Genomic insights from whole genome sequencing of four clonal outbreak Campylobacter jejuni assessed within the global C. jejuni population

Abstract

BackgroundWhole genome sequencing (WGS) is useful for determining clusters of human cases, investigating outbreaks, and defining the population genetics of bacteria. It also provides information about other aspects of bacterial biology, including classical typing results, virulence, and adaptive strategies of the organism. Cell culture invasion and protein expression patterns of four related multilocus sequence type 21 (ST21) C. jejuni isolates from a significant Canadian water-borne outbreak were previously associated with the presence of a CJIE1 prophage. Whole genome sequencing was used to examine the genetic diversity among these isolates and confirm that previous observations could be attributed to differential prophage carriage. Moreover, we sought to determine the presence of genome sequences that could be used as surrogate markers to delineate outbreak-associated isolates.ResultsDifferential carriage of the CJIE1 prophage was identified as the major genetic difference among the four outbreak isolates. High quality single-nucleotide variant (hqSNV) and core genome multilocus sequence typing (cgMLST) clustered these isolates within expanded datasets consisting of additional C. jejuni strains. The number and location of homopolymeric tract regions was identical in all four outbreak isolates but differed from all other C. jejuni examined. Comparative genomics and PCR amplification enabled the identification of large chromosomal inversions of approximately 93 kb and 388 kb within the outbreak isolates associated with transducer-like proteins containing long nucleotide repeat sequences. The 93-kb inversion was characteristic of the outbreak-associated isolates, and the gene content of this inverted region displayed high synteny with the reference strain.ConclusionsThe four outbreak isolates were clonally derived and differed mainly in the presence of the CJIE1 prophage, validating earlier findings linking the prophage to phenotypic differences in virulence assays and protein expression. The identification of large, genetically syntenous chromosomal inversions in the genomes of outbreak-associated isolates provided a unique method for discriminating outbreak isolates from the background population. Transducer-like proteins appear to be associated with the chromosomal inversions. CgMLST and hqSNV analysis also effectively delineated the outbreak isolates within the larger C. jejuni population structure.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3340-8) contains supplementary material, which is available to authorized users.

Whole-Genome Sequencing in Epidemiology of Campylobacter jejuni Infections

“…In all of those studies, epidemiologically linked strains were clearly separated from nonrelated control strains. Due to variations in the numbers of genes analyzed and the overall genetic diversity of the studied strains, the allelic differences between control strains and outbreak-associated strains varied between 10 to 15, as observed in the Australian and the Canadian studies (18,19), and 454, as described in the Finnish milk outbreak (15). In real-life settings, however, the possibility that the variation observed among isolates within an outbreak might represent the genomic variation present in the initial inoculum, due to mixed-strain coinfection, cannot be excluded.…”

“…Lahti and colleagues, investigating an Australian outbreak associated with chicken paté by using a reference-based coregenome MLST analysis implemented in SeqSphereϩ (Ridom GmbH), with a total of 1,271 shared loci, described a maximum of 1 allele difference between the clinical isolates (18). Furthermore, four isolates associated with the Walkerton outbreak in Canada differed from one another by a total of 15 SNVs, corresponding to an average of ϳ4 allele differences, using a 732-core-gene schema (19). In all of those studies, epidemiologically linked strains were clearly separated from nonrelated control strains.…”

Foodborne bacteria in dairy products: Detection by molecular techniques

“…and Salmonella spp. (Lambert et al, 2015;Clark et al, 2016;Jackson et al, 2016;Wilson et al, 2016). Furthermore, WGS has the potential to discriminate between sporadic and outbreak isolates which may be indistinguishable by current methods of subtyping (Phillips et al, 2016).…”

Caracterização molecular de linhagens de Campylobacter jejuni de origens diversas isoladas no Brasil

“…A resistência à tetraciclina em completo, dentre outros, vêm sendo utilizados com sucesso na tipagem molecular e nos estudos epidemiológicos e filogenéticos de linhagens de C. jejuni (MEINERSMANN et al, 1997;DINGLE et al, 2001;SAILS et al, 2003;CLARK et al, 2005;KARENLAMPI et al, 2007;SHEPPARD et al, 2009;AQUINO et al, 2010;OPORTO et al, 2011;AHAMED et al, 2012;ABAY et al, 2014;DUARTE et al, 2014;REVEZ et al, 2014;LLARENA et al, 2015;MAROTTA et al, 2015;CLARK et al, 2016;SILVA et al, 2016;FRAZÃO et al, 2017;ROSSI, 2017;OHISHI et al, 2017). HUGENHOLTZ, 2008;BIKARD et al, 2012).…”

“…A metodologia de sequenciamento do genoma completo vem sendo utilizada com êxito em linhagens de C. jejuni, tanto em estudos que abrangem linhagens advindas de surtos, na tentativa de traçar as possíveis rotas de contaminação, quanto em estudos filogenéticos para avaliar a diversidade genética dessa espécie bacteriana (BIGGS et al, 2011;REVEZ et al, 2014;CLARK et al, 2016;DEARLOVE et al, 2016;CODY et al, 2017;LAHTI et al, 2017; LLARENA; TABOADA; ROSSI, 2017).…”