Antimicrobial use in swine production and its effect on the swine gut microbiota and antimicrobial resistance

Improvements of weaned pigs barn hygiene to reduce the spread of antimicrobial resistance

The spread of antimicrobial resistance (AMR) in animal husbandry is usually attributed to the use of antibiotics and poor hygiene and biosecurity. We therefore conducted experimental trials to improve hygiene management in weaned pig houses and assessed the impact on the spread. For each of the two groups examined, the experimental group (EG) and the control group (CG), three replicate batches of piglets from the same pig breeder, kept in pre-cleaned flat decks, were analyzed. In the flat decks of the experimental groups, the hygiene conditions (cleaning, disinfection, dust removal and fly control) were improved, while regular hygiene measures were carried out in the control groups. The occurrence and spread of AMR were determined in Escherichia coli (E. coli; resistance indicator) using cultivation-dependent (CFU) and -independent (qPCR) methods as well as whole genome sequencing of isolates in samples of various origins, including feces, flies, feed, dust and swabs. Surprisingly, there were no significant differences (p > 0.05) in the prevalence of resistant E. coli between the flat decks managed with conventional techniques and those managed with improved techniques. Selective cultivation delivered ampicillin- and sulfonamide-resistant E. coli proportions of up to 100% and 1.2%, respectively. While 0.5% E. coli resistant to cefotaxime and no ciprofloxacin resistance were detected. There was a significant difference (p < 0.01) in the abundance of the blaTEM-1 gene in fecal samples between EG and CG groups. The colonization of piglets with resistant pathogens before arrival, the movement of flies in the barn and the treatment of bacterial infections with antibiotics obscured the effects of hygiene improvement. Biocide tolerance tests showed no development of resistance to the farm regular disinfectant. Managing hygiene alone was insufficient for reducing antimicrobial resistances in piglet rearing. We conclude that the complex factors contributing to the presence and distribution of AMR in piglet barns underscore the necessity for a comprehensive management strategy.

Bacteria populating freshly appeared supraglacial lake possess metals and antibiotic-resistant genes

Antibiotic resistance (AR) has been extensively studied in natural habitats and clinical applications. AR is mainly reported with the use and misuse of antibiotics; however, little is known about its presence in antibiotic-free remote supraglacial lake environments. This study evaluated bacterial strains isolated from supraglacial lake debris and meltwater in Dook Pal Glacier, northern Pakistan, for antibiotic-resistant genes (ARGs) and metal-tolerant genes (MTGs) using conventional PCR. Several distinct ARGs were reported in the bacterial strains isolated from lake debris (92.5%) and meltwater (100%). In lake debris, 57.5% of isolates harbored the blaTEM gene, whereas 58.3% of isolates in meltwater possessed blaTEM and qnrA each. Among the ARGs, qnrA was dominant in debris isolates (19%), whereas in meltwater isolates, qnrA (15.2%) and blaTEM (15.2%) were dominant. ARGs were widely distributed among the bacterial isolates and different bacteria shared similar types of ARGs. Relatively greater number of ARGs were reported in Gram-negative bacterial strains. In addition, 92.5% of bacterial isolates from lake debris and 83.3% of isolates from meltwater harbored MTGs. Gene copA was dominant in meltwater isolates (50%), whereas czcA was greater in debris bacterial isolates (45%). Among the MTGs, czcA (18.75%) was dominant in debris strains, whereas copA (26.0%) was greater in meltwater isolates. This presents the co-occurrence and co-selection of MTGs and ARGs in a freshly appeared supraglacial lake. The same ARGs and MTGs were present in different bacteria, exhibiting horizontal gene transfer (HGT). Both positive and negative correlations were determined between ARGs and MTGs. The research provides insights into the existence of MTGs and ARGs in bacterial strains isolated from remote supraglacial lake environments, signifying the need for a more detailed study of bacteria harboring ARGs and MTGs in supraglacial lakes.

Why Bufo gargarizans tadpoles grow bigger in Pb-contaminated environments? The gut microbiota matter

The impacts of lead/Pb2+ on ecosystems have received widespread attention. Growth suppression is a major toxic effect of Pb compounds on aquatic animals, however, some studies have also reported their growth-promoting effects. These complex outcomes may be explained by anions that accompany Pb2+ or by the multiple toxic mechanisms/pathways of Pb2+. To examine these hypotheses, we tested how Bufo gargarizans tadpoles responded to Pb(NO3)2 (100 and 200 μg/L Pb2+) using transcriptomics and microbiomics, with NaNO3 and blank groups as controls. Tadpoles exposed to Pb(NO3)2 showed delayed development while increased somatic growth in a dose-dependent manner, which can be attributed to the effects of NO3- and Pb2+, respectively. Tadpole transcriptomics revealed that exposure to NO3- downregulated the MAPK pathway at transcriptional level, explaining the development-suppressing effect of NO3-; while Pb2+ upregulated the transcription of detoxification pathways (e.g., xenobiotics metabolism by cytochrome P450 and glutathione metabolism), indicating cellular stress and thus contradicting the growth advantage of Pb2+-exposed tadpoles. Pb2+ exposure changed the tadpole gut microbiota drastically, characterized by increased polysaccharides and carbohydrate utilization while decreased fatty acid and amino acid consumption according to microbial functional analysis. Similar gut microbial variations were observed in field-collected tadpoles from different Pb2+ environments. This metabolic shift in gut microbiota likely improved the overall food utilization efficiency and increased the allocation of fatty acids and amino acids to the host, explaining the growth advantage of Pb2+-exposed tadpoles. In summary, our results suggest multiple toxic pathways of Pb2+, and the gut microbiota may affect the pollution outcomes on animals.

Contribution of Manure-Spreading Operations to Bioaerosols and Antibiotic Resistance Genes' Emission

Manure spreading from farm animals can release antibiotic-resistant bacteria (ARB) carrying antimicrobial resistance genes (ARGs) into the air, posing a potential threat to human and animal health due to the intensive use of antibiotics in the livestock industry. This study analyzed the effect of different manure types and spreading methods on airborne bacterial emissions and antibiotic resistance genes in a controlled setting. Cow, poultry manure, and pig slurry were spread in a confined environment using two types of spreaders (splash plate and dribble bar), and the resulting emissions were collected before, during, and after spreading using high-volume air samplers coupled to a particle counter. Total bacteria, fecal indicators, and a total of 38 different subtypes of ARGs were further quantified by qPCR. Spreading poultry manure resulted in the highest emission rates of total bacteria (10¹¹ 16S gene copies/kg manure spread), Archaea (10⁶ 16S gene copies/kg manure), Enterococcus (10⁵ 16S gene copies/kg manure), and E. coli (10⁴ 16S gene copies/kg manure), followed by cow manure and pig slurry with splash plates and the dribble bar. Manure spreading was associated with the highest rates of airborne aminoglycoside genes for cow and poultry (10⁶ gene copies/kg manure), followed by pig slurry (10⁴ gene copies/kg manure). This study shows that the type of manure and spreading equipment can affect the emission rates of airborne bacteria, and ARGs.

Effect of Red-Beetroot-Supplemented Diet on Gut Microbiota Composition and Metabolite Profile of Weaned Pigs-A Pilot Study

Red beetroot is a well-recognized and established source of bioactive compounds (e.g., betalains and polyphenols) with anti-inflammatory and antimicrobial properties. It is proposed as a potential alternative to zinc oxide with a focus on gut microbiota modulation and metabolite production. In this study, weaned pigs aged 28 days were fed either a control diet, a diet supplemented with zinc oxide (3000 mg/kg), or 2% and 4% pulverized whole red beetroot (CON, ZNO, RB2, and RB4; respectively) for 14 days. After pigs were euthanized, blood and digesta samples were collected for microbial composition and metabolite analyses. The results showed that the diet supplemented with red beetroot at 2% improved the gut microbial richness relative to other diets but marginally influenced the cecal microbial diversity compared to a zinc-oxide-supplemented diet. A further increase in red beetroot levels (4%-RB4) led to loss in cecal diversity and decreased short chain fatty acids and secondary bile acid concentrations. Also, an increased Proteobacteria abundance, presumably due to increased lactate/lactic-acid-producing bacteria was observed. In summary, red beetroot contains several components conceived to improve the gut microbiota and metabolite output of weaned pigs. Future studies investigating individual components of red beetroot will better elucidate their contributions to gut microbiota modulation and pig health.

Use of an Innovative Silage of Agro-Industrial Waste By-Products in Pig Nutrition: A Pilot Study of Its Effects on the Pig Gastrointestinal Microbiota

The aim of this study was to evaluate whether dietary supplementation with an innovative silage (IS) created using 60% olive mill waste, 20% grape pomace, and 20% deproteinised feta cheese waste solids can modulate the composition of the intestinal microbiota in weaned (Exp. 1) and finishing (Exp. 2) pigs. In Exp. 1 (40 day supplementation), forty-five crossbred weaned pigs were randomly assigned to the 0% (Control), 5%, or 10% IS groups (15 replicates/experimental diet). In Exp. 2 (60 day supplementation), eighteen finishing pigs from Exp. 1 were fed the control diet for 8 weeks before being re-assigned to their original experimental groups and fed with the 0% (Control), 5%, or 10% IS diets (six replicates/experimental diet). Performance parameters were recorded. Ileal and caecal digesta and mucosa were collected at the end of each experiment for microbiota analysis using 16S rRNA gene sequencing (five pigs/experimental diet for Exp. 1 and six pigs/experimental diet for Exp. 2). No significant effects on pig growth parameters were observed in both experiments. In Exp. 1, 5% IS supplementation increased the relative abundance of the Prevotellaceae family, Coprococcus genus, and Alloprevotella rava (OTU_48) and reduced the relative abundance of Lactobacillus genus in the caecum compared to the control and/or 10% IS diets (p < 0.05). In Exp. 2, 5% IS supplementation led to compositionally more diverse and different ileal and caecal microbiota compared to the control group (p < 0.05; p = 0.066 for β-diversity in ileum). Supplementation with the 5% IS increased the relative abundance of Clostridium celatum/disporicum/saudiense (OTU_3) in the ileum and caecum and Bifidobacterium pseudolongum (OTU_17) in the caecum and reduced the relative abundance of Streptococcus gallolyticus/alactolyticus (OTU_2) in the caecum compared to the control diet (p < 0.05). Similar effects on C. celatum/disporicum/saudiense and S. gallolyticus/alactolyticus were observed with the 10% IS diet in the caecum (p < 0.05). IS has the potential to beneficially alter the composition of the gastrointestinal microbiota in pigs.

Swine Colibacillosis: Global Epidemiologic and Antimicrobial Scenario

Swine pathogenic infection caused by Escherichia coli, known as swine colibacillosis, represents an epidemiological challenge not only for animal husbandry but also for health authorities. To note, virulent E. coli strains might be transmitted, and also cause disease, in humans. In the last decades, diverse successful multidrug-resistant strains have been detected, mainly due to the growing selective pressure of antibiotic use, in which animal practices have played a relevant role. In fact, according to the different features and particular virulence factor combination, there are four different pathotypes of E. coli that can cause illness in swine: enterotoxigenic E. coli (ETEC), Shiga toxin-producing E. coli (STEC) that comprises edema disease E. coli (EDEC) and enterohemorrhagic E. coli (EHEC), enteropathogenic E. coli (EPEC), and extraintestinal pathogenic E. coli (ExPEC). Nevertheless, the most relevant pathotype in a colibacillosis scenario is ETEC, responsible for neonatal and postweaning diarrhea (PWD), in which some ETEC strains present enhanced fitness and pathogenicity. To explore the distribution of pathogenic ETEC in swine farms and their diversity, resistance, and virulence profiles, this review summarizes the most relevant works on these subjects over the past 10 years and discusses the importance of these bacteria as zoonotic agents.

Cascading effects of Pb on the environmental and symbiotic microbiota and tadpoles' physiology based on field data and laboratory validation

Heavy metal pollution poses a serious threat to ecosystems. Currently, there is a lack of field data that would enable us to gain a systematic understanding of the influences of heavy metals on aquatic ecosystems, especially the interactions between environments and animals. We studied the relationships between the variations in heavy metal concentrations (10 species including Pb in sediments and surface water), the community structure of environmental and symbiotic microbiota, and the gut traits of Bufo gargarizans tadpoles across 16 sampling sites on the Chengdu Plain through rigorous statistical analysis and laboratory validation. The results show that heavy metal concentrations, especially the Pb concentration of the sediment, are linked to the variations in sediment and tadpoles' gut microbiomes but not to water microbiota. For the sediment microbiota, Pb causes a trade-off between the proportions of Burkholderiales and Verrucomicrobiae and affects the methane, sulfide, and nitrate metabolisms. For tadpoles, a high sediment Pb content leads to a low abundance of gut aerobic bacteria and a large relative gut weight under both field and laboratory conditions. In addition, Pb promotes the growth of B. gargarizans tadpoles under laboratory conditions. These effects seem to be beneficial to tadpoles. However, a high Pb content leads to a low abundance of probiotic bacteria (e.g., Verrucomicrobiae, Eubacteriaceae, and Cetobacterium) and a high abundance of pathogenic bacteria in the gut and environment, suggesting potential health risks posed by Pb. Interestingly, there is a causal relationship between Pb-induced variations in sediment and symbiotic microbiotas, and the latter is further linked to the variation in relative gut weight of tadpoles. This suggests a cascading effect of Pb on the ecosystem. In conclusion, our results indicate that among the heavy metals, the Pb in sediment is a critical factor affecting the aquatic ecosystem through an environment-gut-physiology pathway mediated by microbiota.

Predicting the Next Superspreader

The spread of multidrug-resistant zoonotic pathogens, such as Salmonella, within livestock is of concern for food safety. The spread of Salmonella on the farm is escalated by superspreaders, which shed the pathogen at high numbers with their feces. However, there are currently no biomarkers to identify potential superspreaders. Kempf and coworkers determined that a potent early inflammatory response to Salmonella infection and changes in the microbiota composition are associated with the superspreader phenotype in pigs (F. Kempf, G. Cordoni, A.M. Chaussé, R. Drumo, et al., mSystems, in press, https://doi.org/10.1128/msystems.00852-22). Since these biomarkers only develop during Salmonella infection, additional work is needed to predict animals that have the potential to become superspreaders.

Increased Multidrug-Resistant Salmonella enterica I Serotype 4,[5],12:i:- Infections Associated with Pork, United States, 2009-2018

Reports of Salmonella enterica I serotype 4,[5],12:i:- infections resistant to ampicillin, streptomycin, sulphamethoxazole, and tetracycline (ASSuT) have been increasing. We analyzed data from 5 national surveillance systems to describe the epidemiology, resistance traits, and genetics of infections with this Salmonella strain in the United States. We found ASSuT-resistant Salmonella 4,[5],12:i:- increased from 1.1% of Salmonella infections during 2009-2013 to 2.6% during 2014-2018; the proportion of Salmonella 4,[5],12:i:- isolates without this resistance pattern declined from 3.1% to 2.4% during the same timeframe. Among isolates sequenced during 2015-2018, a total of 69% were in the same phylogenetic clade. Within that clade, 77% of isolates had genetic determinants of ASSuT resistance, and 16% had genetic determinants of decreased susceptibility to ciprofloxacin, ceftriaxone, or azithromycin. Among outbreaks related to the multidrug-resistant clade, 63% were associated with pork consumption or contact with swine. Preventing Salmonella 4,[5],12:i:- carriage in swine would likely avert human infections with this strain.

Insights on the effects of antimicrobial and heavy metal usage on the antimicrobial resistance profiles of pigs based on culture-independent studies

Antimicrobial resistance is a global threat to human, animal, and environmental health. In pig production, antimicrobials and heavy metals such as zinc oxide are commonly used for treatment and prevention of disease. Nevertheless, the effects of antimicrobials and heavy metals on the porcine resistome composition and the factors influencing this resistance profile are not fully understood. Advances in technologies to determine the presence of antimicrobial resistance genes in diverse sample types have enabled a more complete understanding of the resistome and the factors which influence its composition. The aim of this review is to provide a greater understanding of the influence of antimicrobial and heavy metal usage on the development and transmission of antimicrobial resistance on pig farms. Furthermore, this review aims to identify additional factors that can affect the porcine resistome. Relevant literature that used high-throughput sequencing or quantitative PCR methods to examine links between antimicrobial resistance and antimicrobial and heavy metal use was identified using a systematic approach with PubMed (NCBI), Scopus (Elsevier), and Web of Science (Clarivate Analytics) databases. In total, 247 unique records were found and 28 publications were identified as eligible for inclusion in this review. Based on these, there is clear evidence that antimicrobial and heavy metal use are positively linked with antimicrobial resistance in pigs. Moreover, associations of genes conferring antimicrobial resistance with mobile genetic elements, the microbiome, and the virome were reported, which were further influenced by the host, the environment, or the treatment itself.

An insight into the commercial piglet's microbial gut colonization: from birth towards weaning

BACKGROUND

The establishment of the gut microbiota can be influenced by several perinatal factors, including, most importantly, the maternal microbiota. Moreover, early-life environmental variation affects gut microbial colonization and the intestinal health of offspring throughout life. The present study aimed to explore the development of piglet gut microbiota from birth to weaning in the commercial practice and also to assess how different farm environments could condition this process. Although it is possible to find in the literature other studies with similar objectives this work probably represents one of the few studies that make a systematic evaluation of such differential factors under a real scenario. To achieve this objective, we performed two trials. In a first Trial, we selected 2 farms in which we performed an intensive sampling (5 samples /animal) to characterize the gut colonization pattern during the first days of life and to identify the time window with the greatest impact. Both farms differed in their health status and the use of antimicrobials in the piglets. In a second Trial, we selected 4 additional farms with variable rearing conditions and a distinctive use of antimicrobials in the sows with a simplified sampling pattern (2 samples/animal). Faecal samples were obtained with swabs and DNA was extracted by using the PSP® Spin Stool DNA Kit and sequencing of the 16S rRNA gene (V3-V4 region) performed by Illumina MiSeq Platform.

RESULTS

The present study contributes to a better understanding of microbiome development during the transition from birth to weaning in commercial conditions. Alpha diversity was strongly affected by age, with an increased richness of species through time. Beta diversity decreased after weaning, suggesting a convergent evolvement among individuals. We pinpointed the early intestinal colonizers belonging to Bacteroides, Escherichia-Shigella, Clostridium sensu stricto 1, and Fusobacterium genera. During lactation(d7-d21 of life), the higher relative abundances of Bacteroides and Lactobacillus genera were correlated with a milk-oriented microbiome. As the piglets aged and after weaning (d36 of life), increasing abundances of genera such as Prevotella, Butyricimonas, Christensenellaceae R-7 group, Dorea, Phascolarctobacterium, Rikenellaceae RC9 gut group, Subdoligranulum, and Ruminococcaceae UCG-002 were observed. These changes indicate the adaptation of the piglets to a cereal-based diet rich in oligosaccharides and starch. Our results also show that the farm can have a significant impact in such a process, evidencing the influence of different environments and rearing systems on the gut microbiota development of the young piglet. Differences between farms were more noticeable after weaning than during lactation with changes in alpha and beta biodiversity and specific taxa. The analysis of such differences suggests that piglets receiving intramuscular amoxicillin (days 2-5 of life) and being offered an acidifying rehydrating solution (Alpha farm in Trial 1) have a greater alpha diversity and more abundant Lactobacillus population. Moreover, the only farm that did not offer any rehydrating solution (Foxtrot farm in Trial 2) showed a lower alpha diversity (day 2 of life) and increased abundance of Enterobacteriaceae (both at 2 and 21 days). The use of in-feed antibiotics in the sows was also associated with structural changes in the piglets' gut ecosystem although without changes in richness or diversity. Significant shifts could be registered in different microbial groups, particularly lower abundances of Fusobacterium in those piglets from medicated sows.

CONCLUSIONS

In conclusion, during the first weeks of life, the pig microbiota showed a relevant succession of microbial groups towards a more homogeneous and stable ecosystem better adapted to the solid dry feed. In this relevant early-age process, the rearing conditions, the farm environment, and particularly the antimicrobial use in piglets and mothers determine changes that could have a relevant impact on gut microbiota maturation. More research is needed to elucidate the relative impact of these farm-induced early life-long changes in the growing pig.

ARGs distribution and high-risk ARGs identification based on continuous application of manure in purple soil

Tetracyclines (TCs) are one of the most widely used antibiotics in livestock and poultry industry. Sichuan province and Chongqing city are the provinces and cities with the most concentrated purple soil distribution in China, as well as the largest livestock and poultry breeding scale. Purple soils with low organic carbon content and poor structure, and manure fertilizers were heavily applied to improve soil quality. However, the research on antibiotic resistance genes (ARGs) dispersal in purple soils is limited. Overall, 234 ARGs subtypes belonging to 15 types were detected in all soils. Long-term application of livestock manures significantly changed the characteristics of ARGs, mobile genetic elements (MGEs), pathogen species and bacterial communities in the soil, and increased by 103.2 %, 13.1 %, 188.6 % and 43.7 % in chicken manure treatments compared with the control, respectively. Partial equation PLS-PM analysis further reveals that the main driving factor of ARGs is bacterial abundance, while bacterial diversity has a negative effect on ARGs abundance. Through ANOVA and network analysis, it was found that 30 ARGs were significantly affected by manure, its relative abundance is 0.8-1.4 times that of the control treatment. The qPCR results also proved that the relative abundance of ARGs including sul2, etc. increased with the increase of manure application and these resistance genes in chicken manure treatments were higher than in pig manure treatments. These resistance genes pose a high risk to public health, and chicken manure application posed a higher risk than pig manure. The TC content in the 40-60 cm soil layer was higher in medium- and high-volume pig manure, which was at risk of being transported to groundwater. Our research results deepen the understanding of ARGs transmission in purple soil under agricultural activities and emphasize the species and distribution of antibiotic resistance genes may differ across soil and manure types.

Too Much of a Good Thing: Rethinking Feed Formulation and Feeding Practices for Zinc in Swine Diets to Achieve One Health and Environmental Sustainability

The objectives of this review were to summarize current knowledge of Zn in swine nutrition, environmental concerns, potential contribution to antimicrobial resistance, and explore the use of alternative feeding strategies to reduce Zn excretion in manure while capturing improvements in productivity. Zinc is a required nutrient for pigs but is commonly supplemented at concentrations that greatly exceed estimated requirements. Feeding pharmacological concentrations of Zn from ZnO to pigs for 1 to 2 weeks post-weaning reduces post-weaning diarrhea and improves growth performance. Feeding elevated dietary levels of Zn to sows during the last 30 days of gestation can reduce the incidence of low-birth-weight pigs and pre-weaning mortality. Most of the dietary Zn consumed by pigs is not retained in the body and is subsequently excreted in manure, which led several countries to impose regulations restricting dietary Zn concentrations to reduce environmental impacts. Although restricting Zn supplementation in swine diets is a reasonable approach for reducing environmental pollution, it does not allow capturing health and productivity benefits from strategic use of elevated dietary Zn concentrations. Therefore, we propose feeding strategies that allow strategic use of high dietary concentrations of Zn while also reducing Zn excretion in manure compared with current feeding practices.

Detection of Acquired Antibiotic Resistance Genes in Domestic Pig (Sus scrofa) and Common Carp (Cyprinus carpio) Intestinal Samples by Metagenomics Analyses in Hungary

The aim of this study was metagenomics analyses of acquired antibiotic-resistance genes (ARGs) in the intestinal microbiome of two important food-animal species in Hungary from a One Health perspective. Intestinal content samples were collected from 12 domestic pigs (Sus scrofa) and from a common carp (Cyprinus carpio). Shotgun metagenomic sequencing of DNA purified from the intestinal samples was performed on the Illumina platform. The ResFinder database was applied for detecting acquired ARGs in the assembled metagenomic contigs. Altogether, 59 acquired ARG types were identified, 51 genes from domestic pig and 12 genes from the carp intestinal microbiome. ARG types belonged to the antibiotic classes aminoglycosides (27.1%), tetracyclines (25.4%), β-lactams (16.9%), and others. Of the identified ARGs, tet(E), a bla_OXA-_48-like β-lactamase gene, as well as cphA4, ampS, aadA2, qnrS2, and sul1, were identified only in carp but not in swine samples. Several of the detected acquired ARGs have not yet been described from food animals in Hungary. The tet(Q), tet(W), tet(O), and mef(A) genes detected in the intestinal microbiome of domestic pigs had also been identified from free-living wild boars in Hungary, suggesting a possible relationship between the occurrence of acquired ARGs in domestic and wild animal populations.

Impact of Raised without Antibiotics Measures on Antimicrobial Resistance and Prevalence of Pathogens in Sow Barns

The growing concern over the emergence of antimicrobial resistance (AMR) in animal production as a result of extensive and inappropriate antibiotic use has prompted many swine farmers to raise their animals without antibiotics (RWA). In this study, the impact of implementing an RWA production approach in sow barns on actual on-farm antibiotic use, the emergence of AMR, and the abundance of pathogens was investigated. Over a 13-month period, fecal and nasopharynx samples were collected at 3-month intervals from sows raised in RWA barns and sows in conventional barns using antibiotics in accordance with the new regulations (non-RWA). Whole genome sequencing (WGS) was used to determine the prevalence of AMR and the presence of pathogens in those samples. Records of all drug use from the 13-month longitudinal study indicated a significant reduction in antimicrobial usage in sows from RWA barns compared to conventional non-RWA barns. Antifolates were commonly administered to non-RWA sows, whereas β-lactams were widely used to treat sows in RWA barns. Metagenomic analyses demonstrated an increased abundance of pathogenic Actinobacteria, Firmicutes, and Proteobacteria in the nasopharynx microbiome of RWA sows relative to non-RWA sows. However, WGS analyses revealed that the nasal microbiome of sows raised under RWA production exhibited a significant increase in the frequency of resistance genes coding for β-lactams, MDR, and tetracycline.

Thermal desorption behavior of fluoroquinolones in contaminated soil of livestock and poultry breeding

As a kind of typical veterinary drug, fluoroquinolone antibiotics (FQs) are widely used in the field of livestock and poultry breeding, but these FQs escape to surrounding soil through various pathways, polluting soil through long-term accumulation. Current study proposed a clean technology named thermal desorption to deal with FQs contaminated soils. It was observed that time, temperature and soil particle size were the critical factors in FQs thermal desorption. Results of the study showed that higher temperature was more effective in the removal of FQs, while removal of FQs attached with finer particles was more difficult compared to coarse particles. Fine soil particles (0.6-0.85 mm) were decontaminated up 99.4% when treated with 400 °C for 60min. Thermal desorption of FQs from contaminated soil was governed by first-order kinetics. Based on the detection of exhaust gas components, a possible thermal desorption mechanism was proposed. Study suggested that thermal desorption was a clean and effective remediation method to treat FQs-contaminated soils without generating any further waste.

The role of gut microbiota in the development of colorectal cancer: a review

PURPOSE

Colorectal cancer (CRC) is the cancer of the colon and rectum. Recent research has found a link between CRC and human gut microbiota. This review explores the effect of gut microbiota on colorectal carcinogenesis and the development of chemoresistance.

METHODS

A literature overview was performed to identify the gut microbiota species that showed altered abundance in CRC patients and the mechanisms by which some of them aid in the development of chemoresistance.

RESULTS

Types of gut microbiota present and methods of analyzing them were discussed. We observed that numerous microbiota showed altered abundance in CRC patients and could act as a biomarker for CRC diagnosis and treatment. Further, it was demonstrated that microbes also have a role in the development of chemoresistance by mechanisms like immune system activation, drug modification, and autophagy modulation. Finally, the key issue of the growing global problem of antimicrobial resistance and its relationship with CRC was highlighted.

CONCLUSION

This review discussed the role of gut microbiota dysbiosis on colorectal cancer progression and the development of chemoresistance.

Immunocyte Populations Observed from Birth to Weaning in Blood, Spleen and Mesenteric Lymph Nodes of Piglets

Susceptibility to pathogen infections and efficacy of vaccination highly depend on the immune status of the piglet. Here, we measured immunocytes in piglets from birth to weaning to elucidate how immunocyte populations change during development and are affected by weaning. Crossbred piglets were used. Suckling piglets were euthanized at 1, 7, 14, 21, 28 or 35 days old (3~4 piglets at each time point). In addition, seven piglets were weaned at 21 days old, with four being euthanized at 28 days old and the remaining at 35 days old. Piglet carcasses were dissected, and blood, mesenteric lymph nodes (MLN) and spleen were sampled. In total, seven antibodies were used to stain the immunocyte population. Dynamics of myeloid (CD3−SWC3+CD16+), natural killer (NK; CD3−SWC3−CD16+), killer T (CD3+CD8+), helper T (CD3+CD4+) and B (CD3−CD21+) cells were analyzed. Percentage of innate immunity cells such as myeloid cells declined (p < 0.05) from the first day after birth. In contrast, percentage of NK cells increased in piglets while they were still suckling. Killer T, helper T, and B cell populations increased around 2~3 weeks after birth. No significant differences in the populations of the evaluated cell types were observed between suckling and weaned piglets at least for 14 days post weaning.

Antibiotic resistance of fecal carriage of Escherichia coli from pig farms in China: a meta-analysis

Fecal carriage of bacteria is a major source of antibiotic resistance genes (ARGs) and a public health risk, but the antibiotic resistance of Escherichia coli (E. coli) in Chinese pig farms remains a major gap in the available literature. Our goal was to conduct a meta-analysis of studies reporting antibiotic resistance of fecal carriage of E. coli from pig farms in China, calculating the pooled resistance rates and summarizing factors associated with it. We searched PubMed and Web of Science for studies published in English up to February 28, 2021. We also searched bibliographic indices and corresponded with the authors. We chose ciprofloxacin, gentamicin, tetracycline, ampicillin, and florfenicol from five major types of antibiotics to comprehensively evaluate the resistance rate of E. coli. We used a random-effects model and Freeman-Tukey double arcsine transformation to calculate the resistance rate and 95% confidence interval. Among the 120 retrieved manuscripts, 16 studies (1985 E. coli isolates) were deemed eligible for our analysis. The combined resistance rate of E. coli from feces was 58.8% (95% CI: 45.3-71.7%) to ciprofloxacin, 54.3% (95% CI: 35.3-72.6%) to gentamicin, 91.0% (95% CI: 83.1-96.7%) to tetracycline, 81.4% (95% CI: 62.0-95.1%) to ampicillin, and 65.4% (95% CI: 33.9-90.9%) to florfenicol. In conclusion, fecal carriage of E. coli in Chinese pig farms shows high resistance to ciprofloxacin, gentamicin, tetracycline, ampicillin, and florfenicol. Subgroup analysis showed that the resistance of E. coli to antibiotics was closely related to the sample size and the health condition of the pigs. Specifically, ESBL-producing E. coli has a higher ratio of resistance to other antibiotics. Future collection of antibiotic resistance and other information in pig farms should be more precise and depend on local surveys.

Intestinal Exposure to Ceftiofur and Cefquinome after Intramuscular Treatment and the Impact of Ceftiofur on the Pig Fecal Microbiome and Resistome

Optimization of antimicrobial treatment during a bacterial infection in livestock requires in-depth knowledge of the impact of antimicrobial therapy on the pathogen and commensal microbiota. Once administered antimicrobials and/or their metabolites are excreted either by the kidneys through urine and/or by the intestinal tract through feces, causing antimicrobial pressure and possibly the emergence of resistance in the gastro-intestinal tract. So far, the excretion of ceftiofur and cefquinome in the intestinal tract of pigs has not been described. The objective of this study was to investigate the excretion of ceftiofur and cefquinome in the different segments of the gut and feces after intramuscular administration. Therefore, 16 pigs were treated either with ceftiofur (n = 8) or cefquinome (n = 8), and feces were collected during the entire treatment period. The presence of ceftiofur and desfuroylceftiofuracetamide or cefquinome were quantified via liquid chromatography−tandem mass spectrometry. At the end of the treatment, pigs were euthanized, and samples from the duodenum, jejunum, ileum and cecum were analyzed. In feces, no active antimicrobial residues could be measured, except for one ceftiofur-treated pig. In the gut segments, the concentration of both antimicrobials increased from duodenum toward the ileum, with a maximum in the ileum (187.8 ± 101.7 ng·g−1 ceftiofur-related residues, 57.8 ± 37.5 ng·g−1 cefquinome) and sharply decreased in the cecum (below the limit of quantification for ceftiofur-related residues, 6.4 ± 4.2 ng·g−1 cefquinome). Additionally, long-read Nanopore sequencing and targeted quantitative polymerase chain reaction (qPCR) were performed in an attempt to clarify the discrepancy in fecal excretion of ceftiofur-related residues between pigs. In general, there was an increase in Prevotella, Bacteroides and Faecalibacterium and a decrease in Escherichia and Clostridium after ceftiofur administration (q-value < 0.05). The sequencing and qPCR could not provide an explanation for the unexpected excretion of ceftiofur-related residues in one pig out of eight. Overall, this study provides valuable information on the gut excretion of parenteral administered ceftiofur and cefquinome.

Heavy metal-induced selection and proliferation of antibiotic resistance: A review

Antibiotic resistance is recognized as a global threat to public health. The selection and evolution of antibiotic resistance in clinical pathogens was believed to be majorly driven by the imprudent use of antibiotics. However, concerns regarding the same, through selection pressure by a multitude of other antimicrobial agents, such as heavy metals, are also growing. Heavy metal contamination co-selects antibiotic and metal resistance through numerous mechanisms, such as co-resistance and cross-resistance. Here, we have reviewed the role of heavy metals as antimicrobial resistance driving agents and the underlying concept and mechanisms of co-selection, while also highlighting the scarcity in studies explicitly inspecting the process of co-selection in clinical settings. Prospective strategies to manage heavy metal-induced antibiotic resistance have also been deliberated, underlining the need to find specific inhibitors so that alternate medicinal combinations can be added to the existing therapeutic armamentarium.

Removal of antibiotic thiamphenicol by bacterium Aeromonas hydrophila HS01

Thiamphenicol (TAP) is an amphenicol antibiotic, which has a broad-spectrum inhibitory effect on both gram-positive and gram-negative bacteria. Since it is widely used in animals and aquaculture, its residues in environment may bring potential risk for human health and ecosystems. While TAP can be removed through conventional physical or chemical methods, its bioremediation using microorganisms is less studied. Here, we report the removal of TAP by a bacterial strain, Aeromonas hydrophila HS01, which can remove more than 90.0% of TAP in a living cell-dependent manner. Our results indicated that its removal efficiency can be greatly affected by the growth condition. Proteomics studies revealed a number of differentially expressed proteins of HS01 in the presence of TAP, which may play critical roles in the transportation and degradation of TAP. All these results indicate bacterial strain A. hydrophila HS01 is a new microbial resource for efficiently removing TAP, and may shed new insights in developing bioremediation approaches for TAP pollution.

Antimicrobial Use and Susceptibility of Indicator Escherichia coli in Finnish Integrated Pork Production

In pigs, antimicrobial use (AMU) practices vary at different production phases between herds and between countries. Antimicrobial resistance (AMR) development is linked to AMU but recognized as a multi-factorial issue, and thus, any information increasing knowledge of AMU and AMR relationships is valuable. We described AMU and screened the carriage of different AMR phenotypes of indicator Escherichia coli in 25 selected Finnish piglet-producing and finishing herds that formed nine birth-to-slaughter production lines. Moreover, we studied associations between AMU and AMR in both herd types and throughout the production line. Treatment records were obtained from the national Sikava register for 1year, and AMU was quantified as mg/PCU (population correction unit) and TIs (treatment incidences). For phenotypic antimicrobial susceptibility testing, ten pen-level pooled feces samples (n=250) in each herd were collected from one room representing the oldest weaned piglets or the oldest finishing pigs. Majority of the medications (96.8%) was administered parenterally, and penicillin was the predominant antimicrobial in every herd. More different antimicrobial substances were used in piglet-producing than in finishing herds (median 5 and 1, respectively, p<0.001). As mg/PCU, sows had the highest AMU and suckling piglets had the highest TIs, whereas finishing pigs were the least treated age group. The proportion of susceptible indicator E. coli isolates of all studied isolates was 59.6%. Resistance was found most commonly against tetracycline, sulfamethoxazole, trimethoprim, and ampicillin, and multi-resistant (MR) isolates (46.5% of all resistant isolates) were resistant to a maximum of four different antimicrobials. Quinolone resistance was rare, and no resistance against 3rd-generation cephalosporins, meropenem, azithromycin, colistin, gentamicin, or tigecycline was detected. The main associations between AMU and AMR were found at antimicrobial group level when use was compared with the presence of AMR phenotypes. The proportion of resistant isolates was not associated with AMU, and herd size was not associated with either AMU or AMR. We suggest that the use of narrow-spectrum beta-lactams as a primary treatment option and lack of wide application of oral group medications potentially favors a good resistance pattern in integrated pork production.

Enrofloxacin Alters Fecal Microbiota and Resistome Irrespective of Its Dose in Calves

Enrofloxacin is a fluoroquinolone drug used to prevent and control bovine respiratory disease (BRD) complex in multiple or single doses, ranging from 7.5 to 12.5 mg/kg body weight. Here, we examined the effects of high and low doses of a single subcutaneously injected enrofloxacin on gut microbiota and resistome in calves. Thirty-five calves sourced for this study were divided into five groups: control (n = 7), two low dose groups (n = 14, 7.5 mg/kg), and two high dose groups (n = 14, 12.5 mg/kg). One group in the low and high dose groups was challenged with Mannheimia haemolytica to induce BRD. Both alpha and beta diversities were significantly different between pre- and post-treatment microbial communities (q < 0.05). The high dose caused a shift in a larger number of genera than the low dose. Using metagenomic ProxiMeta Hi-C, 32 unique antimicrobial resistance genes (ARGs) conferring resistance to six antibiotic classes were detected with their reservoirs, and the high dose favored clonal expansion of ARG-carrying bacterial hosts. In conclusion, enrofloxacin treatment can alter fecal microbiota and resistome irrespective of its dose. Hi-C sequencing provides significant benefits for unlocking new insights into the ARG ecology of complex samples; however, limitations in sample size and sequencing depth suggest that further work is required to validate the findings.

Metagenomic Analysis of the Fecal Archaeome in Suckling Piglets Following Perinatal Tulathromycin Metaphylaxis

Simple Summary

The archaeal population, or ‘archaeome’, is comprised of unicellular microorganisms with a distinct biology compared with bacteria and has been shown to be an important component of host-associated microbes. While the impact of antimicrobial administration on gastrointestinal microbiota has been widely evaluated, no metagenomics-based analysis has been performed to assess the impact of an early life antimicrobials intervention on the fecal archaeome in swine. The aim of this study was therefore to investigate the impact of perinatal tulathromycin (TUL) administration on the fecal archaeome composition and diversity in suckling piglets using metagenomic sequencing analysis. Our results suggest that perinatal TUL metaphylaxis seems to have a minimal effect on the gut archaeome composition and diversity in sucking piglets.

Abstract

The gastrointestinal microbiome plays an important role in swine health and wellbeing, but the gut archaeome structure and function in swine remain largely unexplored. To date, no metagenomics-based analysis has been done to assess the impact of an early life antimicrobials intervention on the gut archaeome. The aim of this study was to investigate the effects of perinatal tulathromycin (TUL) administration on the fecal archaeome composition and diversity in suckling piglets using metagenomic sequencing analysis. Sixteen litters were administered one of two treatments (TUL; 2.5 mg/kg IM and control (CONT); saline 1cc IM) soon after birth. Deep fecal swabs were collected from all piglets on days 0 (prior to treatment), 5, and 20 post intervention. Each piglet’s fecal archaeome was composed of rich and diverse communities that showed significant changes over time during the suckling period. At the phylum level, 98.24% of the fecal archaeome across all samples belonged to Euryarchaeota. At the genus level, the predominant archaeal genera across all samples were Methanobrevibacter (43.31%), Methanosarcina (10.84%), Methanococcus (6.51%), and Methanocorpusculum (6.01%). The composition and diversity of the fecal archaeome between the TUL and CONT groups at the same time points were statistically insignificant. Our findings indicate that perinatal TUL metaphylaxis seems to have a minimal effect on the gut archaeome composition and diversity in sucking piglets. This study improves our current understanding of the fecal archaeome structure in sucking piglets and provides a rationale for future studies to decipher its role in and impact on host robustness during this critical phase of production.

Use of Lactobacillus plantarum (strains 22F and 25F) and Pediococcus acidilactici (strain 72N) as replacements for antibiotic-growth promotants in pigs

The lactic acid bacteria (LAB) Lactobacillus plantarum (strains 22F and 25F) and Pediococcus acidilactici (strain 72N) have appeared promising as replacements for antibiotics in in vitro studies. Microencapsulation, especially by the spray-drying method, has been used to preserve their numbers and characteristics during storage and digestion. This study compared the efficacy of these strains and their microencapsulated form with antibiotic usage on growth performance, faecal microbial counts, and intestinal morphology in nursing-finishing pigs. A total of 240 healthy neonatal pigs were treated on days 0, 3, 6, 9, and 12 after cross-fostering. Sterile peptone water was delivered orally to the control and antibiotic groups. Spray-dried Lactobacillus plantarum strain 22F stored for 6-months was administered to piglets in the spraydry group. Three ml of each the three fresh strains (10⁹ CFU/mL) were orally administered to piglets in each group. All pigs received the basal diets, but these were supplemented with routine antibiotic for the antibiotic group. Pigs in all the probiotic supplemented groups exhibited a better average daily gain and feed conversion ratio than those of the controls in the nursery and grower phases. Probiotic supplementation increased viable lactobacilli and decreased enterobacterial counts. Antibiotic additives reduced both enterobacterial and lactobacilli counts. Villous height and villous height:crypt depth ratio were greater in probiotic and antibiotic supplemented pigs comparing to the controls, especially in the jejunum. The results demonstrated the feasibility of using these strains as a substitute for antibiotics and the practicality of the microencapsulation protocol for use in swine farms.

Porcine enterotoxigenic Escherichia coli: Antimicrobial resistance and development of microbial-based alternative control strategies

Strains of enterotoxigenic Escherichia coli (ETEC) causing post-weaning diarrhoea (PWD) in piglets have a widespread and detrimental impact on animal health and the economics of pork production. Traditional approaches to control and prevention have placed a strong emphasis on antimicrobial use (AMU) to the extent that current prevalent porcine ETEC strains have developed moderate to severe resistance. This complicates treatment of ETEC infection by limiting therapeutic options, increasing diagnostic costs and increasing mortality rates. Management factors, the use of supra-physiological levels of zinc oxide and selected feed additives have all been documented to lower the incidence of ETEC infection in pigs; however, each intervention has its own limitations and cannot solely be relied upon as an alternative to AMU. Consequently, treatment options for porcine ETEC are moving towards the use of newer antimicrobials of higher public health significance. This review focuses on microorganisms and microbial-derived products that could provide a naturally evolved solution to ETEC infection and disease. This category holds a plethora of yet to be explored possibilities, however studies based around bacteriophage therapy, probiotics and the use of probiotic fermentation products as postbiotics have demonstrated promise. Ultimately, pig producers and veterinarians need these solutions to reduce the reliance on critically important antimicrobials (CIAs), to improve economic and animal welfare outcomes, and to lessen the One Health threat potentiated by the dissemination of AMR through the food chain.

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.

Timely Control of Gastrointestinal Eubiosis: A Strategic Pillar of Pig Health

The pig gastrointestinal tract (GIT) is an open ecosystem in which microorganisms and their host are mutually involved and continually adapt to different factors and problems which may or may not be host dependent or due to the production system. The aim of the present review is to highlight the factors affecting the GIT microbial balance in young pigs, focusing on the pre- and post-weaning phases, to define a road map for improving pig health and the production efficiency of the food chain. Birth and weaning body weight, physiological maturation, colostrum and milk (composition and intake), genetic background, environmental stressors and management practices, antibiotic use and diet composition are considered. Overall, there is a lack of knowledge regarding the effect that some factors, including weaning age, the use of creep feed, the composition of the colostrum and milk and the use of antibiotics, may have on the gut microbiome of piglets. Furthermore, the information on the gut microbiome of piglets is mainly based on the taxonomy description, while there is a lack of knowledge regarding the functional modification of the microbiota, essential for the exploitation of microbiota potential for modulating pig physiology.

The role of protein restriction and interaction with antibiotics in the regulation of compensatory growth in pigs: growth performance, serum hormone concentrations, and messenger RNA levels in component tissues of the endocrine growth axis

The present study investigated the effects of protein restriction and antibiotics on the hypothalamus-pituitary-liver growth axis during the compensatory growth of growing and finishing pigs. Growth performance, serum hormones, and messenger RNA (mRNA) levels of hormones and their receptors in growth axis tissues were recorded for analyses. A total of 64 piglets (large white × Landrace × Duroc cross) with an initial weight of 10.07 ± 0.14 kg were randomly divided into 4 treatment groups of 16 piglets per group. The dietary treatments consisted of 2 protein levels (14% and 20%) and 2 antibiotic levels (no antibiotics and 20 mg/kg colistin sulfate with 50 mg/kg kitasamycin) in a 2 × 2 factorial arrangement. The study was performed over 30 d for the first stage (S1, restriction phase) and 74 d for the second stage (S2, realimentation phase). The 4 treatment diets were maintained throughout the duration in the restriction phase. The 4 groups were fed the same diet in the realimentation phase. The trial period totaled 104 d. Protein restriction decreased BW, average daily food intake, and ADG in weaning pigs (P < 0.01) and induced compensatory growth after feeding a normal diet during the growth of finishing pigs. Average daily gain increased during the last phase of compensatory growth (P < 0.01). Protein restriction increased serum GH and leptin (LEP) and the mRNA levels of liver IGF-1 receptor (IGF-1-R; P < 0.01) but decreased serum IGF-1 (P < 0.01) and the mRNA levels of liver GH receptor (GH-R; P < 0.01) and IGF-1 (P < 0.05) in weaning piglets. Serum GH was increased, but serum IGF-1 was decreased during the realimentation phase (P < 0.05). Antibiotics increased the mRNA levels of GHRH (P < 0.05) and decreased somatostatin (P < 0.01) in the hypothalamus of weaning pigs. Protein restriction and antibiotics had no interactions across the entire trial. In conclusion, the slowing of growth caused by early protein restriction may be compensated for in the later stages of pig raising, and the mechanism of compensation is related to the regulation of GH, IGF-1, GH-R, and IGF-1-R.

Identification of drug-resistant phenotypes and resistance genes in Enterococcus faecalis isolates from animal feces originating in Xinjiang, People’s Republic of China

This study examined the presence and the antibiotic resistance patterns of Enterococcus faecalis isolated from the feces of 285 animals. Polymerase chain reaction tests verified the presence of E. faecalis from 49 pigs, 20 cows, 174 sheep, 17 horses, 21 chickens, and four dung beetles. Bacterial strains from different animals showed differences in susceptibility and resistance to the tested antimicrobials. The isolates exhibited resistance to ampicillin (6.32%), ciprofloxacin (40.00%), nitrofurantoin (1.40%), erythromycin (54.04%), streptomycin (82.11%), tetracycline (45.26%), amoxicillin (64.91%), penicillin (92.28%), and vancomycin (0.35%). The resistant strains also possessed varying complements of resistance genes including tem (77.89%), tetM (33.68%), gyrA (37.54%), parC (34.74%), aph(3′)-III (22.46%), aac(6′)/aph2″ (10.88%), and ant(6′)-I (8.42%). Genes for vancomycin resistance (vanB and vanC) and erythromycin resistance (mefA) were not detected. These results indicate high levels of antibiotic resistance among the isolates, although no positive correlation was observed between resistance genes and antibiotic resistance spectrum.

Preliminary investigation of the use of dietary supplementation with probiotic Bacillus subtilis strain QST713 shows that it attenuates antimicrobial-induced dysbiosis in weaned piglets

Growth performance of pigs has been associated with healthy gut microbiota. To improve production, pigs are usually treated with antimicrobials. Nonetheless, while antimicrobials harm the gut-indigenous microbiota, probiotic supplementation seems to help keep it healthy. Here, using antimicrobials, we artificially induced dysbiosis in pigs and evaluated a possible preventive effect of probiotic supplementation. Three 6-week-old piglets were given a basal feed, and 3 more the feed supplemented with 2.0 × 10⁶  CFU of Bacillus subtilis QST713/g of feed. After 14 days, antimicrobial enrofloxacin (5 mg/kg B.W.) was injected intramuscularly to all pigs on days 14-16. Feces were collected on days 14, 17, 19, 21, and 23. Total bacteria count was unaffected by enrofloxacin or QST713. However, Lactobacillus spp. and, in particular, Escherichia coli were affected by enrofloxacin, the latter not being observed in the feces on days 17 and 19. Interestingly, a reciprocal increase in E. coli was observed in control pigs on days 21 and 23, although in QST713-supplemented piglets, this increase was attenuated. While the gut microbiota composition did not return to initial levels in antimicrobial-administered piglets, it did in QST713-supplemented piglets. QST713 supplementation was likely crucial to keep the microbiota of piglets healthy.

RNA-based thermoregulation of a Campylobacter jejuni zinc resistance determinant

RNA thermometers (RNATs) trigger bacterial virulence factor expression in response to the temperature shift on entering a warm-blooded host. At lower temperatures these secondary structures sequester ribosome-binding sites (RBSs) to prevent translation initiation, whereas at elevated temperatures they "melt" allowing translation. Campylobacter jejuni is the leading bacterial cause of human gastroenteritis worldwide yet little is known about how it interacts with the host including host induced gene regulation. Here we demonstrate that an RNAT regulates a C. jejuni gene, Cj1163c or czcD, encoding a member of the Cation Diffusion Facilitator family. The czcD upstream untranslated region contains a predicted stem loop within the mRNA that sequesters the RBS to inhibit translation at temperatures below 37°C. Mutations that disrupt or enhance predicted secondary structure have significant and predictable effects on temperature regulation. We also show that in an RNAT independent manner, CzcD expression is induced by Zn(II). Mutants lacking czcD are hypersensitive to Zn(II) and also over-accumulate Zn(II) relative to wild-type, all consistent with CzcD functioning as a Zn(II) exporter. Importantly, we demonstrate that C. jejuni Zn(II)-tolerance at 32°C, a temperature at which the RNAT limits CzcD production, is increased by RNAT disruption. Finally we show that czcD inactivation attenuates larval killing in a Galleria infection model and that at 32°C disrupting RNAT secondary structure to allow CzcD production can enhance killing. We hypothesise that CzcD regulation by metals and temperature provides a mechanism for C. jejuni to overcome innate immune system-mediated Zn(II) toxicity in warm-blooded animal hosts.

Distribution of antibiotic and metal resistance genes in two glaciers of North Sikkim, India

Glacier studies as of late have ruffled many eyeballs, exploring this frigid ecology to understand the impact of climate change. Mapquesting the glaciers led to the discovery of concealed world of "psychrophiles" harboring in it. In the present study, the antibiotic resistance genes (ARGs) and heavy metal resistance genes (MRGs) were evaluated through both the culture-dependent and culture-independent methods. Samples were collected from two different glaciers, i.e., debris-covered glacier (Changme Khangpu) and debris-free glacier (Changme Khang). Functional metagenomics of both the glacier samples, provided evidence of presence of resistant genes against various antibiotic groups. Bacitracin resistant gene (bacA) was the predominant ARG in both the glaciers. MRGs in both the glacier samples were diversified as the genes detected were resistant against various heavy metals such as arsenic, tungsten, mercury, zinc, chromium, copper, cobalt, and iron. Unique MRGs identified from Changme Khangpu glacier were resistant to copper (cutA, cutE, cutC, cutF, cueR, copC, and copB) and chromium (yelf, ruvB, nfsA, chrR, and chrA) whereas, from Changme Khang glacier they showed resistance against cobalt (mgtA, dmef, corD, corC, corB, and cnrA), and iron (yefD, yefC, yefB, and yefA) heavy metals. ARGs aligned maximum identity with Gram-negative psychrotolerant bacteria. The cultured bacterial isolates showed tolerance to high concentrations of tested heavy metal solutions. Interestingly, some of the antibiotic resistant bacterial isolates also showed tolerance towards the higher concentrations of heavy metals. Thus, an introspection of the hypothesis of co-occurrence and/co-selection of ARGs and MRGs in such environments has been highlighted here.

Whole-genome characterisation of multidrug resistant monophasic variants of Salmonella Typhimurium from pig production in Thailand

Background

Monophasic Salmonella Typhimurium or S. enterica 1,4,[5],12:i:- is among the top five serotypes reported in Thailand. In this study, nineteen monophasic S. Typhimurium from the pig production chain in Chiang Mai and Lamphun provinces during 2011–2014 were sequenced and compared to a globally disseminated clone. Isolates were probed in silico for the presence of antimicrobial resistance genes and Salmonella virulence factors, including Pathogenicity Islands.

Results

All isolates were from sequence type 34 (ST-34) and clustered similarly in core and pangenome genealogies. The two closest related isolates showed differences in only eighteen loci from whole-genome multilocus sequence typing analysis. All 19 isolates carried aminoglycoside and beta-lactam class resistance genes and genes for five or more different antibiotic classes. Seven out of 14 known SPIs were detected, including SPI-5, SPI-13 and SPI-14, which were detected in all isolates.

Conclusions

The multi-drug resistant clone, ST-34 was sampled at all stages of pork production. This clone has infiltrated global agricultural processes and poses a significant public health risk. Differences in the core and accessory genomes of the isolates we collected suggest that strains persist though the pork production process, with evidence of mutation within the core-genome and horizontal acquisition of genes, potentially via sharing of pathogenicity islands and plasmids. This highlights the importance of surveillance and targeted intervention measures to successfully control Salmonella contamination.

Antimicrobial resistance genes in bacteria from animal-based foods

Antimicrobial resistance is a worldwide public health threat. Farm animals are important sources of bacteria containing antimicrobial resistance genes (ARGs). Although the use of antimicrobials in aquaculture and livestock has been reduced in several countries, these compounds are still routinely applied in animal production, and contribute to ARGs emergence and spread among bacteria. ARGs are transmitted to humans mainly through the consumption of products of animal origin (PAO). Bacteria can present intrinsic resistance, and once antimicrobials are administered, this resistance may be selected and multiply. The exchange of genetic material is another mechanism used by bacteria to acquire resistance. Some of the main ARGs found in bacteria present in PAO are the bla, mcr-1, cfr and tet genes, which are directly associated to antibiotic resistance in the human clinic.

Antibiotic Treatment Administered to Pigs and Antibiotic Resistance of Escherichia coli Isolated from Their Feces and Carcasses

Antimicrobial resistance (AMR) in bacteria is a frequent and widespread phenomenon. The European Food Safety Authority (EFSA) reports that multidrug resistant (MDR) Escherichia coli is considered an important hazard to public health. The lack of data on the correlation between the administration of antibiotics to pigs and the diffusion of MDR E. coli necessitates an in-depth study. The aims of our study were first of all to determine the presence of MDR and/or extended spectrum β-lactamase (ESβL) E. coli isolated from feces and carcasses of pigs; and second, to evaluate the correlation between antibiotic resistance and the antibiotic treatment administrated to the animals considered. The examined E. coli was isolated from 100 fecal swabs and 100 carcass sponges taken from farms and slaughterhouses located in Reggio Emilia province in Italy. The MDR isolates were tested following the protocol defined by EUCAST (2015). Subsequently, a real-time PCR and an endpoint-PCR were used for the genomic analysis. Data highlighted 76.5% of MDR E. coli with a marked presence of the ampicillin (AMP)-streptomycin (STRE)-tetracycline (TETRA) pattern. Moreover, 13 isolates were ESβL producers, and the bla_CTXM gene was the most frequently observed in genomic analysis. Results confirm the complexity of the AMR phenomenon showing a partial correlation between the administration of antibiotics and the resistance observed. Pigs destined to the production of Protected Designation of Origin items are colonized by bacteria resistant to a wide range of antibiotic classes even if data are encouraging for colistin and third generation cephalosporin. Furthermore, in-depth study focused on food production could be useful in a view of high safety standards for consumers.

Influence of modern treatment regimens on serum biochemical parameters in piglets with gastroenteritis

The article presents analyses of biochemical parameters of blood serum in weaned piglets with non-contagious gastroenteritis and after their treatment with a probiotic (live spores of Bacillus cereus var. toyoi; silicic acid; calcium carbonate) and a phytobiotic (natural extracts of Oreganum vulgare, Cinnamomun cassia and Capsicum annuum; hydrogenated rapeseed oil) as part of the basic ration in combination with antibiotic (10% solution of enrofloxacin hydrochloride) on a modern pig farm. In animals of the experimental groups with gastroenteritis we established hypoproteinemia, hypoalbuminemia, hypoglycemia, hypoureaemia, hypercreatininemia, hyperbilirubinemia and increase of enzyme activity compared to parameters of clinically healthy piglets. The study established that the use of probiotics and phytobiotics for weaned piglets had a positive influence on protein synthesis function of the liver, as indicated by the normalization of serum total protein and albumins. Also, we found a positive influence of probiotics and phytobiotics on intensity of protein metabolism, as indicated by an increase of serum urea to the level of clinically healthy piglets. Use of phytobiotics for piglets had a positive influence on the process of gluconeogenesis in their body, which is indicated by the normalization of serum glucose to the level of clinically healthy piglets. Also, the use of probiotics and phytobiotics had a positive influence on the pigment-forming function of the liver, as indicated by the reduction of serum total bilirubin to the level of clinically healthy piglets. The use of probiotics and phytobiotics reduced activity of serum alanine and aspartate aminotransferases in the piglets of the experimental groups, indicating the stabilization of hepatocytes’ cell structures (mitochondrial and cytosolic). The study established positive influence of probiotics and phytobiotics on the functioning of the liver and biliary tract, as indicated by decreased activity of serum alkaline phosphatase and gamaglutamiltranspeptidase to the level of clinically healthy piglets. So, addition of probiotics and phytobiotics to mixed fodder up to 45 days of age, normalizes functioning of the kidneys and liver in weaned piglets with gastroenteritis.

Antimicrobial Effects on Swine Gastrointestinal Microbiota and Their Accompanying Antibiotic Resistome

Antimicrobials are the most commonly prescribed drugs in the swine industry. While antimicrobials are an effective treatment for serious bacterial infections, their use has been associated with major adverse effects on health. It has been shown that antimicrobials have substantial direct and indirect impacts on the swine gastrointestinal (GI) microbiota and their accompanying antimicrobial resistome. Antimicrobials have also been associated with a significant public health concern through selection of resistant opportunistic pathogens and increased emergence of antimicrobial resistance genes (ARGs). Since the mutualistic microbiota play a crucial role in host immune regulation and in providing colonization resistance against potential pathogens, the detrimental impacts of antimicrobial treatment on the microbiota structure and its metabolic activity may lead to further health complications later in life. In this review, we present an overview of antimicrobial use in the swine industry and their role in the emergence of antimicrobial resistance. Additionally, we review our current understanding of GI microbiota and their role in swine health. Finally, we investigate the effects of antimicrobial administration on the swine GI microbiota and their accompanying antibiotic resistome. The presented data is crucial for the development of robust non-antibiotic alternative strategies to restore the GI microbiota functionality and guarantee effective continued use of antimicrobials in the livestock production system.

Nanoparticles in Equine Nutrition: Mechanism of Action and Application as Feed Additives

Several concerns exist regarding horse rearing such as environmental pollution, antibiotics resistance, digestive disorders, mycotoxins contamination of animal feed, gut health management, and improvement of feed efficiency. Nanoparticles have the potential to address these issues and thus could be used as feed additive. Citrate reduces and stabilizes gold nanoparticles, alongside biosynthesized silver nanoparticles have the potential to prolong and improve digestive enzyme activity, which would enhance starch digestibility in the stomach. Zinc oxide and selenium nanoparticles could be used to improve feed digestibility and volatile fatty acids production. Magnesium oxide, silver, and copper nanoparticles exhibit strong antimicrobial activity against gram-positive and gram-negative microbes and weaken the biofilm formation of the microbial community. Calcium, zinc, and silver nanoparticles could be used to prevent periodontal disease in horses. In addition, silver nanoparticles may be applied as antifasciolitics and potentially against other gastrointestinal parasites. Environmental concern of equines could be addressed by using cerium oxide, silver, and cobalt nanoparticles to reduce methane emission and zinc oxide could help to reduce fecal mineral output. Fullerol C₆₀[OH]_24, a honey-derived silver nanoparticle and zinc oxide nanoparticles exhibit attractive antibacterial properties because of increased specific surface area as the reduced particle enhance unit surface reactivity. Gut health management of equines could be solved with nanoparticles because of the ability of ferrous oxide and copper nanoparticles to improve microbial growth, whereas zinc oxide improves villus height, crypt depth, and villous surface area. It is required to explore in depth the beneficial effects of these nanoparticles as a novel area in the equine industry's both in vitro and in vivo before recommendation to equine owners.

Prevalence of Antibiotic Resistance Genes in Air-Conditioning Systems in Hospitals, Farms, and Residences

High-throughput quantitative PCR combined with Illumina sequencing and network analysis were used to characterize the antibiotic resistance gene (ARG) profiles in air-conditioning filters from different environments. In total, 177 ARGs comprising 10 ARG types were determined. The detectable numbers and the relative abundance of ARGs in hospitals and farms were significantly higher than those in city and village residences. Compared to hospitals, farms had a higher level of tetracycline, multidrug, integrase, and macrolide⁻lincosamide⁻streptogramin (MLS) B resistance genes but a lower level of beta-lactam resistance genes. The bl3_cpha gene was the most abundant resistance gene subtype in hospital samples with an abundance of 2.01 × 10^-4 copies/16S rRNA, while a level of only 5.08 × 10^-12 copies/16S rRNA was observed in farm samples. There was no significant difference in bacterial diversity among the hospitals, farms, and residences, and Proteobacteria was the most abundant phylum. Network analysis revealed that Proteobacteria and Actinobacteria were possible hosts of the beta-lactam, MLSB, aminoglycoside, multidrug, sulfonamide, and tetracycline resistance genes. The results demonstrate that ARGs exist in indoor environments and that farms and hospitals are important sources. This study provides a useful reference for understanding the distribution patterns and risk management of ARGs in indoor environments.

Piglet gut microbial shifts early in life: causes and effects

The gut microbiome has long been known to play fundamentally important roles in the animal health and the well-being of its host. As such, the establishment and maintenance of a beneficial gut microbiota early in life is crucial in pigs, since early gut colonizers are pivotal in the establishment of permanent microbial community structures affecting the health and growth performance of pigs later in life. Emphasizing this importance of early gut colonizers, it is critical to understand the factors impacting the establishment of the piglet gut microbiome at weaning. Factors include, among others, diet, in-feed antibiotics, probiotics and prebiotic administration. The impact of these factors on establishment of the gut microbiome of piglets at weaning includes effects on piglet gut microbial diversity, structure, and succession. In this review, we thoroughly reviewed the most recent findings on the piglet gut microbiome shifts as influenced by weaning, and how these microbiome changes brought about by various factors that have been shown to affect the development of microbiota in piglets. This review will provide a general overview of recent studies that can help to facilitate the design of new strategies to modulate the gut microbiome in order to enhance gastrointestinal health, growth performance and well-being of piglets.

Co-selection of multi-antibiotic resistance in bacterial pathogens in metal and microplastic contaminated environments: An emerging health threat

Misuse/over use of antibiotics increases the threats to human health since this is a main reason behind evolution of antibiotic resistant bacterial pathogens. However, metals such as mercury, lead, zinc, copper and cadmium are accumulating to critical concentration in the environment and triggering co-selection of antibiotic resistance in bacteria. The co-selection of metal driven antibiotic resistance in bacteria is achieved through co-resistance or cross resistance. Metal driven antibiotic resistant determinants evolved in bacteria and present on same mobile genetic elements are horizontally transferred to distantly related bacterial human pathogens. Additionally, in marine environment persistent pollutants like microplastics is recognized as a vector for the proliferation of metal/antibiotics and human pathogens. Recently published research confirmed that horizontal gene transfer between phylogenetically distinct microbes present on microplastics is much faster than free living microbes. Therefore, microplastics act as an emerging hotspot for metal driven co-selection of multidrug resistant human pathogens and pose serious threat to humans which do recreational activities in marine environment and ingest marine derived foods. Therefore, marine environment co-polluted with metal, antibiotics, human pathogens and microplastics pose an emerging health threat globally.

Microbial shifts in the swine nasal microbiota in response to parenteral antimicrobial administration

The continuous administration of antimicrobials in swine production has been widely criticized with the increase of antimicrobial-resistant bacteria and dysbiosis of the beneficial microbial communities. While an increasing number of studies investigate the effects of antimicrobial administration on swine gastrointestinal microbiota biodiversity, the impact of their use on the composition and diversity of nasal microbial communities has not been widely explored. The objective of this study was to characterize the short-term impact of different parenteral antibiotics administration on the composition and diversity of nasal microbial communities in growing pigs. Five antimicrobial treatment groups, each consisting of four, eight-week old piglets, were administered one of the antimicrobials; Ceftiofur Crystalline free acid (CCFA), Ceftiofur hydrochloride (CHC), Tulathromycin (TUL), Oxytetracycline (OTC), and Procaine Penicillin G (PPG) at label dose and route. Individual deep nasal swabs were collected immediately before antimicrobial administration (control = day 0), and again on days 1, 3, 7, and 14 after dosing. The nasal microbiota across all the samples were dominated by Firmicutes, proteobacteria and Bacteroidetes. While, the predominant bacterial genera were Moraxella, Clostridium and Streptococcus. Linear discriminant analysis, showed a pronounced, antimicrobial-dependent microbial shift in the composition of nasal microbiota and over time from day 0. By day 14, the nasal microbial compositions of the groups receiving CCFA and OTC had returned to a distribution that closely resembled that observed on day 0. In contrast, pigs that received CHC, TUL and PPG appeared to deviate away from the day 0 composition by day 14. Based on our results, it appears that the impact of parenteral antibiotics on the swine nasal microbiota is variable and has a considerable impact in modulating the nasal microbiota structure. Our results will aid in developing alternative strategies for antibiotics to improve swine health and consequently production.

Association between the gut microbiota and mineral metabolism

The aim of this review is to present the most recent scientific evidence of interactions between the intestinal microbiota and minerals, and the effect of this interaction on the health of the host. The Web of Science database from the years 2013-2017 on this topic was reviewed. Numerous in vitro studies have shown that iron significantly affects the intestinal microbiota. However, Bifidobacteriaceae are capable of binding iron in the large intestine, thereby limiting the formation of free radicals synthesized in the presence of iron, and thus reducing the risk of colorectal cancer. Animal studies have revealed that supplementation with probiotics, prebiotics and synbiotics has a significant effect on bone calcium, phosphate and bone metabolism. The dynamic interaction between microbiota and zinc was shown. Human studies have provided evidence of the influence of probiotic bacteria on parathormone, calcium and phosphate levels and thus on bone resorption. Recent studies have produced new information mainly on the impact of the intestinal bacteria on the metabolism of calcium and iron. From a scientific perspective, the most urgent fields that remain to be investigated are the identification of all human gut microbes and new therapies targeting the interaction between intestinal bacteria and minerals. © 2017 Society of Chemical Industry.

Review of antibiotic resistance in China and its environment

Antibiotic resistance is a global health crisis linked to increased, and often unrestricted, antibiotic use in humans and animals. As one of the world's largest producers and consumers of antibiotics, China is witness to some of the most acute symptoms of this crisis. Antibiotics and antibiotic resistance genes (ARGs) are widely distributed in surface water, sewage treatment plant effluent, soils and animal wastes. The emergence and increased prevalence of ARGs in the clinic/hospitals, especially carbapenem-resistant gram negative bacteria, has raised the concern of public health officials. It is important to understand the current state of antibiotic use in China and its relationship to ARG prevalence and diversity in the environment. Here we review these relationships and their relevance to antimicrobial resistance (AMR) trends witnessed in the clinical setting. This review highlights the issues of enrichment and dissemination of ARGs in the environment, and also future needs in mitigating the spread of antibiotic resistance in the environment, particularly under the 'planetary health' perspective, i.e., the systems that sustain or threaten human health.