Characterization of recurrent and sporadic Listeria monocytogenes isolates from raw milk and nondairy foods by pulsed-field gel electrophoresis, monocin typing, plasmid profiling, and cadmium and antibiotic resistance determination

Following previous surveys to assess the incidence of Listeria monocytogenes in raw milk and nondairy foods processed in Northern Ireland, isolates were characterized as recurrent or sporadic on the basis of multilocus enzyme electrophoresis (MEE) analysis and restriction fragment length polymorphism typing. In the present study, 45 representative recurrent and sporadic electrophoretic types (ETs) previously identified by MEE were subjected to pulsed-field gel electrophoresis (PFGE) of genomic DNA macrorestriction fragments, monocin typing, plasmid profiling, and an examination of resistance to cadmium and nine different antibiotics. Although PFGE proved to be capable of subdividing a number of recurrent and sporadic ETs, the grouping of strains arrived at by PFGE and MEE were in broad agreement, and previous conclusions regarding the designation of L. monocytogenes strains as recurrent or sporadic remained unaltered. It is considered that PFGE was able to detect minor genetic changes in recurrent ETs which occurred during the time period in which food surveys were carried out. Production of type E monocin (Types A to E were found among the 45 strains), plasmid carriage, and resistance to cadmium occurred more frequently in recurrent than in sporadic strains and may be important with regard to the ability of L. monocytogenes to persist in food and food-processing environments. Only 2 of 45 strains showed resistance to any of the nine antibiotics tested: two sporadic strains were resistant to tetracycline (MIC, 64 microg x ml(-1)).     

Genotypic characterization of Salmonella by multilocus sequence typing, pulsed-field gel electrophoresis and amplified fragment length polymorphism

Molecular typing is an important tool in surveillance and outbreak investigations of human Salmonella infections. In this study, three molecular typing methods were used to investigate the discriminatory ability, reproducibility and the genetic relationship between 110 Salmonella enterica subspecies enterica isolates. A total of 25 serotypes were investigated that had been isolated from humans or veterinary sources in Denmark between 1995 and 2001. All isolates were genotyped by multilocus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE) and amplified fragment length polymorphism (AFLP). When making genetic trees, all three methods resulted in similar clustering that often corresponded with serotype, although some serotypes displayed more diversity than others. Of the three techniques, MLST was the easiest to interpret and compare between laboratories. Unfortunately the seven housekeeping genes used in this MLST scheme lacked diversity and the ability to discriminate between isolates were higher with both PFGE and AFLP. The discriminatory power of AFLP and PFGE were similar but PFGE fingerprints were both easier to reproduce, interpret and less time-consuming to analyze when compared to AFLP. PFGE is the therefore the preferred molecular typing method for surveillance and outbreak investigations, whereas AFLP is most useful for local outbreak investigations.     

Typing of food-borne Listeria monocytogenes by polymerase chain reaction-restriction enzyme analysis and amplified fragment length polymorphism

The applicability of polymerase chain reaction-restriction enzyme analysis (PCR-REA) and amplified fragment length polymorphism (AFLP) for typing of food borne Listeria monocytogenes strains was tested. A panel of 43 L. monocytogenes strains isolated from food, mostly serovars 1/2b or 1/2a, were analysed by the optimized PCR-REA oriented to inlA and inlB genes and by AFLP. By PCR-REA, five types of profiles were obtained. By AFLP, the strains were separated into 11 types and 18 subtypes forming two major clusters. PCR REA was a relatively straightforward method for typing food-borne L. monocytogenes with a moderate discrimination power. AFLP was a more complex but a highly discriminative and reproducible method.     

Molecular analysis of Leptospira spp. isolated from humans by restriction fragment length polymorphism, real-time PCR and pulsed-field gel electrophoresis

A total of 17 Leptospira clinical strains isolated from humans in Croatia were serologically and genetically analysed. For serovar identification, the microscopic agglutination test (MAT) and pulsed-field gel electrophoresis (PFGE) were used. To identify isolates on genomic species level, PCR-based restriction fragment length polymorphism (RFLP) and real-time PCR were performed. MAT revealed the following serogroup affinities: Grippotyphosa (seven isolates), Icterohaemorrhagiae (eight isolates) and Javanica (two isolates). RFLP of PCR products from a 331-bp-long fragment of rrs (16S rRNA gene) digested with endonucleases MnlI and DdeI and real-time PCR revealed three Leptospira genomic species. Grippotyphosa isolates belonged to Leptospira kirschneri , Icterohaemorrhagiae isolates to Leptospira interrogans and Javanica isolates to Leptospira borgpetersenii . Genomic DNA from 17 leptospiral isolates was digested with NotI and SgrAI restriction enzymes and analysed by PFGE. Results showed that seven isolates have the same binding pattern to serovar Grippotyphosa, eight isolates to serovar Icterohaemorrhagiae and two isolates to serovar Poi. Results demonstrate the diversity of leptospires circulating in Croatia. We point out the usefulness of a combination of PFGE, RFLP and real-time PCR as appropriate molecular methods in molecular analysis of leptospires.     

Application of multilocus enzyme electrophoresis in studies of the epidemiology of Listeria monocytogenes in Denmark.

A total of 245 strains of Listeria monocytogenes were investigated. These strains were isolated from human and animal cases of listeriosis as well as from different kinds of raw and processed foods. Thirty-three electrophoretic types (ETs) were identified among the 245 strains. The strains investigated included all human clinical strains isolated in Denmark during 1989 and 1990. Seventy-three percent of the strains isolated in this period were assigned to one of only two ETs (ET 1 and ET 4). ET 1, which was found to be the most frequently occurring ET among strains isolated from human clinical cases, was also found to occur rather frequently in animal clinical cases. ET 1 was, however, found only sporadically among strains isolated from foods and food factories. The data indicate that there might be something distinctive about the physiology or ecology of the ET 1 clone which makes it more likely to bring about disease in human beings either because of high pathogenicity or because of a special ability to multiply to infectious doses in processed foods. Another type, designated ET 4, was found to be the next most frequently occurring ET, after ET 1, among human clinical isolates. This could be explained by the fact that ET 4 was found to be the most frequently occurring ET within food isolates.     

Transmission of intestinal Bifidobacterium longum subsp. longum strains from mother to infant, determined by multilocus sequencing typing and amplified fragment length polymorphism

The gastrointestinal tracts of neonates are colonized by bacteria immediately after birth. It has been discussed that the intestinal microbiota of neonates includes strains transferred from the mothers. Although some studies have indicated possible bacterial transfer from the mother to the newborn, this is the first report confirming the transfer of bifidobacteria at the strain level. Here, we investigated the mother-to-infant transmission of Bifidobacterium longum subsp. longum by genotyping bacterial isolates from the feces of mothers before delivery and of their infants after delivery. Two hundred seven isolates from 8 pairs of mothers and infants were discriminated by multilocus sequencing typing (MLST) and amplified fragment length polymorphism (AFLP) analysis. By both methods, 11 strains of B. longum subsp. longum were found to be monophyletic for the feces of the mother and her infant. This finding confirms that these strains were transferred from the intestine of the mother to that of the infant. These strains were found in the first feces (meconium) of the infant and in the feces at days 3, 7, 30, and 90 after birth, indicating that they stably colonize the infant's intestine immediately after birth. The strains isolated from each family did not belong to clusters derived from any of the other families, suggesting that each mother-infant pair might have unique family-specific strains.     

Characterization of Listeria monocytogenes isolated from poultry products and from the poultry-processing environment by random amplification of polymorphic DNA and multilocus enzyme electrophoresis.

A total of 289 Listeria monocytogenes strains isolated from a poultry-processing environment and poultry products over a 6-month period were characterized by random amplification of polymorphic DNA, (RAPD) to pinpoint sources of contamination within the plant and gain some measure of the persistence of individual genotypes within this environment. Eighteen RAPD profiles (A through R) were identified within this group, with 64% (184 of 289) of all strains displaying a single RAPD profile, RAPD type A. This genotype was more prevalent in the raw-poultry-processing environment, where, although its origin within this environment appeared to be the incoming birds, it was also widespread on food contact surfaces, floors, and drains. This was the only genotype which persisted throughout the entire 6-month period, and it and RAPD type B were the only two genotypes found in both the raw- and cooked-poultry-processing environments. L. monocytogenes strains isolated from cooked poultry products and the cooked-poultry-processing environment up to 1 year later (17 strains) contained only RAPD types A and B, highlighting the potential which exists for persistent strains to cross-contaminate foods processed in that environment. The other genotypes (C through R) occurred more sporadically, suggesting varied sources of contamination. These were confined to either the raw- or the cooked-poultry-processing environment and were relatively short-lived. Further characterization of a selection of RAPD type A strains, together with strains of RAPD types B through R, was carried out by multilocus enzyme electrophoresis. Strains of RAPD type A contained two electrophoretic types, one of which was serotype 1/2a and the other was 1/2c.(ABSTRACT TRUNCATED AT 250 WORDS)     

Typing of human, animal, food, and environmental isolates of Listeria monocytogenes by multilocus enzyme electrophoresis.

In order to elucidate some aspects of the epidemiology of listeriosis in Switzerland, 181 strains of Listeria monocytogenes isolated from humans, animals, food, and the environment have been analyzed by multilocus enzyme electrophoresis at 21 enzyme loci. The clone responsible for several recent food-borne outbreaks in Switzerland and in North America (marked by electrophoretic type 1 and serovar 4b) has been found frequently among strains isolated from animals. Thus, animals may represent a major source of diffusion of this clone in the environment and in food, in which it has been found only sporadically, however. Two other unrelated clones (including strains belonging to serovars 1/2b and 1/2c) have often been isolated from meat but not from animals. These findings indicate that contamination of meat with L. monocytogenes might originate mainly from the environment in which it is processed rather than from animals themselves. This could explain the differences in the distribution of L. monocytogenes serovars isolated from meat and from animals.     

Characterisation of persistent and sporadic Listeria monocytogenes strains by pulsed-field gel electrophoresis (PFGE) and amplified fragment length polymorphism (AFLP)

This study was set up to evaluate the genetic similarity or dissimilarity of persistent and sporadic Listeria monocytogenes strains existing in eleven food processing facilities, including fish, dairy, meat and poultry processing plants. In each plant persistent and sporadic strains were selected on the basis of PFGE typing results. A total of 17 strains representing persistent strains and 38 sporadic strains originating from eleven food processing plants were included in the study. PFGE macrorestriction patterns of persistent and sporadic strains from different processing plants were compared and the strains were further studied by amplified fragment length polymorphism (AFLP), being a characterisation method giving more whole genome based information. The 17 persistent and 38 sporadic strains showed 14 and 35 pulsotypes, 14 and 28 AFLP types, respectively. The combination of PFGE and AFLP typing results yielded a total of 48 genotypes. Thirteen of 15 genotypes presented by persistent strains were only associated with persistent strains and similarly 94% (33/35) of genotypes showed by sporadic strains were recovered among sporadic strains only. Our results showed that L. monocytogenes strains causing persistent contamination differ from sporadic strains. In AFLP analysis persistent strains did not, however, form any specific clusters and neither was there any difference between the known two genomic groups. These results indicate that even though persistent strains differ from sporadic strains there seems not to be any specific evolutional lineage of persistent strains.     

A comparison between starch and polyacrylamide gels for the analysis of Listeria monocytogenes using multilocus enzyme electrophoresis

S.H. FLINT, N.J. HARTLEY, S.M. AVERY AND J.A. HUDSON. 1996. Forty-seven Listeria monocytogenes isolates were analysed using multilocus enzyme electrophoresis in two laboratories. Both assayed for the same six enzymes, but one used a starch gel method and the other polyacrylamide gels. The starch gel method distinguished six electrophoretic types whereas the polyacrylamide gel method produced 17 different electrophoretic types. The polyacrylamide gel method was more discriminatory than the starch gel method.     

PCR/restriction fragment length polymorphism (RFLP) typing of human and poultry Campylobacter jejuni strains

AIMS: The PCR/RFLP typing of 156 isolates Campylobacter jejuni originating from poultry and humans was performed (101 human and 55 poultry strains). METHODS AND RESULTS: On the basis of restrictive digest, six types were identified with AfaI, seven types with MboI and five types with HaeIII. With a combination of these three enzymes, 22 types were found. In human strains, the most frequently occurring types were Cj.4 (28%), Cj.1 (19%), Cj. 13 (13%) and Cj. 2 (5%). In the case of poultry strains, the most frequent types were Cj. 1 (34%), Cj. 11 (22%), C.j. 21 (16%) and Cj. 15 (11%). CONCLUSIONS: The findings support the hypothesis that poultry is a significant source but not sole source of Campylobacter sp. in relation to humans. SIGNIFICANCE AND IMPACT OF THE STUDY: The typing of Campylobacter sp. forms the basis for an evaluation of the current state and risk assessment of various Campylobacter sp. sources in relation to humans.     

Typing of human, animal, food, and environmental isolates of Listeria monocytogenes by multilocus enzyme electrophoresis

In order to elucidate some aspects of the epidemiology of listeriosis in Switzerland, 181 strains of Listeria monocytogenes isolated from humans, animals, food, and the environment have been analyzed by multilocus enzyme electrophoresis at 21 enzyme loci. The clone responsible for several recent food-borne outbreaks in Switzerland and in North America (marked by electrophoretic type 1 and serovar 4b) has been found frequently among strains isolated from animals. Thus, animals may represent a major source of diffusion of this clone in the environment and in food, in which it has been found only sporadically, however. Two other unrelated clones (including strains belonging to serovars 1/2b and 1/2c) have often been isolated from meat but not from animals. These findings indicate that contamination of meat with L. monocytogenes might originate mainly from the environment in which it is processed rather than from animals themselves. This could explain the differences in the distribution of L. monocytogenes serovars isolated from meat and from animals.     

Analysis of Clostridium botulinum serotype E strains by using multilocus sequence typing, amplified fragment length polymorphism, variable-number tandem-repeat analysis, and botulinum neurotoxin gene sequencing

A total of 41 Clostridium botulinum serotype E strains from different geographic regions, including Canada, Denmark, Finland, France, Greenland, Japan, and the United States, were compared by multilocus sequence typing (MLST), amplified fragment length polymorphism (AFLP) analysis, variable-number tandem-repeat (VNTR) analysis, and botulinum neurotoxin (bont) E gene sequencing. The strains, representing environmental, food-borne, and infant botulism samples collected from 1932 to 2007, were analyzed to compare serotype E strains from different geographic regions and types of botulism and to determine whether each of the strains contained the transposon-associated recombinase rarA, involved with bont/E insertion. MLST examination using 15 genes clustered the strains into several clades, with most members within a cluster sharing the same BoNT/E subtype (BoNT/E1, E2, E3, or E6). Sequencing of the bont/E gene identified two new variants (E7, E8) that showed regions of recombination with other E subtypes. The AFLP dendrogram clustered the 41 strains similarly to the MLST dendrogram. Strains that could not be differentiated by AFLP, MLST, or bont gene sequencing were further examined using three VNTR regions. Both intact and split rarA genes were amplified by PCR in each of the strains, and their identities were confirmed in 11 strains by amplicon sequencing. The findings suggest that (i) the C. botulinum serotype E strains result from the targeted insertion of the bont/E gene into genetically conserved bacteria and (ii) recombination events (not random mutations) within bont/E result in toxin variants or subtypes within strains.     

Division of Listeria monocytogenes serovar 4b strains into two groups by PCR and restriction enzyme analysis.

Altogether, 133 strains of Listeria monocytogenes serovar 4b were investigated. A segment of 2,916 bp containing parts of the two genes inlA and inlB in L. monocytogenes was amplified by the PCR technique. The PCR product obtained was cleaved with the restriction enzyme AluI, and the fragments generated were separated by gel electrophoresis, leading to two distinct groups: PCR-restriction enzyme analysis groups I and II, containing 37 and 96 strains, respectively. The PCR-restriction enzyme analysis method described in this paper could be a useful tool for the subtyping of L. monocytogenes serovar 4b strains.     

Prevalence and fingerprinting of Listeria monocytogenes strains isolated from raw whole milk in farm bulk tanks and in dairy plant receiving tanks

The incidence of Listeria species in raw whole milk from farm bulk tanks and from raw milk in storage at a Swedish dairy plant was studied. Listeria monocytogenes was found in 1.0% and Listeria innocua was found in 2.3% of the 294 farm bulk tank (farm tank) milk specimens. One farm tank specimen contained 60 CFU of L. monocytogenes ml(-1). L. monocytogenes was detected in 19.6% and L. innocua was detected in 8.5% of the milk specimens from the silo receiving tanks at the dairy (dairy silos). More dairy silo specimens were positive for both Listeria species during winter than during summer. Restriction enzyme analysis and pulsed-field gel electrophoresis were applied to 65 isolates of L. monocytogenes, resulting in 16 different clonal types. Two clonal types were shared by the farm tank milk and the dairy silo milk. All except one clonal type belonged to serovar 1/2a. In the dairy silo milk five clonal types were found more frequently and for a longer period than the others. No Listeria species were found in any other samples from the plant.     

Identification of Thiobacillus ferrooxidans strains based on restriction fragment length polymorphism analysis of 16S rDNA.

The 16S rDNA sequences from ten strains of Thiobacillus ferrooxidans were amplified by PCR. The products were compared by performing restriction fragment length polymorphism (RFLP) analysis with restriction endonucleases Alu I, Hap II, Hha I, and Hae III. The RFLP patterns revealed that T. ferrooxidans could be distinguished from other iron- or sulphur-oxidizing bacteria such as T. thiooxidans NB1-3, T. caldus GO-1, Leptospirillum ferrooxidans and the marine iron-oxidizing bacterium strain KU2-11. The RFLP patterns obtained with Alu I, Hap II, and Hae III were the same for nine strains of T. ferrooxidans except for strain ATCC 13661. The RFLP patterns for strains NASF-1 and ATCC 13661 with Hha I were distinct from those for other T. ferrooxidans strains. The 16S rDNA sequence of T. ferrooxidans NASF-1 possessed an additional restriction site for Hha I. These results show that iron-oxidizing bacteria isolated from natural environments were rapidly identified as T. ferrooxidans by the method combining RFLP analysis with physiological analysis.     

Molecular genotyping of Mycobacterium tuberculosis strains isolated from patients in the Samara region by the restriction DNA fragment length polymorphism

The typing of 106 M. tuberculosis (MBT) strains isolated from patients in the Samara region by the restriction DNA fragment length polymorphism (RFLP) IS6110 revealed that most of the strains (71.7%) belonged to the W family, 5 MBT strains (4.7%) belonged to the AI family, one culture was the mixture of two strains, AI and W. In addition, 24 MBT strains (22.6%) classified with other genotypes were detected. The analysis of the sensitivity of the MBT strains to rifampicin and isoniazid, with the method of absolute concentrations and by point mutations, demonstrated that 29 MBT strains (27.3%) were sensitive to rifampicin and isoniazid and 56 MBT strains (52.9%) were resistant to rifampicin and isoniazid simultaneously. Among the MBT strains of different RFLP families, strains both sensitive and resistant to these two preparations could be detected, but strains with multiple drug resistance prevailed in the W family (61.8%).     

Comparison of direct genome restriction enzyme analysis and pulsed-field gel electrophoresis for typing of Vibrio vulnificus and their correspondence with multilocus sequence typing data

We compared the potential of direct genome restriction enzyme analysis (DGREA) and pulsed-field gel electrophoresis (PFGE) for discriminating Vibrio vulnificus isolates from clinical (23) and environmental (17) sources. The genotypes generated by both methodologies were compared to previous multilocus sequence typing (MLST) data. DGREA established clearer relationships among V. vulnificus strains and was more consistent with MLST than with PFGE. DGREA is a very promising tool for epidemiological and ecological studies of V. vulnificus.