A prevalence study of Salmonella spp., Yersinia spp., Toxoplasma gondii and porcine reproductive and respiratory syndrome virus in UK pigs at slaughter

Bayesian evaluation of meat juice ELISA for detecting Salmonella in slaughtered pigs without specifying a cut-off

BACKGROUND

Consumption of pork and pork products is a major source of human infection with Salmonella. Salmonella is typically subclinical in pigs, making it difficult to identify infected pigs. Therefore, effective surveillance of Salmonella in pigs critically relies on good knowledge on how well the diagnostic tests used perform. A test that has been used in several countries for Salmonella monitoring is serological testing of meat juice using an ELISA (MJ ELISA) to detect antibodies against Salmonella. This MJ ELISA data could be used to estimate infection prevalence and trends. However, as the MJ ELISA output is a sample-to-positive (S/P) ratio, which is a continuous outcome rather than a binary (positive/negative) result, the interpretation of this data depends upon a chosen cut-off.

AIM

To apply Bayesian latent class models (BLCMs) to estimate diagnostic accuracy of the MJ ELISA test values in the absence of a gold standard without needing to apply a cut-off.

METHODS AND RESULTS

BLCMs were fitted to data from a UK abattoir survey carried out in 2006 in order to estimate the diagnostic accuracy of MJ ELISA with respect to the prevalence of active Salmonella infection. This survey consisted of a MJ ELISA applied in parallel with the bacteriological testing of caecal contents, carcass swabs and lymph nodes (n = 625). A BLCM was also fitted to the same data but with dichotomisation of the MJ ELISA results, in order to compare with the model using continuous outcomes. Estimates were obtained for sensitivity and specificity of the ELISA over a range of S/P values and for the bacteriological tests and were found to be similar between the models using continuous and dichotomous ELISA outcomes.

CONCLUSION

The Bayesian method without specifying a cut-off does allow prevalence to be inferred without specifying a cut-off for the ELISA. The study results will be useful for estimating infection prevalence from serological surveillance data.

Occurrence of Salmonella spp. in animal patients and the hospital environment at a veterinary academic hospital in South Africa

Background and Aims

Nosocomial infections caused by Salmonella spp. are common in veterinary facilities. The early identification of high-risk patients and sources of infection is important for mitigating the spread of infections to animal patients and humans. This study investigated the occurrence of Salmonella spp. among patients at a veterinary academic hospital in South Africa. In addition, this study describes the environmental factors that contribute to the spread of Salmonella spp. in the veterinary facility.

Materials and Methods

This study used a dataset of Salmonella-positive animals and environmental samples submitted to the bacteriology laboratory between 2012 and 2019. The occurrence of Salmonella isolates at the veterinary hospital was described based on source, month, season, year, and location. Proportions and 95% confidence intervals were calculated for each variable.

Results

A total of 715 Salmonella isolates were recorded, of which 67.6% (483/715) came from animals and the remainder (32.4%, 232/715) came from environmental samples. The highest proportion (29.2%) of Salmonella isolates was recorded in 2016 and most isolates were reported in November (17.4%). The winter season had the lowest (14.6%) proportion of isolates reported compared to spring (31.3%), summer (27.8%), and autumn (26.4%). Salmonella Typhimurium (20.0%) was the most frequently reported serotype among the samples tested, followed by Salmonella Anatum (11.2%). Among the positive animal cases, most (86.3%) came from equine clinics. Most reported isolates differed based on animal species with S. Typhimurium being common in equines and S. Anatum in bovines.

Conclusion

In this study, S. Typhimurium emerged as the predominant strain in animal and environmental samples. Equines were the most affected animals; however, Salmonella serotypes were also detected in the production animals. Environmental contamination was also a major source of Salmonella species in this study. To reduce the risk of transmission, strict infection prevention and control measures (biosecurity) must be implemented.

Biosecurity measures to control hepatitis E virus on European pig farms

Hepatitis E virus (HEV) genotype 3 is a prevalent zoonotic pathogen in European pig farms, posing a significant public health risk primarily through the foodborne route. The study aimed to identify effective biosecurity measures for controlling HEV transmission on pig farms, addressing a critical gap in current knowledge. Utilizing a cross-sectional design, fecal samples from gilts, dry sows, and fatteners were collected on 231 pig farms of all farm types across nine European countries. Real-time RT-PCR was employed to test these samples for HEV. Simultaneously, a comprehensive biosecurity questionnaire captured data on various potential measures to control HEV. The dependent variable was HEV risk, categorized as lower or higher based on the percentage of positive pooled fecal samples on each farm (25% cut-off). The data were analyzed using generalized linear models (one for finisher samples and one for all samples) with a logit link function with country and farm type as a priori fixed factors. The results of the final multivariable models identified key biosecurity measures associated with lower HEV risk, which were the use of a hygienogram in the breeding (OR: 0.06, p = 0.001) and/or fattening area after cleaning (OR: 0.21, p = 0.019), the presence of a quarantine area (OR: 0.29, p = 0.025), testing and/or treating purchased feed against Salmonella (OR: 0.35, p = 0.021), the presence of other livestock species on the farm, and having five or fewer persons in charge of the pigs. Contrary to expectations, some biosecurity measures were associated with higher HEV risk, e.g., downtime of 3 days or longer after cleaning in the fattening area (OR: 3.49, p = 0.005) or mandatory handwashing for farm personnel when changing barn sections (OR: 3.4, p = 0.026). This novel study unveils critical insights into biosecurity measures effective in controlling HEV on European pig farms. The identification of both protective and risk-associated measures contributes to improving strategies for managing HEV and underscores the complexity of biosecurity in pig farming.

Isolation, characterization and antimicrobial resistance of Yersinia enterocolitica from Polish cattle and their carcasses

BACKGROUND

Yersinia enterocolitica is a heterogeneous bacterial species that has been divided into six biotypes and more than 70 serotypes. Each year, the European Food Safety Authority classifies yersiniosis caused by Y. enterocolitica as one of the most important zoonotic diseases. The prevalence of Y. enterocolitica in cattle has not been thoroughly analyzed in Poland, and beef and bovine carcasses contaminated with antimicrobial resistant Y. enterocolitica pose a health risk for both, farm workers and consumers. Therefore, the aim of this study was to evaluate the prevalence of Y. enterocolitica in cattle and to determine the antimicrobial susceptibility of the isolated strains.

RESULTS

A total of 1020 samples were analyzed, including 660 rectal swabs collected from live cattle and 360 swabs from cold-stored beef carcasses. The results of this study indicate that Y. enterocolitica was isolated from three of the 15 examined cattle herds and the prevalence within these herds ranged from 0% to nearly 32%. Y. enterocolitica was isolated from 14.7% of the examined heifers, 7.4% of calves and 5.5% of adult cows. More than 65% of the strains were isolated from cold enrichment. The strains isolated from live cattle tested positive for the ystB gene, while ail and ystA genes were not found. Most of the isolated strains belonged to bioserotype 1A/NT. The majority of the isolated strains were resistant to ampicillin, cefalexin and amoxicillin with clavulanic acid, however these are expected phenotypes for Y. enterocolitica.

CONCLUSIONS

The results of this study indicate that Y. enterocolitica is present in cattle herds in Poland. The strains isolated from live cattle were ystB-positive, most of them belonged to bioserotype 1A/NT. The prevalence of Y. enterocolitica strains was generally low in cold-stored beef carcasses.

Assessing pig farm biosecurity measures for the control of Salmonella on European farms

Salmonella spp. is a common zoonotic pathogen, causing gastrointestinal infections in people. Pigs and pig meat are a major source of infection. Although farm biosecurity is believed to be important for controlling Salmonella transmission, robust evidence is lacking on which measures are most effective. This study enrolled 250 pig farms across nine European countries. From each farm, 20 pooled faecal samples (or similar information) were collected and analysed for Salmonella presence. Based on the proportion of positive results, farms were categorised as at higher or lower Salmonella risk, and associations with variables from a comprehensive questionnaire investigated. Multivariable analysis indicated that farms were less likely to be in the higher-risk category if they had '<400 sows'; used rodent baits close to pig enclosures; isolated stay-behind (sick) pigs; did not answer that the hygiene lock/ anteroom was easy to clean; did not have a full perimeter fence; did apply downtime of at least 3 days between farrowing batches; and had fully slatted flooring in all fattener buildings. A principal components analysis assessed the sources of variation between farms, and correlation between variables. The study results suggest simple control measures that could be prioritised on European pig farms to control Salmonella.

Yersinia enterocolitica in wild and peridomestic rodents within Great Britain, a prevalence study

Yersinia enterocolitica is a human pathogen transmitted via the faecal-oral route among animals and humans and is a major foodborne public health hazard. This study explores the role of Y. enterocolitica transmission at the livestock-wildlife interface and investigates the potential role wild and peridomestic rodents play as a source of this zoonotic pathogen. The total of 342 faecal samples collected from the seven rodent species and one insectivore was examined using an optimized protocol to culture and identify Y. enterocolitica. Positive samples were also bioserotyped for grouping and determination of sample pathogenicity. Wildlife species sampled in this study were separated into two sample groups: randomly sampled (brown rats, house mice, wood mice, bank voles, field voles and the common shrew), as well as targeted sampling (red and grey squirrels). The overall prevalence of Y. enterocolitica in the randomly sampled population was 3.73%. Brown rats were chosen as sentinel species and tested to determine if location (pig farm vs non-pig farm) was a significant factor affecting Y. enterocolitica prevalence. In this study, location was not significant. All positive samples were found to be of biotype 1A, deemed non-pathogenic. Three of the samples were serotype 09, six were serotype 27 and five had an unidentifiable serotype. This study represents the first time Y. enterocolitica has been identified in these species of wildlife within mainland Britain. In addition, this study's findings are entirely novel and overall with regard to field voles and common shrews. However, the role of wild and peridomestic rodents in the transmission of pathogenic Y. enterocolitica remains unknown, as this study was unable to detect the presence of pathogenic Y. enterocolitica strains in these species.

Prophylactic Delivery of a Bacteriophage Cocktail in Feed Significantly Reduces Salmonella Colonization in Pigs

Nontyphoidal Salmonella spp. are a leading cause of human food poisoning and can be transmitted to humans via consuming contaminated pork. To reduce Salmonella spread to the human food chain, bacteriophage (phage) therapy could be used to reduce bacteria from animals' preslaughter. We aimed to determine if adding a two-phage cocktail to feed reduces Salmonella colonization in piglets. This first required spray drying phages to allow them to be added as a powder to feed, and phages were spray dried in different excipients to establish maximum recovery. Although laboratory phage yields were not maintained during scale up in a commercial spray dryer (titers fell from 3 × 108 to 2.4 × 106 PFU/g respectively), the phage titers were high enough to progress. Spray dried phages survived mixing and pelleting in a commercial feed mill, and sustained no further loss in titer when stored at 4°C or barn conditions over 6 months. Salmonella-challenged piglets that were prophylactically fed the phage-feed diet had significantly reduced Salmonella colonization in different gut compartments (P < 0.01). 16S rRNA gene sequencing of fecal and gut samples showed phages did not negatively impact microbial communities as they were similar between healthy control piglets and those treated with phage. Our study shows delivering dried phages via feed effectively reduces Salmonella colonization in pigs. IMPORTANCE Infections caused by Salmonella spp. cause 93.8 million cases of human food poisoning worldwide, each year of which 11.7% are due to consumption of contaminated pork products. An increasing number of swine infections are caused by multidrug-resistant (MDR) Salmonella strains, many of which have entered, and continue to enter the human food chain. Antibiotics are losing their efficacy against these MDR strains, and thus antimicrobial alternatives are needed. Phages could be developed as an alternative approach, but research is required to determine the optimal method to deliver phages to pigs and to determine if phage treatment is effective at reducing Salmonella colonization in pigs. The results presented in this study address these two aspects of phage development and show that phages delivered via feed prophylactically to pigs reduces Salmonella colonization in challenged pigs.

Salmonella Shedding in Slaughter Pigs and the Use of Esterified Formic Acid in the Drinking Water as a Potential Abattoir-Based Mitigation Measure

Pigs shedding Salmonella at slaughter are considered a source of carcass contamination and human infection. To assess this potential risk, the proportion of Salmonella shedders that arrive for slaughter was evaluated in a population of 1068 pigs from 24 farms. Shedding was present in 27.3% of the pigs, and the monophasic variant of Salmonella Typhimurium, an emerging zoonotic serotype, was the most prevalent (46.9%). Antimicrobial resistance (AMR) in Salmonella isolates was common, but few isolates showed AMR to antimicrobials of critical importance for humans such as third-generation cephalosporins (5%), colistin (0%), or carbapenems (0%). However, AMR to tigecycline was moderately high (15%). The efficacy of an esterified formic acid in the lairage drinking water (3 kg formic acid/1000 L) was also assessed as a potential abattoir-based strategy to reduce Salmonella shedding. It was able to reduce the proportion of shedders (60.7% in the control group (CG) vs. 44.3% in the treatment group (TG); p < 0.01). After considering clustering and confounding factors, the odds of shedding Salmonella in the CG were 2.75 (95% CI = 1.80−4.21) times higher than those of the TG, suggesting a potential efficacy of reduction in shedding as high as 63.6%. This strategy may contribute to mitigating the burden of abattoir environmental contamination.

Prevalence of Salmonella spp. in slaughter pigs and carcasses in Irish abattoirs and their antimicrobial resistance

Background

Salmonella is an important zoonotic pathogen and is one of the main causes of foodborne outbreaks and infections in the European Union. Pigs are a significant reservoir and are frequently subclinical carriers of this organism. Salmonella can be shed in the faeces allowing infection to spread to other pigs, the environment, transport vehicles, lairages and other areas. Inadvertent spillage of gut contents during the slaughter process also leads to contamination. A pig Salmonella control programme has operated in Ireland since 2002 but many local surveys and an EUMS baseline survey in 2008 continued to indicate high levels of the organism in the pig sector. The objectives of this study were to generate updated information on the prevalence of Salmonella spp, in slaughter pigs and carcasses in Irish abattoirs. Five pigs from each of 164 herds were randomly sampled over a 14-week period during 2016. One sample from each of the five pigs of; caecal content, ileo-caecal lymph nodes and carcass swabs (pre-chill) were collected. The five caeca and lymph node samples from each herd were processed as one pool of caecal samples and one pool of lymph node samples, respectively, while the five carcass swabs were tested as individual samples. All isolates were characterised by serotyping and antimicrobial susceptibility.

Results

In total, 235 Salmonella spp. were isolated from 820 individual carcass swabs, 164 pooled lymph nodes and 164 caecal contents. Salmonella spp. were isolated from 54.3% of the caecal contents and from 31.7% of the ileo-caecal lymph node sample pools. A total of 11.5% of carcass-swab samples yielded Salmonella spp. S. Typhimurium 4,[5],12:i:1,2 or its monophasic variant 4,[5],12:i:-: predominated among isolates from all positive samples; accounting for 73% of lymph nodes, 68% of caecal contents and 56% of carcass swab isolates. S. London and S. Derby were the next most common isolated serotypes.

Conclusions

These results confirm continuing high levels of Salmonella in fattening pigs in Ireland although reductions in carcass contamination compared to previous surveys were noted. A high prevalence of Salmonella in lymph nodes suggests that it remains a significant problem pre slaughter and a challenge to abattoirs in adhering to process hygiene requirements. The high prevalence of monophasic S. Typhimurim 4,[5],12:i:-: is of serious concern.

Therefore, it is important to identify contributing factors in the dissemination of this pathogen in the pork industry in order to minimise the risk of human salmonellosis cases.

Non-diarrhoeic pigs as source of highly virulent and multidrug-resistant non-typhoidal Salmonella

Food-producing animals act as reservoirs of non-typhoidal Salmonella (NTS) serovars with potential food safety and public health implications. The present cross-sectional study aimed at determining the prevalence of Salmonella serotypes in non-diarrhoeic pigs and characterizing the isolates using molecular tools. Salmonella isolates (n = 22) recovered from faecal samples of 194 randomly selected pigs were characterized for virulence and antimicrobial resistance and subtyped using XbaI-PFGE. The prevalence of Salmonella in apparently healthy non-diarrhoeic pigs was 11.3% (95%CI, 4.3-19.5%), with S. Weltevreden (81.8%) and S. Enteritidis (18.2%) being the serotypes detected. Salmonella isolates harboured virulence genes such as invA (100%), stn (100%), spvR/spvC (86.3%) and fimA (22.7%). Phenotypically, isolates showed sensitivity to chloramphenicol, levofloxacin and ciprofloxacin and resistance to tetracycline and ampicillin (100%), streptomycin (86.4%), amoxicillin-clavulanate (63.6%), cefotaxime (22.7%) and ceftriaxone (9.1%). Notably, 18.2% isolates were multidrug-resistant (≥ 3 antimicrobial class) with multiple antimicrobial resistance (MAR) index of 0.56-0.67 (18.2%), 0.44 (45.5%), 0.33 (31.8%) and 0.22 (4.5%). Genotypically, isolates carried various antibiotic resistance genes: ESBL (bla_TEM and bla_OXA), aminoglycoside (strA, strB and aadA1), sulphonamide (sul1, sul2 and dfrA1), tetracycline (tetA and tetB) and plasmid AmpC beta-lactamase (ACC, FOX, MOX, DHA, CIT and EBC). The present investigation emphasizes the epidemiological significance of PFGE typing in the detection of emerging strains of highly virulent and multidrug-resistant S. Weltevreden and S. Enteritidis in non-diarrhoeic pigs that pose serious public health implications in the pork supply chain environment. More extensive longitudinal study is warranted to provide epidemiological links between environmental reservoirs and animal and human infections in piggery settings.

Transcriptome profiling identifies immune response genes against porcine reproductive and respiratory syndrome virus and Haemophilus parasuis co-infection in the lungs of piglets

Background

Co-infections of the porcine reproductive and respiratory syndrome virus (PRRSV) and the Haemophilus parasuis (HPS) are severe in Chinese pigs, but the immune response genes against co-infected with 2 pathogens in the lungs have not been reported.

Objectives

To understand the effect of PRRSV and/or HPS infection on the genes expression associated with lung immune function.

Methods

The expression of the immune-related genes was analyzed using RNA-sequencing and bioinformatics. Differentially expressed genes (DEGs) were detected and identified by quantitative real-time polymerase chain reaction (qRT-PCR), immunohistochemistry (IHC) and western blotting assays.

Results

All experimental pigs showed clinical symptoms and lung lesions. RNA-seq analysis showed that 922 DEGs in co-challenged pigs were more than in the HPS group (709 DEGs) and the PRRSV group (676 DEGs). Eleven DEGs validated by qRT-PCR were consistent with the RNA sequencing results. Eleven common Kyoto Encyclopedia of Genes and Genomes pathways related to infection and immune were found in single-infected and co-challenged pigs, including autophagy, cytokine-cytokine receptor interaction, and antigen processing and presentation, involving different DEGs. A model of immune response to infection with PRRSV and HPS was predicted among the DEGs in the co-challenged pigs. Dual oxidase 1 (DUOX1) and interleukin-21 (IL21) were detected by IHC and western blot and showed significant differences between the co-challenged pigs and the controls.

Conclusions

These findings elucidated the transcriptome changes in the lungs after PRRSV and/or HPS infections, providing ideas for further study to inhibit ROS production and promote pulmonary fibrosis caused by co-challenging with PRRSV and HPS.

Toxoplasma gondii Infection in Swine: Implications for Public Health

Toxoplasmosis, due to Toxoplasma gondii, is a parasitic disease with global importance. Among livestock, chronic T. gondii infection has been reported in higher rates in pigs and small ruminants, but with subclinical infections in case commonly encountered in pigs. Seroprevalence in the global pig population ranges according to the age or species of pigs, geographical distribution, production programs, and systems. Generally, T. gondii infections are noticed in low prevalence rates in conventional pig farms with high hygiene standards. In contrast, higher prevalence is common on free-ranging farms, outdoor or backyard small pig fams, as well as in farmed or hunted wild boars. The T. gondii average worldwide seroprevalence in pigs is reported to be 13% in Europe, 21% in Africa, 25% in North America, 21% in Asia, and 23% in South America. Human toxoplasmosis outbreaks have been correlated with the consumption of raw or undercooked meat, especially from infected pigs or wild boars, as well as of contaminated drinking water. The risk of infection in processed pork products is lower compared with fresh pork, as meat processing can reduce or inactivate T. gondii tissue cysts. Hence, the prevalence of T. gondii in the pig population may be a useful indicator of the risk of human toxoplasmosis associated with the consumption of pork products. The lack of obligatory screening methods at farm level for the detection of antibodies in farmed animals or the viable T. gondii in carcasses at slaughterhouse level increases the risk of contaminated pork or meat products. For this reason, the application of biosecurity and surveillance programs at farm level is very important to prevent a T. gondii infection.

Abattoir-based study of Salmonella prevalence in pigs at slaughter in Great Britain

Consumption of pork and pork products can be associated with outbreaks of human salmonellosis. Salmonella infection is usually subclinical in pigs, and farm-based control measures are challenging to implement. To obtain data on Salmonella prevalence, samples can be collected from pigs during the slaughter process. Here we report the results of a Great Britain (GB) based abattoir survey conducted by sampling caecal contents from pigs in nine British pig abattoirs during 2019. Samples were collected according to a randomised stratified scheme, and pigs originating from 286 GB farms were included in this survey. Salmonella was isolated from 112 pig caecal samples; a prevalence of 32.2% [95% confidence interval (CI) 27.4–37.4]. Twelve different Salmonella serovars were isolated, with the most common serovars being S. 4,[5],12:i:-, a monophasic variant of Salmonella Typhimurium (36.6% of Salmonella-positive samples), followed by S. Derby (25.9% of Salmonella-positive samples). There was no significant difference compared to the estimate of overall prevalence (30.5% (95% CI 26.5–34.6)) obtained in the last abattoir survey conducted in the UK (2013). Abattoir-based control measures are often effective in the reduction of Salmonella contamination of carcasses entering the food chain. In this study, the effect of abattoir hygiene practices on the prevalence of Salmonella on carcasses was not assessed. Continuing Salmonella surveillance at slaughter is recommended to assess effect of farm-based and abattoir-based interventions and to monitor potential public health risk associated with consumption of Salmonella-contaminated pork products.

Porcine reproductive and respiratory syndrome virus seroprevalence in Scottish finishing pigs between 2006 and 2018

BACKGROUND

Porcine reproductive and respiratory syndrome (PRRS) is a major endemic pig disease worldwide and is associated with considerable economic costs.

METHODS

In Scotland, three abattoir surveys were conducted in 2006 (158 farms), 2012-2013 (94 farms) and 2017-2018 (97 farms) to estimate seroprevalence to PRRS virus (PRRSV) in commercial finishing pigs. These surveys covered around 79%, 59% and 66% of the Quality Meat Scotland assured farms slaughtering pigs in Scotland in 2006, 2012-13 and, 2017-18 respectively. In the 2006 survey, six pigs per farm were sampled and tested using the CIVTEST SUIS PRRS E/S test. In the 2012-2013 and 2017-2018 surveys, 10 pigs per farm were sampled and tested using the IDEXX PRRS X3 Ab test. A farm was considered positive if it had one or more seropositive samples.

RESULTS

The prevalence of positive farms was 45.6% (95% CI: 38.0-53.4), 47.8% (95% CI: 38.1-57.9) and 45.4% (95% CI: 35.8-55.3) in the 2006, 2012-2013 and 2017-2018 surveys, respectively, and 70%-75.5% farms did not change their status between sampling periods.

CONCLUSION

The prevalence of PRRSV exposure in Scottish pig herds was high and changed little from 2006 to 2018. These surveys have informed planning for a prospective PRRS control programme in Scotland.

Meat Safety from Farm to Slaughter—Risk-Based Control of Yersinia enterocolitica and Toxoplasma gondii

The implementation of the traditional meat safety control system has significantly contributed to increasing food safety and public health protection. However, several biological hazards have emerged in meat production, requiring a comprehensive approach to their control, as traditional methods of meat inspection at the slaughterhouse are not able to detect them. While national control programs exist for the most important meat-related hazards, similar data are still lacking for certain neglected threats, such as Yersinia enterocolitica or Toxoplasma gondii. The obstacle in controlling these hazards in the meat chain is their presence in latently infected, asymptomatic animals. Their effective control can only be achieved through systematic preventive measures, surveillance or monitoring, and antimicrobial interventions on farms and in slaughterhouses. To establish such a system, it is important to collect all relevant data on hazard-related epidemiological indicators from the meat chain, which should provide relevant guidance for interventions at the harvest and post-harvest stage. The proposed approach is expected to improve the existing system and provide many opportunities to improve food safety and public health.

Ecological niche adaptation of Salmonella Typhimurium U288 is associated with altered pathogenicity and reduced zoonotic potential

The emergence of new bacterial pathogens is a continuing challenge for agriculture and food safety. Salmonella Typhimurium is a major cause of foodborne illness worldwide, with pigs a major zoonotic reservoir. Two phylogenetically distinct variants, U288 and ST34, emerged in UK pigs around the same time but present different risk to food safety. Here we show using genomic epidemiology that ST34 accounts for over half of all S. Typhimurium infections in people while U288 less than 2%. That the U288 clade evolved in the recent past by acquiring AMR genes, indels in the virulence plasmid pU288-1, and accumulation of loss-of-function polymorphisms in coding sequences. U288 replicates more slowly and is more sensitive to desiccation than ST34 isolates and exhibited distinct pathogenicity in the murine model of colitis and in pigs. U288 infection was more disseminated in the lymph nodes while ST34 were recovered in greater numbers in the intestinal contents. These data are consistent with the evolution of S. Typhimurium U288 adaptation to pigs that may determine their reduced zoonotic potential.

Reduction of Salmonella prevalence at slaughter in Lawsonia intracellularis co-infected swine herds by Enterisol® Ileitis vaccination

Salmonella spp. remains a wide-spread pathogen among pig herds and its control has major impact on food borne Salmonella infections in humans. The objective of the study was to investigate the influence of an Enterisol® Ileitis vaccination on Salmonella seroprevalence in Lawsonia intracellularis (L. intracellularis) and Salmonella spp. co-infected pig herds under field conditions. This study compared vaccinated and non-vaccinated pigs of consecutive piglet batches, housed on four different finishing units. Prior to study start, endemic field infections of L. intracellularis and Salmonella spp. were confirmed by serology in the nursery and in all finishing units. Field infection of L. intracellularis occurred at the middle of the nursery phase. In total twenty-five batches of finishing pigs were included in the study, pigs were investigated for four (non-vaccinated group, n = 9) or six months (vaccinated group, n = 16). The primary outcome parameter was Salmonella serology (antibody titers) at the end of fattening. Secondary parameters comprised serology for L. intracellularis and performance parameters, including average daily weight gain (g), duration of fattening period (days), feed conversion (kg/kg) and mortality (%). A total of 709 blood samples were assessed, deriving from vaccinated (n = 439) and non-vaccinated finishing pigs (n = 270). Evaluation of the antibody titers demonstrated that vaccination significantly reduced the Salmonella seroprevalence in the finishing pigs on all four farms. The average OD% values were reduced from 32.7% to 13.4% in addition to a reduced variability in the vaccinated pigs compared to the control group. The Salmonella category of all finishing farms improved by at least one category in accordance with the German Salmonella monitoring program. In addition, vaccination had a positive tendency on the average daily weight gain, fattening duration and reduced mortality. In conclusion, this study demonstrates that vaccination with Enterisol® Ileitis has a positive and direct impact on reduction of Salmonella infection in co-infected herds.

Bayesian Source Attribution of Salmonella Typhimurium Isolates From Human Patients and Farm Animals in England and Wales

The purpose of the study was to apply a Bayesian source attribution model to England and Wales based data on Salmonella Typhimurium (ST) and monophasic variants (MST), using different subtyping approaches based on sequence data. The data consisted of laboratory confirmed human cases and mainly livestock samples collected from surveillance or monitoring schemes. Three different subtyping methods were used, 7-loci Multi-Locus Sequence Typing (MLST), Core-genome MLST, and Single Nucleotide Polymorphism distance, with the impact of varying the genetic distance over which isolates would be grouped together being varied for the latter two approaches. A Bayesian frequency matching method, known as the modified Hald method, was applied to the data from each of the subtyping approaches. Pigs were found to be the main contributor to human infection for ST/MST, with approximately 60% of human cases attributed to them, followed by other mammals (mostly horses) and cattle. It was found that the use of different clustering methods based on sequence data had minimal impact on the estimates of source attribution. However, there was an impact of genetic distance over which isolates were grouped: grouping isolates which were relatively closely related increased uncertainty but tended to have a better model fit.

All about Toxoplasma gondii infections in pigs: 2009-2020

Toxoplasma gondii infections are common in humans and animals worldwide. Toxoplasma gondii infection in pigs continues to be of public health concern. Pigs are important for the economy of many countries, particularly, USA, China, and European countries. Among the many food animals, pigs are considered the most important for T. gondii transmission in USA and China because viable parasites have rarely been isolated from beef or indoor raised chickens. Besides public health issues, T. gondii causes outbreaks of clinical toxoplasmosis in pigs in China, associated with a unique genotype of T. gondii (ToxoDB genotype #9 or Chinese 1), rarely found in other countries. The safety of ready to eat pork products with respect to T. gondii infection is a matter of recent debate. Here, we review in detail seroprevalence, prevalence of viable and nonviable T. gondii, epidemiology, risk assessment, diagnosis, and curing of pork products containing T. gondii for the past decade. This review will be of interest to biologists, parasitologists, veterinarians, and public health workers.

ESTABLISHMENT OF THE EFFICIENCY OF ANIMAL BREEDING PREMISES DISINFECTION BY MODERN DISINFECTANTS

The technological complex of veterinary-sanitary and organization-economic arrangements, conducted for prophylaxis and fight against infectious diseases inevitably includes disinfection, directed on inactivation of pathogenic agents in the environment. At applying new disinfectants in practice in the whole structure of the technological process of animal husbandry products, it is necessary to determine their sensitivity to the circulating microflora. The aim of the study was to establish the effectiveness of using new disinfecting preparations of different chemical groups and to determine regimes of their application in the whole complex of anti-epizootic prophylactic arrangements. Disinfecting preparations “Hermicidan FF plus”, “Peroxan forte”, “Viro-xal” were used in experiments. The quality of the conducted disinfection was controlled by separation of sanitary-representative microorganisms – bacteria of the colon bacillus group. It has been established, that the disinfecting preparations “Hermicidan FF plus”, “Peroxan forte”, “Viro-xal” have bactericidal properties relative to the sanitary-representative microorganisms and can be used in the general complex of sanitary-hygienic arrangements. The disinfectant “Hermicidan FF plus” has bactericidal properties in concentration 0,5 % at exposition 1 hour, preparation “Peroxan Forte” is effective at using in concentration 1,0 % at exposition 1 hour, and the disinfecting means “Viro xal” acts bactericidially in concentration 1,0 % at exposition 3 hours. For today the question of search for new technological, high-effective disinfecting preparations that correspond to existent requirements of biological safety and protection remains urgent.

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

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.

The global seroprevalence of Toxoplasma gondii in pigs: A systematic review and meta-analysis

Toxoplasmosis, caused by the protozoan parasite Toxoplasma gondii, is an important disease with worldwide distribution. Infection can occur from ingesting raw or undercooked infected meat, and among food animal species, pork is known to be one of the main sources of meat-borne infection. Here, we present results of the first systematic review and meta-analysis on the global T. gondii seroprevalence in pigs. PubMed/MEDLINE, Scopus, and EMBASE databases were comprehensively searched for relevant studies published between January 1, 1990 and October 25, 2018. We used a random effects model to calculate pooled seroprevalence estimates with 95% confidence intervals (CI) and analyzed data from five continents. We also conducted subgroup and meta-regression analyses to evaluate the effects of geographical and climate variables on pooled seroprevalence rates. Among 1542 publications identified, 148 studies containing 150 datasets were included in the meta-analysis, and comprised 148,092 pigs from 47 countries. The pooled global T. gondii seroprevalence in pigs was estimated to be 19% (95%CI, 17-22%; 23,696/148,092), with the lowest seroprevalence in Europe (13%; 10-15%) and highest seroprevalence in Africa (25%; 17-34%) and North America (25%; 19-33%). The seropositivity rates in Asia and South America regions were (21%, 16-26%) and (23%; 17-30%), respectively. A significantly higher T. gondii seroprevalence was associated with higher mean annual temperature and lower geographical latitude. The presence of cats on farms was identified as a potential risk factor for T. gondii seropositivity (OR, 1.41; 95%CI, 1.00-2.02). Our findings highlight the importance of pigs as a possible source of human T. gondii infections.

Persistent Infection and Long-Term Carriage of Typhoidal and Nontyphoidal Salmonellae

The ability of pathogenic bacteria to affect higher organisms and cause disease is one of the most dramatic properties of microorganisms. Some pathogens can establish transient colonization only, but others are capable of infecting their host for many years or even for a lifetime. Long-term infection is called persistence, and this phenotype is fundamental for the biology of important human pathogens, including Helicobacter pylori, Mycobacterium tuberculosis, and Salmonella enterica Both typhoidal and nontyphoidal serovars of the species Salmonella enterica can cause persistent infection in humans; however, as these two Salmonella groups cause clinically distinct diseases, the characteristics of their persistent infections in humans differ significantly. Here, following a general summary of Salmonella pathogenicity, host specificity, epidemiology, and laboratory diagnosis, I review the current knowledge about Salmonella persistence and discuss the relevant epidemiology of persistence (including carrier rate, duration of shedding, and host and pathogen risk factors), the host response to Salmonella persistence, Salmonella genes involved in this lifestyle, as well as genetic and phenotypic changes acquired during prolonged infection within the host. Additionally, I highlight differences between the persistence of typhoidal and nontyphoidal Salmonella strains in humans and summarize the current gaps and limitations in our understanding, diagnosis, and curing of persistent Salmonella infections.

Molecular and in vitro characterisation of hepatitis E virus from UK pigs

Hepatitis E virus (HEV) infection is widespread in the global pig population. Although clinically inapparent in pigs, HEV infection is the cause of Hepatitis E in humans and transmission via the food chain has been established. Following a 2013 study that investigated prevalence of HEV infection in UK slaughter-age pigs samples indicating highest viral load were selected for further characterisation. High throughput sequencing was used to obtain the complete coding sequence from five samples. An in-frame insertion was observed within the HEV hypervariable region in two samples. To interrogate whether this mutation may be the cause of high-level viraemia and faecal shedding as observed in the sampled pigs virus isolation and culture was conducted. Based on viral growth kinetics there was no evidence that these insertions affected replication efficiency in vitro, suggesting as yet undetermined host factors may affect the course of infection and consequently the risk of foodborne transmission.

Assessment of the feasibility of serological monitoring and on-farm information about health status for the future meat inspection of fattening pigs

Current macroscopic meat inspection cannot detect the most common pork-borne pathogens (Salmonella spp., Yersinia enterocolitica and Toxoplasma gondii). Furthermore, food chain information (FCI) may not provide sufficient data for visual-only inspection, which is supposed to be the common way of inspection of pigs in the European Union. Our observational study aimed to evaluate the serological monitoring and the clinical evaluation of on-farm health status of pigs and assess the feasibility of these data as part of the FCI in meat inspection. We studied the serological status of Salmonella spp., Yersinia spp. and T. gondii in pigs during the fattening period. Additionally, we evaluated the association between on-farm health status and meat inspection findings. On 57 indoor fattening pig farms in Finland, we collected blood samples (mean of 20 pigs/farm) and assessed the on-farm health (coughing, tail biting, lameness) at the end of the fattening period. We visited 34 of these farms also at the beginning of the fattening for sampling and on-farm health evaluation of the same pigs. Meat inspection results were obtained after slaughter for all 57 farms. Salmonella seroprevalence was low at the end of the fattening period: it was 17.6%, 10.6% or 1.9%, with the cut-off values of OD15% (recommended by the test manufacturer), OD20% (used by Danish monitoring programme) and OD40% (used by German monitoring programme), respectively. The overall seroprevalence of Salmonella spp. and Yersinia spp. increased significantly (P < 0.001) during the fattening period (from 8.1% to 17.2% and from 30.3% to 72.3%, respectively), while the seroprevalence of T. gondii remained low (<1%). The within-farm seroprevalences of Salmonella spp. and Yersinia spp. differed significantly between the farms and this farm-level serological data could be used as FCI for risk-based decisions to improve food safety. Such potentially feasible decisions could include additional carcass testing, carcass decontamination, carcass processing, slaughtering arrangements and improved biosecurity measures at the farm. However, risk mitigation targets and procedures must be carefully adjusted for each pathogen regarding also economic aspects. Tail biting observed on farm was associated with partial carcass condemnations and arthritis at slaughter. This information could be included in the FCI and used when making decisions regarding meat inspection procedure: visual-only or additional inspections.

How do pig farms maintain low Salmonella prevalence: a case-control study

Salmonella prevalence in UK pigs is amongst the highest in Europe, highlighting the need to investigate pig farms which have managed to maintain a low Salmonella seroprevalence. A total of 19 pig farms that had a consistently low (<10%) seroprevalence over 4 years (named Platinum farms) were compared against 38 randomly selected Control farms, chosen to match the same distribution of production types and geographical distribution of the Platinum farms. Each farm was visited and floor faeces and environmental samples were collected. It was shown that Control farms had a significantly higher median percentage of pooled faecal samples positive for Salmonella compared with the Platinum farms (12.1% and 0.4% for pooled faecal samples, respectively) and were more likely to have serovars of public health importance detected (S. Typhimurium/ monophasic variants or S. Enteritidis). Considering the comprehensive on-farm sampling, the identification of farms negative for Salmonella, along with the identification of those that had maintained low prevalence over a long period is important. The risk factor analyses identified pelleted feed, feed deliveries crossing farm perimeter and regular antibiotic use as associated with being a Control farm. Performance data indicated that Platinum farms were performing better for slaughter live weight than Controls. Limited assessments of available pig movement records suggested that the source of pigs was not key to Platinum status, but further study would be needed to confirm this finding. These results emphasise that maintaining very low prevalence on UK farms is achievable.

Prevalence, risk factors and genetic characterization of Toxoplasma gondii in sick pigs and stray cats in Jiangsu Province, eastern China

Toxoplasma gondii is an obligate intracellular parasitic protozoan with a worldwide distribution. The parasites in edible tissues of pigs and oocysts from cats are the major sources of T. gondii infection in humans. However, there are no data from sick pigs in veterinary clinics or from stray cats in Jiangsu Province, eastern China. In total, biological samples from 141 sick pigs and 64 stray cats were collected from this region. The rate of T. gondii infection in sick pigs was 46.81% using a polymerase chain reaction (PCR), and the overall prevalence of toxoplasmosis in stray cats was 34.38% by PCR and an enzyme-linked immunosorbent assay (ELISA). T. gondii was significantly more prevalent in lungs and heart than in liver and spleen (P < 0.05). Age and geographic region were considered to be the main risk factors associated with T. gondii infection in these pigs. The DNA samples from 17 sick pigs and seven stray cats, were successfully genotyped by multilocus PCR-restriction fragment length polymorphism (PCR-RFLP) with 10 genetic markers [SAG1, SAG2 (5'-3'SAG2, alt. SAG2), SAG3, GRA6, PK1, c22-8, c29-2, BTUB, L358 and Apico]. Six distinct genotypes were found, which were designated ToxoDB PCR-RFLP genotypes #9 (Chinese I), #10 (Type I), #213, and #89, and New 1 and New 2. Chinese I is the most prevalent T. gondii genotype in this region. The two new genotypes (designated New 1 and New 2) are reported and the ToxoDB PCR-RFLP genotype #89 is found for the first time in China. Such information will be useful for the prevention, diagnosis and treatment of porcine toxoplasmosis in Jiangsu Province, eastern China.

UK Pigs at the Time of Slaughter: Investigation into the Correlation of Infection with PRRSV and HEV

Hepatitis E virus (HEV) and porcine reproductive and respiratory syndrome virus (PRRSV) and are both globally prevalent in the pig population. While HEV does not cause clinical disease in pigs, its zoonotic potential has raised concerns in the food safety sector. PRRS has become endemic in the United Kingdom (UK) since its introduction in 1991, and continues to cause considerable economic losses to the swine industry. A better understanding of the current prevalence and diversity of PRRSV and HEV in the UK, and their potential association, is needed to assess risks and target control measures appropriately. This study used plasma, tonsil, and cecal content samples previously collected from pigs in 14 abattoirs in England and Northern Ireland to study the prevalence of several pathogens including PRRSV and HEV. The diversity of PRRSV strains detected in these samples was analyzed by sequencing open reading frame 5 (ORF5), revealing no substantial difference in PRRSV strains from these clinically unaffected pigs relative to those from clinical cases of disease in the UK. Despite the potential immuno-modulatory effect of PRRSV infection, previously demonstrated to affect Salmonella and HEV shedding profiles, no significant association was found between positive PRRSV status and positive HEV status.

Evaluation of an enhanced cleaning and disinfection protocol in Salmonella contaminated pig holdings in the United Kingdom

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.

Salmonella in the pork production chain and its impact on human health in the European Union

Salmonella spp. comprise the second most common food-borne pathogens in the European Union (EU). The role of pigs as carriers of Salmonella has been intensively studied both on farm and at slaughter. Salmonella infection in pigs may cause fever, diarrhoea, prostration and mortality. However, most infected pigs remain healthy carriers, and those infected at the end of the fattening period could pose a threat to human health. Contamination of pig carcasses can occur on the slaughter line, and it is linked to cross-contamination from other carcasses and the presence of Salmonella in the environment. Therefore, Salmonella serovars present on pig carcasses can be different from those detected in the same bathes on the farm. In recent years, S. Typhimurium, S. Derby and S. serotype 4,[5],12:i:- (a monophasic variant of S. Typhimurium) have been the most common serovars to be detected in pigs in EU countries, but S. Rissen, S. Infantis, S. Enteritidis and S. Brandenburg have also been reported. In humans, several cases of salmonellosis have been linked to the consumption of raw or undercooked pork and pork products. Among the main serovars of porcine origin detected in confirmed human cases, S. Typhimurium, the monophasic variant S. 4,[5],12:i:- and S. Derby are certainly the most important.

Cross-Sectional Study of Toxoplasma gondii Infection in Pig Farms in England

Ingestion of undercooked meat has been proposed as an important source of human Toxoplasma gondii infection. To ascertain the contribution of meat consumption to the risk of human infection, estimates of the prevalence of infection in meat-producing animals are required. A cross-sectional study was conducted to assess T. gondii infection in pigs raised in England, to identify risk factors for infection, and to compare performance of two serological tests: modified agglutination test (MAT) and enzyme-linked immunosorbent assay (ELISA). Blood samples from 2071 slaughter pigs originating from 131 farms were collected and 75 (3.6%) were found to be positive by MAT. Positive pigs originated from 24 farms. A subset of samples (n = 492) were tested using ELISA, and a significant disagreement (p < 0.001) was found between the two tests. An empirical Bayes approach was used to estimate the farm-level prevalence and the probability of each individual farm having at least one positive animal, considering the uncertainty arising from the sampling strategy and the imperfect test performance. The adjusted farm-level prevalence was 11.5% (95% credible interval of positive farms 8.4-16.0%). Two different criteria were used for classifying farms as infected: (1) ≥50% probability of having at least one infected pig (n = 5, 6.8%) and (2) ≥10% probability (n = 15, 20.5%). Data on putative risk factors were obtained for 73 farms. Using a 10% cutoff, the relative risk (RR) of infection was higher in farms where cats have direct access to pigs' food (RR = 2.6; p = 0.04), pigs have outdoor access (RR = 3.0; p = 0.04), and farms keeping ≤200 pigs (RR = 3.9; p = 0.02), with strong collinearity between the three variables. The findings suggest a low level of T. gondii infection in the farms studied, most of which are likely to send to slaughter batches comprising 100% uninfected pigs. These results provide key inputs to quantitatively assess the T. gondii risk posed by pork to consumers.