ABSTRACT
Campylobacter is a leading cause of foodborne illness in humans, and improving our understanding of the epidemiology of this organism is essential. The objective of this study was to identify the genes that discriminate isolates of C. jejuni by analysis with whole-genome DNA microarrays. Statistical analyses of whole-genome data from 95 geographically diverse cattle, chicken, and human C. jejuni isolates identified 142 most significant variable genes. Of this total, 125 (88%) belonged to genomic prophage and hypervariable regions. The significance of genomic prophage and hypervariable regions in determining C. jejuni isolate genomic diversity is emphasized by these results. These genes will be useful as biomarkers and components of genotyping systems for C. jejuni to improve our understanding of the epidemiology and population genetics of this major foodborne pathogen.
Subject(s)
Campylobacter Infections/microbiology , Campylobacter jejuni/classification , Campylobacter jejuni/genetics , Genetic Variation , Meat/microbiology , Prophages/classification , Prophages/genetics , Animals , Campylobacter jejuni/isolation & purification , Campylobacter jejuni/metabolism , Cattle , Chickens , DNA, Bacterial/genetics , DNA, Bacterial/isolation & purification , DNA, Bacterial/metabolism , Food Microbiology/methods , Foodborne Diseases/microbiology , Genetic Loci , Genome-Wide Association Study , Genotyping Techniques , Humans , Internet , Oligonucleotide Array Sequence Analysis , Population Surveillance , Prophages/isolation & purification , Prophages/metabolism , United StatesABSTRACT
A novel influenza A (H1N1) virus detected in April 2009 rapidly spread around the world. North American provincial and state laboratories have well-defined roles and responsibilities, including providing accurate, timely test results for patients and information for regional public health and other decision makers. We used the multidisciplinary response and rapid implementation of process changes based on Lean methods at the provincial public health laboratory in British Columbia, Canada, to improve laboratory surge capacity in the 2009 influenza pandemic. Observed and computer simulating evaluation results from rapid processes changes showed that use of Lean tools successfully expanded surge capacity, which enabled response to the 10-fold increase in testing demands.
Subject(s)
Influenza, Human/epidemiology , Laboratories/organization & administration , Pandemics , Public Health/standards , Canada/epidemiology , Humans , Influenza A Virus, H1N1 Subtype/isolation & purification , Influenza, Human/diagnosis , Laboratories/standards , Reverse Transcriptase Polymerase Chain Reaction , Time FactorsABSTRACT
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.
