Genomic relatedness within five common Finnish Campylobacter jejuni pulsed-field gel electrophoresis genotypes studied by amplified fragment length polymorphism analysis, ribotyping, and serotyping

Development of Multiple-Locus Variable-Number Tandem-Repeat Analysis for Molecular Subtyping of Campylobacter jejuni by Using Capillary Electrophoresis

Campylobacter jejuni is a common cause of the frequently reported food-borne diseases in developed and developing nations. This study describes the development of multiple-locus variable-number tandem-repeat (VNTR) analysis (MLVA) using capillary electrophoresis as a novel typing method for microbial source tracking and epidemiological investigation of C. jejuni. Among 36 tandem repeat loci detected by the Tandem Repeat Finder program, 7 VNTR loci were selected and used for characterizing 60 isolates recovered from chicken meat samples from retail shops, samples from chicken meat processing factory, and stool samples. The discrimination ability of MLVA was compared with that of multilocus sequence typing (MLST). MLVA (diversity index of 0.97 with 31 MLVA types) provided slightly higher discrimination than MLST (diversity index of 0.95 with 25 MLST types). The overall concordance between MLVA and MLST was estimated at 63% by adjusted Rand coefficient. MLVA predicted MLST type better than MLST predicted MLVA type, as reflected by Wallace coefficient (Wallace coefficient for MLVA to MLST versus MLST to MLVA, 86% versus 51%). MLVA is a useful tool and can be used for effective monitoring of C. jejuni and investigation of epidemics caused by C. jejuni.

Genome analysis of Campylobacter jejuni strains isolated from a waterborne outbreak

BACKGROUND

Waterborne Campylobacter jejuni outbreaks are common in the Nordic countries, and PFGE (pulsed field gel electrophoresis) remains the genotyping method of choice in outbreak investigations. However, PFGE cannot assess the clonal relationship between isolates, leading to difficulties in molecular epidemiological investigations. Here, we explored the applicability of whole genome sequencing to outbreak investigation by re-analysing three C. jejuni strains (one isolated from water and two from patients) from an earlier resolved Finnish waterborne outbreak from the year 2000.

RESULTS

One of the patient strains had the same PFGE profile, as well as an identical overall gene synteny and three polymorphisms in comparison with the water strain. However, the other patient isolate, which showed only minor differences in the PFGE pattern relative to the water strain, harboured several polymorphisms as well as rearrangements in the integrated element CJIE2. We reconstructed the genealogy of these strains with ClonalFrame including in the analysis four C. jejuni isolated from chicken in 2012 having the same PFGE profile and sequence type as the outbreak strains. The three outbreak strains exhibited a paraphyletic relationship, implying that the drinking water from 2000 was probably contaminated with at least two different, but related, C. jejuni strains.

CONCLUSIONS

Our results emphasize the capability of whole genome sequencing to unambiguously resolve the clonal relationship between isolates of C. jejuni in an outbreak situation and evaluate the diversity of the C. jejuni population.

Arcobacter species and their pulsed-field gel electrophoresis genotypes in Finnish raw milk during summer 2011

The aim of this study was to investigate the occurrence of Arcobacter species in raw milk in Finland. A total of 177 raw milk samples, each from a separate farm, were examined from June to August 2011. Arcobacter species were isolated using an enrichment and selective detection procedure. Overall, 26 (15 % ) of the 177 samples yielded Arcobacter spp. Samples from 25 farms were positive for Arcobacter butzleri and from 1 farm for Arcobacter cryaerophilus. Moreover, both Arcobacter butzleri and A. cryaerophilus were recovered from 1 positive sample. To evaluate a possible genetic variability, one strain of A. butzleri from each farm and the A. cryaerophilus sample were analyzed by pulsed-field gel electrophoresis. Genotyping revealed that Arcobacter spp. populations are heterogeneous, and no dominant clone has spread in the investigated samples. Our study is the first report on the isolation of both A. butzleri and A. cryaerophilus in raw milk in Finland. Based on our findings, the presence of Arcobacter species in raw milk may pose a potential hazard for human health, in particular for consumers who prefer drinking unpasteurized milk.

Genetic heterogeneity of Campylobacter jejuni NCTC 11168 upon human infection

Campylobacter jejuni NCTC 11168 variants before and after accidental human infection were sequenced with Illumina technology and mapped against the isogenic reference genome applying the Breseq pipeline. Only the frequencies of length variations of homopolymeric tracts in the contingency genes Cj0045c, Cj0456c, Cj1139c, Cj1145c, and Cj1306c and a deletion in Cj0184c were significantly different after human passage (p<0.01). Our results highlight differences in the selection of C. jejuni variants after human infection compared with those observed in animal models, emphasizing the genetic diversity of C. jejuni NCTC 11168 and the possible role of the host in the selection of bacterial determinants that might be involved in the adaptation and disease development.

Finnish Campylobacter jejuni strains of multilocus sequence type ST-22 complex have two lineages with different characteristics

BACKGROUND

Campylobacter jejuni is the major cause of human bacterial gastroenteritis worldwide, and in a minority of cases, post-infectious complications may occur. ST-22 complex (usually Penner serotype 19) strains have been overrepresented among patients with postinfectious complications of campylobacteriosis. We here present a characterization of a collection of 27 Finnish C. jejuni strains of ST-22 complex, from humans (22 strains) and animal sources (five strains), with the aim of contributing to our knowledge of the pathogenesis of C. jejuni infections.

METHODOLOGY/PRINCIPAL FINDINGS

All strains were analyzed by pulsed-field gel electrophoresis (PFGE) genotyping, lipo-oligosaccharide (LOS) locus class, Y-glutamyl transpeptidase (GGT) activity, in vitro biofilm formation ability, invasion and adhesion in HeLa cells and induction of IL-8 production. ST-22 complex contained five STs (ST-22; ST-1947; ST-1966; ST-3892; ST-3996) which were homogeneous in having sialylated LOS class A(1) but on the other hand were distinguished into two major lineages according to the major STs (ST-22 and ST-1947) by different PFGE genotypes and certain other characteristics. All ST-22 strains had similar SmaI PFGE profiles, were GGT positive, and formed biofilms, except one strain, while ST-1947 strains were all GGT negative, did not form biofilm, had significantly higher motility than ST-22 (p<0.05) and had their SmaI PFGE profile. Invasion and adhesion as well as induction of IL-8 production on HeLa cells were strain-dependent characteristics.

CONCLUSIONS/SIGNIFICANCE

ST-22 complex strains, reveal potential for molecular mimicry in host interactions upon infection as they all express sialylated LOS class A(1). The two major STs, ST-22 and ST-1947 formed two homogeneous lineages, which differed from each other both phenotypically and genetically, suggesting that the strains may have evolved separately, perhaps by interacting with different spectra of hosts. Further studies are needed in order to understand if these two lineages are associated with different disease outcomes.

Genotypic and phenotypic properties of Candida parapsilosis sensu strictu strains isolated from different geographic regions and body sites

BACKGROUND

Candida parapsilosis is known to show limited genetic variability, despite different karyotypes and phenotypes have been described. To further investigate this aspect, a collection of 62 sensu strictu C. parapsilosis independent isolates from 4 geographic regions (Italy, n = 19; New Zealand, n = 15; Argentina, n = 14; and Hungary, n = 14) and different body sites (superficial and deep seated) were analysed for their genetic and phenotypic traits. Amplification fragment length polymorphism (AFLP) analysis was used to confirm species identification and to evaluate intraspecific genetic variability. Phenotypic characterisation included clinically relevant traits, such as drug susceptibility, in vitro biofilm formation and aspartyl protease secretion.

RESULTS

AFLP genotyping showed little variation among isolates, when the presence/absence of bands was considered. However, when AFLP profiles were compared by relative intensity for each fragment, a significant level of variation and geographical clustering was observed. All isolates were found to be susceptible to commonly used antifungals, although a reduced susceptibility to echinocandins was observed in all isolates. C. parapsilosis isolates from different geographic origins varied in the number of biofilm producers, with a higher prevalence of producers isolated in Hungary and Argentina. The frequency of secreted proteinase producers also varied in isolates obtained from different areas, with a higher number of proteinase producers found in Italy and New Zealand. Interestingly, biofilm production and proteinase secretion were negatively correlated. This finding could be explained by assuming that proteinase activity plays a role in detachment and release from a mature biofilm, via degradation of C. parapsilosis adhesins and/or extracellular matrix components, as observed for other microorganisms.

CONCLUSIONS

The low number of polymorphic AFLP bands (18 out of 80) obtained for C. parapsilosis isolates is in agreement with the limited sequence variability described for this species. However, when band intensity was included in the analysis, geographical clustering was observed. Expression of virulence factors varied among strains isolated from different geographical regions, with biofilm and proteinase producers more frequently isolated from Hungary and Italy, respectively.

Comparative genotyping of Campylobacter jejuni strains from patients with Guillain-Barré syndrome in Bangladesh

BACKGROUND

Campylobacter jejuni is a common cause of acute gastroenteritis and is associated with post-infectious neuropathies such as the Guillain-Barré syndrome (GBS) and the Miller Fisher syndrome (MFS). We here present comparative genotyping of 49 C. jejuni strains from Bangladesh that were recovered from patients with enteritis or GBS. All strains were serotyped and analyzed by lipo-oligosaccharide (LOS) genotyping, amplified fragment length polymorphism (AFLP) analysis, multilocus sequence typing (MLST), and pulsed-field gel electrophoresis (PFGE).

METHODOLOGY/PRINCIPAL FINDINGS

C. jejuni HS:23 was a predominant serotype among GBS patients (50%), and no specific serotype was significantly associated with GBS compared to enteritis. PCR screening showed that 38/49 (78%) of strains could be assigned to LOS classes A, B, C, or E. The class A locus (4/7 vs 3/39; p<0.01) was significantly associated in the GBS-related strains as compared to enteritis strains. All GBS/oculomotor related strains contained the class B locus; which was also detected in 46% of control strains. Overlapping clonal groups were defined by MLST, AFLP and PFGE for strains from patients with gastroenteritis and GBS. MLST defined 22 sequence types (STs) and 7 clonal complexes including 7 STs not previously identified (ST-3742, ST-3741, ST-3743, ST-3748, ST-3968, ST-3969 and ST-3970). C. jejuni HS:23 strains from patients with GBS or enteritis were clonal and all strains belonged to ST-403 complex. Concordance between LOS class B and ST-403 complex was revealed. AFLP defined 25 different types at 90% similarity. The predominant AFLP type AF-20 coincided with the C. jejuni HS:23 and ST-403 complex.

CONCLUSION/SIGNIFICANCE

LOS genotyping, MLST, AFLP and PFGE helped to identify the HS:23 strains from GBS or enteritis patients as clonal. Overall, genotypes exclusive for enteritis or for GBS-related strains were not obtained although LOS class A was significantly associated with GBS strains. Particularly, the presence of a clonal and putative neuropathogenic C. jejuni HS:23 serotype may contribute to the high prevalence of C. jejuni related GBS in Bangladesh.

Characterization of genetically matched isolates of Campylobacter jejuni reveals that mutations in genes involved in flagellar biosynthesis alter the organism's virulence potential

Phenotypic and genotypic evidence suggests that not all Campylobacter jejuni isolates are pathogenic for humans. We hypothesized that differences in gene content or gene expression alter the degree of pathogenicity of C. jejuni isolates. A C. jejuni isolate (Turkey) recovered from a turkey and a second C. jejuni isolate (CS) recovered from a chicken differed in their degrees of in vitro and in vivo virulence. The C. jejuni Turkey isolate invaded INT 407 human epithelial cells and secreted the Cia (Campylobacter invasion antigen) proteins, while the C. jejuni CS isolate was noninvasive for human epithelial cells and did not secrete the Cia proteins. Newborn piglets inoculated with the C. jejuni Turkey isolate developed more severe clinical signs of campylobacteriosis than piglets inoculated with the C. jejuni CS isolate. Additional work revealed that flagellin was not expressed in the C. jejuni CS isolate. Microarray and real-time reverse transcription-PCR analyses revealed that all flagellar class II genes were significantly downregulated in the C. jejuni CS isolate compared to the C. jejuni Turkey isolate. Finally, nucleotide sequencing of the flgR gene revealed the presence of a single residue that was different in the FlgR proteins of the C. jejuni Turkey and CS isolates. Complementation of the C. jejuni CS isolate with a wild-type copy of the flgR gene restored the isolate's motility. Collectively, these findings support the hypothesis that critical differences in gene content or gene expression can alter the pathogenic potential of C. jejuni isolates.

Predominant strains of thermophilic Campylobacter spp. in a German poultry slaughterhouse

Campylobacter causes bacterial diarrhoea in man and is a common foodborne pathogen, that has been associated mainly with poultry carcasses and processed poultry products as well as with drinking water. Genotyping of Campylobacter spp. from poultry was done in order to prove if predominant stable strains in the food chain are present. The influence of the slaughter process on the stability should be determined. Thermophilic Campylobacter spp. from eight poultry flocks were isolated from cloacal swabs, carcasses and offal at different abattoir processing steps to determine their stability. DNA-fingerprinting was done using Pulsed-Field Gel Electrophoresis (PFGE) with two enzymes (SmaI and KpnI) and ribotyping. More than 150 Campylobacter strains were ribotyped and these data were combined with the results of PFGE. Molecular typing showed that strains found in cloacal swabs before processing could also be isolated from carcasses and offal at different processing steps representing predominating stable strains. Strains with varying molecular pattern could additionally be detected at different processing steps. Both genotyping methods identified in agreement flock-specific strains. These remained stable through the slaughter of poultry and were not altered through the slaughter process. Despite the known genetic variability of thermophilic Campylobacter, stable predominant strains could be identified in the poultry slaughter process and those strains can thus enter the food chain.

High level of ciprofloxacin resistance and its molecular background among Campylobacter jejuni strains isolated in the United Arab Emirates

The antibiotic sensitivity and the serotype and molecular type (MT) distribution of 41 Campylobacter jejuni strains isolated from individual patients in Tawam Hospital, Al Ain, United Arab Emirates, were investigated. While all strains were sensitive to erythromycin (MIC 0.5-4 mg l(-1)), 35 isolates (85.4 %) exhibited resistance to ciprofloxacin (MIC 8-64 mg l(-1)). All resistant strains carried the Thr-86 to Ile mutation in the gyrase A (gyrA) gene, as shown by mismatch amplification mutation assay (MAMA) and confirmed by sequencing. Based on the partial sequences of gyrA, resistant isolates carried 10 distinct alleles, eight of them representing new variants. Strains were assigned to 30 MTs based on the combined results of PFGE and flaA PCR-RFLP typing. Eight of the 35 ciprofloxacin-resistant strains, isolated over a period of more than 1 year, represented the largest MT, also carrying the same allelic variant of the gyrA gene. These results show that the local incidence of fluoroquinolone resistance among C. jejuni is one of the highest reported worldwide. It was also demonstrated that stable MTs could persist for a relatively long time among the clonally unrelated antibiotic-resistant isolates of C. jejuni. The data also emphasize the need to replace fluoroquinolones as empirical therapy for diarrhoea of undiagnosed aetiology.

Genetic variability of Campylobacter jejuni isolated from fresh and frozen broiler carcasses

AIMS

The aim of this study was to determine the genetic variability of Campylobacter jejuni isolates from poultry before and after freezing treatment in order to identify genotypes that would survive the treatment.

METHODS AND RESULTS

C. jejuni was isolated from both fresh and frozen halves of the same carcass after freezing for 2 or more than 20 days at -20 degrees C. From 36 carcasses, representing five unrelated flocks in Norway, a total of 209 isolates were included in the study. Thirty-two of the isolates were recovered with a qualitative method while the remaining 177 were isolated using a quantitative method. Isolates were genotyped with fluorescent amplified fragment length polymorphism using MfeI and BglII restriction enzymes. Nine different genotypes were identified, however, one genotype was shown to be dominant in three different flocks. This genotype and the dominant genotype of another flock were found among isolates from fresh and frozen broiler halves. They were also shown to be identical to genotypes frequently identified among strains isolated from humans, cattle and poultry flocks in previous years.

CONCLUSIONS

Freezing treatment or isolation method appeared not to select for a particular genotype.

SIGNIFICANCE AND IMPACT OF THE STUDY

The results of the present study indicate that the freezing tolerance of strains is not genotype dependent.

Stress Response of Campylobacter spp. and its Role in Food Processing

In many temperate countries Campylobacter spp. are the most common bacterial causes of human infectious intestinal disease. Yet the aetiology of this infection has only partly been described. A majority of human campylobacteriosis cases are associated with food of animal origin. Despite being very sensitive to environmental stressors Campylobacter spp. are able to persist in the food chain and can pose a threat to the consumer. In this review, the survival potential and stress response of Campylobacter spp. in food will be summarized and the importance of food preservation technologies will be discussed.

PCR-based restriction fragment length polymorphism (RFLP) analysis of Campylobacter jejuni isolates from humans, chickens and dogs in northern Taiwan

Two hundred and twenty strains of Campylobacter jejuni (70 human, 51 canine and 99 chicken strains) were isolated from September 2003 to September 2004 in northern Taiwan. These strains were subtyped by PCR-RFLP analysis of the flagellin (FlaA) gene. On the basis of restrictive digest, six types were identified with AfaI, seven types with MboI and five types with HaeIII. With the combination of these three enzymes, 47 distinct PCR-RFLP patterns were observed-25 each from human and chicken isolates, and 9 from canine isolates. In human strains, the most frequently occurring types were Cj-28 (14.3%), Cj-17 (10%), Cj-16 (8.6%), Cj-37 (7.1%) and Cj-46 (7.1%). In canine strains, the most prevalent types were Cj-1 (33.3%), Cj-26 (19.6%), Cj-3 (15.7%), Cj-2 (9.8%) and Cj-10 (9.8%). In chicken strains, the most frequently occurring types were Cj-46 (40.4%), Cj-29 (9.1%), Cj-45 (7.1%) and Cj-41 (5.1%). The results suggest that poultry is a source, but not the sole source, of C. jejuni infection in humans. Two RFLP types, Cj-17 and Cj-37, frequently occurring in human isolates in this study have also been found to be prevalent in human isolates in Japan, China and the Czech Republic, indicating a possible international clonal spread.

Heterogeneity of non-serotypable Campylobacter jejuni isolates

Several phenotypic and genotypic methods are currently used to identify subtypes of Campylobacter jejuni isolates. Of the phenotypic methods one, i.e. serotyping based on the heat stable antigen, is often hindered by the relatively large number of un-typable (NT) strains. Little is known, however, about the heterogeneity of the group formed by these NT strains. Therefore we serotyped 92 Hungarian, non-outbreak C. jejuni isolates and subjected the 28 NT strains to molecular analysis using PCR-RFLP of the flaA gene and to pulsed-field gel electrophoresis. With both methods the NT strains were classified into several molecular types (17 and 25, respectively), while the number of subgroups based on the results of the two techniques combined was twenty-six. These results indicate that the NT group of strains is extremely heterogeneous in Hungary, and the epidemiological connection between two NT isolates cannot be established or excluded without the use of molecular typing techniques.

Amplified fragment length polymorphism, serotyping, and quinolone resistance of Campylobacter jejuni and Campylobacter coli strains from chicken-related samples and humans in Taiwan

The high-resolution genotyping method of amplified fragment length polymorphism (AFLP) analysis was used to study the genetic relationships between Campylobacter jejuni isolates from chicken-related samples (n = 32) and humans (n = 27) as well as between Campylobacter coli isolates from chicken-related samples (n = 27) and humans (n = 5). These isolates were collected between 1994 and 2003 in Taiwan. All C. jejuni and C. coli isolates showed highly heterogeneous fingerprints. C. jejuni isolates were separated in two distinct genetic clusters (A and B) at 40% genetic similarity and 42 different AFLP types at 90% similarity. However, three clusters at 40% genetic similarity and 33 different AFLP types at 90% similarity were observed in C. coli isolates. These results showed that AFLP analysis could be used to identify individual isolates of two Campylobacter species. Among C. jejuni isolates, the predominant AFLP type 1 was observed in five (7.9%) isolates, and types 5 and 12 in four (6.3%) isolates each. Cluster B consisted of 10 isolates, while the majority of isolates (n = 53) belonged to cluster A. In some AFLP types (1, 5, 12, 14 and 31), AFLP fingerprints of chicken-related isolates were closely related genetically to those of isolates from humans with gastroenteritis. The predominant serotypes in C. jejuni isolates were B:2 and Y:37. All isolates belonging to serotype O:19 grouped into one single AFLP type. Some chicken samples yielded multiple isolates of Campylobacter harboring simultaneously quinolone-resistant and quinolone-sensitive isolates attributed to the same species, or harboring C. jejuni and C. coli that have the characteristics of quinolone resistance.

Genetic profiling of Campylobacter jejuni strains from humans infected in Sweden or in Thailand, and from healthy Swedish chickens, studied by pulsed-field gel electrophoresis (PFGE)

The major objective of the study was to explore the genomic diversity between Campylobacter jejuni (C.jejuni) from different sources as a tool for epidemiological considerations. Subtyping was performed using pulsed-field gel electrophoresis (PFGE) and the enzyme used for cleavage was SmaI. Isolates originated from humans infected in Sweden (n=49) and Thailand (n=32) and from healthy Swedish chickens (n=51). Eight PFGE groups were formed in a dendrogram and 48% of the isolates belonged to 1 of these groups. In 2 PFGE groups, strains from humans infected in both Sweden and Thailand were represented. Four of the PFGE groups comprised high frequencies of strains from domestic human infection, as well as from healthy chickens. The PFGE pattern was also compared with the antibiotic resistance pattern in all the above-mentioned isolates. In conclusion, C.jejuni was a diverse group based on PFGE genotyping; about 24% of the clones from Swedish patients and healthy Swedish chickens were similar; and there was no correlation between the antibiotic resistance pattern and the PFGE profiling among the studied strains. Our findings are also in accordance with our hypothesis that there may be similarities between Swedish and Thai strains, which might support a theory of globally occurring C.jejuni.

Use of the oxford multilocus sequence typing protocol and sequencing of the flagellin short variable region to characterize isolates from a large outbreak of waterborne Campylobacter sp. strains in Walkerton, Ontario, Canada

The Walkerton (Ontario, Canada) outbreak of waterborne Escherichia coli O157:H7 and Campylobacter jejuni was quite limited in both space and time, making it a good model for exploring the utility of different typing and subtyping methods for the characterization of relationships among isolates of these organisms. We have extended previous work with these organisms through analysis by the Oxford multilocus sequence typing (MLST) and the flagellin short variable region (fla-SVR) sequencing methods. Additional isolates not epidemiologically related to the Walkerton outbreak have also been included. Both sequencing methods identified and differentiated between Walkerton outbreak strains 1 and 2. When these strains were compared with isolates that were not part of the outbreak, the information produced by the fla-SVR method more often correlated with epidemiological findings than that produced by MLST, though both methods were required for optimal discrimination. The MLST data were more relevant in terms of the overall population structure of the organisms. Both mutation and recombination appeared to be responsible for generating diversity among the isolates tested.

Swimming and Campylobacter infections

A matched case-control study was conducted to study risk factors for domestically acquired sporadic Campylobacter infections in Finland. Swimming in natural sources of water was a novel risk factor. Eating undercooked meat and drinking dug-well water were also independent risk factors for Campylobacter infection.

Application of molecular genetic methods in diagnostics and epidemiology of food-borne bacterial pathogens

Salmonella enterica, Campylobacter and Yersinia species, Shiga toxin-producing Escherichia coli (STEC), Listeria monocytogenes and Clostridium perfringens are the bacterial pathogens constituting the greatest burden of food-borne disease in Finland. Several molecular genetic methods have been applied to diagnose, discriminate and survey these bacteria. PCR, PCR-RFLP and PFGE are the most widely and successfully used. However, these methods are unable to replace conventional and internationally standardised phenotyping. Electronic database libraries of the different genomic profiles will enable continuous surveillance of infections and detection of possible infection clusters at an early stage. Furthermore, whole-genome sequence data have opened up new insights into epidemiological surveillance. Laboratory-based surveillance performed in a timely manner and exploiting adequate methods, and co-operation at local, national and international levels are among the key elements in preventing food-borne diseases. This paper reviews different applications of molecular genetic methods for investigating enteric bacterial pathogens and gives examples of the methods successfully used in diagnostics and epidemiological studies in Finland.

Longitudinal study of Campylobacter jejuni bacteriophages and their hosts from broiler chickens

A longitudinal study of bacteriophages and their hosts was carried out at a broiler house that had been identified as having a population of Campylobacter-specific bacteriophages. Cloacal and excreta samples were collected from three successive broiler flocks reared in the same barn. Campylobacter jejuni was isolated from each flock, whereas bacteriophages could be isolated from flocks 1 and 2 but were not isolated from flock 3. The bacteriophages isolated from flocks 1 and 2 were closely related to each other in terms of host range, morphology, genome size, and genetic content. All Campylobacter isolates from flock 1 were genotypically indistinguishable by pulsed-field gel electrophoresis (PFGE). PFGE and multilocus sequence typing indicated that this C. jejuni type was maintained from flock 1 to flock 2 but was largely superseded by three genetically distinct C. jejuni types insensitive to the resident bacteriophages. All isolates from the third batch of birds were insensitive to bacteriophages and genotypically distinct. These results are significant because this is the first study of an environmental population of C. jejuni bacteriophages and their influence on the Campylobacter populations of broiler house chickens. The role of developing bacteriophage resistance was investigated as this is a possible obstacle to the use of bacteriophage therapy to reduce the numbers of campylobacters in chickens. In this broiler house succession was largely due to incursion of new genotypes rather than to de novo development of resistance.

An outbreak of gastroenteritis from a non-chlorinated community water supply

STUDY OBJECTIVE

To determine the source and the extent of a community wide outbreak of gastroenteritis.

DESIGN

A matched case-control study with postal questionnaires. Subtyping of campylobacter strains by pulsed field gel electrophoresis (PFGE).

SETTING

A rural municipality with a population of 8600 in southern Finland, August 2000. Two thirds of the population receive non-chlorinated ground water from the municipal water supply.

PARTICIPANTS

Cases were randomly selected among residents of the municipality who contacted the municipal health centre because of gastroenteritis and had illness onset between 31 July and 20 August 2000. Community controls were identified from the population registry and matched according to sex, year of birth, and postal code.

MAIN RESULTS

Four hundred and sixty three persons contacted the municipal health centre because of gastroenteritis. Campylobacter jejuni was isolated from stool samples of 24 persons. One hundred and thirty seven cases and 388 controls were enrolled in the case-control study. In multivariate analysis, drinking unboiled water from the municipal supply was significantly associated with illness (odds ratio 11.1, 95% confidence interval 1.4 to 90.2). C jejuni was isolated from one tap water sample. The water isolate and all but one of the patient isolates were indistinguishable by PFGE.

CONCLUSIONS

Combining epidemiological investigation with molecular subtyping methods provided strong evidence that water was the source of the outbreak. Non-chlorinated small ground water systems may be susceptible to waterborne outbreaks and constitute a risk to rural populations.

Ribotyping characterisation of campylobacter isolates randomly collected from different sources in Italy

In this study the potential for using the automated PstI ribotyping as a primary library typing method to survey Campylobacter and for identification of two thermophilic Campylobacter jejuni and Campylobacter coli species was evaluated. A total of 158 isolates randomly collected in Italy from different sources were analyzed. A large percentage of chicken (28%), turkey (27%) and turkey meat (25%) isolates shared their ribotyping profiles (ribotypes) with those of humans, whereas the swine isolates had unique profiles. The identification results obtained by ribotyping corresponded to those collected by using a multiplex PCR protocol specifically designed for C. jejuni and C. coli detection. The comparison of the PstI ribotyping profiles obtained in this research with those of the isolates collected over time will facilitate determining the ribotypes that are more frequently transmitted to humans in comparison to those that are normally harboured only in animals, foods and in the environment.

Molecular epidemiology in the public health and hospital environments

The increasing speed and ease of genomic sequencing coupled with available funding to sequence multiple, unrelated strains of the same species will lead inevitably to the identification of candidate genes that can be used as molecular typing tools (MLST, SLST, microarray approach). However, it is important to note that even the most sophisticated typing tool should never replace a full epidemiologic investigation in which all available information is taken into account. Nevertheless, the typing methods discussed in this article and those yet to be developed have significantly improved the quality of health care worldwide.

Effect of incubation temperature on isolation of Campylobacter jejuni genotypes from foodstuffs enriched in Preston broth

Preston broth and agar incubated at either 37 or 42 degrees C have been widely used to isolate campylobacters from foodstuffs. The consequences of using either incubation temperature were investigated. Retail packs of raw chicken (n = 24) and raw lamb liver (n = 30) were purchased. Samples were incubated in Preston broth at 37 and 42 degrees C and then streaked onto Preston agar and incubated as before. Two Campylobacter isolates per treatment were characterized. Poultry isolates were genotyped by random amplification of polymorphic DNA (RAPD), pulsed-field gel electrophoresis (PFGE), and flagellin PCR-restriction fragment length polymorphism, and lamb isolates were genotyped by RAPD only. In total, 96% of the poultry and 73% of the lamb samples yielded campylobacters. The lamb isolates were all Campylobacter jejuni, as were 96% of the poultry isolates, with the remainder being Campylobacter lari. The incubation temperature had no significant effect on the number of positive samples or on the species isolated. However, genotyping of the C. jejuni isolates revealed profound differences in the types obtained. Overall (from poultry and lamb), the use of a single incubation temperature, 37 degrees C, gave 56% of the total number of RAPD C. jejuni genotypes, and hence, 44% remained undetected. The effect was especially marked in the poultry samples, where incubation at 37 degrees C gave 47% of the PFGE genotypes but 53% were exclusively recovered after incubation at 42 degrees C. Thus, the incubation temperature of Preston media selects for certain genotypes of C. jejuni, and to detect the widest range, samples should be incubated at both 37 and 42 degrees C. Conversely, genotyping results arising from the use of a single incubation temperature should be interpreted with caution.

Comparison of eight phenotypic methods for subspecies characterization of thermophilic Campylobacter spp. isolated from pig liver

Four hundred pork livers from bacon pigs (37 herds) obtained at six pig-processing plants were studied to assess the Campylobacter contamination rate. Deep tissue areas were sampled immediately after evisceration. Approximately 6% of livers were infected with Campylobacter spp., including Campylobacter coli (67%), Campylobacter jejuni (30%), and Campylobacter lari (3%). The 60 resulting isolates (39 C. coli isolates, 19 C. jejuni isolates, and 2 C. lari isolates) employed in this study were characterized at the subspecies level in a comparison of eight phenotyping schemes, including four biotyping, two serotyping, and two phage-typing schemes. The Skirrow-Benjamin biotyping scheme produced two biotypes for C. jejuni, i.e., biotype 2 (95%) and biotype 1 (5%). The Lior biotyping scheme subdivided C. coli into biotype 1 (41%) and biotype 2 (59%), while biotype 4 was the dominant type (95%) for C. jejuni. The Roop scheme allowed further differentiation of C. coli into three biovars, i.e., biovar 1 (57%), biovar 2 (40%), and biovar 3 (3%), and it subdivided C. jejuni into two biotypes, i.e., biovar 1 (95%) and biovar 2 (5%). Preston biotyping produced the largest degree of subspecies differentiation, with 18 C. coli biotypes and 7 C. jejuni biotypes being identified. The most common were biotypes 2650 and 6030, representing 18 and 42% of all C. coli and C. jejuni isolates, respectively. The Penner-Hennessy serotyping scheme successfully serotyped 89% of the isolates, with 10 serotypes being identified; 30% of the serotypeable isolates were accounted for by Penner 23, followed by Penner 20 (16%) and Penner 39 (14%). The Lior serotyping scheme successfully serotyped only 45% of the strains, and eight serogroups were identified, with Lior 36 (31%), Lior 20 (23%), and Lior 5 being the most frequent. The Preston scheme and the Khakhria-Lior phage-typing scheme were able to type 16 and 25% of the isolates, respectively. The Preston scheme produced three phage groups, i.e., 69 (56%), 90 (22%), and 116 (22%), and the Khakhria-Lior scheme also produced three phage types, i.e., 44 (40%), 27 (33%), and 37 (20%), as well as atypical lysis patterns (7%). The results of this study demonstrate the role of Preston biotyping in the phenotyping of isolates, particularly in diagnostic laboratories that have no access or limited access to molecular typing equipment.

Detection and typing of Campylobacter jejuni and Campylobacter coli and analysis of indicator organisms in three waterborne outbreaks in Finland

Waterborne outbreaks associated with contamination of drinking water by Campylobacter jejuni are rather common in the Nordic countries Sweden, Norway, and Finland, where in sparsely populated districts groundwater is commonly used without disinfection. Campylobacters, Escherichia coli, or other coliforms have rarely been detected in potential sources. We studied three waterborne outbreaks in Finland caused by C. jejuni and used sample volumes of 4,000 to 20,000 ml for analysis of campylobacters and sample volumes of 1 to 5,000 ml for analysis of coliforms and E. coli, depending on the sampling site. Multiple samples obtained from possible sources (water distribution systems and environmental water sources) and the use of large sample volumes (several liters) increased the chance of detecting the pathogen C. jejuni in water. Filtration of a large volume (1,000 to 2,000 ml) also increased the rate of detection of coliforms and E. coli. To confirm the association between drinking water contamination and illness, a combination of Penner serotyping and pulsed-field gel electrophoresis (digestion with SmaI and KpnI) was found to be useful. This combination reliably verified similarity or dissimilarity of C. jejuni isolates from patient samples, from drinking water, and from other environmental sources, thus confirming the likely reservoir of an outbreak.

Comparative genotyping of Campylobacter jejuni by amplified fragment length polymorphism, multilocus sequence typing, and short repeat sequencing: strain diversity, host range, and recombination

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.

Combined use of two genetic fingerprinting methods, pulsed-field gel electrophoresis and ribotyping, for characterization of Escherichia coli O157 isolates from food animals, retail meats, and cases of human disease

Two genetic fingerprinting techniques, pulsed-field gel electrophoresis (PFGE) and ribotyping, were used to characterize 207 Escherichia coli O157 isolates from food animals, foods of animal origin, and cases of human disease (206 of the isolates were from the United Kingdom). In addition, 164 of these isolates were also phage typed. The isolates were divided into two general groups: (i) unrelated isolates not known to be epidemiologically linked (n = 154) and originating from food animals, foods and the environment, or humans and (ii) epidemiologically related isolates (n = 53) comprised of four related groups (RGs) originating either from one farm plus the abattoir where cattle from that farm were slaughtered or from one of three different English abattoirs. PFGE was conducted with the restriction endonuclease XbaI, while for ribotyping, two restriction endonucleases (PstI and SphI) were combined to digest genomic DNAs simultaneously. The 207 E. coli O157 isolates produced 97 PFGE profiles and 51 ribotypes. The two genetic fingerprinting methods had similar powers to discriminate the 154 epidemiologically unrelated E. coli O157 isolates in the study (Simpson's index of diversity [D] = 0.98 and 0.94 for PFGE typing and ribotyping, respectively). There was no correlation between the source of an isolate (healthy meat or milk animals, retail meats, or cases of human infection) and either particular PFGE or ribotype profiles or clusters. Combination of the results of both genetic fingerprinting methods produced 146 types, significantly more than when either of the two methods was used individually. Consequently, the superior discriminatory performance of the PFGE-ribotyping combination was proven in two ways: (i) by demonstrating that the majority of the E. coli O157 isolates with unrelated histories were indeed distinguishable types and (ii) by identifying some clonal groups among two of the four RGs of E. coli O157 isolates (comprising PFGE types different by just one or two bands), the relatedness of which would have remained unconfirmed otherwise.

Diversity of Campylobacter isolates from retail poultry carcasses and from humans as demonstrated by pulsed-field gel electrophoresis

Campylobacter spp. are a major contaminant of poultry. Eating undercooked chicken and handling raw poultry have been identified as risk factors for campylobacteriosis in humans. Previous studies have found Campylobacter spp. on 90% of poultry carcasses. In the present study, pulsed-field gel electrophoresis (PFGE) was used to assess the genetic diversity of strains on retail poultry carcasses. PFGE patterns of isolates from campylobacteriosis cases were compared to those from the poultry isolates. Over a 1-year study period (March 2000 through February 2001), whole fresh young chickens (n = 72) were obtained from three retail outlets in an urban community in the south-central United States. Campylobacter spp. were isolated from 82% of these carcasses. Strains (n = 70) were defined on the basis of their PFGE pattern. Sixty-seven percent of the carcasses from which Campylobacter spp. were isolated were contaminated with more than one PFGE-distinguishable strain. During the 1-year study period, most of the PFGE patterns (59%) were limited to isolates obtained from a single carcass. Forty-one percent of the PFGE-distinguishable strains were recovered from more than one carcass. Ninety-seven percent of the carcasses contaminated with the same strain were purchased at the same time from the same store. To examine the degree of genetic stability, four strains were followed in vitro over an estimated 1,000 doublings. The PFGE pattern of one of these isolates underwent minor changes during in vitro growth. The data indicate extensive variability in the PFGE patterns of Campylobacter spp. isolated from humans and from poultry carcasses. In spite of difficulties caused by such diversity and the fact that some carcasses are contaminated with more than one strain, the pattern variation provides a useful method for linking a particular strain to its source.