Antibiotic Resistance: From Pig to Meat

The use of oral fluids and sock samples for monitoring key pathogens in pig populations for surveillance purposes

Despite the prevalence of co-infections and the association of over 50 viral and 46 bacterial pathogens with pig diseases, little is known about their simultaneous occurrence, particularly in commercial pig farming environments where health programs are in place. To address this knowledge gap, this study aimed to evaluate the pathogen threshold of respiratory and enteric pathogens in pig herds using the Pork MultiPath™ (PMP1 and PMP2, respiratory and enteric respectively) technology, which detects multiple pathogens simultaneously in a single reaction with high sensitivity and specificity. In this study the most prevalent respiratory pathogens, Mycoplasma hyrohinis, Pasteurella multocida, and Haemophilus parasuis detected by PMP1 were effectively controlled during the nursery stage through strategic treatment with tiamulin. Even though the major respiratory incidences were reduced, the recorded coughing and sneezing rates were associated with the levels of H. parasuis and M. hyrohinis, which were set at 1356 and 1275 copies/reaction, respectively. In addition, one of the identified co-infection patterns indicated a strong relationship between the occurrence of H. parasuis and M. hyorhinis at the sample and pen levels, highlighting the high likelihood of detecting these two pathogens together. Testing with enteric panel PMP2 revealed that the most frequently detected virulence factors during the early nursery stage were Escherichia coli genes for toxins - ST1, ST2, and fimbriae - F4 and F18. Moreover, a co-infection with Rotavirus B and C was often observed during the nursery stage, and a strong positive correlation between these two markers has been identified. Additionally, the levels of several markers, namely E. coli F4, F5, F18, LT, ST1, and ST2, have been associated with a higher likelihood of sickness in pig populations. In addition, the onset of Brachyspira pilosicoli during the nursery and grower stages was found to be associated with an increased risk of diarrhoea, with a set threshold at around 500 copies/reaction. Although simultaneous detection of multiple pathogens is not yet widely used in the pig industry, it offers a significant advantage in capturing the diversity and interactions of co-infections. Testing pooled samples with Pork MultiPath™ is cost-effective and practical to regularly monitor the health status of pig populations.

The Potential of Cold Atmospheric Pressure Plasmas for the Direct Degradation of Organic Pollutants Derived from the Food Production Industry

Specialized chemicals are used for intensifying food production, including boosting meat and crop yields. Among the applied formulations, antibiotics and pesticides pose a severe threat to the natural balance of the ecosystem, as they either contribute to the development of multidrug resistance among pathogens or exhibit ecotoxic and mutagenic actions of a persistent character. Recently, cold atmospheric pressure plasmas (CAPPs) have emerged as promising technologies for degradation of these organic pollutants. CAPP-based technologies show eco-friendliness and potency for the removal of organic pollutants of diverse chemical formulas and different modes of action. For this reason, various types of CAPP-based systems are presented in this review and assessed in terms of their constructions, types of discharges, operating parameters, and efficiencies in the degradation of antibiotics and persistent organic pollutants. Additionally, the key role of reactive oxygen and nitrogen species (RONS) is highlighted. Moreover, optimization of the CAPP operating parameters seems crucial to effectively remove contaminants. Finally, the CAPP-related paths and technologies are further considered in terms of biological and environmental effects associated with the treatments, including changes in antibacterial properties and toxicity of the exposed solutions, as well as the potential of the CAPP-based strategies for limiting the spread of multidrug resistance.

Defined Pig Microbiota Mixture as Promising Strategy against Salmonellosis in Gnotobiotic Piglets

Probiotics are a potential strategy for salmonellosis control. A defined pig microbiota (DPM) mixture of nine bacterial strains previously exhibited probiotic and anti-Salmonella properties in vitro. Therefore, we evaluated its gut colonization ability and protection effect against S. typhimurium LT2-induced infection in the gnotobiotic piglet model. The DPM mixture successfully colonized the piglet gut and was stable and safe until the end of the experiment. The colon was inhabited by about 9 log CFU g-1 with a significant representation of bifidobacteria and lactobacilli compared to ileal levels around 7-8 log CFU g-1. Spore-forming clostridia and bacilli seemed to inhabit the environment only temporarily. The bacterial consortium contributed to the colonization of the gut at an entire length. The amplicon profile analysis supported the cultivation trend with a considerable representation of lactobacilli with bacilli in the ileum and bifidobacteria with clostridia in the colon. Although there was no significant Salmonella-positive elimination, it seems that the administered bacteria conferred the protection of infected piglets because of the slowed delayed infection manifestation without translocations of Salmonella cells to the blood circulation. Due to its colonization stability and potential protective anti-Salmonella traits, the DPM mixture has promising potential in pig production applications. However, advanced immunological tests are needed.

Dispersion of antimicrobial resistant bacteria in pig farms and in the surrounding environment

BACKGROUND

Antimicrobial resistance has been identified as a major threat to global health. The pig food chain is considered an important source of antimicrobial resistance genes (ARGs). However, there is still a lack of knowledge on the dispersion of ARGs in pig production system, including the external environment.

RESULTS

In the present study, we longitudinally followed one swine farm located in Italy from the weaning phase to the slaughterhouse to comprehensively assess the diversity of ARGs, their diffusion, and the bacteria associated with them. We obtained shotgun metagenomic sequences from 294 samples, including pig feces, farm environment, soil around the farm, wastewater, and slaughterhouse environment. We identified a total of 530 species-level genome bins (SGBs), which allowed us to assess the dispersion of microorganisms and their associated ARGs in the farm system. We identified 309 SGBs being shared between the animals gut microbiome, the internal and external farm environments. Specifically, these SGBs were characterized by a diverse and complex resistome, with ARGs active against 18 different classes of antibiotic compounds, well matching antibiotic use in the pig food chain in Europe.

CONCLUSIONS

Collectively, our results highlight the urgency to implement more effective countermeasures to limit the dispersion of ARGs in the pig food systems and the relevance of metagenomics-based approaches to monitor the spread of ARGs for the safety of the farm working environment and the surrounding ecosystems.

Effect of a probiotic and an antibiotic on the mobilome of the porcine microbiota

Introduction: To consider the growing health issues caused by antibiotic resistance from a "one health" perspective, the contribution of meat production needs to be addressed. While antibiotic resistance is naturally present in microbial communities, the treatment of farm animals with antibiotics causes an increase in antibiotic resistance genes (ARG) in the gut microbiome. Pigs are among the most prevalent animals in agriculture; therefore, reducing the prevalence of antibiotic-resistant bacteria in the pig gut microbiome could reduce the spread of antibiotic resistance. Probiotics are often studied as a way to modulate the microbiome and are, therefore, an interesting way to potentially decrease antibiotic resistance. Methods: To assess the efficacy of a probiotic to reduce the prevalence of ARGs in the pig microbiome, six pigs received either treatment with antibiotics (tylvalosin), probiotics (Pediococcus acidilactici MA18/5M; Biopower® PA), or a combination of both. Their faeces and ileal digesta were collected and DNA was extracted for whole genome shotgun sequencing. The reads were compared with taxonomy and ARG databases to identify the taxa and resistance genes in the samples. Results: The results showed that the ARG profiles in the faeces of the antibiotic and combination treatments were similar, and both were different from the profiles of the probiotic treatment (p < 0.05). The effects of the treatments were different in the digesta and faeces. Many macrolide resistance genes were detected in a higher proportion in the microbiome of the pigs treated with antibiotics or the combination of probiotics and antibiotics. Resistance-carrying conjugative plasmids and horizontal transfer genes were also amplified in faeces samples for the antibiotic and combined treatments. There was no effect of treatment on the short chain fatty acid content in the digesta or the faeces. Conclusion: There is no positive effect of adding probiotics to an antibiotic treatment when these treatments are administered simultaneously.

Effects of supplemental bacteriophage on the gut microbiota and nutrient digestibility of ileal-cannulated pigs

This study measured the potential changes of the microbiota in the gastrointestinal tract and energy and nutrient digestibility by supplemental bacteriophages in pigs. Twelve castrated male pigs (initial mean body weight = 29.5 ± 2.3 kg) were surgically cannulated using T-cannula. The animals were housed individually in pens equipped with a feeder and a nipple waterer. The pigs were allotted to 1 of 3 experimental diets in a quadruplicated 3 × 2 Latin square design with 3 experimental diets, 2 periods, and 12 pigs resulting in 8 replicates per diet. The 3 diets were a control mainly based on corn and soybean meal with no antibiotics or bacteriophages, a diet containing 0.1% antibiotics, and a diet containing 0.2% bacteriophages. On day 5 of the experimental period, feces were collected and on days 6 and 7, ileal digesta were collected. Genomic DNA for bacteria were extracted from the ileal digesta and feces and the V4 region of the 16S rRNA gene was amplified. The ileal and fecal digestibility of energy, dry matter, organic matter, crude protein, and fiber was unaffected by dietary antibiotics or bacteriophages. At the phylum level, the supplemental antibiotic or bacteriophage tended to result in a higher proportion of Firmicutes (p = 0.059) and a lower proportion of Bacteroidetes (p = 0.099) in the ileal digesta samples compared with the control group with no difference between the antibiotic and bacteriophage groups. At the genus level, the supplemental antibiotic or bacteriophage tended to result in a higher proportion of Lactobacillus (p = 0.062) and a lower proportion of Bacteroides (p = 0.074) and Streptococcus (p = 0.088) in the ileal digesta compared with the control group with no difference between the antibiotic and bacteriophage groups. In the feces, supplemental antibiotics or bacteriophages reduced the proportion of Bifidobacterium compared with the control group (p = 0.029) with no difference between the antibiotic and bacteriophage groups. Overall, supplemental antibiotics and bacteriophages showed positive effect on the microbiota of in the ileal digesta without largely affecting energy or nutrient digestibility, with no differences between the antibiotic and bacteriophage groups in growing pigs.

Bacterial profile of pork from production to retail based on high-throughput sequencing

Pork is a common vehicle for foodborne pathogens, including Salmonella spp. and Yersinia enterocolitica. Cross-contamination can occur at any stage of the pork production chain, from farm to market. In the present study, high-throughput sequencing was used to characterize bacterial profiles and track their changes along the whole supply chain. Tracked meat samples (pig on the farm, carcass in the slaughterhouse, unprocessed carcass and processed meat in the processing plant, and fresh pork at the local retail stores) and their associated environmental samples (e.g., water, floor, feed, feces, and workers' gloves) were collected from sequential stages (n = 96) and subjected to 16S rRNA metataxonomic analyses. At the farm, a total of 652 genera and 146 exclusive genera were identified in animal and environmental samples (pig, drain, floor, fan, and feces). Based on beta diversity analysis, it was demonstrated that the microbial composition of animal samples collected at the same processing step is similar to that of environmental samples (e.g., drain, fan, feces, feed, floor, gloves, knives, tables, and water). All animal and environmental samples from the slaughterhouse were dominated by Acinetobacter (55.37 %). At the processing plant, belly meat and neck meat samples were dominated by Psychrobacter (55.49 %). At the retail level, key bacterial players, which are potential problematic bacteria and important members with a high relative abundance in the samples, included Acinetobacter (8.13 %), Pseudomonas (6.27 %), and Staphylococcus (2.13 %). In addition, the number of confirmed genera varied by more than twice that identified in the processing plant. Source tracking was performed to identify bacterial contamination routes in pork processing. Animal samples, including the processing plant's carcass, the pig from the farm, and the unwashed carcass from the slaughterhouse (77.45 %), along with the processing plant's gloves (5.71 %), were the primary bacterial sources in the final product. The present study provides in-depth knowledge about the bacterial players and contamination points within the pork production chain. Effective control measures are needed to control pathogens and major pollutants at each stage of pork production to improve food safety.

Chlortetracycline Concentration Impact on Salmonella Typhimurium Sustainability in the Presence of Porcine Gastrointestinal Tract Bacteria Maintained in Continuous Culture

Concern exists that the continued use of antibiotics in animal feeds may lead to an increased prevalence of resistant bacteria within the host animal's gastrointestinal tract. To evaluate the effect of chlortetracycline on the persistence of Salmonella enterica serotype Typhimurium within a diverse population of porcine cecal bacteria, we cultured a mixed population of cecal bacteria without or with added chlortetracycline. When grown at a 24 h vessel turnover rate, chlortetracycline-susceptible S. Typhimurium exhibited more than 2.5 times faster (p < 0.05) disappearance rates than theoretically expected (0.301 log10 colony-forming unit/mL per day) but did not differ whether treated or not with 55 mg of chlortetracycline/L. Chlortetracycline-resistant S. Typhimurium was not recovered from any of these cultures. When the mixed cultures were inoculated with a chlortetracycline-resistant S. Typhimurium, rates of disappearance were nearly two times slower (p < 0.05) than those observed earlier with chlortetracycline-susceptible S. Typhimurium, and cultures persisted at >2 log10 colony-forming units/mL for up to 14 days of treatment with 110 mg of chlortetracycline/L. Under the conditions of this study, chlortetracycline-resistant S. Typhimurium was competitively enabled to persist longer within the mixed populations of porcine gut bacteria than chlortetracycline-susceptible S. Typhimurium, regardless of the presence or absence of added chlortetracycline.

Transmission of β-lactamases in the pork food chain: A public health concern

Antimicrobial resistance (AMR) is a risk for public health that requires management in a One Health perspective, including humans, animals, and the environment. The food production chain has been identified as a possible route of transmission of AMR bacteria to humans. The most critical issue regards resistance to the Critically Important Antimicrobials (CIAs), such as β-lactams antibiotics. Here, pigs were analysed along the entire food producing chain, including feces, carcasses and pork products (fresh meat, fermented and seasoned products) ensuring treaciability of all samples. Escherichia coli were isolated and their ability to produce ESBL and AmpC β-lactamases was evaluated both phenotypically and genotypically. Strains with the same AMR profile from feces, carcasses, and meat products were selected for phylogenetic and comparative genomic analyses to evaluate the possible "farm-to-fork" transmission of β-lactams resistant bacteria. Results showed that the percentage of ESBL strains in fecal E. coli was approximately 7% and increased slightly in the pork food chain: the 10% of ESBL E. coli isolated from carcasses and the 12.5% of isolates from fresh meat products. AmpC E. coli were found only in feces, carcasses, and fresh meat with a low prevalence. Results showed that of the 243 pigs followed along the entire food chain genetic similarities in E. coli isolated from farm-to-fork were found in only one pig (feces, carcasses and fresh meat). Frequent similarities were shown in resistant E. coli isolates from carcasses and fresh meat or fermented product (three pork food chain). Moreover, in one case, bacteria isolated from fresh meat and fermented product were genotypically similar. Concluding, direct transmission of β-lactams resistance from farm-to-fork is possible but not frequent. Further studies are needed to improve risk communication to consumers and access to clear and reliable information and health concerns on food.

Brazilian Clinical Strains of Actinobacillus pleuropneumoniae and Pasteurella multocida: Capsular Diversity, Antimicrobial Susceptibility (In Vitro) and Proof of Concept for Prevention of Natural Colonization by Multi-Doses Protocol of Tildipirosin

One hundred Actinobacillus pleuropneumoniae (App) and sixty Pasteurella multocida subsp. multocida serogroup A (PmA) isolates were recovered from porcine pneumonic lungs collected from eight central or southern states of Brazil between 2014 and 2018 (App) or between 2017 and 2021 (PmA). A. pleuropneumoniae clinical isolates were typed by multiplex PCR and the most prevalent serovars were 8, 7 and 5 (43, 25% and 18%, respectively). In addition, three virulence genes were assessed in P. multocida isolates, all being positive to capA (PmA) and kmt1 genes, all negative to capD and toxA, and most of them (85%) negative to pfhA gene. The susceptibility of both pathogens to tildipirosin was investigated using a broth microdilution assay. The percentage of isolates susceptible to tildipirosin was 95% for App and 73.3% for PmA. The MIC50 values were 0.25 and 1 μg/mL and the MIC90 values were 4 and >64 μg/mL for App and PmA, respectively. Finally, a multiple-dose protocol of tildipirosin was tested in suckling piglets on a farm endemic for both pathogens. Tildipirosin was able to prevent the natural colonization of the tonsils by App and PmA and significantly (p < 0.0001) reduced the burden of Glaesserella parasuis in this tissue. In summary, our results demonstrate that: (i) tildipirosin can be included in the list of antibiotics to control outbreaks of lung disease caused by App regardless of the capsular type, and (ii) in the case of clinical strains of App and PmA that are sensitive to tildipirosin based on susceptibility testing, the use of this antibiotic in eradication programs for A. pleuropneumoniae and P. multocida can be strongly recommended.

Fatty Acid Profile and Lipid Quality Indexes of the Meat and Backfat from Porkers Supplemented with EM Bokashi Probiotic

The study aimed to assess the effect of supplementation of pig diet with the Bokashi probiotic on the fatty acid profile of longissimus lumborum (LL) muscles and backfat. The research involved 120 hybrid pigs deriving from Naïma sows and P-76 boars. The experimental group's pigs received probiotics in their feed (containing Saccharomyces cerevisiae, Lactobacillus casei, and Lactobacillus plantarum). To analyze the fatty acid profile in intramuscular fat (IMF) of LL and backfat, 24 pig carcasses from the control group and 26 from the probiotic-supplemented group were randomly selected. Probiotic supplementation increased the Atherogenic Index, reduced the proportion of C20:4, and increased C12:0 and C18:2 n-6 in IMF LL, without affecting ΣSFA, ΣMUFA, and ΣPUFA. In backfat, probiotic supplementation decreased C18:1 and C18:2 n-6 proportion and increased C18:3 n-3, C20:3 n-6, and C20:4 n-6. These changes resulted in significantly higher ΣMUFA, ΣPUFA, PUFA Σn-3/Σn-6, and lower Saturation Index (SI). From a consumer health and technological point of view, probiotic supplementation improved the lipid profile of backfat to a greater extent than LL muscle. Bokashi, at a dose of 3 g/kg of feed in the last stage of pig production, had no significant effect on the fatty acid profile of the meat.

Evaluation of Antimicrobial Resistance Profiles of Bacteria Isolated from Biofilm in Meat Processing Units

The aim of this study was to assess the hygiene of pork, beef, and poultry carcasses and to determine the phenotypic antibiotic susceptibility of the bacteria embedded in the biofilm formed on the carcasses kept in cooling chambers for at least three days. The level of hygiene was assessed by determining the total aerobic colony count (TACC) and the Enterobacteriaceae level in different sampling points of the carcasses, along with the detection of E. coli and Pseudomonas spp. embedded in the biofilm. Furthermore, the E. coli and Pseudomonas spp. isolates were tested for antimicrobial resistance profiles. A total of 130 samples collected from pork, beef, and poultry from processing units were analyzed to determine the total aerobic colony count as well as to measure the level of Enterobacteriaceae found on the carcasses. The antimicrobial susceptibility of 44 Escherichia coli and eight Pseudomonas spp. strains isolated from the carcasses were assessed using the Vitek 2 system using two different cards. Overall, the regulatory limits for the TACC were exceeded in 7.6% of the samples, and 65% of the samples exceeded the regulatory limits for Enterobacteriaceae levels. The antimicrobial susceptibility tests of the E. coli isolates analyzed with the AST-GN27 card revealed the highest resistance to be that towards ampicillin (76.1%), followed by cefazolin (71.4%), amoxicillin/clavulanic acid (61.9%), nitrofurantoin (52.3%), cefoxitin (47.6%), tetracycline (38.1%), piperacillin, norfloxacin (19%), trimethoprim-sulfamethoxazole (11.9%), cefotaxime (9.5%), ceftazidime, cefazolin, amikacin, gentamicin, and ciprofloxacin (4.7%). However, all of the isolates were sensitive to piperacillin-tazobactam and imipenem. Thirty-two (61.5%; 95% CI 47.9-73.5) out of fifty-two isolates exhibited multidrug resistance, resulting in the expression of 10 resistance profiles. The findings of this study highlight serious hygienic and sanitary deficiencies within the meat processing units and demonstrate that the resulting meat can harbor Multidrug-resistant Escherichia coli and Pseudomonas spp., both of which pose a serious public health risk. However, further research with a larger number of samples is required to reach thorough results.

A cyclophosphamide-induced immunosuppression Swiss Albino mouse model unveils a potential role for cow urine distillate as a feed additive

BACKGROUND

Traditional and natural immunomodulators are increasingly used as supplements in animal feeds and as interventions in the prevention and treatment of disease in animals.

OBJECTIVE

The aim of this study was to examine the immunomodulatory characteristics of distilled cow urine in vivo using two mouse models, a normal mouse model and an immunosuppressive mouse model.

METHODOLOGY

We divided 144 Swiss Albino mice weighing between 15 g and 30 g, aged between two and three months, into two groups of 72 mice each. In the first group, we subdivided the animals into six subgroups of 12 each. In this group paramerters such as, body weight, organ weights of liver and kidney, haemagglutination titre, Jerne plaque-forming assay, and bone marrow cellularity were measured. We divided the second group into six subgroups for the assessment of delayed-type hypersensitivity (DTH).

RESULTS

As compared to normal control mice, immunocompetent and immunosuppressed mice (given cow urine distillate) had significant increases in body weight, spleen weight, liver weight, total leucocyte count, lymphocyte count, serum protein, and globulin contents. In the treatment groups, the titre of antibodies, the number of antibody- producing cells, the cellularity of bone marrow, and foot pad thickness also increased. In the treatment group, both humoral and cellular immunity were altered compared to the control group, suggesting cow urine distillate to be a potential animal feed ingredient for immunoregulation.

CONCLUSION

This study was able to demonstrate the experimental validity of natural compounds as immunomodulators that can be used in feed supplements for animals. Various compounds could be tested for immunomodulatory effects using this technique in experimental animals.

Genomic Characterization of a Tetracycline-Resistant Strain of Brochothrix thermosphacta Highlights Plasmids Partially Shared between Various Strains

The Gram-positive bacterium Brochothrix thermosphacta is a spoilage agent commonly found on meat products. While the tet(L) gene, which confers resistance to tetracycline, has been identified in certain strains of B. thermosphacta, only a limited number of studies have investigated this gene and its potential presence on mobile DNA elements. This study aims to analyze the tetracycline-resistant strain B. thermosphacta BT469 at the genomic level to gain insight into the molecular determinants responsible for this resistance. Three plasmids have been identified in the strain: pBT469-1, which contains a tetR gene; pBT469-2, which harbours the tet(L) gene responsible for tetracycline resistance; and pBT469-3, which carries genes encoding for a thioredoxin and a phospholipase A2. Homology searches among sequences in public databases have revealed that the plasmid pBT469-2 is currently unique to the BT469 strain. However, the pBT469-1 plasmid is also found in three other strains of B. thermosphacta. Notably, sequences similar to pBT469-1 and pBT469-2 were also found in other bacterial genera, suggesting that these plasmids may be part of a diverse family present in several bacterial genera. Interestingly, sequences of various strains of B. thermosphacta show a high level of similarity with pBT469-3, suggesting that variants of this plasmid could be frequently found in this bacterium.

One Health challenges for pig reproduction

The current state of the world challenges pig reproduction as an important part of One Health, which involves interrelationships between animal, human and environmental health. The One Health concept underlines a comparative aspect in reproductive physiology and disease occurrence, bridging knowledge from one species to another. Seasonal changes in the environment affect pig reproduction and climate change may further strengthen those effects. Endocrine-disrupting chemicals (EDCs), and specifically phthalates and heavy metals, interfere with endocrine function, and thereby sexual behavior, fertilization capacity and steroidogenesis. Reproductive infections and extended semen storage are important indications for antimicrobial use. Innovative solutions are needed to explore alternatives to antimicrobials. Efforts to ensure reproductive efficiency have prolonged farrowing as litter size has doubled over the past three decades, compromising immune transfer and welfare. Physiological, metabolic and programming related events around parturition are key areas for future One Health research in pig reproduction. In conclusion, climate change challenges reproductive management and breeding. More resilient pigs that can tolerate harsh environment but maintain high reproductive performance are needed. EDCs continue to grow as an environmental challenge for reproductive management and alternatives to antibiotics will be required.

Application of nematicide avermectin enriched antibiotic-resistant bacteria and antibiotic resistance genes in farmland soil

The extensive use of antibiotics in medicine and agriculture has resulted in the accumulation of antibiotic-resistant microorganisms and antibiotic resistance genes (ARGs) in environments, which threaten human health and contaminate environment. Nematicide avermectin is widely applied to control root-knot nematodes. The effect of five-years application of avermectin on rhizosphere microbiome and resistome of sick tobacco plants in farmland were investigated in present study. The environmental risks of avermectin was assessed adequately. Metagenomic method was used to analyze antibiotic-resistant bacteria and antibiotic resistance genes in the avermectin-treated soil. The abundance and distribution of antibiotic-resistant bacteria and their antibiotic resistance genes were affected by avermectin application. The antibiotic resistant Proteobacteria occupied the highest percentage (36%) in rhizosphere soil and carried 530 ARGs. Opportunistic human pathogens carrying antibiotic resistance genes were enriched in the avermectin-treated soil. Avermectin application increased the counts of many types of antibiotic resistance genes. The relative abundances of genes adeF, BahA, fusH, ileS, and tlrB in the avermectin-treated soil were significantly greater than in the untreated control soil. Different resistance mechanisms were revealed in the avermectin-treated soil. The efflux of antibiotic (670 ARGs), inactivation of antibiotic (475 ARGs), and alteration of antibiotic target (267 ARGs) were the main resistance mechanisms. Rigid control the avermectin dose and use frequency and other pesticides can decrease soil antibiotic resistance genes and protect agricultural products' safety and public health. Overall, application of nematicide avermectin enriched antibiotic-resistant bacteria and antibiotic resistance genes in farmland soil, which should be on the alert for environment protection.

Antimicrobial Resistance and Clonal Lineages of Escherichia coli from Food-Producing Animals

Escherichia coli are one of the most important pathogenic bacteria readily found in the livestock and widely studied as an indicator that carries drug-resistant genes between humans, animals, and the environment. The use of antimicrobials in the food chain, particularly in food-producing animals, is recognized as a significant contributor to the development and spread of antimicrobial resistance (AMR) and resistance genes can be transferred from the farm through the food-chain. The objective of this review is to highlight the background of the antimicrobials use in food-producing animals, more specifically, to study clonal lineages and the resistance profiles observed in E. coli, as well as in extended spectrum beta-lactamases (ESBL) producing E. coli, in a set of food-production animals with greater relevance in food consumption, such as pigs, poultry, cattle, fish farming and rabbits. Regarding the prevalence of ESBL-producing E. coli among farm animals, high-to-moderate prevalence was observed, and the highest resistance rates to tetracycline and ampicillin was detected in different farms in all geographic regions. Worldwide pandemic clones and high-risk zoonotic E. coli clones have been identified in most food-producing animals, and some of these clones are already disseminated in different niches, such as the environment and humans. A better understanding of the epidemiology of E. coli and ESBL-producing E. coli in livestock is urgently needed. Animal production is one of the major causes of the antibiotic resistance problem worldwide and a One Health approach is needed.

The Genetic Diversity and Antimicrobial Resistance of Pyogenic Pathogens Isolated from Porcine Lymph Nodes

According to the Food and Agriculture Organization of the United Nations, pork remains the most consumed meat in the world. Consequently, it is very important to ensure that it is of the highest microbiological quality. Many of the pathogens that cause lymph node lesions in pigs are zoonotic agents, and the most commonly isolated bacteria are Mycobacterium spp., Streptococcus spp., Staphylococcus aureus and Rhodococcus equi (synonymous with Prescottella equi). The prevention and treatment of zoonotic infections caused by these bacteria are mainly based on antimicrobials. However, an overuse of antimicrobials contributes to the emergence and high prevalence of antimicrobial-resistant strains, which are becoming a serious challenge in many countries. The aim of this study was to evaluate the genetic diversity and antimicrobial resistance of the Streptococcus spp. (n = 48), S. aureus (n = 5) and R. equi (n = 17) strains isolated from swine lymph nodes with and without lesions. All isolates of S. dysgalactiae, S. aureus and R. equi were subjected to PFGE analysis, which showed the genetic relatedness of the tested bacteria in the studied pig populations. Additionally, selected tetracycline and macrolide resistance genes in the streptococcal strains were also studied. The results obtained in the present study provide valuable data on the prevalence, diversity, and antimicrobial resistance of the studied bacteria. Numerous isolated bacterial Streptococcus spp. strains presented resistance to doxycycline, and almost half of them carried tetracycline resistance genes. In addition, R. equi and S. aureus bacteria presented a high level of resistance to beta-lactam antibiotics and to cefotaxime, respectively.

Adhesion factors and antimicrobial resistance of Escherichia coli strains associated with colibacillosis in piglets in Colombia

Background and Aims

The pathogenicity of Escherichia coli is determined by the presence of genes that mediate virulence factors such as adherence capacity and toxin production. This research aimed to identify the adhesion factors and antibiotic resistance capacity of E. coli strains associated with diarrhea in piglets in Colombia.

Materials and Methods

Presumptive E. coli strains were isolated from the rectal swabs of piglets in swine farms between 4 and 40 days of age with evidence of diarrhea. Presumptive E. coli strains were tested for antibiotic resistance. The hemolytic capacity of presumptive E. coli strains was measured and molecularly identified. Strains confirmed as hemolytic E. coli was evaluated for the presence of five adhesion factors (F4, F5, F6, F18, and F41) and resistance to 11 antibiotics.

Results

Fifty-two putative E. coli strains were isolated, six of which showed a hemolytic capacity. The hemolytic strains were molecularly identified as E. coli. Adhesive fimbriae were found in five of six β-hemolytic E. coli isolates. Combinations of the adhesion factors F6-F18 and F6-F41 were linked to antibiotic resistance capacity.

Conclusion

The phenomenon of E. coli strains resistant to multiple antibiotics on pig farms represents a constant risk factor for public health and pig production.

Molecular Detection of Metronidazole and Tetracycline Resistance Genes in Helicobacter pylori-Like Positive Gastric Samples from Pigs

Antimicrobial resistance is a major public health concern. The aim of this study was to assess the presence of antibiotic resistance genes, previously reported in Helicobacter pylori, in gastric samples of 36 pigs, in which DNA of H. pylori-like organisms had been detected. Based on PCR and sequencing analysis, two samples were positive for the 16S rRNA mutation gene, conferring tetracycline resistance, and one sample was positive for the frxA gene with a single nucleotide polymorphism, conferring metronidazole resistance. All three amplicons showed the highest homology with H. pylori-associated antibiotic resistance gene sequences. These findings indicate that acquired antimicrobial resistance may occur in H. pylori-like organisms associated with pigs.

Characterization of Lactic Acid Bacteria Isolated from Spontaneously Fermented Sausages: Bioprotective, Technological and Functional Properties

Fermentation is one of the most ancient strategies to improve safety and extend shelf-life of the products. Starter cultures are mainly represented by lactic acid bacteria (LAB), which may also be bioprotective agents controlling the fermentation process, the native microbiota and pathogen outgrowth. This work aimed to select new LAB strains from spontaneously fermented sausages produced in different areas of Italy, which can be effective as starter cultures and bioprotective agents in fermented salami. The strains, mainly belonging to the Latilactobacillus sakei species, were characterized for their ability to inhibit major meat pathogens, the presence of antibiotic resistances and amine production. Moreover, technological performances, such as growth and acidification kinetics at increasing NaCl concentrations, were studied. As a result, new autochthonous Lat. sakei strains were obtained, lacking antibiotic resistance, possessing antimicrobial activity against Clostridium sporogenes, Listeria monocytogenes, Salmonella and Escherichia coli and with high growth performance under osmotic pressure. These strains have the potential for future application to improve the safety of fermented meats, even under conditions in which chemical preservatives are reduced or eliminated. Moreover, studies on autochthonous cultures are pivotal for guaranteeing specific characteristics of traditional products that represent an important cultural heritage.

Identification and characterization of extrachromosomal circular DNA in Wei and Large White pigs by high-throughput sequencing

Wei pig (WP) and Large White pig (LP) are fatty and lean breeds, respectively. Extrachromosomal circular DNA (eccDNA) plays an important role in regulating signaling pathway processes of cell. However, there are few reports regarding the eccDNA and ecDNA profiles in WP and LP. The present work aimed to investigate the eccDNA and ecDNA profiles between WP and LP. Three WPs and three LPs (100 ± 1.3 kg) were selected for analysis of eccDNA and ecDNA in the ear samples. Results showed that there were 39,686,953,656-58,411,217,258 and 53,824,168,657-58,311,810,737 clean data for WP and LP, respectively. Sequencing yielded 15,587-25,479 and 71,123-79,605 eccDNAs from the ear samples of WP and LP, respectively. There were 15,111 and 22,594 eccDNA-derived genes in the WP and LP, respectively, and 13,807 eccDNA-derived genes were common in the ear samples of both pigs. Sequencing yielded 13-19 and 27-43 ecDNAs in the ears of WP and LP, respectively. There were 1,005 and 1,777 ecDNA-derived genes in WP and LP, respectively, and 351 ecDNA-derived genes were common in the ear samples of both pigs. The most significant KEGG pathways of eccDNA-derived genes were axon guidance, focal adhesion, metabolic pathways, MAPK signaling pathway, Hedgehog signaling pathway, microRNAs in cancer, tight junction, phospholipase D signaling pathway, endocytosis, and sphingolipid signaling pathway. Furthermore, the most significant KEGG pathways of ecDNA-derived genes were olfactory transduction, B cell receptor signaling pathway, and chemical carcinogenesis. The eccDNA00044301 was lower abundance, while the ecDNA00000060 was higher abundance in WP compared with that in LP. Summary, we found that eccDNAs and ecDNAs are common in WP and LP and occur in sizes large enough to carry one or several partial or complete genes. These findings have expanded the knowledge repertoire of circular DNA in pig and will provide a reference for the use of pigs as a medical model and help discovery of new genetic markers to select high-quality breeds.

Presence of Staphylococcus spp. carriers of the mecA gene in the nasal cavity of piglets in the nursery phase

The presence of Staphylococcus spp. resistant to methicillin in the nasal cavity of swine has been previously reported. Considering the possible occurrence of bacterial resistance and presence of resistance genes in intensive swine breeding and the known transmissibility and dispersion potential of such genes, this study aimed to investigate the prevalence of resistance to different antibiotics and the presence of the mecA resistance gene in Staphylococcus spp. from piglets recently housed in a nursery. For this, 60 nasal swabs were collected from piglets at the time of their housing in the nursery, and then Staphylococcus spp. were isolated and identified in coagulase-positive (CoPS) and coagulase-negative (CoNS) isolates. These isolates were subjected to the disk-diffusion test to evaluate the bacterial resistance profile and then subjected to molecular identification of Staphylococcus aureus and analyses of the mecA gene through polymerase chain reaction. Of the 60 samples collected, 60 Staphylococcus spp. were isolated, of which 38 (63.33%) were classified as CoNS and 22 (36.67%) as CoPS. Of these, ten (45.45%) were identified as Staphylococcus aureus. The resistance profile of these isolates showed high resistance to different antibiotics, with 100% of the isolates resistant to chloramphenicol, clindamycin, and erythromycin, 98.33% resistant to doxycycline, 95% resistant to oxacillin, and 85% resistant to cefoxitin. Regarding the mecA gene, 27 (45%) samples were positive for the presence of this gene, and three (11.11%) were phenotypically sensitive to oxacillin and cefoxitin. This finding highlights the importance of researching the phenotypic profile of resistance to different antimicrobials and resistance genes in the different phases of pig rearing to identify the real risk of these isolates from a One Health perspective. The present study revealed the presence of samples resistant to different antibiotics in recently weaned production animal that had not been markedly exposed to antimicrobials as growth promoters or even as prophylactics. This information highlights the need for more research on the possible sharing of bacteria between sows and piglets, the environmental pressure within production environments, and the exposure of handlers during their transport, especially considering the community, hospital, and political importance of the presence of circulating resistant strains.

Reassessment of Historical Clinical Trials Supports the Effectiveness of Phage Therapy

Phage therapy has become a hot topic in medical research due to the increasing prevalence of antibiotic-resistant bacteria strains. In the treatment of bacterial infections, bacteriophages have several advantages over antibiotics, including strain specificity, lack of serious side effects, and low development costs. However, scientists dismissed the clinical success of early clinical trials in the 1940s, slowing the adoption of this promising antibacterial application in Western countries. The current study used statistical methods commonly used in modern meta-analysis to reevaluate early 20th-century studies and compare them with clinical trials conducted in the last 20 years. Using a random effect model, the development of disease after treatment with or without phages was measured in odds ratios (OR) with 95% confidence intervals (CI). Based on the findings of 17 clinical trials conducted between 1921 and 1940, phage therapy was effective (OR = 0.21, 95% CI = 0.10 to 0.44, P value < 0.0001). The current study includes a topic review on modern clinical trials; four could be analyzed, indicating a noneffective therapy (OR = 2.84, 95% CI = 1.53 to 5.27, P value = 0.0009). The results suggest phage therapy was surprisingly less effective than standard treatments in resolving bacterial infections. However, the results were affected by the small sample set size. This work also contextualizes the development of phage therapy in the early 20th century and highlights the expansion of phage applications in the last few years. In conclusion, the current review shows phage therapy is no longer an underestimated tool in the treatment of bacterial infections.

Use of Microorganisms as Nutritional and Functional Feedstuffs for Nursery Pigs and Broilers

The objectives of this review paper are to introduce the structures and composition of various microorganisms, to show some applications of single cells as alternative protein supplements or energy feeds in swine and poultry diets, and to discuss the functional effects of microorganisms as feed additives on the growth performance and intestinal health of nursery pigs and broilers. Microorganisms, including bacteria, yeasts, and microalgae, have been commonly supplemented in animal diets because they are cost-effective, stable, and have quantitative production that provides nutritional and functional benefits to pigs and broilers. Microorganisms could be alternative antibiotics to enhance intestinal health due to bioactive components from cell wall components, which interact with receptors on epithelial and immune cells. In addition, bioactive components could be digested by intestinal microbiota to produce short-chain fatty acids and enhance energy utilization. Otherwise, microorganisms such as single-cell protein (SCP) and single-cell oils (SCOs) are sustainable and economic choices to replace conventional protein supplements and energy feeds. Supplementing microorganisms as feedstuffs and feed additives improved the average daily gain by 1.83%, the daily feed intake by 0.24%, and the feed efficiency by 1.46% in pigs and broilers. Based on the properties of each microorganism, traditional protein supplements, energy feeds, and functional feed additives could be replaced by microorganisms, which have shown benefits to animal's growth and health. Therefore, specific microorganisms could be promising alternatives as nutritional and functional feedstuffs in animal diets.

Garlic essential oil in water nanoemulsion prepared by high-power ultrasound: Properties, stability and its antibacterial mechanism against MRSA isolated from pork

Food-borne methicillin-resistance Staphylococcus aureus (MRSA) has caused significant health threats and economic loss in livestock and poultry products. Garlic essential oil (GEO) is an effective antibacterial agent but presents strong instability and hydrophobicity. In this study, GEO in water nanoemulsion (GEON) with good stability was produced by emulsification technique of high-power ultrasound. Its antibacterial activity and underlying mechanism against MRSA isolated from retailed pork were investigated. Results showed that ultrasonic treatment significantly reduced the particle size of GENO from 820.3 to 215.0 nm as time increased from 0 to 10 min. Comparatively, GEON of 10 min ultrasound was more stable than other GEONs (0, 1, 5 min) during 30 d storage. It also displayed good thermal stability and relatively good ion stability (NaCl, MgCl₂, and glucose). Antibacterial analysis showed that GEON (10 min) exhibited the best anti-MRSA activity among all GEONs, and the minimum inhibitory concentration of GEO in this nanoemulsion was 0.125 % (1.25 mg/mL). Treatment of GEON (10 min) significantly suppressed the cell proliferation of MRSA, which was mainly achieved by damaging the cell membrane as evidenced by membrane depolarization and considerable leakage of intracellular nucleic acids and protein. Laser scanning confocal microscope and scanning electron microscopy showed that treatment of GEON (10 min) significantly altered the membrane integrity and severely damaged the cellular membrane and structure. The present work illustrated that GEON produced by ultrasonic emulsification is a promising alternative to inhibit the contamination and spread of MRSA in livestock and poultry products.

Taxonomical Identification and Safety Characterization of Lactobacillaceae from Mediterranean Natural Fermented Sausages

Fermented meat products represent an important industrial sector in Europe, particularly in the Mediterranean Countries (MC), where the presence of numerous local productions, still obtained through spontaneous fermentation, is recognized as a formidable treasure chest of unexplored microbial biodiversity. Lactobacillaceae naturally occurring in fifteen spontaneously fermented sausages from MC (Italy, Spain, Croatia, and Slovenia) were isolated and taxonomically characterized using molecular techniques. Additionally, a safety assessment for the presence of antibiotic resistances and biogenic amine (BA) production was performed to determine their suitability as autochthonous starter cultures. Molecular typing, performed using REP-PCR, discriminated 151 strains belonging to Latilactobacillus sakei (59.6%), Latilactobacillus curvatus (26.5%) and Companilactobacillus alimentarius (13.9%). The minimum inhibitory concentrations (MICs) of eight different antibiotics revealed a high resistance to streptomycin (27%), tetracycline (16%), followed by gentamycin (14%) and kanamycin (13%). Interestingly, the results showed a geographical distribution of resistant biotypes. tetM/tetS or ermB genes were identified in only six strains. The amino-biogenic potential of the strains was assessed, confirming the absence of this trait among L. sakei, while a high number of producer strains was found among L. curvatus. On the 151 analyzed strains, 45 demonstrated safety traits for their future use as starter food cultures. These results open the way to further studies on the technological properties of these promising autochthonous strains, strongly linked to the Mediterranean environment.

Emergence and spread of antibiotic-resistant foodborne pathogens from farm to table

Antibiotics have been overused and misused for preventive and therapeutic purposes. Specifically, antibiotics are frequently used as growth promoters for improving productivity and performance of food-producing animals such as pigs, cattle, and poultry. The increasing use of antibiotics has been of great concern worldwide due to the emergence of antibiotic resistant bacteria. Food-producing animals are considered reservoirs for antibiotic resistance genes (ARGs) and residual antibiotics that transfer from the farm through the table. The accumulation of residual antibiotics can lead to additional antibiotic resistance in bacteria. Therefore, this review evaluates the risk of carriage and spread of antibiotic resistance through food chain and the potential impact of antibiotic use in food-producing animals on food safety. This review also includes in-depth discussion of promising antibiotic alternatives such as vaccines, immune modulators, phytochemicals, antimicrobial peptides, probiotics, and bacteriophages.

Knowledge, Attitudes and Practices Regarding Antibiotic Use and Antibiotic Resistance: A Latent Class Analysis of a Romanian Population

Considering the major limitations of the latest studies conducted in Romania on the knowledge, attitudes and practices (KAPs) of antibiotic use and antibiotic resistance, we conducted this study to assess this major public health threat. A cross-sectional survey based on a validated questionnaire was conducted among the general population of Romania for a period of 5 months, i.e., September 2021-January 2022. The questionnaire was distributed using Google Form and it covered demographic characteristics and KAP assessments consisting of 12 items on knowledge, 10 items on attitudes and 3 items on practices. Latent class analyses (LCAs) were conducted to group respondents based on their responses. The response rate was 77%, of which females responded in a greater number (n = 1251) compared to males (n = 674). For most of the respondents (67.32%, n = 1296), the education level was high school, while 23.58% (n = 454) of respondents were college graduates. One in three Romanians (33.3%) know the WHO predictions related to this topic. Overall, the Romanian population is less disciplined when it comes to completing antibiotic treatments, as 29.19% of the respondents stop the course of antibiotic administration if their symptoms improve. The key findings from the present study may help policy makers in designing targeted interventions to decrease confusion, ambiguity or misconceptions about antibiotic use.

The Role of Gut Microbiota in the Skeletal Muscle Development and Fat Deposition in Pigs

Pork quality is a factor increasingly considered in consumer preferences for pork. The formation mechanisms determining meat quality are complicated, including endogenous and exogenous factors. Despite a lot of research on meat quality, unexpected variation in meat quality is still a major problem in the meat industry. Currently, gut microbiota and their metabolites have attracted increased attention in the animal breeding industry, and recent research demonstrated their significance in muscle fiber development and fat deposition. The purpose of this paper is to summarize the research on the effects of gut microbiota on pig muscle and fat deposition. The factors affecting gut microbiota composition will also be discussed, including host genetics, dietary composition, antibiotics, prebiotics, and probiotics. We provide an overall understanding of the relationship between gut microbiota and meat quality in pigs, and how manipulation of gut microbiota may contribute to increasing pork quality for human consumption.

Assessment of listing and categorisation of animal diseases within the framework of the Animal Health Law (Regulation (EU) No 2016/429): antimicrobial‐resistant Escherichia coli in dogs and cats, horses, swine, poultry, cattle, sheep and goats

Escherichia coli (E. coli) was identified among the most relevant antimicrobial‐resistant (AMR) bacteria in the EU for dogs and cats, horses, swine, poultry, cattle, sheep and goats in previous scientific opinions. Thus, it has been assessed according to the criteria of the Animal Health Law (AHL), in particular criteria of Article 7 on disease profile and impacts, Article 5 on its eligibility to be listed, Annex IV for its categorisation according to disease prevention and control rules as in Article 9 and Article 8 for listing animal species related to the bacterium. The assessment has been performed following a methodology previously published. The outcome is the median of the probability ranges provided by the experts, which indicates whether each criterion is fulfilled (lower bound ≥ 66%) or not (upper bound ≤ 33%), or whether there is uncertainty about fulfilment. Reasoning points are reported for criteria with uncertain outcome. According to the assessment here performed, it is uncertain whether AMR E. coli can be considered eligible to be listed for Union intervention according to Article 5 of the AHL (33–66% probability). According to the criteria in Annex IV, for the purpose of categorisation related to the level of prevention and control as in Article 9 of the AHL, the AHAW Panel concluded that the bacterium does not meet the criteria in Sections 1, 2, 3 and 4 (Categories A, B, C and D; 0–5%, 5–10%, 10–33% and 10–33% probability of meeting the criteria, respectively) and the AHAW Panel was uncertain whether it meets the criteria in Section 5 (Category E, 33–66% probability of meeting the criteria). The animal species to be listed for AMR E. coli according to Article 8 criteria include mammals, birds, reptiles and fish.

Impact of Antibiotic Therapies on Resistance Genes Dynamic and Composition of the Animal Gut Microbiota

Antibiotics are major disruptors of the gastrointestinal microbiota, depleting bacterial species beneficial for the host health and favoring the emergence of potential pathogens. Furthermore, the intestine is a reactor of antibiotic resistance emergence, and the presence of antibiotics exacerbates the selection of resistant bacteria that can disseminate in the environment and propagate to further hosts. We reviewed studies analyzing the effect of antibiotics on the intestinal microbiota and antibiotic resistance conducted on animals, focusing on the main food-producing and companion animals. Irrespective of antibiotic classes and animal hosts, therapeutic dosage decreased species diversity and richness favoring the bloom of potential enteropathogens and the selection of antibiotic resistance. These negative effects of antibiotic therapies seem ineluctable but often were mitigated when an antibiotic was administered by parenteral route. Sub-therapeutic dosages caused the augmentation of taxa involved in sugar metabolism, suggesting a link with weight gain. This result should not be interpreted positively, considering that parallel information on antibiotic resistance selection was rarely reported and selection of antibiotic resistance is known to occur also at low antibiotic concentration. However, studies on the effect of antibiotics as growth promoters put the basis for understanding the gut microbiota composition and function in this situation. This knowledge could inspire alternative strategies to antibiotics, such as probiotics, for improving animal performance. This review encompasses the analysis of the main animal hosts and all antibiotic classes, and highlights the future challenges and gaps of knowledge that should be filled. Further studies are necessary for elucidating pharmacodynamics in animals in order to improve therapy duration, antibiotic dosages, and administration routes for mitigating negative effects of antibiotic therapies. Furthermore, this review highlights that studies on aminoglycosides are almost inexistent, and they should be increased, considering that aminoglycosides are the first most commonly used antibiotic family in companion animals. Harmonization of experimental procedures is necessary in this research field. In fact, current studies are based on different experimental set-up varying for antibiotic dosage, regimen, administration, and downstream microbiota analysis. In the future, shotgun metagenomics coupled with long-reads sequencing should become a standard experimental approach enabling to gather comprehensive knowledge on GIM in terms of composition and taxonomic functions, and of ARGs. Decorticating GIM in animals will unveil revolutionary strategies for medication and improvement of animals' health status, with positive consequences on global health.