos J.; González-Escalona, Narjol

doi:10.1128/mra.00535-20

Cited by 3 publications

(8 citation statements)

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“…Since most of our sequenced strains correspond to draft genome assemblies, we could not determine whether the T6SSs were plasmid or chromosomally encoded in most of them. However, we have closed the genomes of 2 of these strains (CFSAN093238 and CFSAN093227) [ 15 ]. In both of them, T6SS was inserted in the chromosomal CjIE3 element, while in strain CFSAN093246, it was plasmid-encoded.…”

Section: Resultsmentioning

confidence: 99%

“…jejuni and 12 C . coli human clinical strains isolated from patients with an enteric infection visiting Clínica Alemana in Santiago, Chile, during a 2-year period (2017–2019) [ 14 , 15 ]. This represents the largest genome collection of clinical Campylobacter strains from Chile and one of the few collections available from South America.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2021

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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.

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Section: Resultsmentioning

confidence: 99%

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

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“…The genome sequence dataset analyzed in this study is listed in Table S1 and includes our recently published collection of human clinical strains of C. jejuni and C. coli from Chile [14,15]. We additionally sequenced C. jejuni strain CFSAN096303.…”

Section: Methodsmentioning

confidence: 99%

“…We additionally sequenced C. jejuni strain CFSAN096303. This strain was sequenced as described in [14] using the NextSeq sequencer (Illumina) obtaining an estimated genome average coverage of 90X. The genome was assembled using the CLC Genomics Workbench v9.5.2 (Qiagen) following the previously used pipeline [14] and was deposited under accession number WXZQ01000000.…”

Section: Methodsmentioning

confidence: 99%

“…We recently made available the whole genome sequences of 69 C. jejuni and 12 C. coli human clinical strains isolated from patients with an enteric infection visiting Clínica Alemana in Santiago, Chile, during a 2-year period (2017-2019) [14,15]. This represents the largest genome collection of clinical Campylobacter strains from Chile and one of the few collections available from South America.…”

Section: Introductionmentioning

confidence: 99%

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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

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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.

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Whole-genome sequencing reveals changes in genomic diversity and distinctive repertoires of T3SS and T6SS effector candidates in Chilean clinical Campylobacter strains

Katz,

Porte,

Weitzel

et al. 2023

Front. Cell. Infect. Microbiol.

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Campylobacter is the leading cause of bacterial gastroenteritis worldwide and an emerging and neglected pathogen in South America. This zoonotic pathogen colonizes the gastrointestinal tract of a wide range of mammals and birds, with poultry as the most important reservoir for human infections. Apart from its high morbidity rates, the emergence of resistant strains is of global concern. The aims of this work were to determine genetic diversity, presence of antimicrobial resistance determinants and virulence potential of Campylobacter spp. isolated from patients with acute gastrointestinal disease at ‘Clinica Alemana’, Santiago de Chile. The study considered the isolation of Campylobacter spp., from stool samples during a 20-month period (January 2020 to September 2021). We sequenced (NextSeq, Illumina) and performed an in-depth analysis of the genome sequences of 88 Campylobacter jejuni and 2 Campylobacter coli strains isolated from clinical samples in Chile. We identified a high genetic diversity among C. jejuni strains and the emergence of prevalent clonal complexes, which were not identified in our previous reports. While ~40% of strains harbored a mutation in the gyrA gene associated with fluoroquinolone resistance, no macrolide-resistance determinants were detected. Interestingly, gene clusters encoding virulence factors such as the T6SS or genes associated with long-term sequelae such as Guillain-Barré syndrome showed lineage-relatedness. In addition, our analysis revealed a high degree of variability regarding the presence of fT3SS and T6SS effector proteins in comparison to type strains 81-176, F38011, and NCTC 11168 and 488. Our study provides important insights into the molecular epidemiology of this emerging foodborne pathogen. In addition, the differences observed regarding the repertoire of fT3SS and T6SS effector proteins could have an impact on the pathogenic potential and transmissibility of these Latin American isolates, posing another challenge in characterizing the infection dynamics of this emergent and neglected bacterial pathogen.

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Complete Genome Sequences of 17 Clinical Campylobacter jejuni Strains from Chile

Abstract: Campylobacter jejuni is the leading cause of bacterial foodborne disease worldwide. Here, we report the complete annotated genomes and plasmid sequences of 17 Campylobacter jejuni strains isolated from patients with gastroenteritis in Santiago, Chile.

Cited by 3 publications

References 12 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

Whole-genome sequencing reveals changes in genomic diversity and distinctive repertoires of T3SS and T6SS effector candidates in Chilean clinical Campylobacter strains

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