Whole genome sequence analysis indicates recent diversification of mammal-associated Campylobacter fetus and implicates a genetic factor associated with H2S production

Bloois, Linda van der Graaf–van; Duim, Birgitta; Miller, William G.; Forbes, Ken J.; Wagenaar, Jaap A.; Zomer, Aldert

doi:10.1186/s12864-016-3058-7

Cited by 23 publications

(39 citation statements)

References 38 publications

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“…, this work provides a molecular tool linked to H 2 S production in C. fetus and supports the findings of the pioneering study of van deerGraaf-van Bloois et al (2016).…”

supporting

confidence: 84%

“…testudinum (Cft), the last subspecies proposed of C. fetus, has a complete version of the operon. This is the case of the strain Cft 03/427 (whose genome is the representative of the species) which has been concordantly described as an H 2 S-producing strain elsewhere (van der Graaf -van Bloois et al, 2016). To date, this subspecies has not been described in cattle, and for this reason it was excluded of this study.…”

Section: Discussionmentioning

confidence: 99%

“…This emphasizes a real need to go further toward current C. fetus classification and identification, which will have a significant impact on the diagnostic practice. As mentioned above, although this issue has been addressed in the literature and genomic studies have broadened and strengthened our knowledge of this bacterium (van der Graaf -van Bloois et al, 2014;van der Graaf -van Bloois et al, 2016;Iraola et al, 2017), a concerted action toward C. fetus subspecies classification and differentiation has been neglected. There are no molecular markers associated to tropism or virulence of Cfv that could help with a differential diagnosis of the bovine genital campylobacteriosis (Gilbert et al, 2018).…”

Section: Manuscript To Be Reviewedmentioning

confidence: 99%

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Peer Review #2 of "L-cysteine transporter-PCR to detect hydrogen sulfide-producing Campylobacter fetus (v0.1)"

2019

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Phenotypic differences between Campylobacter fetus fetus and Campylobacter fetus venerealis subspecies allow the differential diagnosis of bovine genital campylobacteriosis. The hydrogen sulfide production, for example, is a trait exclusive to Campylobacter fetus fetus and Campylobacter fetus venerealis biovar intermedius. This gas that can be biochemically tested can be produced from L-cysteine. Herein we report a novel multiplex-PCR to differentiate Campylobacter fetus based on the evaluation of a deletion of an ATPbinding cassette-type L-cysteine transporter that could be involved in hydrogen sulfide production, as previously described. A wet lab approach combined with an in silico whole genome data analysis showed complete agreement between this L-cysteine transporter-PCR and the hydrogen sulfide production biochemical test. This multiplex-PCR may complement the tests currently employed for the differential diagnosis of Campylobacter fetus.

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“…, this work provides a molecular tool linked to H 2 S production in C. fetus and supports the findings of the pioneering study of van deerGraaf-van Bloois et al (2016).…”

supporting

confidence: 84%

Section: Discussionmentioning

confidence: 99%

Section: Manuscript To Be Reviewedmentioning

confidence: 99%

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Peer Review #2 of "L-cysteine transporter-PCR to detect hydrogen sulfide-producing Campylobacter fetus (v0.1)"

2019

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“…Whole-genome sequencing has provided important insights into the genetics and evolution of Campylobacter species that occupy different host niches (Miller et al, 2014a ; Gilbert et al, 2016 ; Graaf-van Bloois et al, 2016 ; van der Graaf-van Bloois et al, 2016 ). However, little is known about how variation in species and strains relates to sub-structure within the chicken gut niche, and how this correlates with the emergence of diseases such as SLD.…”

Section: Introductionmentioning

confidence: 99%

Genome Reduction for Niche Association in Campylobacter Hepaticus, A Cause of Spotty Liver Disease in Poultry

Petrovska

Tang

Rensburg

et al. 2017

Front. Cell. Infect. Microbiol.

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The term “spotty liver disease” (SLD) has been used since the late 1990s for a condition seen in the UK and Australia that primarily affects free range laying hens around peak lay, causing acute mortality and a fall in egg production. A novel thermophilic SLD-associated Campylobacter was reported in the United Kingdom (UK) in 2015. Subsequently, similar isolates occurring in Australia were formally described as a new species, Campylobacter hepaticus. We describe the comparative genomics of 10 C. hepaticus isolates recovered from 5 geographically distinct poultry holdings in the UK between 2010 and 2012. Hierarchical gene-by-gene analyses of the study isolates and representatives of 24 known Campylobacter species indicated that C. hepaticus is most closely related to the major pathogens Campylobacter jejuni and Campylobacter coli. We observed low levels of within-farm variation, even between isolates collected over almost 3 years. With respect to C. hepaticus genome features, we noted that the study isolates had a ~140 Kb reduction in genome size, ~144 fewer genes, and a lower GC content compared to C. jejuni. The most notable reduction was in the subsystem containing genes for iron acquisition and metabolism, supported by reduced growth of C. hepaticus in an iron depletion assay. Genome reduction is common among many pathogens and in C. hepaticus has likely been driven at least in part by specialization following the occupation of a new niche, the chicken liver.

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“…Ideally, the analysed samples are also very closely related, which is the case in outbreak or intrapatient divergence studies. In this setting, one of a set of closely related samples may be assembled and used as reference against which all others can be mapped [21,22]. The resulting alignment is then the basis for phylogenetic reconstruction, either directly or after concatenation of the positions showing variance.…”

mentioning

confidence: 99%

Whole genome sequencing options for bacterial strain typing and epidemiologic analysis based on single nucleotide polymorphism versus gene-by-gene–based approaches

Schürch

Arredondo-Alonso

Willems

et al. 2018

Clinical Microbiology and Infection

357

293

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Background: Whole genome sequence (WGS)-based strain typing finds increasing use in the epidemiologic analysis of bacterial pathogens in both public health as well as more localized infection control settings. Aims: This minireview describes methodologic approaches that have been explored for WGS-based epidemiologic analysis and considers the challenges and pitfalls of data interpretation. Sources: Personal collection of relevant publications. Content: When applying WGS to study the molecular epidemiology of bacterial pathogens, genomic variability between strains is translated into measures of distance by determining single nucleotide polymorphisms in core genome alignments or by indexing allelic variation in hundreds to thousands of core genes, assigning types to unique allelic profiles. Interpreting isolate relatedness from these distances is highly organism specific, and attempts to establish species-specific cutoffs are unlikely to be generally applicable. In cases where single nucleotide polymorphism or core gene typing do not provide the resolution necessary for accurate assessment of the epidemiology of bacterial pathogens, inclusion of accessory gene or plasmid sequences may provide the additional required discrimination. Implications: As with all epidemiologic analysis, realizing the full potential of the revolutionary advances in WGS-based approaches requires understanding and dealing with issues related to the fundamental steps of data generation and interpretation.

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Whole genome sequence analysis indicates recent diversification of mammal-associated Campylobacter fetus and implicates a genetic factor associated with H2S production

Cited by 23 publications

References 38 publications

Peer Review #2 of "L-cysteine transporter-PCR to detect hydrogen sulfide-producing Campylobacter fetus (v0.1)"

Peer Review #2 of "L-cysteine transporter-PCR to detect hydrogen sulfide-producing Campylobacter fetus (v0.1)"

Genome Reduction for Niche Association in Campylobacter Hepaticus, A Cause of Spotty Liver Disease in Poultry

Whole genome sequencing options for bacterial strain typing and epidemiologic analysis based on single nucleotide polymorphism versus gene-by-gene–based approaches

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