Comparative Genotyping of Campylobacter jejuni by Amplified Fragment Length Polymorphism, Multilocus Sequence Typing, and Short Repeat Sequencing: Strain Diversity, Host Range, and Recombination

Abstract

Three molecular typing methods were used to study the relationships among 184 Campylobacter strains isolated from humans, cattle, and chickens. All strains were genotyped by amplified fragment length polymorphism (AFLP) analysis, multilocus sequence typing (MLST), and sequence analysis of a genomic region with short tandem repeats designated clustered regularly interspaced short palindromic repeats (CRISPRs). MLST and AFLP analysis yielded more than 100 different profiles and patterns, respectively. These multiple-locus typing methods resulted in similar genetic clustering, indicating that both are useful in disclosing genetic relationships between Campylobacter jejuni isolates. Group separation analysis of the AFLP analysis and MLST data revealed an unexpected association between cattle and human strains, suggesting a common source of infection. Analysis of the polymorphic CRISPR region carrying short repeats allowed about two-thirds of the typeable strains to be distinguished, similar to AFLP analysis and MLST. The three methods proved to be equally powerful in identifying strains from outbreaks of human campylobacteriosis. Analysis of the MLST data showed that intra-and interspecies recombination occurs frequently and that the role of recombination in sequence variation is 50 times greater than that of mutation. Examination of strains cultured from cecum swabs revealed that individual chickens harbored multiple Campylobacter strain types and that some genotypes were found in more than one chicken. We conclude that typing of Campylobacter strains is useful for identification of outbreaks but is probably not useful for source tracing and global epidemiology because of carriage of strains of multiple types and an extremely high diversity of strains in animals.

CRISPR — a widespread system that provides acquired resistance against phages in bacteria and archaea

“…This has become the standard method for genotyping of M. tuberculosis strains as part of ongoing efforts to control tuberculosis outbreaks 37,38 , and is also used for the typing of Corynebacterium diphtheriae 39 . Nonspoligotyping based methods for strain typing using CRISPR arrays are also used to study Campylobacter jejuni, Thermotoga neapolitana and other bacterial strains 40,41 , and Russell and colleagues recently filed a patent application on CRISPR-based methods to type Lactobacillus strains (US Patent application 20060199190).…”

Campylobacter sequence typing databases: applications and future prospects

“…The Campylobacter populations that infect broiler flocks can be complex, containing multiple genotypes, and flocks may be colonized by a succession of different genotypes over time (Bull et al, 2006;Colles et al, 2008bColles et al, , 2011aSchouls et al, 2003). Most information is available for broiler flocks which are slaughtered at a young age; however, a longitudinal study of a free-range broiler breeder flock over the course of a year indicated that Campylobacter populations naturally become more diverse as flocks age (Colles et al, 2011a).…”

Risk factors for infection withCampylobacter jejuni flaAgenotypes

“…In addition, a variety of methods have been used to compare animal and human isolates. Some studies have concluded that finding the same subtype in animal and human isolates is evidence of transmission from animals to humans or is evidence of a common source for animals and humans [17,[24][25][26][27][28]. However, the potential to identify genotypespecific risk factors for sporadic infection is yet to be evaluated.…”