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

Abstract

A subtyping methodology for Campylobacter, Comparative Genomic Fingerprinting (CGF40), has been described recently. The objective of this study was to assess the utility of CGF40 as a tool to enhance routine public health surveillance of campylobacteriosis. Isolates of Campylobacter from across the province were requested and sent for CGF40 subtyping. Epidemiological data from cases reported to public health officials in Nova Scotia, Canada, from January 2012 to March 2015 were linked with blinded CGF40 subtyping results. CGF40 was epidemiologically valid; subtyping discerned known epidemiologically related isolates and augmented case-finding. Predominant sources and locations of subtype detection from the national reference database showed some study subtypes were rare and even novel to the database, while others were more commonly identified over multiple years and with exposures locally and internationally. A case-case study design was applied to examine risk factors for the most common CGF40 subtypes detected. Differences in the epidemiology of different CGF40 subtypes were observed. Statistically significant associations were noted for specific subtypes with rural residence, local exposure, contact with a pet dog or cat, contact with chickens, and drinking unpasteurized milk. With prospective use, CGF40 could potentially identify unrecognized outbreaks and contribute to epidemiological investigations of case clusters.

Frequent Implication of Multistress-TolerantCampylobacter jejuniin Human Infections

“…This CGF subtype is detected more frequently in human clinical cases (59.0%) than in animals (40.5%) in the Canadian Campylobacter CGF database ( 21 ). According to a recent study from Nova Scotia, a province geographically distant from Alberta, the predominant CGF subtype 0083.001.002 in MST clade IV is also the most common CGF subtype found in human clinical isolates of C. jejuni in this province ( 22 ). CGF subtype 0083.001.002 is primarily associated with chicken ( 22 ), and strains in 0083.001.002 were highly tolerant to PAA, freezing, and heat treatment ( Figure 4 ).…”

“…According to a recent study from Nova Scotia, a province geographically distant from Alberta, the predominant CGF subtype 0083.001.002 in MST clade IV is also the most common CGF subtype found in human clinical isolates of C. jejuni in this province ( 22 ). CGF subtype 0083.001.002 is primarily associated with chicken ( 22 ), and strains in 0083.001.002 were highly tolerant to PAA, freezing, and heat treatment ( Figure 4 ). This finding suggests that multistress tolerance may facilitate C. jejuni survival in poultry processing, preservation, and cooking, and consequently might increase chances of food contamination and human exposure.…”

Molecular Detection, Typing, and Quantification of Campylobacter spp. in Foods of Animal Origin

“…It can also detect the level of genetic diversity of species and predict interspecies transmission, as reported for experiments on pig and poultry farms (Ceuppens and others ), and to determine genetic relatedness between C. jejuni and C. coli isolates from retail meat sources (Noormohamed and Fakhr ) and Campylobacter isolates from chicken flocks on 2 farms (Zhang and others ). MLST has also been used in reports of outbreaks and for determining public health cases (Schleihauf and others ) and epidemiological relationships of C. jejuni strains from chickens and humans (Oh and others ). In all these studies, STs and clonal complexes were assigned using the C. jejuni or C. coli PubMLST database.…”

“…Thus, it is easier and faster to employ molecular biology techniques such as polymerase chain reaction (PCR) and sequencing for identification purposes. In addition, tools such as pulsed‐field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) are the currently the most commonly used for typing (Goering ; Miller and others ; Behringer and others ; Gharst and others ; Manfreda and others ; Pan and others ; Vidal and others ; Oh and others ; Schleihauf and others ; Vinueza‐Burgos and others ; Zhang and others ).…”

Inquiring into the Gaps of Campylobacter Surveillance Methods

“…However, microarrays are ultimately abandoned and cannot be considered as optimal tools for subtyping because they offer limited throughput in real-time outbreak investigation and constitute a costly and a technique that is difficult to standardize. Another method of comparative genomics is the recent typing method of comparative genomic fingerprinting (CGF), which has improved routine campylobacteriosis surveillance [ 101 ]. The CGF is the preferred method for the detection of Campylobacter genes with high variability among the different species of bacterial clusters that have been previously identified by the MCGH method [ 102 ].…”