Array-based comparative genomics of Campylobacter jejuni sheep abortion isolates
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ABSTRACT:
ORGANISM(S): Campylobacter jejuni
PROVIDER: GSE54860 | GEO | 2014/02/11
SECONDARY ACCESSION(S): PRJNA237829
REPOSITORIES: GEO
Similar Datasets
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2014-02-11 | E-GEOD-54860 | biostudies-arrayexpress
Project description:Campylobacter jejuni has become the predominant cause of sheep abortions in the U.S. However, little is know about the genetic diversity among the isolates collected from different time periods. In this study, the genetic diversity of sheep aborion isolates of C. jejuni was investigated by Array-based CGH
2014-02-11 | GSE54859 | GEO
Project description:Campylobacter jejuni has become the predominant cause of sheep abortions in the U.S. However, little is know about the genetic diversity among the isolates collected from different time periods. In this study, the genetic diversity of sheep abortion isolates of C. jejuni was investigated by Array-based CGH
2014-02-11 | GSE54858 | GEO
Project description:Campylobacter jejuni has become the predominant cause of sheep abortions in the U.S. However, little is know about the genetic diversity among the isolates collected from different time periods. In this study, the genetic diversity of sheep aborion isolates of C. jejuni was investigated by Array-based CGH Each isolate was compared to IA3902, a dye-swap replicate was applied for each isolate
2014-02-11 | E-GEOD-54859 | biostudies-arrayexpress
Project description:Campylobacter jejuni has become the predominant cause of sheep abortions in the U.S. However, little is know about the genetic diversity among the isolates collected from different time periods. In this study, the genetic diversity of sheep abortion isolates of C. jejuni was investigated by Array-based CGH Each isolate was compared to IA3902, a dye-swap replicate was applied for each isolate
2014-02-11 | E-GEOD-54858 | biostudies-arrayexpress
Project description:Campylobacter jejuni is a leading cause of human gastrointestinal disease and small ruminant abortions in the United States. The recent emergence of a highly virulent, tetracycline-resistant C. jejuni subsp. jejuni sheep abortion clone (clone SA) in the United States, and that strain's association with human disease, has resulted in a heightened awareness of the zoonotic potential of this organism. Pacific Biosciences' Single Molecule, Real-Time sequencing technology was used to explore the variation in the genome-wide methylation patterns of the abortifacient clone SA (IA3902) and phenotypically distinct gastrointestinal-specific C. jejuni strains (NCTC 11168 and 81-176). Several notable differences were discovered that distinguished the methylome of IA3902 from that of 11168 and 81-176: identification of motifs novel to IA3902, genome-specific hypo- and hypermethylated regions, strain level variability in genes methylated, and differences in the types of methylation motifs present in each strain. These observations suggest a possible role of methylation in the contrasting disease presentations of these three C. jejuni strains. In addition, the methylation profiles between IA3902 and a luxS mutant were explored to determine if variations in methylation patterns could be identified that might explain the role of LuxS-dependent methyl recycling in IA3902 abortifacient potential.
| S-EPMC4294202 | biostudies-literature
Project description:Campylobacter infection is a leading cause of ovine abortion worldwide. Historically, genetically diverse Campylobacter fetus and Campylobacter jejuni strains have been implicated in such infections, but since 2003 a highly pathogenic, tetracycline-resistant C. jejuni clone (named SA) has become the predominant cause of sheep abortions in the United States. Whether clone SA was present in earlier U.S. abortion isolates (before 2000) and is associated with sheep abortions outside the United States are unknown. Here, we analyzed 54 C. jejuni isolates collected from U.S. sheep abortions at different time periods and compared them with 42 C. jejuni isolates associated with sheep abortion during 2002 to 2008 in Great Britain, using multilocus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE), and array-based comparative genomic hybridization (CGH). Although clone SA (ST-8) was present in the early U.S. isolates, it was not as tetracycline resistant (19% versus 100%) or predominant (66% versus 91%) as it was in the late U.S isolates. In contrast, C. jejuni isolates from Great Britain were genetically diverse, comprising 19 STs and lacking ST-8. PFGE and CGH analyses of representative strains further confirmed the population structure of the abortion isolates. Notably, the Great Britain isolates were essentially susceptible to most tested antibiotics, including tetracycline, while the late U.S. isolates were universally resistant to this antibiotic, which could be explained by the common use of tetracyclines for control of sheep abortions in the United States but not in Great Britain. These results suggest that the dominance of clone SA in sheep abortions is unique to the United States, and the use of tetracyclines may have facilitated selection of this highly pathogenic clone.
| S-EPMC4042809 | biostudies-literature
Project description:Campylobacter jejuni is a major pathogen in bacterial gastroenteritis worldwide and can cause bacteremia in severe cases. C. jejuni is highly structured into clonal lineages of which the ST677CC lineage has been overrepresented among C. jejuni isolates derived from blood. In this study, we characterized the genomes of 31 C. jejuni blood isolates and 24 faecal isolates belonging to ST677CC in order to study the genome biology related to C. jejuni invasiveness. We combined the genome analyses with phenotypical evidence on serum resistance which was associated with phase variation of wcbK; a GDP-mannose 4,6-dehydratase involved in capsular biosynthesis. We also describe the finding of a Type III restriction-modification system unique to the ST-794 sublineage. However, features previously considered to be related to pathogenesis of C. jejuni were either absent or disrupted among our strains. Our results refine the role of capsule features associated with invasive disease and accentuate the possibility of methylation and restriction enzymes in the potential of C. jejuni to establish invasive infections. Our findings underline the importance of studying clinically relevant well-characterized bacterial strains in order to understand pathogenesis mechanisms important in human infections.
| S-EPMC4658567 | biostudies-literature
Project description:BackgroundCampylobacter jejuni is a pervasive pathogen of major public health concern with a complex ecology requiring accurate and informative approaches to define pathogen diversity during outbreak investigations. Source attribution analysis may be confounded if the genetic diversity of a C. jejuni population is not adequately captured in a single specimen. The aim of this study was to determine the genomic diversity of C. jejuni within individual stool specimens from four campylobacteriosis patients. Direct plating and pre-culture filtration of one stool specimen per patient was used to culture multiple isolates per stool specimen. Whole genome sequencing and pangenome level analysis were used to investigate genomic diversity of C. jejuni within a patient.ResultsA total 92 C. jejuni isolates were recovered from four patients presenting with gastroenteritis. The number of isolates ranged from 13 to 30 per patient stool. Three patients yielded a single C. jejuni multilocus sequence type: ST-21 (n = 26, patient 4), ST-61 (n = 30, patient 1) and ST-2066 (n = 23, patient 2). Patient 3 was infected with two different sequence types [ST-51 (n = 12) and ST-354 (n = 1)]. Isolates belonging to the same sequence type from the same patient specimen shared 12-43 core non-recombinant SNPs and 0-20 frameshifts with each other, and the pangenomes of each sequence type consisted of 1406-1491 core genes and 231-264 accessory genes. However, neither the mutation nor the accessory genes were connected to a specific functional gene category.ConclusionsOur findings show that the C. jejuni population recovered from an individual patient's stool are genetically diverse even within the same ST and may have shared common ancestors before specimens were obtained. The population is unlikely to have evolved from a single isolate at the time point of initial patient infection, leading us to conclude that patients were likely infected with a heterogeneous C. jejuni population. The diversity of the C. jejuni population found within individual stool specimens can inform future methodological approaches to attribution and outbreak investigations.
| S-EPMC9727990 | biostudies-literature
Project description:Campylobacter is the most common bacterial cause of gastroenteritis in the European Union with over 200,000 laboratory-confirmed cases reported annually. This is the first study to describe findings related to comparative genomics analyses of the sequence type (ST)-677 clonal complex (CC), a Campylobacter jejuni lineage associated with bacteremia cases in humans. We performed whole-genome sequencing, using Illumina HiSeq sequencing technology, on five related ST-677 CC isolates from two chicken farms to identify microevolution taking place at the farms. Our further aim was to identify novel putative virulence determinants from the ST-677 CC genomes. For this purpose, clinical isolates of the same CC were included in comparative genomic analyses against well-known reference strains of C. jejuni. Overall, the ST-677 CC was recognized as a highly clonal lineage with relatively small differences between the genomes. Among the farm isolates differences were identified mainly in the lengths of the homopolymeric tracts in genes related to the capsule, lipo-oligosaccharide, and flagella. We identified genomic features shared with C. jejuni subsp. doylei, which has also been shown to be associated with bacteremia in humans. These included the degradation of the cytolethal distending toxin operon and similarities between the capsular polysaccharide biosynthesis loci. The phase-variable GDP-mannose 4,6-dehydratase (EC 4.2.1.47) (wcbK, CAMP1649), associated with the capsular polysaccharide biosynthesis locus, may play a central role in ST-677 CC conferring acid and serum resistance during different stages of infection. Homology-based searches revealed several additional novel features and characteristics, including two putative type Vb secretion systems and a novel restriction modification/methyltransferase gene cluster, putatively associated with pathogenesis and niche adaptation.
| S-EPMC4202330 | biostudies-literature