Genomic diversity of Campylobacter coli and Campylobacter jejuni isolates recovered from free-range broiler farms and comparison with isolates of various origins.

In many industrialized countries, the incidence of campylobacteriosis exceeds that of salmonellosis. Campylobacter bacteria are transmitted to humans mainly in food, especially poultry meat products. Total prevention of Campylobacter colonization in broiler flocks is the best way to reduce (or eliminate) the contamination of poultry products. The aim of this study was to establish the sources and routes of contamination of broilers at the farm level. Molecular typing methods (DNA macrorestriction pulsed-field gel electrophoresis and analysis of gene polymorphism by PCR-restriction fragment length polymorphism) were used to characterize isolates collected from seven broiler farms. The relative genomic diversity of Campylobacter coli and Campylobacter jejuni was determined. Analysis of the similarity among 116 defined genotypes was used to determine clusters within the two species. Furthermore, evidence of recombination suggested that there were genomic rearrangements within the Campylobacter populations. Recovery of related clusters from different broiler farms showed that some Campylobacter strains might be specifically adapted to poultry. Analysis of the Campylobacter cluster distribution on three broiler farms showed that soil in the area around the poultry house was a potential source of Campylobacter contamination. The broilers were infected by Campylobacter spp. between days 15 and 36 during rearing, and the type of contamination changed during the rearing period. A study of the effect of sanitary barriers showed that the chickens stayed Campylobacter spp. free until they had access to the open area. They were then rapidly colonized by the Campylobacter strains isolated from the soil.

Molecular epidemiology of Listeria monocytogenes isolates collected from the environment, raw meat and raw products in two poultry- and pork-processing plants.

AIMS: In order to study the transmission of Listeria monocytogenes in a poultry and a pork meat plant, we analysed the contamination by this pathogen over several months. METHODS AND RESULTS: Five hundred and two isolates of L. monocytogenes were collected and characterized by genotyping and serotyping. Thirty-seven genotypes were obtained by ApaI-restriction analysis-pulsed field gel electrophoresis (REA-PFGE) and 35 by SmaI-REA-PFGE and resulted in 50 combined genotypes. The tracing of the contamination in both plants showed that some clones were able to survive for several months. However, some other clones were found only during processing operations, were not detectable after cleaning and seemed to enter continuously into the plant. CONCLUSIONS: Some L. monocytogenes strains may persist for a long period in the plant environment. Different genotypes can be associated with poultry as well as pork meat. SIGNIFICANCE AND IMPACT OF THE STUDY: Listeria monocytogenes contamination can be due to contaminated raw materials, bacterial spread and also ineffective cleaning procedures.

Campylobacter contamination in French chicken production from farm to consumers. Use of a PCR assay for detection and identification of Campylobacter jejuni and Camp. coli.

AIMS: Campylobacter contamination in French chicken production from the farm to the consumer was determined using a PCR assay for bacteria detection and identification. METHODS AND RESULTS: Samples were bird droppings from poultry houses, neck skins, livers, hearts, gizzards, wings, legs and escalopes from slaughterhouses and gizzards, legs, drumstick, breast and escalopes from a supermarket. Bacterial DNA extraction was performed after an enrichment step in a broth and was followed by PCR. An internal control (IC) was used for both DNA extraction and PCR. Campylobacter were detected in 79.2% of poultry houses. Of the 303 samples, 201 were Campylobacter-positive (i.e. 66.3%) including 43.2% faecal samples, 5.6% slaughterhouse samples and 17.5% supermarket samples. There was no significant difference between the molecular method and the conventional culture technique for Campylobacter detection whatever the samples. The sensitivity was 5 UFC g(-1) of samples and 1.5 x 10(3) UFC ml(-1) of enrichment broth. The use of IC revealed PCR inhibition in 13 samples and problems in the DNA extraction in five samples. CONCLUSION: Significant Campylobacter contamination affects all stages of French chicken production. SIGNIFICANCE AND IMPACT OF THE STUDY: The understanding of Campylobacter contamination at different levels of chicken production and the determination of the best place(s) for intervention are important for significantly decreasing Campylobacteriosis. Our technique is rapid and can be used on different chicken samples for Campylobacter detection and identification.

Tracing of Salmonella spp. in two pork slaughter and cutting plants using serotyping and macrorestriction genotyping.

AIMS: The origin of Salmonella contamination of pork products is not well established. In order to further this knowledge, the transmission of Salmonella spp. from live pigs to pork cuts was investigated in two pork slaughter and cutting plants. METHODS AND RESULTS: Salmonella spp. were isolated from both pork (pigs, carcasses, cuts) and the environment before and during slaughterhouse activities. Eight serotypes were identified. XbaI and SpeI macrorestriction distinguished 20 genotypes of Salmonella Typhimurium and 16 genotypes of Salmonella Derby. A major cluster of Salmonella Typhimurium genotypes was common to both plants and all pig-related genotypes, while a predominant pig-related Salmonella Derby genotype was common to both plants. CONCLUSION: None of the Salmonella strains persisted for long periods in the pork-processing environments. SIGNIFICANCE AND IMPACT OF THE STUDY: This work shows that contaminated live pigs, because of bacterial spread due to the process and ineffective cleaning procedures, are involved in Salmonella contamination.

Some safety aspects of Salmonella vaccines for poultry: in vivo study of the genetic stability of three Salmonella typhimurium live vaccines.

Live vaccine strains of Salmonella should be avirulent, immunogenic and genetically stable. Some isolates of three commercially available live vaccine strains of Salmonella typhimurium, sampled during a study on their persistence in a vaccinated flock of chickens, were analyzed for genetic stability using macrorestriction analysis of their genome. Two out of the three vaccine strains showed genetic instabilities. Two of the 51 isolates of Zoosaloral vaccine strain and nine of the 32 analyzed isolates of chi(3985), a genetically modified organism, were variants and showed different macrorestriction profiles.

Physicochemical surface properties of five Listeria monocytogenes strains from a pork-processing environment in relation to serotypes, genotypes and growth temperature.

Physicochemical surface properties, related to electrostatic, van der Waals and Lewis acid-base interactions, of five Listeria monocytogenes strains isolated from pork-processing environments were determined after two subcultures at 37 degrees C and a final culture at three temperatures: 37, 10 and 4 degrees C. Three strains (Lm1, Lm114 and Lm191) were genetically related while two were unrelated (Lm25 and Lm74) according to ApaI-macrorestriction and pulsed-field gel electrophoresis (PFGE) typing. Listeria monocytogenes cell surfaces were generally negatively charged regardless of pH and tended to be hydrophilic due to a basic character. However, variable physicochemical surface properties of the five Listeria monocytogenes isolates were observed after growth at 37 degrees C. After growth at 10 degrees C, the three genetically related isolates exhibited similar surface properties and were slightly more hydrophilic and basic than the others. After growth at 4 degrees C, the five isolates displayed the same weak affinity for all kinds of solvents and low electrophoretic mobility values. A sharp decrease of temperature and subsequent growth of various Listeria monocytogenes strains resulted in loss of the physicochemical surface property variability, which may suggest the role of common chill adaptation mechanisms affecting surface properties.

Survival and recovery of viable but noncultivable forms of Campylobacter in aqueous microcosm.

Previous studies suggesting that the persistence of thermotolerant Campylobacter in water, especially as a viable but non-cultivable form (VNC), was involved in human campylobacteriosis, the capacities of survival and resuscitation of a significant collection of 85 strains in aqueous microcosms were investigated. Two-thirds of these strains (68%) were not detectable on agar medium after a stay of 14-21 days, whereas 21% reached this state before 14 days and 11% were non-cultivable after a stay of 21 days. Some strains remained cultivable after 35 days in a shaken aqueous microcosm and beyond 60 days without shaking. After 30 days, 51% of the non-detectable strains by conventional culture were recovered after injection in 9-day fertilised chicken eggs. A kinetic study showed that the age of the viable but non-cultivable forms and characteristics of the strains could explain the variations of recovery. These results suggest that viable but non-cultivable forms of Campylobacter could be a potential risk of colonisation of human or animals and that an embryonic factor seems to be essential to allow resuscitation.

An immunoconcentration-PCR assay to detect Salmonella in the environment of poultry houses.

An immunoconcentration-PCR assay was developed for the rapid and specific detection of Salmonella. This assay was evaluated against a conventional bacteriological method for the detection of Salmonella from environmental swabs of poultry houses. The 120 samples investigated were pre-enriched in phosphate buffered peptone water and Salmonella was separated by an immunoconcentration process using an automated system (VIDAS bioMérieux, Marcy l'Etoile, France) prior to PCR. The specificity of the assay was high as no false-positives were found. The sensitivity of the assay was 70%. The correlation between the ICS-PCR assay and the bacteriological method was 84%.

Identification by a multiplex PCR-based assay of Salmonella typhimurium and Salmonella enteritidis strains from environmental swabs of poultry houses.

A multiplex-PCR-based assay (m-PCR) was developed for the detection of Salmonella and for the identification of the two serotypes Enteritidis and Typhimurium. Three sets of primers selected from different genomic sequences amplified a 429 bp fragment specific for the genus Salmonella within a randomly cloned sequence, a 559 bp target specific for Salmonella Typhimurium within the fliC gene and a 312 bp fragment specific for Salmonella Enteritidis within the sefA gene. The m-PCR-based assay was used for detecting Salmonella from 1078 environmental swabs of poultry houses. Prior to PCR, these swabs were pre-enriched in phosphate-buffered peptone water for 18-20 h and then sub-cultured on a Modified Semi-solid Rappaport Vassiliadis medium (MSRV) for 18-20 h. The m-PCR combined with MSRV had a better sensitivity (95%) than the bacteriological method (92.5%). The MSRV-m-PCR assay and the bacteriological method had an agreement rate of 95.6%.

Evaluation of a multiplex PCR assay for simultaneous identification of Salmonella sp., Salmonella enteritidis and Salmonella typhimurium from environmental swabs of poultry houses.

A Multiplex PCR-based assay (m-PCR) with three sets of primers was developed for the detection of all serotypes of Salmonella enterica and the identification of Salmonella Enteritidis and Salmonella Typhimurium. This method was evaluated against a bacteriological method for the analysis of environmental swabs of poultry houses. Samples were preenriched in phosphate-buffered peptone water for 24 h and subjected to three different protocols prior to PCR: (i) an immunomagnetic separation using Dynabeads anti-Salmonella (Dynal); (ii) a DNA extraction procedure using the Instagene matrix; (iii) an additional step of culture on an MSRV medium. With protocols 1 and 2, eight positive results were found by PCR and 20 with the bacteriological method. Protocol 3 combining MSRV and PCR gave similar results to those obtained from bacteriological methods and allowed Salmonella detection within 2 days.

Listeria monocytogenes in pork slaughtering and cutting plants. Use of RAPD, PFGE and PCR-REA for tracing and molecular epidemiology.

In order to determine the origin of pork cuts contamination by Listeria monocytogenes, 287 isolates, collected from five French pork slaughtering and cutting plants, from live pigs to pork cuts, were characterised using three molecular typing methods: random amplification of polymorphic DNA (RAPD) carried out with five different primers, genomic macrorestriction using ApaI with pulsed-field gel electrophoresis (PFGE) and a PCR-restriction enzyme analysis (PCR-REA) based on the polymorphism existing within the inlA and inlB genes. Results obtained from RAPD and PFGE were closely related and distinguished respectively 17 RAPD types (r1-r17) and 17 PFGE types (a1-a17) among the 287 isolates, whereas the PCR-REA analysis only yielded two profiles (p1 and p2). Considering the combined results obtained with the three molecular typing methods, 19 Listeria monocytogenes genotypes (1-19) were distinguished. Serotyping led at least four serotypes being distinguished: 1/2a, 3a, 1/2c and 3c. The application of genotyping identified the predominance of a Listeria monocytogenes strain of type (1) and other very closely related ones (5, 9, 10, 12, 13, 14, 16 and 19) which were present on pork as well as in the environment within the five investigated plants. This study also pointed out the presence of these closely related Listeria monocytogenes strains over a 1-year period in the environments of two plants, even after cleaning and disinfection procedures. This highlights the possibility for some Listeria monocytogenes strains to persist in pork processing environments and raises the problem of the efficiency of cleaning and disinfection procedures used in pork slaughterhouses, chilling and cutting rooms.

Molecular characterization of the diversity of Campylobacter spp. isolates collected from a poultry slaughterhouse: analysis of cross-contamination.

Investigations of a free-range broiler flock during the rearing period and at the slaughterhouse by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) of the flagellin (flaA) gene (flaA typing) have shown that poultry carcasses are contaminated by Campylobacter spp. strains which were previously present in the poultry faces. Moreover, the investigation of the previous and the following batches in the processing plant using flaA typing have shown that cross-contamination between batches coming from different flocks occurs and is also a risk factor for the presence of Campylobacter spp. on poultry carcasses.

Development of a m-PCR assay for simultaneous identification of Campylobacter jejuni and C. coli.

Multiplex PCR assay (m-PCR) with three sets of primers was developed for simultaneous identification of Campylobacter jejuni and C. coli. Poultry faecal samples were enriched in Preston broth for 24 h and streaking on selective media was performed before and after enrichment. m-PCR was applied on bacterial cultures harvested from media plates. The data showed a selective effect of Preston broth which favoured the growth of C. coli. Identification of the species by the hippurate hydrolysis test and by the m-PCR was performed on 294 isolates of Campylobacter. The efficiency of the identification by the biochemical test is only 34% in comparison to 100% efficiency with the PCR. The use of our m-PCR in combination with the culture method allowed reliable detection and identification of C. jejuni and C. coli within 3-4 d.

Development of a multiplex PCR gene fingerprinting method using gyrA and pflA polymorphisms to identify genotypic relatedness within Campylobacter jejuni species.

The two genes gyrA and pflA, whose sequence variability had been previously described, were evaluated separately for their potential value in discriminating strains of Campylobacter jejuni. A single method was then developed by which the two loci were simultaneously amplified using a multiplex PCR procedure, and banding patterns were generated using a pre-selected set of restriction endonuclease enzymes. The method was applied to 18 strains of Camp. jejuni from different poultry sources varying in geographical origin and year of isolation. Results were combined and compared by means of numerical analysis with the classification obtained by flaA-typing and macrorestriction SmaI and KpnI. The usefulness of PCR fingerprinting of the gyrA/pflA genes for rapid ordering of strains by genotypic relatedness and providing additional information for estimating the degree of linkage between strains was demonstrated.

Detection of Salmonella spp. in food products by polymerase chain reaction and hybridization assay in microplate format.

Here, hybridization assay of amplified products is described which detect Salmonella spp. from chicken fillets and other food homogenates within 24 h. This technique is composed of four steps: (1) sample is pre-enriched overnight in phosphate buffered peptone water; (2) total DNA is extracted; (3) a Salmonella spp. specific DNA target sequence is amplified by polymerase chain reaction; (4) amplified products are captured by a probe covalently bound onto NH-Covalink (Nunc, Danemark) microwells and detected by a chemiluminescent enzymatic reaction. This hybridization of amplified products was demonstrated as sensitive as their analysis on agarose gel. Compared to a bacteriological method for Salmonella spp. detection, its specificity was estimated at 100% and its sensitivity was 93.2% from analysis of 207 naturally contaminated chicken fillets samples.

Chemiluminescent and colorimetric enzymatic assays for the detection of PCR-amplified Salmonella sp. products in microplates.

To improve Salmonella detection, we developed nonradioactive hybridization assays of amplified products from pure Salmonella cultures. Biotin-labeled PCR products were trapped by internal probes covalently bound to CovaLink-NH MicroWells and detected by colorimetric or chemiluminescent enzymatic reactions. The sensitivities of colorimetric assays using peroxidase and alkaline phosphatase were similar to those obtained with an ethidium bromide-stained agarose gel; both procedures allow the detection of 50 Salmonella cells. Chemiluminescence was 10-fold more sensitive than colorimetry.

Partial sequencing of hog cholera virus Alfort strain genome and its comparison with other pestivirus strains.

After molecular RNA cloning of the Alfort strain (Alfort/LCRV) of hog cholera virus (HCV), the nucleotide sequence of about 70% of the total genome was determined. This sequence was compared with homologous parts of previously published pestivirus genomes. The average homology with another clone of the Alfort strain (Alfort/FRC) was found to be lower (86.1%) than with Brescia strain of HCV (94.3%), while, compared with NADL, Osloss and SD-1 (3 different strains of bovine viral diarrhea virus, BVDV), the average homology was 67%. Although the amino-acid sequences show a higher degree of conservation, they had a similar degree of homology (92.7, 96.7, 69, 68.2 and 69%, respectively). Partial sequence comparison also revealed that Alfort/LCRV strain was more closely related to Alfort 187 (98.6% for the nucleotides and amino acids) and Weybridge (97.3% for the nucleotides and 96.1% for the amino acids) strains of HCV than it was to Alfort/FRC. These results may indicate that the Alfort/FRC strain has undergone more genomic variations during its historical passage. Genomic relationships among the pestiviruses are discussed.

Evaluation of different DNA extraction procedures for the detection of Salmonella from chicken products by polymerase chain reaction.

Polymerase chain reaction (PCR) was used after a short pre-enrichment culture to detect Salmonella subspecies in chicken fillets. A direct PCR assay performed with chicken meat inoculated with Salmonella Typhimurium produced no PCR products. Six different DNA extraction protocols were tested to recover efficiently Salmonella DNA after a short incubation period. Three of them gave results that were reliable, rapid and sensitive. Successful protocols used Proteinase K and/or a centrifugation step to concentrate the samples. For reliable detection of Salmonella subspecies, a few thousand bacterial cells per ml must be present. To obtain this number of bacterial cells with an inoculation of about one cell in 25 g of ionized food products, it was necessary to incubate samples for at least 10 h before PCR. A larger inoculum of approximately 10 cells in 25 g of ionized food products, required 8 h in culture broth to give positive results by PCR-based assay.

Genetic studies of lactococcal bacteriophages--taxonomic differentiations and DNA analysis: evidence for 3' cohesive ends.

Twenty-four bacteriophages of Lactococcus lactis subsp. lactis and L. lactis subsp. cremoris were classified. Two groups of bacteriophages morphologically defined as prolate or isometric types by electron microscopy were examined for their genome sizes, protein patterns and DNA homologies. These criteria showed that prolate phages are quite homogeneous. In contrast, isometric phages exhibit more differences, particularly in particle sizes and protein compositions. Analysis of DNA hybridizations confirmed that prolate phages can be grouped together as can be isometric phages but for one exception, phage I52. These two families were clearly defined. The unique phage which does not fit in either group probably belongs to a third one which is much less represented. No obvious relationships between these criteria and the lytic spectra were detected. Evidence of the presence of cohesive ends in phage genomes is also presented in this study. A more detailed analysis performed on one member of the prolate group revealed 3' protruding ends made up of around 13 nucleotides on complementary single strands.