Dataset Information

Genomic Characterization of Jumbo Salmonella Phages That Effectively Target United Kingdom Pig-Associated Salmonella Serotypes.

ABSTRACT: A common cause of human food poisoning is through ingestion of pork products contaminated with Salmonella spp. Worryingly multi-drug resistant (MDR) Salmonella strains have been isolated from pigs, which motivates the need for alternative antimicrobials. In this study isolation and characterization of 21 lytic Salmonella phages is described. All 21 phages, labeled as SPFM phages were shown to efficiently infect MDR Salmonella strains isolated from United Kingdom pigs and phages SPFM1, SPFM3, SPFM10, SPFM14, SPFM15, SPFM17, and SPFM19 could lyse 100% of strains tested. The phage genome sizes range from 233 to 242 Kb, which qualifies them as jumbo phages. All SPFM phage genomes are approximately 95% similar to each other by average nucleotide identity, they encode between 258-307 coding sequences and share 188 core genes. Phylogenetic analysis shows these phages are most similar to phages of the genus Seoulvirus and to further characterize phages within the genus, genes under positive selection were identified. Several of the genes under evolutionary selection pressure were predicted to encode for proteins that interact with bacteria. We describe the phenotypic and genetic characterization of this novel Salmonella phage set. As the phages efficiently kill MDR Salmonella strains, they may offer a promising alternative to antibiotics.

SUBMITTER: Thanki AM

PROVIDER: S-EPMC6614189 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Salmonella is the second most commonly reported zoonotic gastrointestinal pathogen in the European Union, and a significant proportion of the cases are linked to the consumption of contaminated pork. Reduction of Salmonella at the farm level helps to mininimise the contamination pressure at the slaughterhouse, and therefore the number of Salmonella bacteria entering the food chain. Cleaning and disinfection (C&D) between batches of pigs is an intervention measure that has potential to reduce the transmission of Salmonella contamination within farms. In this study, two pig finisher buildings in each of 10 Salmonella positive farms were sampled pre-C&D, post-C&D, post-restocking with the following batch of pigs, and shortly before these pigs were sent to slaughter. The incoming batch of pigs was also sampled before it reached the study building (pre-restocking). At each visit, pooled and individual faecal samples were collected and Salmonella isolation was carried out according to an ISO 6579:2002 Annex D-based method. One building on each farm (intervention) was cleaned and disinfected according to a rigorous protocol consisting of several steps and a Defra-approved disinfectant used at the General Orders concentration, whilst the other building (control) was cleaned and disinfected as per normal farm routine. At the post-C&D visit, Enterobacteriaceae and total bacterial counts were determined to evaluate residual faecal contamination and general hygiene levels. Rodent specialists visited the farms before and after C&D and rodent carcasses were collected for Salmonella testing. The intervention buildings were significantly less likely (p = 0.004) to be positive for Salmonella after C&D. The pre-restocking pigs had the highest likelihood (p<0.001) of being Salmonella positive (often with multiple serovars) and there was no significant difference between intervention and control buildings in Salmonella prevalence at the post-restocking visit (p = 0.199). However, the pigs housed in the intervention buildings were significantly less likely (p = 0.004) to be positive for Salmonella at slaughter age. Multivariable analysis suggested that cleaning all fixtures of buildings, leaving the pens empty for 2-3 days and using an effective disinfectant are factors significantly improving the likelihood of removing Salmonella contamination during C&D. Signs of rodents were recorded in all farms, but rodent activity and harbourage availability decreased between visits. All the rats tested were Salmonella negative. S. Typhimurium or its monophasic variants were isolated from 6 mouse carcasses in 3 farms where the same serovars were isolated from pigs. This study demonstrates that an appropriate C&D programme significantly reduces the likelihood of residual contamination in Salmonella positive pig buildings, and suggests a significant reduction in the prevalence of Salmonella in the pigs in appropriately cleaned and disinfected buildings when sampled before slaughter. Due to a high prevalence of infection in replacement pigs, control of Salmonella in pig farms is challenging. Rodents may also contribute to the carry-over of infection between batches. C&D is a useful measure to help reduce the number of infected pigs going to the slaughterhouse, but should be supplemented by other control measures along the pig breeding and production chain.

Project description:BackgroundThe EU Regulation No 2160/2003 imposes a reduction in the prevalence of Salmonella in pigs. The efficiency of control programmes for Salmonella in pigs, reported among the EU Member States, varies and definitive eradication seems very difficult. Control measures currently recommended for Salmonella are not serotype-specific. Is it possible that the risk factors for different Salmonella serotypes are different? The aim of this study was to investigate potential risk factors for two groups of Salmonella sp serotypes using pen faecal samples from breeding pig holdings representative of the Portuguese pig sector.MethodsThe data used come from the Baseline Survey for the Prevalence of Salmonella in breeding pigs in Portugal. A total of 1670 pen faecal samples from 167 herds were tested, and 170 samples were positive for Salmonella. The presence of Salmonella in each sample (outcome variable) was classified in three categories: i) no Salmonella, ii) Salmonella Typhimurium or S. Typhimurium-like strains with the antigenic formula: 1,4,5,12:i:-, , and iii) other serotypes. Along with the sample collection, a questionnaire concerning herd management and potential risk factors was utilised. The data have a "natural" hierarchical structure so a categorical multilevel analysis of the dataset was carried out using a Bayesian hierarchical model. The model was estimated using Markov Chain Monte Carlo methods, implemented in the software WinBUGS.ResultsThe significant associations found (when compared to category "no Salmonella"), for category "serotype Typhimurium or S. Typhimurium-like strains with the antigenic formula: 1,4,5,12:i:-" were: age of breeding sows, size of the herd, number of pigs/pen and source of semen. For the category "other serotypes" the significant associations found were: control of rodents, region of the country, source of semen, breeding sector room and source of feed.ConclusionsThe risk factors significantly associated with Salmonella shedding from the category "serotype Typhimurium or serotype 1,4,5,12:i:-" were more related to animal factors, whereas those associated with "other serotypes" were more related to environmental factors. Our findings suggest that different control measures could be used to control different Salmonella serotypes in breeding pigs.

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Genomic Characterization of Jumbo Salmonella Phages That Effectively Target United Kingdom Pig-Associated Salmonella Serotypes.

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