Monitoring of Pig Slaughter Stages and Correlation in the Prevalence of Pathogens and Levels of Microorganisms That Indicate Microbiological Quality and Hygiene Using a Predictive Model

Pig production is relevant to the Brazilian economy. Different stages of the raising and slaughtering process influence the microbiological quality of pig products and by-products. Microbiological analysis and hazard analysis and critical control points (HACCPs) are tools for monitoring microbiological quality indicator microorganisms. The construction of predictive models can assist the process of monitoring the microbiological quality of pig products. This study aimed to map the slaughter stages and develop a model to predict the absence or presence of Salmonella based on the process variables (distance from the farm to the slaughterhouse and aerobic mesophilic) and analyze their influence on contamination indicator microorganisms. A total of 810 samples were collected at nine stages of the slaughter process (bleeding, scalding, dehairing, singeing, washing, evisceration, inspection, final washing, and chilling). The binary class predictive model was used as a microbiological quality predictor at the slaughter stages. Salmonella was identified at all process stages, with lower contamination levels at the scalding and chilling stages, whereas the highest levels were found at the dehairing and bleeding stages. The predictive model revealed an accuracy of about 85% for Salmonella being a tool to monitor the microbiological quality of pig slaughter.

Microbiological Quality of Pig Carcasses in a Slaughterhouse under Risk-Based Inspection System

Meat product inspection is one of the procedures adopted more than a century ago to guarantee food quality and safety for consumption. Due to technology and regulation advancement for farming and slaughtering pigs, a change in zoonotic profile attributed to pork has been identified. Thus, a global movement began to establish inspection parameters based on epidemiological risk profiles, culminating in the publication of a new regulation in Brazil in 2018. This normative instruction establishes that slaughterhouses under federal inspection must implement risk-based inspection until 2028. Changes in the inspection system can generate questions and objections on the part of customers and consumer markets. In order to assess microbiological contamination when adopting a risk-based inspection system, the occurrence of Salmonella spp. and the quantification of Enterobacteriaceae and mesophilic aerobic counts were compared in pig carcasses slaughtered under traditional and risk-based inspection systems. A statistical significance reduction was identified regarding the quantification of Enterobacteriaceae (log -0.18 to -1.61 CFU/cm²) and mesophilic aerobic counts (log 4.60 to 3.49 CFU/cm²). The occurrence of Salmonella spp. did not show a significant difference (4% to 5.3%). The results allowed us to conclude that adopting risk-based inspection systems improves food safety through Enterobacteriaceae and mesophilic aerobic counts reduction.

Different Swine Production Systems Can Shape Slurry Resistome at Mechanism and Class Levels Based on Swine Manure Evaluation

Antimicrobial resistance is a major threat to public health. Antimicrobial use in animal husbandry is a major concern since it can favor an increase in antimicrobial resistance among farms. Herein, we aim to better understand and characterize the main resistome profiles in microbial communities found in pig farms. Sampling of swine manure was performed in two different timepoints (October 2019 and January 2020) in each of the 14 different swine farms, located in the mesoregion of Western Santa Catarina state in Brazil, a pole of swine product production of worldwide importance. Samples were divided into three groups: farms with the opened regimen and no usage of antimicrobials (F1; n = 10), farms with the closed regimen and usage of antimicrobials (F2; n = 16), and farms with the closed regimen and no usage of antimicrobials (F3; n = 2). The metagenomic evaluation was performed to obtain and identify genetic elements related to antimicrobial resistance using nanopore sequencing. We used ResistoXplorer software to perform composition, alpha and beta diversity, and clustering analysis. In addition, PCR reactions were performed to confirm the presence or absence of seven different beta-lactamase family genes and five phosphoethanolamine transferase gene variants clinically relevant. Our findings based on the identification of resistance genes at the mechanism level showed a prevalence of alteration of the drug target (72.3%) profile, followed by drug inactivation (17.5%) and drug efflux (10.1%). We identified predominantly aminoglycosides (45.3%), tetracyclines (15.9%), and multiclass (11,2%) resistance genes. PCoA analysis indicates differences between F1 and F2 profiles. F2 samples showed increased diversity when compared to the F1 group. In addition, herein we first report the identification of mcr-4 in a slurry sample (C1F1.1) in Santa Catarina State. In general, our findings reinforce that many factors on the practices of animal husbandry are involved in the resistome profile at the mechanism and class levels. Further studies to better understand microbiome and mobilome aspects of these elements are necessary to elucidate transmission pathways between different bacteria and environments.

Removal or substitution of in feed antimicrobials in swine production

Antimicrobial substitutes are being used in pig production systems, to maintain the health of the animals without compromising their performance. The aim of this study is to evaluate the impact of either the removal of in feed antimicrobials or their substitution for feed additives, at the nursery and growing/finishing stages. At weaning, 1091 piglets were sexed, vaccinated, homogenized by weight and allocated to six treatments during the nursery stage (26-63 d): T1- feed with no antimicrobials nor additives; T2 - feed with antimicrobials; T3 - feed with prebiotic; T4 - feed with probiotic; T5 - feed with essential oils; T6 - feed with organic acids. The same treatments were applied to 840 pigs during the growing/finishing stages (64-167 d). There was no effect of the treatments on feed conversion at the nursery (P = 0.222) and the growing/finishing (P = 0.809) stages. The average daily gain did not differ across treatments in the nursery (P = 0.342) and in growing/finishing (P = 0.050). The cost of the interventions with injectable drugs was not different between the treatments neither at the nursery (P = 0.990) nor at the growing/finishing (P = 0.310). However, the pneumonia and pleurisy index for all treatments was equal or above 1.0, which indicates a respiratory challenge. There was an increase in the cost with antimicrobials or additives per kg of feed produced, which impacts the cost per kg of pig produced. In conclusion, the removal of antimicrobials in pig diets is financially feasible and their substitution by additives did not impact growing performance.

Phylogenetic relationship and genomic characterization of Salmonella Typhimurium strains isolated from swine in Brazil

Salmonella Typhimurium has been transmitted between humans and animals. Although, Brazil has been one of the largest pork meat exporters worldwide, there are few studies that characterized epidemiologically S. Typhimurium strains from swine. The aims of this work were to study the phylogenetic relationship of S. Typhimurium genomes isolated from swine in Brazil among themselves and with other genomes isolated from several sources and countries using wgMLST and cgMLST and to perform the search of Salmonella pathogenicity islands (SPIs). In addition, for S. Typhimurium strains from swine to compare the virulence and antimicrobial resistance genes by VFDB and ResFinder, genetic content by BLAST Atlas and orthologous proteins clusters by OrthoVenn. The constructed phylogenetic trees by wgMLST and cgMLST grouped the majority (92.3% and 80.7%, respectively) of the strains isolated from swine in Brazil into the same group. All the isolates contained important SPIs (SPI-1, SPI-2, SPI-3, SPI-5 and SPI-9). A total of 100 and 31 virulence and resistance genes were detected in the S. Typhimurium strains isolated from swine, respectively. The BLAST Atlas and orthologous proteins analysis found regions of phages and differences in metabolic, regulatory and cellular processes among S. Typhimurium LT2 and S. Typhimurium isolates from swine. In conclusion, molecular typing based in the wgMLST and cgMLST suggested that the S. Typhimurium isolates from swine studied were genetically related. The pathogenic potential of the strains studied was corroborated by the presence of important SPIs and virulence genes. The high number of antimicrobial resistance genes detected is worrying and reinforced their potential risk in swine in Brazil. The comparison by BLAST Atlas suggested differences in mobile genetic elements among S. Typhimurium LT2 and S. Typhimurium isolates from swine in Brazil. The orthologous proteins analysis revealed unique genes related to important cellular processes in the strains from swine.

Effect of gaseous ozone application during chilling on microbial and quality attributes of pig carcasses

Ozone application has been suggested as an additional measure to the slaughter animals under hygiene programs. In this study, we determined the efficacy of gaseous ozone applied to pig carcasses during chilling (16 h at 2-5°C). Forty carcasses were allocated to each treatment: control, without ozone application (T1) and 5 ppm gaseous ozone application (T2), divided in two 4-h periods. The carcasses were sampled before and after chilling. The average counts of total aerobic mesophilic (TAM) bacteria before chilling were not different (p = 0.55) between T1 and T2. In turn, after chilling, the ozone-treated carcasses had significantly reduced about 0.4 colony-forming units (CFU)/cm² of TAM counts (p < 0.001) than the control carcasses. No significant reduction was observed in the number of carcasses positive for Listeria sp. and Escherichia coli after gaseous ozone treatment; while a tendency (p = 0.08) of lower number of Salmonella positive carcasses in T2 was observed. Common macrorestriction (pulsed-field gel electrophoresis) patterns of S. enterica were observed in the carcasses before and after chilling. Pork samples from treated and untreated carcasses with ozone showed no lipid oxidation or altered color and pH. The results indicate that the gaseous ozone in the tested protocol is effective in reducing TAM populations, but not effective in decreasing the number of carcasses positive for E. coli and Listeria sp. Regarding Salmonella, the tendency of positive carcasses reduction may encourage further studies by testing other protocols of gaseous ozone application inside the chilling chamber.

Antimicrobial resistance in commensal Escherichia coli and Enterococcus spp. isolated from pigs subjected to different antimicrobial administration protocols

The antimicrobial resistance (AMR) in human and animal pathogens is a global concern, and antimicrobial use (AMU) is considered the most important driver for its increase. The aim of this study was to assess AMR in Escherichia coli and Enterococcus spp. in faecal samples of pigs subjected to four different AMU protocols from birth to finishing: G1, no in-feed antimicrobials; G2: a total average dose 6018 mg antimicrobials/pig; G3: a total average dose 8127 mg antimicrobials/pig; and G4: a total average dose 15,678 mg antimicrobials/pig. Faecal samples were collected at six time points and AMR was assessed in both bacteria. The microbiota composition was assessed by 16S rRNA sequencing. Minor differences on the microbiota profile was observed among groups, but a lower Firmicutes:Bacteroidetes ratio was noted in G4. Escherichia coli and Enterococcus spp. strains isolated from all groups showed a high level of multi-drug resistance (MDR). The amount of antimicrobials used was significantly positively associated with the probability of MDR in both bacteria. Approximately 43% of the variation in MIC₉₀ for colistin could be explained by AMU, and a one-day increase in administration of colistin increased MIC₉₀ by 0.05 μg mL^-1. In conclusion, the results suggest that the higher the use of antimicrobials in farms, the higher the MDR frequency and resistance to the highest priority critically important antimicrobials for humans in commensal gut bacteria of pigs.

Re-Emergence of Salmonellosis in Hog Farms: Outbreak and Bacteriological Characterization

Clinical salmonellosis has been increasing significantly in Brazil in recent years. A total of 130 outbreaks distributed among 10 swine-producing states were investigated. One representative Salmonella isolate from each outbreak was characterized through serotyping, antimicrobial resistance profiles, PFGE, and WGS. From 130 outbreaks: 50 were enteric, 48 were septicemic, 17 cases were characterized as hepato-biliary invasive, 13 as nodal and two were not classified. The most prevalent serovars were a monophasic variant of S. typhimurium (55/130), Choleraesuis (46/130), and Typhimurium (14/130). Most of the strains (86.92%) demonstrated a high rate of multi-drug resistance. The identification of a major Choleraesuis clonal group in several Brazilian states sharing the same resistance genes suggested that these strains were closely related. Six strains from this clonal group were sequenced, revealing the same ST-145 and 11 to 47 different SNPs. The detected plasmid type showed multiple marker genes as RepA_1_pKPC-CAV1321, the first to be reported in Salmonella. All AMR genes detected in the genomes were likely present on plasmids, and their phenotype was related to genotypic resistance genes. These findings reveal that salmonellosis is endemic in the most important pig-producing states in Brazil, emphasizing the need to make data available to aid in reducing its occurrence.

Synthetic gene as target to assess the sensitivity of PCR to detect Trichinella spp. larvae in meat from a non-endemic region

Trichinellosis is a zoonotic disease exotic in Brazil but commonly found worldwide including South American countries like Argentina. International trading of swine meat needs an official Trichinella-free diagnosis commonly carried out by pepsin-HCl digestion of diaphragm tissue fragments followed by microscopic examination for the presence or absence of Trichinella larvae. The easiness of this diagnostic method allows it to be performed at slaughtering plants but, in contrast, it lacks sensitivity and does not allow species differentiation, which is fundamental for determining geographical and species distribution of different genotypes. In our study, we aimed to evaluate a highly sensitive diagnostic method based on the polymerase chain reaction (PCR) that would allow us to detect and classify different species of Trichinella. Thus, we designed a synthetic gene and selected five sets of primers targeting specific regions of the Trichinella genome. The synthetic gene was cloned into a plasmid and then used to optimize PCR conditions. Using our PCR, we were able to detect 0.001 pg of the synthetic gene, which corresponded to 0.01 larvae. Then, we collected 175 samples of Suidae (domestic and wild boars) diaphragm fragments that were pooled into groups, digested with pepsin-HCl, and had the DNA extracted for analysis by PCR. The clinical samples evaluated were negative by PCR. Our results indicate that the PCR-based method might be a useful diagnostic method complementary to the pepsin-HCl digestion method currently in use, mostly in non-endemic areas.

Protection Efficacy of the rLTB-R1 Chimera against Experimental Swine Mycoplasmal Pneumonia

Background: Mycoplasma hyopneumoniaeis the etiological agent of the Swine Mycoplasmal Pneumonia (SMP), one of the most economically significant diseases in the swine industry worldwide. Commonly used vaccines for SMP control consist of inactivated whole cells (bacterins). These vaccines are efficacious against M. hyopneumoniaechallenge, but do not prevent colonization by the pathogen or completely eliminate pneumonia. P97 adhesin is conserved in the M. pneumoniae virulent strains, therefore it is an attractive target to be used in recombinant vaccines against M. hyopneumoniae. The aim of the present study was to evaluate protection afforded by rLTB-R1, a recombinant chimera composed by LTB fused with the R1 repeat region of P97 adhesin of M. hyopneumoniae, in specific-pathogen-free (SPF) piglets vaccinated by intranasal or intramuscular route and challenged with a pathogenic strain of M. hyopneumoniae.Materials, Methods & Results:PCR products of the LTB and R1 coding sequences were fused, then cloned into pETDEST42™ expression vector. The rLTB-R1 was expressed in Escherichia coli BL21 (DE3) Salt induction (SI).They were allocated into three groups: four piglets were intranasally vaccinated with 1 mg of rLTB-R1 solubilized in 1 mL of PBS at 0 and 14 days (IN rLTB-R1 group); four piglets were intramuscularly vaccinated with 1 mg of rLTB-R1 solubilized in 1 mL of PBS at 0 and 14 days (IM rLTB-R1 group);three piglets were intranasally and intramuscularly inoculated with 1 mL of PBS (control group).Two weeks after the last immunization (28 day), piglets were intratracheally challenged with 10 mL of a suspension containing 109color-changing unit (CCU) of pathogenic M. hyopneumoniae 7448 strain on three consecutive days. Until the challenge (28 days), intranasal and intramuscular vaccination with rLTB-R1 induced seroconversions of anti-R1 systemic antibodies of 1.6 and 4.6 ×, respectively. The IN rLTB-R1 group had no pulmonary lesion, rLTB-R1 conferred protection against experimental SMP. On the other hand, IM rLTB-R1 and control groups had on average 7.24% and 8.46% of pulmonary lesion, respectively, showing that intramuscular vaccination with rLTB-R1 did not confer protection.Discussion:The rLTB-R1, when intranasally administrated to mice, elicited production of anti-R1 IgA in trachea and bronchi as well as specific Th1 response, suggesting an adequate stimulation of the mucosal immune system. We believe that rLTB-R1 induced a similar immune response in piglets intranasally vaccinated, conferring protection against experimental SMP. The present study, the rLTB-R1 alone, without any chemical adjuvant, stimulated a significant seroconversion of anti-R1 systemic antibodies in pigs intramuscularly vaccinated, showing the potential of LTB as a parenteral adjuvant in swine vaccination.Previous work has shown that the intramuscular administration route was evaluated in pigs because mice intramuscularly vaccinated with rLTB-R1 presented significant levels of anti-R1 IgA in trachea and bronchi, suggesting that rLTB can stimulate some degree of mucosal immunity even if not delivered by a mucosal route.However, in the present study, piglets intramuscularly vaccinated with rLTB-R1 presented high levels of anti-R1 systemic antibodies, they were not protected.On the other hand, intranasal vaccination of piglets with rLTB-R1 elicited low levels of anti-R1 systemic antibodies (1.6 × at 28 days), but it conferred full protection against experimental SMP. The present study demonstrated that intranasal vaccination of piglets with rLTB-R1 conferred protection against experimental SMP. A more detailed analysis of the protective immune response induced by rLTB-R1 in pigs is currently being performed.

Enumeration, Antimicrobial Resistance and Typing of Salmonella enterica: Profile of Strains Carried in the Intestinal Contents of Pigs at Slaughter in Southern Brazil

Background: Despite a strong association between Salmonella isolation and slaughter hygiene, as measured by the Enterobacteriaceae levels on pre-chill carcass surfaces, a high variation in this association was observed between sampling days within the same slaughterhouse. It was hypothesised that in a scenario of high exposure on the farm, batches with a high prevalence of carrier pigs shedding a high number of Salmonella may enhance the risk of contamination on some slaughter days. Thus, the aim of this study was to assess the profile of Salmonella carried in the intestinal contents of slaughter pigs.Materials, Methods & Results: Ten pig batches slaughtered in a slaughterhouse were investigated for the presence of Salmonella. From each pig, the following samples were taken: i. blood collected at bleeding; ii. sponges rubbed on the carcass surface after bleeding and before chilling; iii. fragment of the ileocecal region of the intestine. Serum samples were subjected to a ELISA-Typhimurium test. Sponges were investigated for the presence of Salmonella and total aerobic mesophilic (TAM) and Enterobacteriaceae (EC) bacterial counts. Salmonella was enumerated in the intestinal contents. Selected Salmonella strains were subjected to an antimicrobial resistance disk diffusion test, macro-restriction with Xba-I (PFGE) and whole genome sequencing (WGS). From the 50 sampled pigs, 96% were positive in the ELISA-Typhimurium test and 64% were Salmonella-positive in the intestinal contents. The amount of Salmonella in the intestinal content samples was highly variable, and the mean log of fitted distributions of Salmonella in the batch ranged from -2.97 to 2.25 cfu.g-1. The slaughter process achieved a logarithmic reduction, ranging from 0.64 to 2.35 log cfu.cm-2 for TAM and from 0.55 to 2.57 log cfu.cm-2 for EC. Salmonella was isolated from 16% of the carcasses after bleeding; this frequency decreased to 8% at the pre-chill step. All positive pre-chill carcasses originated from pigs carrying Salmonella in the intestinal content and from batches with a high number of carrier pigs. Salmonella Typhimurium and its monophasic variant were the most frequent in the intestinal contents and carcasses. Resistance was detected against ampicillin (42.5%), tetracycline (42.5%), sulfonamide (40%), gentamicin (25%) and ciprofloxacin (12.5%). Regarding colistin, 85% of the tested strains were classified as non-susceptible. The monophasic variant S. Typhimurium strains subjected to PFGE and WGS presented different profiles; several antimicrobial resistance genes were identified and all belonged to ST-19.Discussion: In this study, almost all sampled pigs entering the slaughter line had been exposed to Salmonella on the farm and a high number were carrying Salmonella in their guts. While the three batches with Salmonella-positive carcasses at the pre-chill step presented TAM media that was not significantly different from the other batches, there was a higher number of positive pigs carrying Salmonella in their intestinal contents. Moreover, the batch with the highest number of positive carcasses also presented the highest Salmonella mean count in their intestinal contents. The profile of Salmonella carried in the intestinal content of slaughter pigs proved to be highly variable in terms of the frequency, number of bacteria, serovars, antimicrobial resistance, and genotypes. Results indicate that the day-to-day variability in the prevalence and number of Salmonella in the intestinal contents of slaughter batches is likely to influence the frequency of contaminated pre-chill carcasses. Salmonella Typhimurium isolated from the intestinal contents of slaughter pigs may belong to genotypes involved in human disease and may carry several antimicrobial resistance genes. These aspects should be taken into account when planning Salmonella control in swine.

Pathogenic variability among Pasteurella multocida type A isolates from Brazilian pig farms

Background

Pasteurella multocida type A (PmA) is considered a secondary agent of pneumonia in pigs. The role of PmA as a primary pathogen was investigated by challenging pigs with eight field strains isolated from pneumonia and serositis in six Brazilian states. Eight groups of eight pigs each were intranasally inoculated with different strains of PmA (1.5 mL/nostril of 10e7 CFU/mL). The control group (n = 12) received sterile PBS. The pigs were euthanized by electrocution and necropsied by 5 dpi. Macroscopic lesions were recorded, and swabs and fragments of thoracic and abdominal organs were analyzed by bacteriological and pathological assays. The PmA strains were analyzed for four virulence genes (toxA: toxin; pfhA: adhesion; tbpA and hgbB: iron acquisition) by PCR and sequencing and submitted to multilocus sequence typing (MLST).

Results

The eight PmA strains were classified as follows: five as highly pathogenic (HP) for causing necrotic bronchopneumonia and diffuse fibrinous pleuritis and pericarditis; one as low pathogenic for causing only focal bronchopneumonia; and two as nonpathogenic because they did not cause injury to any pig. PCR for the gene pfhA was positive for all five HP isolates. Sequencing demonstrated that the pfhA region of the HP strains comprised four genes: tpsB1, pfhA1, tpsB2 and pfhA2. The low and nonpathogenic strains did not contain the genes tpsB2 and pfhA2. A deletion of four bases was observed in the pfhA gene in the low pathogenic strain, and an insertion of 37 kb of phage DNA was observed in the nonpathogenic strains. MLST clustered the HP isolates in one group and the low and nonpathogenic isolates in another. Only the nonpathogenic isolates matched sequence type 10; the other isolates did not match any type available in the MLST database.

Conclusions

The hypothesis that some PmA strains are primary pathogens and cause disease in pigs without any co-factor was confirmed. The pfhA region, comprising the genes tpsB1, tpsB2, pfhA1 and pfhA2, is related to the pathogenicity of PmA. The HP strains can cause necrotic bronchopneumonia, fibrinous pleuritis and pericarditis in pigs and can be identified by PCR amplification of the gene pfhA2.

Genotyping and antimicrobial resistance in Escherichia coli from pig carcasses

ABSTRACT: The increasing antimicrobial resistance observed worldwide in bacteria isolated from human and animals is a matter of extreme concern and has led to the monitoring of antimicrobial resistance in pathogenic and commensal bacteria. The aim of this study was to evaluate the antimicrobial resistance profile of Escherichia coli isolated from pig carcasses and to assess the occurrence of relevant resistance genes. A total of 319 E. coli isolates were tested for antimicrobial susceptibility against different antimicrobial agents. Moreover, the presence of extended-spectrum β-lactamase (ESBL) and inducible ampC-β-lactamase producers was investigated. Eighteen multi-resistant strains were chosen for resistance gene detection and PFGE characterization. The study showed that resistance to antimicrobials is widespread in E. coli isolated from pig carcasses, since 86.2% of the strains were resistant to at least one antimicrobial and 71.5% displayed multi-resistance profiles. No ampC-producing isolates were detected and only one ESBL-producing E. coli was identified. Genes strA (n=15), floR (n=14), aac(3)IVa (n=13), tetB (n=13), sul2 (n=12), tetA (n=11), aph(3)Ia (n=8) and sul3 (n=5) were detected by PCR. PFGE analysis of these multi-resistant E. coli strains showed less than 80% similarity among them. We conclude that antimicrobial multi-resistant E. coli strains are common on pig carcasses and present highly diverse genotypes and resistance phenotypes and genotypes.

Development and Application of an Enzyme-Linked Immunosorbent Assay to Detect Antibodies against Prevalent Salmonella Serovars in Swine in Southern Brazil

The implementation of Salmonella control programs in the pork production chain demands rapid and cost-effective methods to assess the prevalence of infection in pig herds. The objective of the present study was to develop an in-house enzyme-linked immunosorbent assay (ELISA) based on S. Typhimurium lipopolysaccharides (LPS) to measure the prevalence of infection caused by Salmonella in swine herds. Coating antigen was produced by phenol extraction of S. Typhimurium culture. After standardization of ELISA test conditions, the assay was validated by testing serum samples on different animal categories: pigs orally inoculated with S. Typhimurium and sentinel animals in contact with them, naturally infected animals, colostrum-deprived piglets, and bacterin-immunized pigs. Seroconversion was observed in inoculated pigs (7 days postinfection [DPI]) and in the sentinels (21 DPI). Nonspecific reactions were not detected in the sera of colostrum-deprived animals. Serum samples from animals immunized with Salmonella Agona, Salmonella Derby, Salmonella Panama, and Salmonella Bredeney bacterins showed marked cross-reaction with the LPS from the serovar Typhimurium. Moreover, positive results obtained with the in-house ELISA were associated with Salmonella isolation in 75 infected pig herds. Comparisons with 2 commercial kits showed a linear correlation coefficient of 0.847 between the in-house ELISA and kit A and 0.922 with kit B but a low agreement in the qualitative results. In conclusion, the newly developed in-house ELISA based on S. Typhimurium LPS can be a useful tool to determine the intensity of Salmonella sp. infection in swine herds.

Virulence-associated genes, antimicrobial resistance and molecular typing of Salmonella Typhimurium strains isolated from swine from 2000 to 2012 in Brazil

AIMS

The aims of this study were to assess the pathogenic potential, antimicrobial resistance and genotypic diversity of Salmonella Typhimurium strains isolated in Brazil from swine (22) and the surrounding swine environment (5) from 2000 to 2012 and compare them to the profiles of 43 human strains isolated from 1983 to 2010, which had been previously studied.

METHODS AND RESULTS

The presence of 12 SPI-1, SPI-2 and plasmid genes was assessed by PCR, the antimicrobial susceptibility to 13 antimicrobials was determined by the disc diffusion assay and genotyping was performed using pulsed-field gel electrophoresis (PFGE), multiple-locus variable-number of tandem repeats analysis (MLVA) and ERIC-PCR. More than 77·8% of the swine strains carried 10 or more of the virulence markers. Ten (37%) strains isolated from swine were multi-drug resistant (MDR). All the molecular typing techniques grouped the strains in two main clusters. Some strains isolated from swine and humans were allocated together in the PFGE-B2, MLVA-A1, MLVA-B and ERIC-A1 clusters.

CONCLUSIONS

The genotyping results suggest that some strains isolated from swine and humans may descend from a common subtype and may indicate a possible risk of MDR S. Typhimurium with high frequency of virulence genes isolated from swine to contaminate humans in Brazil.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study provided new information about the pathogenic potential, antimicrobial resistance and genotypic diversity of S. Typhimurium isolates from swine origin in Brazil, the fourth largest producer of pigs worldwide.

Effect of slaughterhouse and day of sample on the probability of a pig carcass being Salmonella-positive according to the Enterobacteriaceae count in the largest Brazilian pork production region

Sources of contamination of carcasses during slaughter include infected pigs as well as environmentally related sources. There are many microbial indicators that can be used in the processing of food to assess food hygiene and the safety of food processing. The presence of some microbial indicators can be viewed as a result of direct or indirect contamination of a food with fecal material. The presence of Enterobacteriaceae is often used as a hygiene indicator, as they are found both in the environment and in the intestine of warm-blooded animals. An association between Salmonella isolation and Enterobacteriaceae count (EC) on pre-chill carcasses has been described, however the impact of slaughterhouse and the day of sampling on the occurrence of Salmonella has not been previously investigated. To this end, mixed logistic regressions (MLRs) with random effects and fixed slopes were performed to assess the change in EC and its correlation with Salmonella occurrence using two data sets. The first describes the EC and Salmonella isolation in 60 pork carcasses in one slaughterhouse sampled at 11 different slaughter steps, including the carcass as a random effect. The second describes the EC and Salmonella isolation on 1150 pre-chill carcasses sampled in 13 slaughterhouses over 230 sampling days, and the model combined two random intercepts, slaughterhouse and date of sampling nested with slaughterhouse (day/slaughterhouse). Statistically significant associations (p<0.0001) between the log of the EC and Salmonella occurrence were found in all models. Nevertheless, although a strong association was found between Enterobacteriaceae and Salmonella contamination in pork carcasses, this association was not constant, given that there was a high variation in the probability of a carcass being positive for Salmonella according to the EC mainly between days of samples. The effect of the day of sampling on Salmonella prevalence was so large that the predictive value of the EC count for Salmonella isolation on a daily basis was compromised. It is possible that on some days batches with a high prevalence of Salmonella carriers shedding a high number of Salmonella were slaughtered. On these days, the potential for contamination/cross-contamination of carcasses will be so large that even hygienic slaughter, confirmed by the low EC on carcasses, will not be able to prevent the presence of Salmonella on some carcasses. The results of this study demonstrate that, despite the statistically significant association found, it may be difficult to predict when hygiene failure measured via EC actually indicates Salmonella contamination, and neither the inverse.

Detection of Genotipically Related Multi-resistant Escherichia coli Isolates in Pig Feces and Carcasses

Background: Antimicrobial resistant bacteria are considered a hazard not only for the treatment of animal diseases but also for public health. Commensal bacteria, such as Escherichia coli are considered a good indicator of antimicrobial resistance in the population, because it is a gut inhabitant and thus undergoes constant pressure of selection by the administration of antimicrobials. Regarding the public health, it is important to evaluate if resistant bacteria carried in the intestinal content of slaughter pigs can be found on the surface of pre chill carcasses. Therefore, the aims of this study were to evaluate the frequency of antimicrobial resistance in E. coli isolated from feces and pig carcasses; and to assess if multi-resistant isolates from both sources were phenotypically and genotypically related.Materials, Methods & Results: Two sampling cycles were conducted in three pig slaughterhouses (A, B and C). In each cycle, samples were collected form: i. feces deposited on the pen floor of the lairage; ii. surface of carcasses at the prechill step. Samples were submitted to a protocol of isolation and confirmation of Escherichia coli. Isolates were grouped according to the origin: feces (n = 355); carcasses (n = 319); and evaluated for antimicrobial resistance by agar diffusion test. Ninety two isolates presenting multidrug resistance profile were analyzed by pulsed-field gel eletrophoresis (PFGE). Among the 674 isolates of E. coli, 7.4% were susceptible to all tested antibiotics while 79.5% (536/674) were multi-resistant. The most frequent resistance patterns were displayed to tetracycline (Tet, 85.9%), ampicillin (Amp, 73.0%), sulfonamide (Sul, 70.0%), florfenicol (Flo, 65.0%) and nalidixic acid (Nal, 58.9%). The most frequent multi-resistance profile among isolates from both origins was [AmpFloNalSulTet]. Multiresistant isolates originated from feces and carcasses displaying genotypically related pulsotypes (≥70% similarity) were found in all three slaughterhouses.Discussion: In agreement with other studies, E. coli isolated from pig feces and carcasses demonstrated a high frequency of antimicrobial resistance and multi-resistance. The most frequent resistance profiles included antimicrobials frequently used on farm as well as drugs that have been banned as feed additives some years ago in Brazil. The selection of resistant strains may be related to the selection pressiondue to the use of antimicrobials in the pig production chain as well as the co-selection of resistance mediated by genes located in common genetic elements. Therefore, the ban of an individual drug is not always associated with the immediate disappearance of the resistance phenotype in the bacteria population. The fact that most multi-resistant E. coli isolates from carcasses belonged to pulsotypes related to those originated from feces samples indicates that resistant E. coli isolates selected on farm may be able to survive the slaughter process and be found on the carcass. In this case, the possibility of those strains being able to reach the population through the consumption of pork products may have to be considered. This hazard has motivated the ban of antimicrobial use in animals in some countries. However, the ban of antimicrobials use on farm is a controversial issue, due to the economical losses that may result from this measure. Therefore, the prudent use of antimicrobials on farm should be encouraged and its influence in the multi-resistance profile of the enteric microbiota should be further studied.

Utility of specific biomarkers to assess safety of swine manure for biofertilizing purposes

Swine production is an important economic activity in Brazil, and there is interest in the development of clean production mechanisms to support sustainable agro-industrial activities. The biomass derived from swine manure has good potential to be used as a biofertilizer due to its high nutrient concentration. However, the land application of manure should be based on safety parameters such as the presence of pathogens that can potentially infect animals and people. This study was designed to assess the presence of porcine circovirus-2 (PCV2), porcine adenovirus (PAdV), rotavirus-A (RV-A) and Salmonella spp. in liquid manure, as well the infectivity of two genotypes of circovirus-2 (PCV2a and PCV2b) present in liquid manure. Three swine farms were evaluated: 1) a nursery production farm (manure analyzed before and after anaerobic biodigestion), 2) a grow-finish production farm (analyzed before and after anaerobic biodigestion), and 3) a second grow-finish production farm (raw manure-affluent). PCV2, PAdV and RV-A were present before and after anaerobic biodigestion (either affluent or effluent) at all farms. Salmonella spp. were detected at farm 1 (affluent and effluent) and farm 3 (raw manure-affluent) but not farm 2 (affluent and effluent). When the ability of the anaerobic biodigestion process to reduce viral concentration was evaluated, no significant reduction was observed (P>0.05). Both the PCV2a and PCV2b genotypes were detected, suggesting viral co-infection in swine production. The results revealed infectious PCV2 even after anaerobic biodigestion treatment. The presence of Salmonella spp. and enteric viruses, especially infectious PCV2, in the final effluent from the anaerobic biodigester system suggests that the process is inefficient for pathogen inactivation. Due to the prevalence and infectivity of PCV2 and considering the successful use of molecular methods coupled to cell culture for detecting infectious PCV2, we suggest that this virus can be used as a bioindicator in swine manure treatment systems to check the efficiency of pathogen inactivation and ensure the production of safe biofertilizers from swine manure.

TLR4 single nucleotide polymorphisms (SNPs) associated with Salmonella shedding in pigs

Toll-like receptor 4 (TLR4) is a key factor in the innate immune recognition of lipopolysaccharide (LPS) from Gram-negative bacteria. Previous studies from our group identified differences in the expression profile of TLR4 and genes affected by the TLR4 signaling pathway among pigs that shed varying levels of Salmonella, a Gram-negative bacterium. Therefore, genetic variation in this gene may be involved with the host’s immune response to bacterial infections. The current study screened for single nucleotide polymorphisms (SNPs) in the TLR4 gene and tested their association with Salmonella fecal shedding. Pigs (n = 117) were intranasally challenged at 7 weeks of age with 1 × 10⁹ CFU of S. Typhimurium χ4232 and were classified as low or persistent Salmonella shedders based on the levels of Salmonella being excreted in fecal material. Salmonella fecal shedding was determined by quantitative bacteriology on days 2, 7, 14, and 20/21 post exposure, and the cumulative levels of Salmonella were calculated to identify the low (n = 20) and persistent (n = 20) Salmonella shedder pigs. From those 40 animals, the TLR4 region was sequenced, and 18 single nucleotide polymorphisms (SNPs) in TLR4 were identified. Twelve SNPs have been previously described and six are novel SNPs of which five are in the 5′ untranslated region and one is in intron 2. Single marker association test identified 13 SNPs associated with the qualitative trait of Salmonella fecal shedding, and seven of those SNPs were also associated with a quantitative measurement of fecal shedding (P < 0.05). Using a stepwise regression process, a haplotype composed of SNPs rs80787918 and rs80907449 (P ≤ 4.0 × 10⁻³) spanning a region of 4.9 Kb was identified, thereby providing additional information of the influence of those SNPs on Salmonella fecal shedding in pigs.

Polynucleotide phosphorylase (PNPase) is required for Salmonella enterica serovar Typhimurium colonization in swine

The pnp gene encodes polynucleotide phosphorylase, an exoribonuclease involved in RNA processing and degradation. A mutation in the pnp gene was previously identified by our group in a signature-tagged mutagenesis screen designed to search for Salmonella enterica serovar Typhimurium genes required for survival in an ex vivo swine stomach content assay. In the current study, attenuation and colonization potential of a S. Typhimurium pnp mutant in the porcine host was evaluated. Following intranasal inoculation with 10(9) cfu of either the wild-type S. Typhimurium χ4232 strain or an isogenic derivative lacking the pnp gene (n = 5/group), a significant increase (p < 0.05) in rectal temperature (fever) was observed in the pigs inoculated with wild-type S. Typhimurium compared to the pigs inoculated with the pnp mutant. Fecal shedding of the pnp mutant was significantly reduced during the 7-day study compared to the wild-type strain (p < 0.001). Tissue colonization was also significantly reduced in the pigs inoculated with the pnp mutant compared to the parental strain, including the tonsils, ileocecal lymph nodes, Peyer's Patch region of the ileum, cecum and contents of the cecum (p < 0.05). The data indicate that the pnp gene is required for S. Typhimurium virulence and gastrointestinal colonization of the natural swine host.

Performance of two swine manure treatment systems on chemical composition and on the reduction of pathogens

Swine effluents must be correctly handled to avoid negative environmental impacts. In this study, the profiles of two swine manure treatment systems were evaluated: a solid-liquid separation step, followed by an anaerobic reactor, and an aerobic step (System 1); and a biodigester followed by serial lagoons (System 2). Both systems were described by the assessment of chemical, bacterial and viral parameters. The results showed that in System 1, there was reduction of chemicals (COD, phosphorus, total Kjeldhal nitrogen - TKN - and NH(3)), total coliforms and Escherichia coli; however, the same reduction was not observed for Salmonella sp. Viral particles were significantly reduced but not totally eliminated from the effluent. In System 2, there was a reduction of chemicals, bacteria and viruses with no detection of Salmonella sp., circovirus, parvovirus, and torque teno virus in the effluent. The chemical results indicate that the treated effluent can be reused for cleaning swine facilities. However, the microbiological results show a need of additional treatment to achieve a complete inactivation for cases when direct contact with animals is required.

Use of an avirulent live Salmonella Choleraesuis vaccine to reduce the prevalence of Salmonella carrier pigs at slaughter

This study evaluated the use of an avirulent live Salmonella Choleraesuis vaccine to reduce the seroprevalence and number of Salmonella carrier pigs at slaughter. Seven batches of 500 pigs were included in each of the two study groups: the vaccinated group (VG) that was orally vaccinated and the control group (CG) that received a placebo on the first day of life. The groups were managed in a three-site system and followed up from birth to slaughter. Blood samples (n=378) were collected from each VG and CG to monitor the on-farm seroprevalence in both groups. Mesenteric lymph nodes and blood from animals (n=390) belonging to each group were collected at slaughter. At the first day of life, the seroprevalence in control batches ranged from 77.9 to 96.3 per cent, while in vaccinated batches, it ranged from 66.6 to 92.6 per cent. At weaning (21 days of age), the number of seropositives decreased in both groups (mean of 12 and 3.7 per cent for CG and VG, respectively). At slaughter, batches of VG had a significantly (P<0.0001) lower seroprevalence (46.6±5 per cent) and isolation of Salmonella from lymph nodes (33.1±5 per cent) compared with CG batches (79.7±4 per cent and 59.5±5 per cent, respectively). The results indicate that administration of a Salmonella choleraesuis-attenuated vaccine on the first day of life decreases Salmonella isolation and seroprevalence in pigs at slaughter.

Detection of Mycoplasma hyopneumoniae by polymerase chain reaction in swine presenting respiratory problems

Since Mycoplasma hyopneumoniae isolation in appropriate media is a difficult task and impractical for daily routine diagnostics, Nested-PCR (N-PCR) techniques are currently used to improve the direct diagnostic sensitivity of Swine Enzootic Pneumonia. In a first experiment, this paper describes a N-PCR technique optimization based on three variables: different sampling sites, sample transport media, and DNA extraction methods, using eight pigs. Based on the optimization results, a second experiment was conducted for testing validity using 40 animals. In conclusion, the obtained results of the N-PCR optimization and validation allow us to recommend this test as a routine monitoring diagnostic method for Mycoplasma hyopneumoniae infection in swine herds.

Proteomic survey of the pathogenic Mycoplasma hyopneumoniae strain 7448 and identification of novel post-translationally modified and antigenic proteins

Mycoplasma hyopneumoniae is an important pathogen for pigs, being the causative agent of enzootic pneumonia. Recently, the genome sequences of three strains, J, 7448 and 232 have been reported. Here, we describe the results of a proteomic analysis, based on two-dimensional gel electrophoresis of soluble protein extracts, immunoblot and mass spectrometry, which was carried out aiming the identification of gene products and antigenic proteins from the M. hyopneumoniae pathogenic strain 7448. A preliminary M. hyopneumoniae proteome map in two pH ranges (3-10 and 4-7) was produced. A total of 31 different coding DNA sequences (CDSs), including three hypothetical ones, were experimentally verified with the identification of the corresponding protein products by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. According to the Clusters of Orthologous Groups (COG) functional classification, the identified proteins were assigned to the groups of metabolism (13), cellular processes (5) and information and storage processing (4). Nine of the identified proteins were not classifiable by COG, including some related to cytoadherence and possibly involved in pathogenicity. Moreover, at least five highly antigenic proteins of M. hyopneumoniae were identified by immunoblots, including four novel ones (a heat shock protein 70, an elongation factor Tu, a pyruvate dehydrogenase E1-beta subunit and the P76 membrane protein). The now available proteome map is expected to serve as a reference for comparative analyses between M. hyopneumoniae pathogenic and non-pathogenic strains, and for methabolic studies based on cells cultured under modified conditions.

Variable number of tandem aminoacid repeats in adhesion-related CDS products in Mycoplasma hyopneumoniae strains

The Mycoplasma hyopneumoniae genome contains at least 22 regions with a variable number of tandem nucleotide repeats (VNTRs) within coding DNA sequences (CDSs). In this work, the VNTR-containing CDSs were analysed in order to evaluate their degree of variation, possible correlations with antigenic properties, and their potential to be used as a basis for a strain typing PCR assay. We have analysed the VNTRs in five M. hyopneumoniae strains (J, 7448, 7422, PMS, and 232), based on published genomic sequences and on amplified and sequenced DNA segments. These VNTRs are distributed among 12 genes, most of which encode putative surface proteins, including known adhesins. The number of repeat units in any of the VNTRs is highly variable among the analysed strains, but they are, without exception, translationally in frame, and, therefore, code for a variable number of aminoacid repeats (VNTARs). These VNTARs determine putative structural, physicochemical and antigenic variations in the corresponding proteins, with potential implications for aspects associated to M. hyopneumoniae pathogenicity, such as cell adhesion and interactions with the host immune system. Considering that the characterized VNTARs are relatively stable, at least in vitro, and their sizes are strain-specific, we have developed a VNTR-based PCR assay for M. hyopneumoniae strain identification, useful for enzootic pneumonia (EP) diagnosis, strain typing, and distinction of circulating field isolates from vaccine strains in animals vaccinated against EP.