The Impact of Multilocus Variable-Number Tandem-Repeat Analysis on PulseNet CanadaEscherichia coliO157:H7 Laboratory Surveillance and Outbreak Support, 2008–2012

Abstract

The lack of pattern diversity among pulsed-field gel electrophoresis (PFGE) profiles for Escherichia coli O157:H7 in Canada does not consistently provide optimal discrimination, and therefore, differentiating temporally and/or geographically associated sporadic cases from potential outbreak cases can at times impede investigations. To address this limitation, DNA sequence-based methods such as multilocus variable-number tandem-repeat analysis (MLVA) have been explored. To assess the performance of MLVA as a supplemental method to PFGE from the Canadian perspective, a retrospective analysis of all E. coli O157:H7 isolated in Canada from January 2008 to December 2012 (inclusive) was conducted. A total of 2285 E. coli O157:H7 isolates and 63 clusters of cases (by PFGE) were selected for the study. Based on the qualitative analysis, the addition of MLVA improved the categorization of cases for 60% of clusters and no change was observed for ∼40% of clusters investigated. In such situations, MLVA serves to confirm PFGE results, but may not add further information per se. The findings of this study demonstrate that MLVA data, when used in combination with PFGE-based analyses, provide additional resolution to the detection of clusters lacking PFGE diversity as well as demonstrate good epidemiological concordance. In addition, MLVA is able to identify cluster-associated isolates with variant PFGE pattern combinations that may have been previously missed by PFGE alone. Optimal laboratory surveillance in Canada is achieved with the application of PFGE and MLVA in tandem for routine surveillance, cluster detection, and outbreak response.

Comparative genomic fingerprinting of Campylobacter: application in routine public health surveillance and epidemiological investigations

“…Furthermore, if low level contamination of a widely distributed food product causes illness in a number of jurisdictions, real-time sharing of subtyping results across jurisdictions is required to detect these outbreaks. Protocols could be designed to target public health investigation following the implementation of routine CGF40 subtyping, similar to those in place through PulseNet Canada for Salmonella, Escherichia coli, and Listeria [28,29]. Our data support other findings that small outbreaks are relatively common [30], beyond those detected through routine public health follow up.…”

Evaluation of whole-genome sequencing for outbreak detection of Verotoxigenic Escherichia coli O157:H7 from the Canadian perspective

“…At the time of the investigation, MLVA was primarily used to provide enhanced resolution to selected outbreaks but was not officially implemented for routine characterization of VTEC O157:H7 in Canada until 2013. Historically, given the overall effectiveness of MLVA for VTEC O157:H7 [ 4 , 5 ], the impacts of routine sequencing may not be as substantial for surveillance and cluster detection of this pathogen in Canada; other priority pathogens such as Listeria and Salmonella , for which no interim method offering comparable resolution is available, have taken precedence for WGS implementation in a number of different countries including Denmark, England and the United States [ 31 ]. PulseNet Canada has followed in similar footsteps; routine sequencing of all Listeria and Salmonella species was implemented in Canada in January and May of 2017, respectively.…”

“…To protect and promote the health of Canadians, rapid and accurate identification of foodborne pathogens is of paramount importance for effective laboratory-based surveillance and outbreak detection, and is dependent on well-established, standardized and highly discriminatory typing methods [ 1 – 3 ]. For nearly two decades, pulsed-field gel electrophoresis (PFGE) has been the laboratory gold standard for foodborne bacterial subtyping and has been the primary method used by PulseNet Canada, Canada’s national molecular subtyping network for foodborne bacterial disease cluster detection and outbreak response [ 4 , 5 ]. The most notable strength of applying PFGE not only lies in the expertise and experience in interpreting the data, but also, in the amount of historical PFGE data that exists in Canada’s national databases [ 4 , 6 , 7 ].…”

“…Despite the historical usefulness and robustness of PFGE, it has been widely demonstrated by the scientific community that the method does not consistently provide optimal discrimination, particularly for highly clonal strains, resulting in outbreak investigations of seemingly unrelated cases and in some instances, discriminates among epidemiological related isolates, obscuring useful linkages and cluster detection [ 3 , 8 , 9 ]. To enhance resolution, multilocus variable-number tandem-repeat analysis (MLVA) was implemented (in Canada, as a supplemental subtyping tool, and elsewhere as a primary tool), and has been extremely valuable in discriminating among closely related isolates that would otherwise be indistinguishable by PFGE [ 4 , 10 – 15 ]; however, optimal resolution is often achieved when the results of these typing methods are combined and interpreted together [ 5 ], rendering characterization of foodborne bacterial pathogens to be laborious, time-consuming and expensive, which has prohibited widespread adoption of both methods in many public health laboratories [ 16 , 17 ]. Additionally, MLVA protocols have only been developed for selected pathogens (i.e., Salmonella Enteritidis, Salmonella Typhimurium and Escherichia coli O157:H7) within the PulseNet Canada network, further hindering its overall effectiveness [ 17 ].…”

PulseNet International: Vision for the implementation of whole genome sequencing (WGS) for global food-borne disease surveillance

“…The use of standardised, validated protocols and analysis procedures by all participants coupled with consistent interpretive criteria has enabled countless successful outbreak investigations, both within single countries and also spanning across borders [4]. Current PulseNet methods, PFGE and MLVA, are no longer considered cutting edge but have been extremely efficient in driving the detection, investigation and control of food-borne infection outbreaks in the past 20 years due to the demonstration of high typeability, reproducibility, discriminatory power, and good epidemiological concordance [5]. For timely and effective surveillance and outbreak response, data must remain comparable at all times among laboratories; any modifications on existing methods or introduction of new methods must be carefully validated and implemented by all network members in order to be effective and to avoid disrupting the surveillance due to backwards incompatibility issues [3,6].…”