Description and determinants of the faecal resistome and microbiome of farmers and slaughterhouse workers: A metagenome-wide cross-sectional study

A cross-sectional comparison of gut metagenomes between dairy workers and community controls

BACKGROUND

As a nexus of routine antibiotic use and zoonotic pathogen presence, the livestock farming environment is a potential hotspot for the emergence of zoonotic diseases and antibiotic resistant bacteria. Livestock can further facilitate disease transmission by serving as intermediary hosts for pathogens before a spillover event. In light of this, we aimed to characterize the microbiomes and resistomes of dairy workers, whose exposure to the livestock farming environment places them at risk for facilitating community transmission of antibiotic resistant genes and emerging zoonotic diseases.

RESULTS

Using shotgun sequencing, we investigated differences in the taxonomy, diversity and gene presence of 10 dairy farm workers and 6 community controls' gut metagenomes, contextualizing these samples with additional publicly available gut metagenomes. We found no significant differences in the prevalence of resistance genes, virulence factors, or taxonomic composition between the two groups. The lack of statistical significance may be attributed, in part, to the limited sample size of our study or the potential similarities in exposures between the dairy workers and community controls. We did, however, observe patterns warranting further investigation including greater abundance of tetracycline resistance genes and prevalence of cephamycin resistance genes as well as lower average gene diversity (even after accounting for differential sequencing depth) in dairy workers' metagenomes. We also found evidence of commensal organism association with tetracycline resistance genes in both groups (including Faecalibacterium prausnitzii, Ligilactobacillus animalis, and Simiaoa sunii).

CONCLUSIONS

This study highlights the utility of shotgun metagenomics in examining the microbiomes and resistomes of livestock workers, focusing on a cohort of dairy workers in the United States. While our study revealed no statistically significant differences between groups in taxonomy, diversity and gene presence, we observed patterns in antibiotic resistance gene abundance and prevalence that align with findings from previous studies of livestock workers in China and Europe. Our results lay the groundwork for future research involving larger cohorts of dairy and non-dairy workers to better understand the impact of occupational exposure to livestock farming on the microbiomes and resistomes of workers.

Residential exposure to microbial emissions from livestock farms: Implementation and evaluation of land use regression and random forest spatial models

Adverse health effects have been linked with exposure to livestock farms, likely due to airborne microbial agents. Accurate exposure assessment is crucial in epidemiological studies, however limited studies have modelled bioaerosols. This study used measured concentrations in air of livestock commensals (Escherichia coli (E. coli) and Staphylococcus species (spp.)), and antimicrobial resistance genes (tetW and mecA) at 61 residential sites in a livestock-dense region in the Netherlands. For each microbial agent, land use regression (LUR) and random forest (RF) models were developed using Geographic Information System (GIS)-derived livestock-related characteristics as predictors. The mean and standard deviation of annual average concentrations (gene copies/m3) of E. coli, Staphylococcus spp., tetW and mecA were as follows: 38.9 (±1.98), 2574 (±3.29), 20991 (±2.11), and 15.9 (±2.58). Validated through 10-fold cross-validation (CV), the models moderately explained spatial variation of all microbial agents. The best performing model per agent explained respectively 38.4%, 20.9%, 33.3% and 27.4% of the spatial variation of E. coli, Staphylococcus spp., tetW and mecA. RF models had somewhat better performance than LUR models. Livestock predictors related to poultry and pig farms dominated all models. To conclude, the models developed enable enhanced estimates of airborne livestock-related microbial exposure in future epidemiological studies. Consequently, this will provide valuable insights into the public health implications of exposure to specific microbial agents.

Swine farming shifted the gut antibiotic resistome of local people

Antibiotic resistance genes (ARGs) are prevalent in the livestock environment, but little is known about impacts of animal farming on the gut antibiotic resistome of local people. Here we conducted metagenomic sequencing to investigate gut microbiome and resistome of residents in a swine farming village as well as environmental relevance by comparing with a nearby non-farming village. Results showed a shift of gut microbiome towards unhealthy status in the residents of swine farming village, with an increased abundance and diversity in pathogens and ARGs. The resistome composition in human guts was more similar with that in swine feces and air than that in soil and water. Mobile gene elements were closely associated with the prevalence of gut resistome. Some plasmid-borne ARGs were colocalized in similar genetic contexts in gut and environmental samples. Metagenomic binning obtained 47 ARGs-carrying families in human guts, and therein Enterobacteriaceae posed the highest threats in antibiotic resistance and virulence. Several ARGs-carrying families were shared by gut and environmental samples (mainly in swine feces and air), and the ARGs were evolutionarily conservative within genera. The findings highlight that swine farming can shape gut resistome of local people with close linkage to farm environmental exposures.

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.

Effects of microbes in pig farms on occupational exposed persons and the environment

In terms of pig farming, pig gut microbes have a significant effect on farmers and the farm environment. However, it is still unclear which microbial composition is more likely to contribute to this effect. This study collected a total of 136 samples, including pigs' faeces samples, farmers' faeces samples, samples from individuals who had no contact with any type of farm animal (referred to as 'non-exposed' persons), and environmental dust samples (collected from inside and outside pig houses and the farm) from two pig farms, pig farm A and pig farm B. Whereafter, 16S rRNA sequencing and taxonomic composition analysis were performed. According to the study, compared to non-exposed persons, pig farmers had a significantly higher abundance of 7 genera. In addition, the farmers were grouped according to the duration of their occupational exposure, and it was shown that 4 genera, including Turicibacter, Terrisporobacter, and Clostridium_sensu_stricto_1, exhibited a rise in more frequent contact with pigs. As compared to outside the pig house, the environmental dust has a greater concentration of the 3 bacteria mentioned before. Therefore, these 3 microbes can be considered as co-occurring microbes that may exist both in humans and the environment. Also, the 3 co-occurring microbes are involved in the fermentation and production of short-chain fatty acids and their effectiveness decreased as distance from the farm increased. This study shows that the 3 microbes where pig farmers co-occur with the environment come from pig farms, which provides fresh ideas for preventing the spread of microbial aerosols in pig farms and reducing pollution.

Comparative analyses of the faecal resistome against β-lactam and quinolone antibiotics in humans and livestock using metagenomic sequencing

To assess the prevalence and abundance of antibiotic resistance genes in human and livestock gut microbiomes, 87 humans (healthy individuals and patients with Clostridioides difficile infection (CDI)) and 108 livestock (swine, cattle, and chickens) were enrolled. Gut microbiomes and fluoroquinolone-resistant Escherichia coli isolates were sequenced, and mobile genetic elements adjacent to the β-lactamase (bla) and transferable quinolone resistance (qnr) genes were compared using metagenomic contigs. Each group of humans and livestock exhibited distinctive microbiota and resistome compositions in the gut. Concerning the resistome of bla and qnr, the prevalence rates between chickens and patients with CDI were the most similar (R2 = 0.46); blaTEM, blaOXA, blaCTX-M, and qnrS were highly prevalent in both groups. According to genomic and phylogenetic analyses, blaCTX-M and blaOXA expressed lineage specificity to either humans or livestock, while qnrS and blaTEM displayed a shared lineage between humans and livestock. A qnrS1 mobilome comprising five genes, including two recombinases, a transposase, and a plasmid gene, is commonly found in human and chicken gut microbiomes. Humans and chickens showed the most similar gut resistomes to β-lactams and quinolones. QnrS and blaTEM displayed especially strong co-occurrence between the guts of humans and livestock.

Longitudinal metagenomic study reveals the dynamics of fecal antibiotic resistome in pigs throughout the lifetime

BACKGROUND

The dissemination of antibiotic resistance genes (ARGs) poses a substantial threat to environmental safety and human health. Herein, we present a longitudinal paired study across the swine lifetime from birth to market, coupled with metagenomic sequencing to explore the dynamics of ARGs and their health risk in the swine fecal microbiome.

RESULTS

We systematically characterized the composition and distribution of ARGs among the different growth stages. In total, 829 ARG subtypes belonging to 21 different ARG types were detected, in which tetracycline, aminoglycoside, and MLS were the most abundant types. Indeed, 134 core ARG subtypes were shared in all stages and displayed a growth stage-associated pattern. Furthermore, the correlation between ARGs, gut microbiota and mobile genetic elements (MGEs) revealed Escherichia coli represented the main carrier of ARGs. We also found that in most cases, the dominant ARGs could be transmitted to progeny piglets, suggesting the potential ARGs generation transmission. Finally, the evaluation of the antibiotic resistance threats provides us some early warning of those high health risk ARGs.

CONCLUSIONS

Collectively, this relatively more comprehensive study provides a primary overview of ARG profile in swine microbiome across the lifetime and highlights the health risk and the intergenerational spread of ARGs in pig farm.

Comparative resistome, mobilome, and microbial composition of retail chicken originated from conventional, organic, and antibiotic-free production systems

The aim of this study was to investigate the microbial composition, and the profiles of antimicrobial resistance genes (ARGs, resistome) and mobile genetic elements (mobilome) of retail chicken carcasses originated from conventional intensive production systems (CO), certified antimicrobial-free intensive production systems (AF), and certified organic production systems with restricted antimicrobial use (OR). DNA samples were collected from 72 chicken carcasses according to a cross-sectional study design. Shot-gun metagenomics was performed by means of Illumina high throughput DNA sequencing followed by downstream bioinformatic analyses. Gammaproteobacteria was the most abundant bacterial class in all groups. Although CO, AF, and OR did not differ in terms of alpha- and beta-microbial diversity, the abundance of some taxa differed significantly across the groups, including spoilage-associated organisms such as Pseudomonas and Acinetobacter. The co-resistome comprised 29 ARGs shared by CO, AF and OR, including genes conferring resistance to beta-lactams (blaACT-8, 10, 13, 29; blaOXA-212;blaOXA-275 and ompA), aminoglycosides (aph(3')-IIIa, VI, VIa and spd), tetracyclines (tet KL (W/N/W and M), lincosamides (inu A,C) and fosfomycin (fosA). ARGs were significantly less abundant (P < 0.05) in chicken carcasses from AF and OR compared with CO. Regarding mobile genetic elements (MGEs), transposases accounted for 97.2% of the mapped genes. A higher abundance (P = 0.037) of MGEs was found in CO compared to OR. There were no significant differences in ARGs or MGEs diversity among groups according to the Simpson´s index. In summary, retail frozen chicken carcasses from AF and OR systems show similar ARGs, MGEs and microbiota profiles compared with CO, even though the abundance of ARGs and MGEs was higher in chicken carcasses from CO, probably due to a higher selective pressure.

Resistome expansion in disease-associated human gut microbiomes

BACKGROUND

The resistome, the collection of antibiotic resistance genes (ARGs) in a microbiome, is increasingly recognised as relevant to the development of clinically relevant antibiotic resistance. Many metagenomic studies have reported resistome differences between groups, often in connection with disease and/or antibiotic treatment. However, the consistency of resistome associations with antibiotic- and non-antibiotic-treated diseases has not been established. In this study, we re-analysed human gut microbiome data from 26 case-control studies to assess the link between disease and the resistome.

RESULTS

The human gut resistome is highly variable between individuals both within and between studies, but may also vary significantly between case and control groups even in the absence of large taxonomic differences. We found that for diseases commonly treated with antibiotics, namely cystic fibrosis and diarrhoea, patient microbiomes had significantly elevated ARG abundances compared to controls. Disease-associated resistome expansion was found even when ARG abundance was high in controls, suggesting ongoing and additive ARG acquisition in disease-associated strains. We also found a trend for increased ARG abundance in cases from some studies on diseases that are not treated with antibiotics, such as colorectal cancer.

CONCLUSIONS

Diseases commonly treated with antibiotics are associated with expanded gut resistomes, suggesting that historical exposure to antibiotics has exerted considerable selective pressure for ARG acquisition in disease-associated strains. Video Abstract.

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.

Differences in gut metagenomes between dairy workers and community controls: a cross-sectional study

Background

As a nexus of routine antibiotic use and zoonotic pathogen presence, the livestock farming environment is a potential hotspot for the emergence of zoonotic diseases and antibiotic resistant bacteria. Livestock can further facilitate disease transmission by serving as intermediary hosts for pathogens as they undergo evolution prior to a spillover event. In light of this, we are interested in characterizing the microbiome and resistome of dairy workers, whose exposure to the livestock farming environment places them at risk for facilitating community transmission of antibiotic resistant genes and emerging zoonotic diseases.

Results

Using shotgun sequencing, we investigated differences in the taxonomy, diversity and gene presence of the human gut microbiome of 10 dairy farm workers and 6 community controls, supplementing these samples with additional publicly available gut metagenomes. We observed greater abundance of tetracycline resistance genes and prevalence of cephamycin resistance genes in dairy workers' metagenomes, and lower average gene diversity. We also found evidence of commensal organism association with plasmid-mediated tetracycline resistance genes in both dairy workers and community controls (including Faecalibacterium prausnitzii, Ligilactobacillus animalis, and Simiaoa sunii). However, we did not find significant differences in the prevalence of resistance genes or virulence factors overall, nor differences in the taxonomic composition of dairy worker and community control metagenomes.

Conclusions

This study presents the first metagenomics analysis of United States dairy workers, providing insights into potential risks of exposure to antibiotics and pathogens in animal farming environments. Previous metagenomic studies of livestock workers in China and Europe have reported increased abundance and carriage of antibiotic resistance genes in livestock workers. While our investigation found no strong evidence for differences in the abundance or carriage of antibiotic resistance genes and virulence factors between dairy worker and community control gut metagenomes, we did observe patterns in the abundance of tetracycline resistance genes and the prevalence of cephamycin resistance genes that is consistent with previous work.

Dissecting microbial communities and resistomes for interconnected humans, soil, and livestock

A debate is currently ongoing as to whether intensive livestock farms may constitute reservoirs of clinically relevant antimicrobial resistance (AMR), thus posing a threat to surrounding communities. Here, combining shotgun metagenome sequencing, machine learning (ML), and culture-based methods, we focused on a poultry farm and connected slaughterhouse in China, investigating the gut microbiome of livestock, workers and their households, and microbial communities in carcasses and soil. For both the microbiome and resistomes in this study, differences are observed across environments and hosts. However, at a finer scale, several similar clinically relevant antimicrobial resistance genes (ARGs) and similar associated mobile genetic elements were found in both human and broiler chicken samples. Next, we focused on Escherichia coli, an important indicator for the surveillance of AMR on the farm. Strains of E. coli were found intermixed between humans and chickens. We observed that several ARGs present in the chicken faecal resistome showed correlation to resistance/susceptibility profiles of E. coli isolates cultured from the same samples. Finally, by using environmental sensing these ARGs were found to be correlated to variations in environmental temperature and humidity. Our results show the importance of adopting a multi-domain and multi-scale approach when studying microbial communities and AMR in complex, interconnected environments.

Metagenomic-based surveillance systems for antibiotic resistance in non-clinical settings

The success of antibiotics as a therapeutic agent has led to their ineffectiveness. The continuous use and misuse in clinical and non-clinical areas have led to the emergence and spread of antibiotic-resistant bacteria and its genetic determinants. This is a multi-dimensional problem that has now become a global health crisis. Antibiotic resistance research has primarily focused on the clinical healthcare sectors while overlooking the non-clinical sectors. The increasing antibiotic usage in the environment - including animals, plants, soil, and water - are drivers of antibiotic resistance and function as a transmission route for antibiotic resistant pathogens and is a source for resistance genes. These natural compartments are interconnected with each other and humans, allowing the spread of antibiotic resistance via horizontal gene transfer between commensal and pathogenic bacteria. Identifying and understanding genetic exchange within and between natural compartments can provide insight into the transmission, dissemination, and emergence mechanisms. The development of high-throughput DNA sequencing technologies has made antibiotic resistance research more accessible and feasible. In particular, the combination of metagenomics and powerful bioinformatic tools and platforms have facilitated the identification of microbial communities and has allowed access to genomic data by bypassing the need for isolating and culturing microorganisms. This review aimed to reflect on the different sequencing techniques, metagenomic approaches, and bioinformatics tools and pipelines with their respective advantages and limitations for antibiotic resistance research. These approaches can provide insight into resistance mechanisms, the microbial population, emerging pathogens, resistance genes, and their dissemination. This information can influence policies, develop preventative measures and alleviate the burden caused by antibiotic resistance.

One Health: a holistic approach for food safety in livestock

The food safety of livestock is a critical issue between animals and humans due to their complex interactions. Pathogens have the potential to spread at every stage of the animal food handling process, including breeding, processing, packaging, storage, transportation, marketing and consumption. In addition, application of the antibiotic usage in domestic animals is a controversial issue because, while they can combat food-borne zoonotic pathogens and promote animal growth and productivity, they can also lead to the transmission of antibiotic-resistant microorganisms and antibiotic-resistant genes across species and habitats. Coevolution of microbiomes may occur in humans and animals as well which may alter the structure of the human microbiome through animal food consumption. One Health is a holistic approach to systematically understand the complex relationships among humans, animals and environments which may provide effective countermeasures to solve food safety problems aforementioned. This paper depicts the main pathogen spectrum of livestock and animal products, summarizes the flow of antibiotic-resistant bacteria and genes between humans and livestock along the food-chain production, and the correlation of their microbiome is reviewed as well to advocate for deeper interdisciplinary communication and collaboration among researchers in medicine, epidemiology, veterinary medicine and ecology to promote One Health approaches to address the global food safety challenges.

Comparative Analyses of Antibiotic Resistance Genes in Jejunum Microbiota of Pigs in Different Areas

Antibiotic resistance genes (ARGs) are emerging environmental contaminants that threaten human and animal health. Intestinal microbiota may be an important ARGs repository, and intensive animal farming is a likely contributor to the environmental burden of ARGs. Using metagenomic sequencing, we investigated the structure, function, and drug resistance of the jejunal microbial community in Landrace (LA, Kunming), Saba (SB, Kunming), Dahe (DH, Qujing), and Diannan small-ear piglets (DS, Xishuangbanna) from different areas in Yunnan Province, China. Remarkable differences in jejunal microbial diversity among the different pig breeds, while the microbial composition of pig breeds in close areas tends to be similar. Functional analysis showed that there were abundant metabolic pathways and carbohydrate enzymes in all samples. In total, 32,487 ARGs were detected in all samples, which showed resistance to 38 categories of drugs. The abundance of ARGs in jejunum was not significantly different between LA and SB from the same area, but significantly different between DS, DH and LA or SB from different areas. Therefore, the abundance of ARGs was little affected by pig breeds and microorganism community structure, but it was closely related to geographical location. In addition, as a probiotic, Lactobacillus amylovorus is also an important ARGs producing bacterium. Our results revealed the antibiotic exposure and intestinal microbial resistance of farms in the study areas, which could provide basic knowledge and potential strategies for rational use of antibiotics and reducing the risk of ARGs transmission in animal husbandry.

Understanding transmission pathways and integrated digital surveillance potential of antimicrobial resistance in Ethiopia in a One Health approach: a mixed-method study protocol

INTRODUCTION

Antimicrobial resistance (AMR) has a critical global impact, mostly affecting low- and middle-income countries. A major knowledge gap exists in understanding the transmission pathway of the gut colonisation with AMR bacteria between healthy humans and their animals in addition to the presence of those AMR bacteria in the surrounding environment. A One Health (OH) approach is necessary to address this multisectoral problem.

METHODS AND ANALYSIS

This cross-sectional, mixed-method OH study design will use both quantitative and qualitative methods of data collection. Quantitative methods will be carried out to assess the prevalence and risk factors associated with multidrug resistant Gram-negative bacteria and vancomycin-resistant enterococci in humans, animals (cattle) and the environment. The focus will be on cattle rearing as an exposure risk for AMR among humans. The assessment of AMR in the population of Jimma, Ethiopia with or without exposure to cattle will reinforce the importance of OH research to identify the impending exchange of resistance profile between humans and animals as well as its ultimate dissemination in the surrounding environment.The targeted semistructured key stakeholder interviews will aid to strengthen the OH-AMR surveillance in Ethiopia by understanding the acceptability of an integrated AMR surveillance platform based on the District Health Information Software-2 and the feasibility of its context-specific establishment.

ETHICS AND DISSEMINATION

The study has been approved by the Regional Ethics Committee, Norway, and the Institutional Review Board of Jimma University, Ethiopia. The study's data will be stored on a secure server known as Services for Sensitive Data hosted by the University of Oslo. In addition, the new European Union Global Data Protection Guidelines for data sharing, storage and protection will be followed. We will publish the results in peer-reviewed journals and present the findings at national and international conferences.

Characteristics of the gut microbiota in Bifidobacterium catenulatum LI10 pre-treated rats with lower levels of D-galactosamine-induced liver damage

AIMS

Liver damage has caused great illness in human beings. Bifidobacterium catenulatum LI10 has been determined with protective effect against D-galactosamine-induced liver damage. However, due to the sample limitation, the individual difference in its protective effect was not determined. The current study was designed to characterise the gut microbiota of LI10-pretreated rats with lower levels of liver damage.

METHODS AND RESULTS

A series of experiments and bioinformatic analyses were carried out. Two rat cohorts with different levels of liver damage were determined, i.e., Non-Severe and Severe cohorts. Six out of the seven measured liver function variables were lower in the Non-Severe cohort, while four cytokine variables also yielded differences between the two cohorts. The Non-Severe and Severe cohorts were determined with distinct gut microbiota, among which, ASV14_Parabacteroides and ASV7_Bacteroides were most associated with Non-Severe and Severe cohorts, respectively. Five phylotypes were determined as structural gatekeepers in the microbiota network of Non-Severe cohort, ASV135_Lachnospiraceae_NK4A136 of which contributed most to the stability of the network.

CONCLUSIONS

The relevant findings suggest that some gut bacteria could benefit the protective effect of LI10 on lowering the severity of rat liver damage.

SIGNIFICANCE AND IMPACT OF THE STUDY

The bacteria benefiting the protective effects of potential probiotics could be further investigated for future clinical application.

Multiple Intestinal Bacteria Associated with the Better Protective Effect of Bifidobacterium pseudocatenulatum LI09 against Rat Liver Injury

Bifidobacterium pseudocatenulatum LI09 could protect rats from D-galactosamine- (D-GalN-) induced liver injury. However, individual difference in the protective effects of LI09 on the liver injury remains poorly understood. The present study is aimed at determining the multiple intestinal bacteria associated with the better protective effect of LI09 against D-GalN-induced rat liver injury. Two rat cohorts, i.e., the nonsevere and severe cohorts, were divided based on their liver injury severity. Higher level of ALB and lower levels of ALT, AST, TBA, TB, IL-5, and MIP-3α were determined in the nonsevere cohort than the severe cohort. The alpha diversity indices (i.e., observed species, Shannon, and Pielou indices) did not yield significant differences between the intestinal microbiota of the nonsevere and severe cohorts. The intestinal microbiota composition was different between the two cohorts. Ten phylotypes assigned to Bacteroides, Clostridia_UCG-014, Clostridium Lachnospiraceae, Lachnospiraceae_NK4A136, and Parabacteroides were closely associated with the nonsevere cohort, among which, ASV8_Lachnospiraceae_NK4A136 was the most associated one. At the structure level, two groups of phylotypes with most correlations were determined in the intestinal microbiota networks of the two cohorts. Among them, ASV135_Lachnospiraceae_NK4A136 was the most powerful gatekeeper in the microbiota network of the nonsevere cohort. In conclusion, some intestinal bacteria, e.g., Lachnospiraceae_NK4A136, Parabacteroides, and Clostridium, were associated with the better protective effect of LI09 against D-GalN-induced rat liver injury. They were likely to enhance the effectiveness of LI09, and their clinical application deserves further investigation.

Abundance, diversity and diffusion of antibiotic resistance genes in cat feces and dog feces

The ARG profiles in pet feces, such as cat and dog feces, and their potential threat to environmental safety are still unclear. In this study, ARGs in 45 cat and 28 dog fecal samples were detected, and a diffusion experiment was performed to assess the risk of ARGs diffusion into the air. The results showed that the abundances of ARGs in cat feces and dog feces were high, and the abundance in dog feces (0.89 ± 0.17 copies/bacterial cell) was significantly higher than that in cat feces (0.46 ± 0.09 copies/bacterial cell) (P < 0.05). The bacterial community, especially Firmicutes and Desulfobacterota in cat feces, and Proteobacteria in dog feces, was the main factor affecting the variation in the ARG profiles, contributing to 31.6% and 32.4% of the variation in cat feces and dog feces, respectively. Physicochemical factors (especially NH₄⁺-N) and age also indirectly affected the variation in the ARG profiles by affecting the bacterial community. In addition, the ARGs in cat feces and dog feces diffused into the air, but there was no evidence that this diffusion posed a threat to environmental safety and human health. These results can provide reference data for healthy animal breeding and the prevention and control of ARG pollution.

OUP accepted manuscript

Background

Real-time quantitative PCR (qPCR) is an affordable method to quantify antimicrobial resistance gene (ARG) targets, allowing comparisons of ARG abundance along animal production chains.

Objectives

We present a comparison of ARG abundance across various animal species, production environments and humans in Europe. AMR variation sources were quantified. The correlation of ARG abundance between qPCR data and previously published metagenomic data was assessed.

Methods

A cross-sectional study was conducted in nine European countries, comprising 9572 samples. qPCR was used to quantify abundance of ARGs [aph(3′)-III, erm(B), sul2, tet(W)] and 16S rRNA. Variance component analysis was conducted to explore AMR variation sources. Spearman’s rank correlation of ARG abundance values was evaluated between pooled qPCR data and earlier published pooled metagenomic data.

Results

ARG abundance varied strongly among animal species, environments and humans. This variation was dominated by between-farm variation (pigs) or within-farm variation (broilers, veal calves and turkeys). A decrease in ARG abundance along pig and broiler production chains (‘farm to fork’) was observed. ARG abundance was higher in farmers than in slaughterhouse workers, and lowest in control subjects. ARG abundance showed a high correlation (Spearman’s ρ > 0.7) between qPCR data and metagenomic data of pooled samples.

Conclusions

qPCR analysis is a valuable tool to assess ARG abundance in a large collection of livestock-associated samples. The between-country and between-farm variation of ARG abundance could partially be explained by antimicrobial use and farm biosecurity levels. ARG abundance in human faeces was related to livestock antimicrobial resistance exposure.

Making waves: How does the emergence of antimicrobial resistance affect policymaking?

This article considers current trends in antimicrobial resistance (AMR) research and knowledge gaps relevant to policymaking in the water sector. Specifically, biological indicators of AMR (antibiotic-resistant bacteria and their resistance genes) and detection methods that have been used so far are identified and discussed, as well as the problems with and solutions to the collection of AMR data, sewage surveillance lessons from the COVID-19 pandemic, and the financial burden caused by AMR, which could be synergically used to improve advocacy on AMR issues in the water sector. Finally, this article proposes solutions to overcoming existing hurdles and shortening the time it will take to have an impact on policymaking and regulation in the sector.

A 'time bomb' in the human intestine-the multiple emergence and spread of antibiotic-resistant bacteria

Antibiotics have a strong killing effect on bacteria and are the first choice for the prevention and treatment of bacterial infectious diseases. Therefore, they have been widely used in the medical field, animal husbandry and planting industry. However, with the massive use of antibiotics, more and more antibiotic-resistant bacteria (ARB) have emerged. Because human intestines are rich in nutrients, have suitable temperature, and are high in bacterial abundance, they can easily become a hotbed for the spread of ARB and antibiotic-resistant genes (ARGs). When opportunistic pathogenic bacteria in the intestine acquire ARGs, the infectious diseases caused by such opportunistic pathogens will become more difficult to treat, or even impossible to cure. Therefore, ARB in the human intestine are like a 'time bomb'. In this review, we discuss the sources of intestinal ARB and the transmission routes of ARGs in the human intestine from the perspective of One Health. Further, we describe various methods to prevent the emergence of ARB and inhibit the spread of ARGs in the human intestine. Finally, we may be able to overcome ARB in the human intestine using an interdisciplinary 'One Health' approach.

Antibiotic Resistance: From Pig to Meat

Pork meat is in high demand worldwide and this is expected to increase. Pork is often raised in intensive conditions, which is conducive to the spread of infectious diseases. Vaccines, antibiotics, and other biosafety measures help mitigate the impact of infectious diseases. However, bacterial strains resistant to antibiotics are more and more frequently found in pig farms, animals, and the environment. It is now recognized that a holistic perspective is needed to sustainably fight antibiotic resistance, and that an integrated One Health approach is essential. With this in mind, this review tackles antibiotic resistance throughout the pork raising process, including their microbiome; many factors of their environment (agricultural workers, farms, rivers, etc.); and an overview of the impact of antibiotic resistance on pork meat, which is the end product available to consumers. Antibiotic resistance, while a natural process, is a public health concern. If we react, and act, collectively, it is expected to be, at least partially, reversible with judicious antibiotic usage and the development of innovative strategies and tools to foster animal health.

Variation in Microbial Exposure at the Human-Animal Interface and the Implications for Microbiome-Mediated Health Outcome

The human gut microbiome varies between populations, largely reflecting ecological differences. One ecological variable that is rarely considered but may contribute substantially to microbiome variation is the multifaceted nature of human-animal interfaces. We present the hypothesis that different interactions with animals contribute to shaping the human microbiome globally. We utilize a One Health framework to explore how changes in microbial exposure from human-animal interfaces shape the microbiome and, in turn, contribute to differential human health across populations, focusing on commensal and pathogen exposure, changes in colonization resistance and immune system training, and the potential for other functional shifts. Although human-animal interfaces are known to underlie human health and particularly infectious disease disparities, since their impact on the human microbiome remains woefully understudied, we propose foci for future research. We believe it will be crucial to understand this critical aspect of biology and its impacts on human health around the globe.

More diversified antibiotic resistance genes in chickens and workers of the live poultry markets

BACKGROUND

Poultry farms and LPMs are a reservoir of antimicrobial resistant bacteria and resistance genes from feces. The LPM is an important interface between humans, farm animals, and environments in a typical urban environment, and it is considered a reservoir for ARGs and viruses. However, the antibiotic resistomes shared between chicken farms and LPMs, and that of LPM workers and people who have no contact with the LPMs remains unknown.

METHODS

We characterized the resistome and bacterial microbiome of farm chickens and LPMs and LPM workers and control subjects. The mobile ARGs identified in chickens and the distribution of the mcr-family genes in publicly bacterial genomes and chicken gut metagenomes was analyzed, respectively. In addition, the prevalence of mcr-1 in LPMs following the ban on colistin-positive additives in China was explored.

RESULTS

By profiling the microbiomes and resistomes in chicken farms, LPMs, LPM workers, and LPM environments, we found that the bacterial community composition and resistomes were significantly different between the farms and the LPMs, and the LPM samples possessed more diversified ARGs (59 types) than the farms. Some mobile ARGs, such as mcr-1 and tet(X3), identified in chicken farms, LPMs, LPM workers, and LPM environments were also harbored by human clinical pathogens. Moreover, we found that the resistomes were significantly different between the LPM workers and those who have no contact with the LPMs, and more diversified ARGs (188 types) were observed in the LPM workers. It is also worth noting that mcr-10 was identified in both human (5.2%, 96/1,859) and chicken (1.5%, 14/910) gut microbiomes. Although mcr-1 prevalence decreased significantly in the LPMs across the eight provinces in China, from 190/333 (57.1%) samples in September 2016-March 2017 to 208/544 (38.2%) samples in August 2018-May 2019, it is widespread and continuous in the LPMs.

CONCLUSION

Live poultry trade has a significant effect on the diversity of ARGs in LPM workers, chickens, and environments in China, driven by human selection with the live poultry trade. Our findings highlight the live poultry trade as ARG disseminators into LPMs, which serve as an interface of LPM environments even LPM workers, and that could urge Government to have better control of LPMs in China. Further studies on the factors that promote antibiotic resistance exchange between LPM environments, human commensals, and pathogens, are warranted.

Antibiotic resistome from the One-Health perspective: understanding and controlling antimicrobial resistance transmission

The concept of the antibiotic resistome was introduced just over a decade ago, and since then, active resistome studies have been conducted. In the present study, we describe the previously established concept of the resistome, which encompasses all types of antibiotic resistance genes (ARGs), and the important findings from each One-Health sector considering this concept, thereby emphasizing the significance of the One-Health approach in understanding ARG transmission. Cutting-edge research methodologies are essential for deciphering the complex resistome structure in the microbiomes of humans, animals, and the environment. Based on the recent achievements of resistome studies in multiple One-Health sectors, future directions for resistome research have been suggested to improve the understanding and control of ARG transmission: (1) ranking the critical ARGs and their hosts; (2) understanding ARG transmission at the interfaces of One-Health sectors; (3) identifying selective pressures affecting the emergence, transmission, and evolution of ARGs; and (4) elucidating the mechanisms that allow an organism to overcome taxonomic barriers in ARG transmission.

Metagenomics-Based Approach to Source-Attribution of Antimicrobial Resistance Determinants - Identification of Reservoir Resistome Signatures

Metagenomics can unveil the genetic content of the total microbiota in different environments, such as food products and the guts of humans and livestock. It is therefore considered of great potential to investigate the transmission of foodborne hazards as part of source-attribution studies. Source-attribution of antimicrobial resistance (AMR) has traditionally relied on pathogen isolation, while metagenomics allows investigating the full span of AMR determinants. In this study, we hypothesized that the relative abundance of fecal resistome components can be associated with specific reservoirs, and that resistomes can be used for AMR source-attribution. We used shotgun-sequences from fecal samples of pigs, broilers, turkeys- and veal calves collected across Europe, and fecal samples from humans occupationally exposed to livestock in one country (pig slaughterhouse workers, pig and broiler farmers). We applied both hierarchical and flat forms of the supervised classification ensemble algorithm Random Forests to classify resistomes into corresponding reservoir classes. We identified country-specific and -independent AMR determinants, and assessed the impact of country-specific determinants when attributing AMR resistance in humans. Additionally, we performed a similarity percentage analysis with the full spectrum of AMR determinants to identify resistome signatures for the different reservoirs. We showed that the number of AMR determinants necessary to attribute a resistome into the correct reservoir increases with a larger reservoir heterogeneity, and that the impact of country-specific resistome signatures on prediction varies between countries. We predicted a higher occupational exposure to AMR determinants among workers exposed to pigs than among those exposed to broilers. Additionally, results suggested that AMR exposure on pig farms was higher than in pig slaughterhouses. Human resistomes were more similar to pig and veal calves’ resistomes than to those of broilers and turkeys, and the majority of these resistome dissimilarities can be explained by a small set of AMR determinants. We identified resistome signatures for each individual reservoir, which include AMR determinants significantly associated with on-farm antimicrobial use. We attributed human resistomes to different livestock reservoirs using Random Forests, which allowed identifying pigs as a potential source of AMR in humans. This study thus demonstrates that it is possible to apply metagenomics in AMR source-attribution.

Farm dust resistomes and bacterial microbiomes in European poultry and pig farms

BACKGROUND

Livestock farms are a reservoir of antimicrobial resistant bacteria from feces. Airborne dust-bound bacteria can spread across the barn and to the outdoor environment. Therefore, exposure to farm dust may be of concern for animals, farmers and neighboring residents. Although dust is a potential route of transmission, little is known about the resistome and bacterial microbiome of farm dust.

OBJECTIVES

We describe the resistome and bacterial microbiome of pig and poultry farm dust and their relation with animal feces resistomes and bacterial microbiomes, and on-farm antimicrobial usage (AMU). In addition, the relation between dust and farmers' stool resistomes was explored.

METHODS

In the EFFORT-study, resistomes and bacterial microbiomes of indoor farm dust collected on Electrostatic Dust fall Collectors (EDCs), and animal feces of 35 conventional broiler and 44 farrow-to-finish pig farms from nine European countries were determined by shotgun metagenomic analysis. The analysis also included 79 stool samples from farmers working or living at 12 broiler and 19 pig farms and 46 human controls. Relative abundance of and variation in resistome and bacterial composition of farm dust was described and compared to animal feces and farmers' stool.

RESULTS

The farm dust resistome contained a large variety of antimicrobial resistance genes (ARGs); more than the animal fecal resistome. For both poultry and pigs, composition of dust resistomes finds (partly) its origin in animal feces as dust resistomes correlated significantly with fecal resistomes. The dust bacterial microbiome also correlated significantly with the dust resistome composition. A positive association between AMU in animals on the farm and the total abundance of the dust resistome was found. Occupational exposure to pig farm dust or animal feces may contribute to farmers' resistomes, however no major shifts in farmers resistome towards feces or dust resistomes were found in this study.

CONCLUSION

Poultry and pig farm dust resistomes are rich and abundant and associated with the fecal resistome of the animals and the dust bacterial microbiome.