Genotyping of Campylobacter spp. from retail meats by pulsed-field gel electrophoresis and ribotyping

Genotyping of Campylobacter jejuni Isolates from Poultry by Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)

Campylobacter jejuni is the leading bacterial foodborne pathogen that causes human acute gastrointestinal illness worldwide. Due to its genetic diversity, fastidious growth and sophisticated biochemical requirements, classification of Campylobacter by traditional techniques is problematic. Several molecular typing methods have been explored in this bacterium. One such method is to use clustered regularly interspaced short palindromic repeats (CRISPR). These CRISPRs consist of a direct repeat interspaced with nonrepetitive spacer sequences. In this study, we applied this genotyping method to explore the genetic diversity of C. jejuni isolated from poultry sources. Ninety-nine C. jejuni isolates from poultry environments in four different US states were used. Genomic DNA of the isolates were extracted from cultures using a commercial kit. PCR primers and conditions for CRISPR type 1 amplification were described previously. The amplicons were purified and sequenced by the Sanger dideoxy sequencing method. The direct repeats (DR) and spacers of the CRISPR sequences were identified using the CRISPRFinder. The results show there were 21% isolates no detectable, 30% isolates questionable, and 49% isolates confirmed CRISPR, respectively. The lengths of CRISPR range from 100 to 695 nucleotides. One type of DR was found in CRISPR of these isolates. The number of spacers in CRISPR ranges from 1 to 10 with various sequences. A total of 55 distinctive spacer sequences were identified in 78 isolates. Among them, 33 sequences were found unique in this study. In addition, the CRISPR genotyping had higher the Simpson's index of diversity value than that from flaA nucleotide typing. The results of our study show the CRISPR genotyping on C. jejuni may be complementary to the other genotyping methods.

Genetic diversity of Campylobacter jejuni and Campylobacter coli isolated from poultry meat products sold on the retail market in Southern Brazil

Campylobacter is regarded as the most common bacterial cause of gastroenteritis throughout the world and most cases of human campylobacteriosis can be traced back to the consumption of poultry meat. In Brazil, few studies evaluated the genetic relatedness among Campylobacter isolates. The aim of this research was to evaluate the genetic diversity of Campylobacter spp. isolated from poultry meat products sold on the retail market in Southern Brazil. The presumptive identification of Campylobacter was performed using traditional microbiological analysis, followed by molecular confirmation by PCR. The genetic diversity of isolates was analyzed by pulsed-field gel electrophoresis (PFGE). Campylobacter spp. was isolated from 91.7% (33/36) of the samples, totaling 48 isolates. Campylobacter jejuni was the most prevalent species isolated (90.8%). PFGE data revealed 26 pulsotypes and 18 PFGE patterns composed of only 1 isolate. Campylobacter isolates exhibited high genetic diversity; however, some clones were recurrent in the poultry meat products sold on the retail market. As the south region of Brazil is an important producer and exporter of chicken meat, our results highlight the need to control this pathogen in the food chain in this area of the world to reduce the risks of exposing consumers to campylobacteriosis.

Efficacy of a typing scheme for Campylobacter based on the combination of true and questionable CRISPR

This study evaluates an improved scheme for Campylobacter genotyping based on the combination of true and questionable CRISPR (clustered regularly interspaced short palindromic repeats) elements. A total of 180 Campylobacter strains (Campylobacter jejuni n=93 and Campylobacter coli n=87), isolated from neck skin and caecal content of broilers, poultry meat and sewage water were analysed. Another 97 C. jejuni DNA samples from cases of human campylobacteriosis were assessed. Sixty-three genotypes were found in C. jejuni considering only true CRISPR, and 16 additional genotypes were identified when questionable CRISPR were also taken into account. Likewise in C. coli the number of genotypes increased from eight for only true CRISPR to 14 after including questionable CRISPR elements. The number of typeable C. jejuni and C. coli isolates was 115 (60.5%) and 17 (19.5%) respectively considering only true CRISPR. These percentages increased to 92.7% (n=176) and 39.1% (n=34) respectively when both true and questionable CRISPR were considered. 60.9% of the C. coli isolates were non-typeable by CRISPR due to the lack of any PCR amplifiable CRISPR loci, which raises questions about CRISPR analysis as an appropriate method for C. coli typing. However the assessment of true and questionable CRISPR has proved to be fairly useful for typing C. jejuni due to its high discriminatory power (Simpson's index=0.960) and typeability (92.7%) values. The results of the present work show that our genotyping method based on the combination of true and questionable CRISPR elements may be used as a suitable complementary tool to existing C. jejuni genotyping methods.

Application of pulsed field gel electrophoresis to type Campylobacter jejuni

Pulsed field gel electrophoresis (PFGE) is generally accepted as one of the most discriminatory methods available for genotyping Campylobacter jejuni. PFGE has been extensively used in epidemiological studies, including outbreak investigation, persistence of genotypes in a human population, environmental diversity of sporadic infection isolates, dissemination of antibiotic-resistant strains, and comparison of genotypes within and between hosts. The main purpose of this chapter is to present a working PFGE protocol for those interested in incorporating this technique in their laboratories.

Genetic diversity and antibiotic resistance profiles of Campylobacter jejuni isolates from poultry and humans in Turkey

In this study, the investigation of clonal relations between human and poultry Campylobacter jejuni isolates and the determination of susceptibilities of isolates to various antibiotics were aimed. A total of 200 C. jejuni isolates concurrently obtained from 100 chicken carcasses and 100 humans were genotyped by the Pulsed-Field Gel Electrophoresis (PFGE) and automated Repetitive Extragenic Palindromic PCR (Rep-PCR, DiversiLab system) methods and were tested for their susceptibility to six antibiotics with disk diffusion method. The minimum inhibitory concentration (MIC) values of ciprofloxacin (CI), enrofloxacin (EF) and erythromycin (EM) were evaluated by E-test. By using PFGE 174 of (87.0%) the isolates were able to be typed. The clonally related strains were placed in 35 different clusters and 115 different genotypes were obtained. All of the two hundred isolates could be typed by using Rep-PCR and were divided into 133 different genotypes. One hundred and fourteen clonally related isolates (57.0%) were included in 47 clusters. In disk diffusion test, while the susceptibility rates of AMC and S to human and chicken derived C. jejuni isolates were 84.0%-96.0% and 96.0%-98.0%, respectively, all isolates were susceptible to gentamicin. The resistance rates of human isolates to AMP, NA and TE were detected as 44.0%, 84.0% and 38.0% of the resistances of chicken isolates to these antibiotics were 34.0%, 95.0% and 56.0%, respectively. The MIC values of human and chicken isolates to CI, EF and EM were detected as 81.0-93.0%, 85.0-88.0% and 6.0-7.0%, respectively. The clonal proximity rates were detected between human and poultry origin C. jejuni isolates. The discriminatory power of PFGE and Rep-PCR was similar, with Simpson's diversity indexes of 0.993 and 0.995, respectively. Concordance of the two methods as determined by Adjusted Rand coefficient was 0.198 which showed the low congruence between Rep-PCR and PFGE. High rates of quinolone resistance were detected in C. jejuni isolates. This study demonstrated that chicken meat played an important role for infections caused by C. jejuni in Turkey and erythromycin, amoxicillin clavulanic acid and gentamicin are recommended for the treatment of Campylobacteriosis in humans.

Campylobacter in small ruminants at slaughter: prevalence, pulsotypes and antibiotic resistance

The present study aimed to address the prevalence, pulsotypes, and antimicrobial susceptibility patterns of Campylobacter species present in sheep and goat carcasses at slaughter. In total, 851 samples were collected (343 meat surfaces, 282 ileum contents, 226 liver surfaces) and 835 Campylobacter isolates were detected in 274 out of 343 carcasses (116 kids, 110 lambs, 63 goats and 54 sheep). The contamination rates per carcass category were 78.4% for kids, 94.5% for lambs, 63.5% for goats, and 72.2% for sheep. On average, 30% of the intestinal content samples and more than 70% of carcass and liver surfaces yielded the presence of campylobacters. Multiplex-PCR and RFLP analysis identified Campylobacter coli as the most prevalent species (76.2%) followed by Campylobacter jejuni (21.4%), albeit 2.4% of selected colonies yielded the concurrent presence of both these species. Macrorestriction profiling by pulsed-field gel electrophoresis (PFGE) was applied in order to characterise a subset of isolates. SmaI-PFGE successfully clustered 222 isolates in 82 SmaI-PFGE types indicating high heterogeneity among the campylobacter isolates (67 types among 174C. coli isolates and 15 types among 48C. jejuni isolates). No carcass-type (lamb, kid, sheep, and goat) specific PFGE clusters were recognised since there was a general overlapping of PFGE patterns regarding ovine and caprine isolates. Multiple pulsotypes were simultaneously present on single carcasses in the majority of tested animals. PFGE provided data regarding the potential routes of meat and liver contamination such as spillage of faecal material and cross-contamination during slaughter. Antimicrobial susceptibility patterns of Campylobacter isolates (n=240), determined by disk diffusion method, revealed resistance to tetracycline (47.9%) followed by streptomycin (22.9%) and ciprofloxacin along with nalidixic acid (18.3%). Isolates exhibited low resistance to erythromycin (2.5%) and were susceptible to gentamicin. The findings of the present study confirm the contamination of sheep and goats at slaughter with thermophilic campylobacters and underline their potential input in the epidemiology of human campylobacteriosis.

Importance of the producer on retail broiler meat product contamination with Campylobacter spp

BACKGROUND

Campylobacter spp. are a leading cause of human bacterial gastroenteritis worldwide, with poultry meat being considered the most important source of the infection. To obtain data on broiler meat contamination with Campylobacter spp. in Lithuania, the occurrence, counts and genotypes of these pathogens on raw broiler meat products from different producers were examined.

RESULTS

Out of 312 broiler meat product samples examined, 46.8% were contaminated with Campylobacter spp. Campylobacter jejuni was identified in 51.4% and Campylobacter coli in 37.7% of positive samples. Campylobacter jejuni was more frequently found in the warm period (April-October) and C. coli in the cold period (November-March) of the year (P < 0.05). The overall mean count of Campylobacter spp. was 3.55 and 3.50 log10 colony-forming units (CFU) on wings and drumsticks respectively. The occurrence and counts of Campylobacter spp. varied significantly between producers examined (P < 0.05). Analysis of flaA-RFLP genotyping revealed C. jejuni genotypes common to all producers as well as producer-specific genotypes.

CONCLUSION

Both the occurrence and counts of Campylobacter spp. on broiler meat products were producer-dependent, so this should be kept in mind when risk-based control measures at national level are applied.

Tracing Campylobacter jejuni strains along the poultry meat production chain from farm to retail by pulsed-field gel electrophoresis, and the antimicrobial resistance of isolates

In this study Campylobacter jejuni isolates were recovered from birds, carcasses and carcass portions from two broiler chicken flocks and from equipment used for carcass and meat processing along the production chain from farms to retail stores. Isolates were subjected to pulsed-field gel electrophoresis (PFGE) using SmaI and KpnI restriction enzymes and their antimicrobial susceptibilities were determined. C. jejuni was recovered from product and equipment used with both flocks at each point in the production chain. The prevalence of C. jejuni in poultry products at retail stores was 58.97% (flock 1) and 69.23% (flock 2). SmaI divided 122 C. jejuni strains from flock 1 and 106 from flock 2 into 17 and 13 PFGE types, respectively. PFGE types H and F were present at all steps along the chain, from farms to retail products. Similarly, for both flocks PFGE type D was detected in crates, slaughterhouse and retail stores. Moreover, the PFGE types were highly diverse at the processing and retail steps. Most PFGE types were resistant to ciprofloxacin (95.45%) and tetracycline (81.82%); and multidrug resistant PFGE types were found in the final products. Our study showed that there were several points of cross-contamination of product along the chain, and a high diversity of PFGE types with antimicrobial resistance to ciprofloxacin and tetracycline in the retail products.

Antimicrobial resistance and molecular subtyping of Campylobacter jejuni and Campylobacter coli from retail meats

Campylobacter isolates (n = 297; 202 C. jejuni and 95 C. coli isolates) recovered from 2,513 retail meat samples (chicken breasts, ground turkey, ground beef, and pork chops) were examined for antimicrobial susceptibility. The isolates were further analyzed for genetic relatedness by pulsed-field gel electrophoresis (PFGE) using SmaI and KpnI restriction enzymes, and a subset of isolates (n = 174) were subtyped by multilocus sequence typing (MLST). The resistance most frequently observed was that to doxycycline (27.6%), followed by ciprofloxacin (13.8%) and erythromycin (6.4%). All isolates were susceptible to gentamicin and meropenem. C. coli showed higher resistance to doxycycline than did C. jejuni (42.1 versus 20.8%) and lower resistance to ciprofloxacin than did C. jejuni (10.5 versus 15.3%). Erythromycin resistance was only observed in C. coli. PFGE using SmaI plus KpnI digestion generated 168 clusters from 297 isolates: 115 from C. jejuni and 53 from C. coli. MLST revealed 44 sequence types (STs) under 10 clonal complexes from 120 C. jejuni and 27 STs under two clonal complexes from 54 C. coli. There was a positive association between PFGE and STs; however, PFGE showed greater discriminatory power than MLST. Subtyping data did not correlate with antimicrobial resistance phenotypes.

A pulsed-field gel electrophoresis study of the genetic diversity of Campylobacter jejuni and Campylobacter coli in poultry flocks in Slovenia

Campylobacter jejuni and C. coli have recently become the most frequent cause of bacterial foodborne enteric infection in most industrialised countries. Consumption and handling of undercooked contaminated poultry meat was identified as an important risk factor for human campylobacteriosis. The aim of this study was to ascertain the genetic diversity of C. jejuni and C. coli strains isolated from poultry in Slovenia. A total of 68 isolates (42 C. jejuni , 26 C. coli ) from faeces (n = 48), meat (n = 15) and skin/carcasses (n = 5) of chicken (n = 60) and turkey samples (n = 5) were analysed by pulsed-field gel electrophoresis. Sma I macrorestriction discriminated between C. jejuni and C. coli isolates. C. jejuni isolates exhibited a higher degree of diversity compared to C. coli isolates. In the C. jejuni group, a number of small clusters were apparent, while C. coli strains formed less but larger clusters. Additional Kpn I digestion of selected isolates resulted in poor subtyping. Strains with identical or very similar profiles were found on different farms, either in the same or different regions and time periods. Some of the clones indicated possible cross-contamination at slaughterhouses.

Similarity of Campylobacter coli from pigs, poultry and man

Campylobacteriosis is one of the most frequently occurring acute gastroenteritis in humans and 10% are caused by Campylobacter coli. A total of 136 isolates of C. coli from humans, poultry, and pigs were identified by multiplex polymerase chain reaction (PCR) and genetically characterized and compared by ribotyping. Automatic riboprints were performed with the PstI restriction enzyme and RiboPrinter. All poultry, pig and human strains represented a heterogeneous spectre of ribotypes. Ten of 23 human strains (43%) could be given DUP-ID from the library represented by DUP-PSTI-1200 (n = 7), DUP-PST1-1201 (n = 2) and DUP-PSTI-1211 (n = 1). Eighteen of 28 (64%) poultry strains were given a DUP-ID. Three isolates were closely related to human strains DUP-PSTI-1201 (n = 2) and DUP-PSTI-1200 (n = 1) and may play an important role in the epidemiology of campylobacteriosis. Nineteen of 85 pig isolates (23%) could be given a DUP-ID, but none were common to human isolates. An overlap was found among poultry and pig isolates with DUP-PSTI-1182 and DUP-PSTI-1140.

Clustering analysis of Salmonella enterica serovar Typhi isolates in Korea by PFGE, ribotying, and phage typing

Salmonella enterica serovar Typhi is a Gram-negative bacterium causing the acute febrile disease typhoid fever. In Korea from 2004 to 2006, a total of 51 Salmonella Typhi isolates were identified in stool and blood from healthy carriers and patients with or without overseas travel histories. In this study, antibiogram, pulsed-field gel electrophoresis (PFGE), and automated ribotyping were performed as molecular epidemiological methods with phage typing as a classical subtyping tool of the isolates. Only two isolates were multidrug resistant and 82.3% of the isolates were susceptible to 16 antimicrobial agents tested. When the dendrogram was created based on the PFGE results, the subtypes could be clustered into five groups by 80% similarity criterion. The PFGE patterns of 31 isolates (60.8%) belonged to Cluster 3, the predominant cluster in the study. Three overseas travel-associated cases were differentiated into Cluster 4 of which three isolates were nalidixic acid or multidrug resistant. Major phage type and ribotype were A and PvuII-436-8-S-6, respectively. This study also showed the prevalence of PFGE Cluster 3 in Korea by clustering analysis and the link between some typhoid cases and travel to Cambodia, India, or Indonesia.

Incidence and ecology of Campylobacter jejuni and coli in animals

Since its initial emergence in the 1970s, Campylobacter has become one of the most common causative agents of bacterial foodborne illness. Campylobacter species readily colonize the gastrointestinal tracts of domestic, feral and wild animals and while they rarely cause clinical disease in food animals, they can produce severe acute gastroenteritis in humans. Prevalence of Campylobacter in food animals can exceed 80% thus challenging processors to employ post-harvest pathogen reduction strategies. Reduction of pathogens before arrival to the abattoir is also of interest because the implementation of pre-harvest interventions may compliment existing post-harvest control techniques to further diminish possible retail sources of infection. Such multiple hurdle approaches that simultaneously utilize pre- and post-harvest control techniques are expected to be the most effective approach for decreasing human illness associated with foodborne pathogens.

Similarity of Campylobacter lari among human, animal, and water isolates in Norway

A total of 49 isolates of Campylobacter lari from human, poultry, ducks, pigs, and water were genetically characterized. The species were identified by biotyping and multiplex polymerase chain reaction (PCR). Automatic riboprints were performed with the PstI restriction enzyme and RiboPrinter. The identification of the isolates was predicted when the corresponding pattern matched one of the patterns of the DuPont identification (DUP-ID) library and was then assigned an identification number. Thirty-five (71.4%) of the isolates were given a DUP-ID number. The isolates from water and animals showed a high degree of similarity to the human strains represented by DUP-PST1-1010, DUP-PST1-1166, DUP-PST1-1178, and DUP-PST1-1081. Some profiles (i.e., DUP-PST1-2021 and DUP-PST1-1184) were found only among the human isolates. Dendrogram analysis using BioNumerics grouped isolates into three main clusters. One of those clusters contained DUP-PST1-2021, DUP-PST1-1184, and DUP-PST1-1081, which was found in both humans and ducks. A second cluster generated DUP-PST1-1010, found in both humans and poultry, and DUP-PST1-1079, found in water. The third cluster consisted of two strains, DUP-PST1-1066 and DUP-PST1-1078, originating in humans, animals, and water. Three human strains and two poultry strains were diverse and formed their own clusters and could not be assigned a DUP-ID number. Because of the similarity of C. lari isolated from humans, poultry, ducks, pigs, and water, as well as the limited knowledge of environmental survival and its virulence factors, special hygienic precautions should be taken to avoid the risk of transmitting Campylobacter.

Development of a strain-specific molecular method for quantitating individual campylobacter strains in mixed populations

The identification of sites resulting in cross-contamination of poultry flocks in the abattoir and determination of the survival and persistence of campylobacters at these sites are essential for the development of intervention strategies aimed at reducing the microbial burden on poultry at retail. A novel molecule-based method, using strain- and genus-specific oligonucleotide probes, was developed to detect and enumerate specific campylobacter strains in mixed populations. Strain-specific oligonucleotide probes were designed for the short variable regions (SVR) of the flaA gene in individual Campylobacter jejuni strains. A 16S rRNA Campylobacter genus-specific probe was also used. Both types of probes were used to investigate populations of campylobacters by colony lift hybridization. The specificity and proof of principle of the method were tested using strains with closely related SVR sequences and mixtures of these strains. Colony lifts of campylobacters were hybridized sequentially with up to two labeled strain-specific probes, followed by the generic 16S rRNA probe. SVR probes were highly specific, differentiating down to 1 nucleotide in the target sequence, and were sufficiently sensitive to detect colonies of a single strain in a mixed population. The 16S rRNA probe detected all Campylobacter spp. tested but not closely related species, such as Arcobacter skirrowi and Helicobacter pullorum. Preliminary field studies demonstrated the application of this technique to target strains isolated from poultry transport crate wash tank water. This method is quantitative, sensitive, and highly specific and allows the identification and enumeration of selected strains among all of the campylobacters in environmental samples.