Molecular-based surveillance of campylobacteriosis in New Zealand - from source attribution to genomic epidemiology.

Epi-interactive, Miramar, Wellington, New Zealand.
Eurosurveillance: bulletin europeen sur les maladies transmissibles = European communicable disease bulletin (Impact Factor: 4.66). 01/2013; 18(3).
Source: PubMed
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    ABSTRACT: The rates of foodborne disease caused by gastrointestinal pathogens continue to be a concern in both the developed and developing worlds. The growing world population, the increasing complexity of agri-food networks and the wide range of foods now associated with STEC are potential drivers for increased risk of human disease. It is vital that new developments in technology, such as whole genome sequencing (WGS), are effectively utilized to help address the issues associated with these pathogenic microorganisms. This position paper, arising from an OECD funded workshop, provides a brief overview of next generation sequencing technologies and software. It then uses the agent-host-environment paradigm as a basis to investigate the potential benefits and pitfalls of WGS in the examination of (1) the evolution and virulence of STEC, (2) epidemiology from bedside diagnostics to investigations of outbreaks and sporadic cases and (3) food protection from routine analysis of foodstuffs to global food networks. A number of key recommendations are made that include: validation and standardization of acquisition, processing and storage of sequence data including the development of an open access "WGSNET"; building up of sequence databases from both prospective and retrospective isolates; development of a suite of open-access software specific for STEC accessible to non-bioinformaticians that promotes understanding of both the computational and biological aspects of the problems at hand; prioritization of research funding to both produce and integrate genotypic and phenotypic information suitable for risk assessment; training to develop a supply of individuals working in bioinformatics/software development; training for clinicians, epidemiologists, the food industry and other stakeholders to ensure uptake of the technology and finally review of progress of implementation of WGS. Currently the benefits of WGS are being slowly teased out by academic, government, and industry or private sector researchers around the world. The next phase will require a coordinated international approach to ensure that it's potential to contribute to the challenge of STEC disease can be realized in a cost effective and timely manner.
    International Journal of Food Microbiology 07/2014; 187C:57-72. DOI:10.1016/j.ijfoodmicro.2014.07.002 · 3.16 Impact Factor
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    ABSTRACT: Although it is known that Escherichia coli O157 is capable of long‐term soil survival, little is known about the mechanisms involved. This study investigated the role of the general stress response system RpoS in E. coli soil survival. The results showed that E. coli O157 isolates capable of long‐term survival (longer than 200 days) in manure‐amended soil were characterized by the absence of mutations in their rpoS gene. In contrast, the strains not capable of long‐term survival all possessed mutations in their rpoS gene. In addition, the long‐term surviving strains showed significantly higher levels of acid resistance in simulated gastric fluid (pH 2.5). Sequencing of the rpoS gene of bovine, food and clinical isolates revealed a skewed distribution of rpoS wild‐type and mutant strains among the different sources. Bovine and food isolates had low numbers of mutants (RpoS system is an advantage for survival in the manure‐amended soil environment. Further deletion and complementation studies should provide more evidence on the role of RpoS in the long‐term survival of E. coli O157 in diverse environments.
    FEMS Microbiology Letters 01/2013; 338(1). · 2.72 Impact Factor
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    ABSTRACT: To determine the fecal excretion of C. jejuni by dairy cows that used housing in combination with outdoor grazing. C. jejuni prevalence and concentration were measured in a total of 990 cow fecal samples collected from seven herd home farms (HH), seven stand-off pad farms (SOP) and seven pasture farms (P) over a two-year period. On all the farms, cows had access to pasture but were restricted to narrow grazing strips in winter. The overall C. jejuni prevalence was 55%, 49% and 54% on HH, SOP and P farms, respectively. The C. jejuni concentration ranged from 0 to 6.7 log10 g(-1) feces and was not statistically different among the farm systems. However, C. jejuni prevalence (p=0.014) and concentration (p=0.0001) were significantly greater in winter-beginning of spring after intensive use of HH, SOP and strip-grazing. Typing of 30 C. jejuni isolates revealed a dominance of ruminant-types (MLST CC-61, CC-21, CC-42, and CC-48), which are associated with human disease. No overall difference was observed among systems but seasonal management practices that force cows close together increased the prevalence and concentration of C. jejuni in feces. These findings are important when identifying farm practices that reduce C. jejuni excretion and the associated risk to human health. This article is protected by copyright. All rights reserved.
    Journal of Applied Microbiology 12/2013; DOI:10.1111/jam.12425 · 2.39 Impact Factor