Performance of a 70-mer oligonucleotide microarray for genotyping of Campylobacter jejuni

Rodin, Sandra; Andersson, Anders F.; Wirta, Valtteri; Eriksson, Lena; Ljungström, Marianne; Björkholm, Britta; Lindmark, Hans; Engstrand, Lars

doi:10.1186/1471-2180-8-73

Cited by 17 publications

(16 citation statements)

References 34 publications

(39 reference statements)

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“…A number of studies have demonstrated the potential of the high-resolution subtyping of Campylobacter using comparative genomics and its potential application in the context of molecular epidemiology or population surveys (28,38,50,51). Despite these advances, the past decade has seen very limited transfer of genomic approaches to subtyping beyond proof-of-concept studies.…”

Section: Discussionmentioning

confidence: 99%

Development and Validation of a Comparative Genomic Fingerprinting Method for High-Resolution Genotyping of Campylobacter jejuni

et al. 2012

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e Campylobacter spp. are a leading cause of bacterial gastroenteritis worldwide. The need for molecular subtyping methods with enhanced discrimination in the context of surveillance-and outbreak-based epidemiologic investigations of Campylobacter spp. is critical to our understanding of sources and routes of transmission and the development of mitigation strategies to reduce the incidence of campylobacteriosis. We describe the development and validation of a rapid and high-resolution comparative genomic fingerprinting (CGF) method for C. jejuni. A total of 412 isolates from agricultural, environmental, retail, and human clinical sources obtained from the Canadian national integrated enteric pathogen surveillance program (C-EnterNet) were analyzed using a 40-gene assay (CGF40) and multilocus sequence typing (MLST). The significantly higher Simpson's index of diversity (ID) obtained with CGF40 (ID ‫؍‬ 0.994) suggests that it has a higher discriminatory power than MLST at both the level of clonal complex (ID ‫؍‬ 0.873) and sequence type (ID ‫؍‬ 0.935). High Wallace coefficients obtained when CGF40 was used as the primary typing method suggest that CGF and MLST are highly concordant, and we show that isolates with identical MLST profiles are comprised of isolates with distinct but highly similar CGF profiles. The high concordance with MLST coupled with the ability to discriminate between closely related isolates suggests that CFG40 is useful in differentiating highly prevalent sequence types, such as ST21 and ST45. CGF40 is a high-resolution comparative genomics-based method for C. jejuni subtyping with high discriminatory power that is also rapid, low cost, and easily deployable for routine epidemiologic surveillance and outbreak investigations. Campylobacter spp. are a leading cause of bacterial gastroenteritis worldwide (20), and most cases are thought to be the direct result of infection by C. jejuni or C. coli (20,43). Risk factors for campylobacteriosis include exposure to contaminated water, milk, and various food products, such as poultry (1,3,6,21). The development and implementation of effective control measures for these pathogens hinge on the identification of sources of infection. Although the ingestion of contaminated food or water and animal contact play a significant role in the epidemiology of campylobacteriosis, efforts to track sources of Campylobacter infection are hampered by the sporadic nature of campylobacteriosis (25), the infrequent association with outbreaks of disease, and widespread reservoirs that include water, livestock, domestic animals, and wildlife (8,17,46,65,67).A number of different molecular subtyping methods, such as pulsed-field gel electrophoresis (PFGE), restriction fragment length polymorphism analysis of the flagellin gene (flaA RFLP), and the DNA sequencing of the flagellin gene short variable region (flaA SVR), have been used to identify genotypic clusters of Campylobacter in the context of molecular epidemiology (18, 33). More recently, a multilocus sequence typing (ML...

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Section: Discussionmentioning

confidence: 99%

Development and Validation of a Comparative Genomic Fingerprinting Method for High-Resolution Genotyping of Campylobacter jejuni

et al. 2012

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“…Within these groups of variable genes, all or a portion of 17 of the 18 intraspecies hypervariable regions published by Parker et al (2006) were identified; region 18 (CJE0944-CJE0947) was absent in our analysis. Portions of two additional recently reported (Rodin et al, 2008) variable regions (regions 19 and 21) were also among the variable genes in our data.…”

Section: Cgimentioning

confidence: 62%

GenotypingCampylobacter jejuniby Comparative Genome Indexing: An Evaluation with Pulsed-Field Gel Electrophoresis andflaASVR Sequencing

Pittenger¹,

Englen²,

Parker³

et al. 2009

Foodborne Pathogens and Disease

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Comparative genome indexing (CGI) using whole-genome DNA microarrays was evaluated as a means of genotyping Campylobacter jejuni relative to two standard methods, pulsed-field gel electrophoresis (PFGE) and flaA short variable region sequencing (flaA SVR typing). Thirty-six geographically diverse C. jejuni isolates were selected from a collection of cattle and chicken isolates. The BioNumerics software program was used for cluster analysis of the data from all 36 isolates for each of the three typing methods. Comparative genome indexing assigned a unique type to each isolate while PFGE and flaA SVR distinguished 29 and 35 different types, respectively. The four common types identified by PFGE were also closely related by CGI, and the overall similarity of the CGI results to those for PFGE indicates the value of CGI as a more informative alternative to PFGE. While flaA SVR was very discriminative, the isolates were all highly similar (>78%) resulting in finer distinctions between isolates and fewer genotypic relations to CGI or PFGE. Campylobacter jejuni is one of the most common causative agents of bacterial gastroenteritis in the world. The development of CGI as a molecular typing tool for C. jejuni offers a highly effective and informative means of further understanding the epidemiology of this ubiquitous pathogen.

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“…A specific pattern of array spots will fluoresce, which is then used to infer the genetic makeup in the test sample [170]. Microarray analysis is an emerging technology that has the potential to become a leading trend in bacterial identification in the dairy and overall in the in food and drink industry, allowing both the detection and/or genotyping of pathogenic microorganisms [171][172][173][174][175][176][177][178][179].…”

Section: Biosensors Microarrays Micro and Nano Electro-mechanical-smentioning

confidence: 99%

Nucleic Acid-Based Methods to Identify, Detect and Type Pathogenic Bacteria Occurring in Milk and Dairy Products

Fusco¹,

Quero²

2012

Structure and Function of Food Engineering

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Performance of a 70-mer oligonucleotide microarray for genotyping of Campylobacter jejuni

Cited by 17 publications

References 34 publications

Development and Validation of a Comparative Genomic Fingerprinting Method for High-Resolution Genotyping of Campylobacter jejuni

Development and Validation of a Comparative Genomic Fingerprinting Method for High-Resolution Genotyping of Campylobacter jejuni

GenotypingCampylobacter jejuniby Comparative Genome Indexing: An Evaluation with Pulsed-Field Gel Electrophoresis andflaASVR Sequencing

Nucleic Acid-Based Methods to Identify, Detect and Type Pathogenic Bacteria Occurring in Milk and Dairy Products

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