Molecular typing of Clostridium perfringens from a food-borne disease outbreak in a nursing home: ribotyping versus pulsed-field gel electrophoresis

Pulsed-field gel electrophoresis of enterotoxic Clostridium perfringens type A isolates recovered from humans and animals in Kolkata, India

Clostridium perfringens is one of the most important globally recognised gastroenteric pathogen in humans as well as animals. The present study was aimed to know the similarities/divergence among C. perfringens type A isolates of human and animal origin using the pulsed-field gel electrophoresis (PFGE) as a molecular tool. The enterotoxic isolates obtained by screening of human diarrhoeal cases (n = 130), diarrhoeal cases of pig (n = 52) and goat (n = 50), meat samples viz., pork (n = 59) and chevon (n = 57) were characterized by standard cultural and biochemical methods followed by PCR Assays. Accordingly, a total of 11 C. perfringens type A characterized isolates (16S rRNA+, cpa+, cpb2+ and cpe+) recovered from human diarrhoeal cases (n = 3); diarrhoeal cases of pig (n = 2) and goat (n = 2); meat samples viz. pork (n = 2) and chevon (n = 2) were examined employing PFGE. The observed clustering pattern in PFGE analysis showed the relatedness between isolates from diarrhoeal goat and chevon (90-100%); diarrhoeal pig and pork (65-68%); moreover, isolates from human diarrhoeal cases were exhibiting lineage to cases from goat and pig diarrhoea as well pork and chevon by 62-68% relatedness. The outcome of the present study indicates the probable contamination of this pathogen to the human food chain through faeces from suspected food animals viz. goat and pig and their improperly cooked meat.

Pulsotype Diversity of Clostridium botulinum Strains Containing Serotypes A and/or B Genes

Clostridium botulinum strains are prevalent in the environment and produce a potent neurotoxin that causes botulism, a rare but serious paralytic disease. In 2010, a national PulseNet database was established to curate C. botulinum pulsotypes and facilitate epidemiological investigations, particularly for serotypes A and B strains frequently associated with botulism cases in the United States. Between 2010 and 2014 we performed pulsed-field gel electrophoresis (PFGE) using a PulseNet protocol, uploaded the resulting PFGE patterns into a national database, and analyzed data according to PulseNet criteria (UPGMA clustering, Dice coefficient, 1.5% position tolerance, and 1.5% optimization). A retrospective data analysis was undertaken on 349 entries comprised of type A and B strains isolated from foodborne and infant cases to determine epidemiological relevance, resolution of the method, and the diversity of the database. Most studies to date on the pulsotype diversity of C. botulinum have encompassed very small sets of isolates; this study, with over 300 isolates, is more comprehensive than any published to date. Epidemiologically linked isolates had indistinguishable patterns, except in four instances and there were no obvious geographic trends noted. Simpson's Index of Diversity (D) has historically been used to demonstrate species diversity and abundance within a group, and is considered a standard descriptor for PFGE databases. Simpson's Index was calculated for each restriction endonuclease (SmaI, XhoI), the pattern combination SmaI-XhoI, as well as for each toxin serotype. The D values indicate that both enzymes provided better resolution for serotype B isolates than serotype A. XhoI as the secondary enzyme provided little additional discrimination for C. botulinum. SmaI patterns can be used to exclude unrelated isolates during a foodborne outbreak, but pulsotypes should always be considered concurrently with available epidemiological data.

Genomic diversity of Clostridium perfringens strains isolated from food and human sources

Clostridium perfringens is a serious pathogen which causes enteric diseases in domestic animals and food poisoning in humans. Spores can survive cooking processes and play an important role in the possible onset of disease. In this study, RAPD-PCR and REP-PCR were used to examine the genetic diversity of 49 isolates of C. perfringens type A from three different sources. The results of RAPD-PCR revealed the most genetic diversity among poultry isolates, while human isolates showed the least genetic diversity. Cluster analysis obtained from RAPD-PCR and based on the genetic distances split the 49 strains into five distinct major clusters (A, B, C, D, and E). Cluster A and C were composed of isolates from poultry meat, cluster B was composed of isolates from human stool, cluster D was composed of isolates from minced meat, poultry meat and human stool and cluster E was composed of isolates from minced meat. Further characterization of these strains by using (GTG) 5 fingerprint repetitive sequence-based PCR analysis did not show further differentiation between various types of strains. In conclusion, RAPD-PCR method seems to be very promising for contamination source tracking in the field of food hygiene.

An epidemiological review of gastrointestinal outbreaks associated withClostridium perfringens, North East of England, 2012–2014

An anecdotal increase inC. perfringensoutbreaks was observed in the North East of England during 2012–2014. We describe findings of investigations in order to further understanding of the epidemiology of these outbreaks and inform control measures. All culture-positive (>105c.f.u./g) outbreaks reported to the North East Health Protection Team from 1 January 2012 to 31 December 2014 were included. Epidemiological (attack rate, symptom profile and positive associations with a suspected vehicle of infection), environmental (deficiencies in food preparation or hygiene practices and suspected vehicle of infection) and microbiological investigations are described. Forty-six outbreaks were included (83% reported from care homes). Enterotoxin (cpe) gene-bearerC. perfringenswere detected by PCR in 20/46 (43%) and enterotoxin (by ELISA) and/or enterotoxigenic faecal/food isolates with indistinguishable molecular profiles in 12/46 (26%) outbreaks. Concerns about temperature control of foods were documented in 20/46 (43%) outbreaks. A suspected vehicle of infection was documented in 21/46 (46%) of outbreaks (meat-containing vehicle in 20/21). In 15/21 (71%) identification of the suspected vehicle was based on descriptive evidence alone, in 5/21 (24%) with supporting evidence from an epidemiological study and in 2/21 (10%) with supporting microbiological evidence.C. perfringens-associated illness is preventable and although identification of foodborne outbreaks is challenging, a risk mitigation approach should be taken, particularly in vulnerable populations such as care homes for the elderly.

Enforcement of science-using a Clostridium perfringens outbreak investigation to take legal action

BACKGROUND

We report an outbreak of Clostridium perfringens in a care home in North East England.

METHODS

A retrospective cohort study was used to investigate this outbreak. Faecal samples were obtained from symptomatic residents. Environmental Health Officers carried out a food hygiene inspection and formal statements were taken.

RESULTS

Fifteen residents reported illness and the epidemic curve was suggestive of a point source outbreak. Results suggest that illness was associated with consumption of mince & vegetable pie and/or gravy. There were a number of issues with food served, in particular the mince products had been cooked, cooled, reheated and served again over a period of several days. Faecal sampling revealed the presence of C.perfringens enterotoxin gene and four samples were indistinguishable by fluorescent amplified fragment length polymorphism, indicating a likely common source. The operator of the home was charged with three offences under the General Food Regulations 2004 and the Food Hygiene (England) Regulations 2006 and was convicted on all counts.

CONCLUSIONS

An outbreak of C.perfringens occurred in a care home. The likely cause was consumption of mince & vegetable pie and/or gravy. Epidemiological evidence can be used to help prosecute businesses with food safety offences in such circumstances.

Identification of Clostridium species and DNA fingerprinting of Clostridium perfringens by amplified fragment length polymorphism analysis

An amplified fragment length polymorphism (AFLP) method was applied to 129 strains representing 24 different Clostridium species, with special emphasis on pathogenic clostridia of medical or veterinary interest, to assess the potential of AFLP for identification of clostridia. In addition, the ability of the same AFLP protocol to type clostridia at the strain level was assessed by focusing on Clostridium perfringens strains. All strains were typeable by AFLP, so the method seemed to overcome the problem of extracellular DNase production. AFLP differentiated all Clostridium species tested, except for Clostridium ramosum and Clostridium limosum, which clustered together with a 45% similarity level. Other Clostridium species were divided into species-specific clusters or occupied separate positions. Wide genetic diversity was observed among Clostridium botulinum strains, which were divided into seven species-specific clusters. The same AFLP protocol was also suitable for typing C. perfringens at the strain level. A total of 29 different AFLP types were identified for 37 strains of C. perfringens; strains initially originating from the same isolate showed identical fingerprinting patterns and were distinguished from unrelated strains. AFLP proved to be a highly reproducible, easy-to-perform, and relatively fast method which enables high throughput of samples and can serve in the generation of identification libraries. These results indicate that the AFLP method provides a promising tool for the identification and characterization of Clostridium species.

Genetic diversity of Clostridium perfringens type A isolates from animals, food poisoning outbreaks and sludge

BACKGROUND

Clostridium perfringens, a serious pathogen, causes enteric diseases in domestic animals and food poisoning in humans. The epidemiological relationship between C. perfringens isolates from the same source has previously been investigated chiefly by pulsed-field gel electrophoresis (PFGE). In this study the genetic diversity of C. perfringens isolated from various animals, from food poisoning outbreaks and from sludge was investigated.

RESULTS

We used PFGE to examine the genetic diversity of 95 C. perfringens type A isolates from eight different sources. The isolates were also examined for the presence of the beta2 toxin gene (cpb2) and the enterotoxin gene (cpe). The cpb2 gene from the 28 cpb2-positive isolates was also partially sequenced (519 bp, corresponding to positions 188 to 706 in the consensus cpb2 sequence). The results of PFGE revealed a wide genetic diversity among the C. perfringens type A isolates. The genetic relatedness of the isolates ranged from 58 to 100% and 56 distinct PFGE types were identified. Almost all clusters with similar patterns comprised isolates with a known epidemiological correlation. Most of the isolates from pig, horse and sheep carried the cpb2 gene. All isolates originating from food poisoning outbreaks carried the cpe gene and three of these also carried cpb2. Two evolutionary different populations were identified by sequence analysis of the partially sequenced cpb2 genes from our study and cpb2 sequences previously deposited in GenBank.

CONCLUSION

As revealed by PFGE, there was a wide genetic diversity among C. perfringens isolates from different sources. Epidemiologically related isolates showed a high genetic similarity, as expected, while isolates with no obvious epidemiological relationship expressed a lesser degree of genetic similarity. The wide diversity revealed by PFGE was not reflected in the 16S rRNA sequences, which had a considerable degree of sequence similarity. Sequence comparison of the partially sequenced cpb2 gene revealed two genetically different populations. This is to our knowledge the first study in which the genetic diversity of C. perfringens isolates both from different animals species, from food poisoning outbreaks and from sludge has been investigated.

Clonal relationships among Clostridium perfringens of porcine origin as determined by multilocus sequence typing

Clostridium perfringens is ubiquitous in the environment and the intestinal tracts of most mammals, but this organism also causes gas gangrene and enteritis in human and animal hosts. While expression of specific toxins correlates with specific disease in certain hosts, the other factors involved in commensalism and host pathogenesis have not been clearly identified. A multilocus sequence typing (MLST) scheme was developed for C. perfringens with the aim of grouping isolates with respect to disease presentation and/or host preference. Sequence data were obtained from one virulence and seven housekeeping genes for 132 C. perfringens isolates that comprised all five toxin types and were isolated from 10 host species. Eighty sequence types (STs) were identified, with the majority (75%) containing only one isolate. eBURST analysis identified three clonal complexes, which contained 59.1% of the isolates. Clonal complex (CC) 1 contained 31, predominantly type A isolates from diverse host species. Clonal complex 2 contained 75% of the bovine type E isolates examined in this study. Clonal complex 3 consisted predominantly of porcine type A and type C isolates. Interestingly, these porcine isolates (n=32) all carried consensus cpb2 and cna genes, encoding beta2 toxin and CpCna, a collagen binding protein, respectively. This compares to carriage of both these genes by only 3.6% of porcine isolates not present in clonal complex 3 (n=28). The data obtained indicates that MLST may be used to identify host species relationships with respect to these C. perfringens isolates.

Molecular subtyping of poultry-associated type A Clostridium perfringens isolates by repetitive-element PCR

Clostridium perfringens strains (type A) isolated from an integrated poultry operation were subtyped using repetitive-element PCR with Dt primers. Isolates were obtained from fecal, egg shell, fluff, and carcass rinse samples as part of a previously reported temporally linked epidemiological survey. A total of 48 isolates of C. perfringens were obtained from different stages of the broiler chicken production chain from two separate breeder farms that supplied a single hatchery that in turn provided chicks to a single grow-out farm whose flocks were processed at a single plant. All 48 isolates were typeable (100% typeability) by repetitive-element PCR with Dt primers. This subtyping method was highly reproducible and discriminatory. By repetitive-element PCR with Dt primers, isolates were classified into four major branches with 12 subgroups or clades. The Simpson's index of discrimination was calculated to be 0.96 for groupings of >95% correlation. Toxin gene profiles of the isolates indicated that all of the isolates were C. perfringens alpha-toxin gene positive and 46 of 48 isolates were beta2-toxin gene positive. All strains were negative for beta- and epsilon-toxin genes. Repetitive sequence-based PCR was found to be a technically practical and reproducible means of subtyping C. perfringens libraries from specific epidemiological or production environment settings.

Multiple-locus variable-number tandem repeat analysis for strain typing of Clostridium perfringens

Clostridium perfringens is ubiquitous in the environment and causes diseases in man and animals, with syndromes ranging from enteritis, enterotoxemia, and sudden death to food poisoning and gas gangrene. Understanding the epidemiology of these infections and of the evolution of virulence in C. perfringens necessitate an efficient, time and cost effective strain typing method. Multiple-locus variable-number tandem repeat analysis (MLVA) has been applied to typing of other pathogens and we describe here the development of a MLVA scheme for C. perfringens. We characterized five variable tandem repeat (VNTR) loci, four of which are contained within protein encoding genes and screened 112 C. perfringens isolates to evaluate typability, reproducibility, and discriminatory power of the scheme. All the isolates were assigned a MLVA genotype and the technique has excellent reproducibility, with a numerical index of discrimination for the five VNTR loci of 0.995. Thus MLVA is an efficient tool for C. perfringens strain typing, and being PCR based makes it rapid, easy, and cost effective. In addition, it can be employed in epidemiological, ecological, and evolutionary investigations of the organism.