Genotype and Antibiotic Resistance Analyses of Campylobacter Isolates from Ceca and Carcasses of Slaughtered Broiler Flocks

To obtain genetic information about Campylobacter jejuni and Campylobacter coli from broilers and carcasses at slaughterhouses, we analyzed and compared 340 isolates that were collected in 2008 from the cecum right after slaughter or from the neck skin after processing. We performed rpoB sequence-based identification, multilocus sequence typing (MLST), and flaB sequence-based typing; we additionally analyzed mutations within the 23S rRNA and gyrA genes that confer resistance to macrolide and quinolone antibiotics, respectively. The rpoB-based identification resulted in a distribution of 72.0% C. jejuni and 28.0% C. coli. The MLST analysis revealed that there were 59 known sequence types (STs) and 6 newly defined STs. Most of the STs were grouped into 4 clonal complexes (CC) that are typical for poultry (CC21, CC45, CC257, and CC828), and these represented 61.8% of all of the investigated isolates. The analysis of 95 isolates from the cecum and from the corresponding carcass neck skin covered 44 different STs, and 54.7% of the pairs had matching genotypes. The data indicate that cross-contamination from various sources during slaughter may occur, although the majority of Campylobacter contamination on carcasses appeared to originate from the slaughtered flock itself. Mutations in the 23S rRNA gene were found in 3.1% of C. coli isolates, although no mutations were found in C. jejuni isolates. Mutations in the gyrA gene were observed in 18.9% of C. jejuni and 26.8% of C. coli isolates, which included two C. coli strains that carried mutations conferring resistance to both classes of antibiotics. A relationship between specific genotypes and antibiotic resistance/susceptibility was observed.Campylobacteriosis is the leading food-borne bacterial gastroenteritis worldwide (12, 15). In Switzerland, the number of registered campylobacteriosis cases has rapidly increased to more than 100 per 100,000 inhabitants in the past few years (14), and this trend has also been observed in the European Union (EU) (12). However, the real number of cases is likely higher, because not all cases are reported due to the self-limiting nature of the disease and its potentially mild symptoms.Campylobacter jejuni and Campylobacter coli are commonly associated with human infection, and they can be detected in up to 85% and 15% of cases, respectively (33). Despite the important role that C. jejuni and C. coli play as zoonotic pathogens worldwide, there is little information regarding the route(s) of transmission (17). Numerous case-control and modeling studies on the infection sources of C. jejuni and C. coli have suggested that handling and consumption of contaminated poultry meat are associated with a risk of human campylobacteriosis (17, 45, 47, 49, 51). Initial meat contamination with C. jejuni or C. coli from the chicken intestine may occur during commonly used automated slaughter processing through several routes, such as the air, water, previously slaughtered flocks, or machinery (19, 36, 37).Precise genotyping and continuous comparison of the strains obtained from, e.g., the production site, flocks, slaughterhouse, retail meat, and infected humans would help to trace the source of infection and might indicate possible intervention strategies for the contaminated site.DNA sequence-based typing methods, such as multilocus sequence typing (MLST), are well suited for this purpose (28), and MLST has become the method of choice for genotyping of Campylobacter (6, 8). Moreover, extension of the classical MLST technique for C. jejuni and C. coli with sequencing of the short variable region (SVR) within the flagellin-encoding gene flaB allows a more precise differentiation among strains that have the same MLST sequence type (ST) (9, 29). An extended MLST work flow was recently developed that reduces the associated time and cost (24). In addition, the new approach allows genetic determination of antibiotic resistance to quinolones and macrolides. Resistance to these antibiotics is a worldwide issue of concern, as an increasing number of Campylobacter isolates are resistant to them. Strikingly, a number of strains are resistant to ciprofloxacin (a quinolone) and, to a lesser extent, erythromycin (a macrolide), which is problematic, because these drugs are typically used to treat campylobacteriosis. Resistance to quinolones is mainly associated with a point mutation in the DNA gyrase gene (gyrA) at position C257T, and a transition in the 23S rRNA gene at position A2075G is commonly responsible for macrolide resistance (1). Simple sequence-based analysis of these common mutational positions can therefore provide information about the antibiotic susceptibility or resistance of a strain. Besides the prudent use of antibiotics, knowledge about the genetic composition of the infectious agent can be helpful to both treat the disease and prevent the spread of resistant strains.In the current study, MLST, flaB typing, and sequence-based determination of quinolone and macrolide resistances were used to investigate the genetic background of C. jejuni and C. coli isolates collected from Swiss broilers in a spatiotemporal study in 2008. We addressed the following three aspects: (i) the diversity of Campylobacter isolates that were recovered from pooled cecum samples and the carcass neck skin, (ii) the possible impact of cross- and self-contamination during slaughter, and (iii) the antibiotic resistance of Campylobacter strains from the broiler flocks and chicken carcasses. All of the data, including the strain information and trace files, were entered into a commercial Web-based Campylobacter MLST database (SmartGene, Zug, Switzerland). This database allows users to retrieve and compare information for any analyzed strain for monitoring purposes (24).