Antibiotic Resistome Associated with Small-Scale Poultry Production in Rural Ecuador

Intervention effects of fructooligosaccharide and astragalus polysaccharide, as typical antibiotic alternatives, on antibiotic resistance genes in feces of layer breeding: advantages and defects

Although antibiotic alternatives are widely used in livestock and poultry breeding industry after in-feed antibiotics ban, their intervention effects on antibiotic resistance genes (ARGs) in these food animals' feces remain poorly understood. Here effects of fructooligosaccharide (FOS) and astragalus polysaccharide (APS), as typical antibiotic alternatives in China, on ARGs in layer feces were estimated by performing metagenomic sequencings and fluorescence quantitative PCR. Fructooligosaccharide significantly reduced sum abundance of ARGs and mobile genetic elements (MGEs) by increasing Lactobacillus clones and reducing Escherichia clones which had relatively higher abundances of ARG subtypes and MGE subtypes in layer feces. However, at least parts of core ARGs and MGEs categories were not reduced by FOS, such as aminoglycosides- and tetracyclines-resistant genes, Tn916, Integrase, and so on. MGEs and microbiome, especially Escherichia genus and Lactobacillus genus, were the key factors affecting ARGs' sum abundance. MGEs had a higher correlation coefficient with ARGs' sum abundance than Escherichia genus and Lactobacillus genus. These findings firstly reveal the defects of antibiotic alternatives in controlling bacterial resistance in livestock and poultry breeding after in-feed antibiotics ban, and more strategies are needed to control pollutions and risks of core ARGs and MGEs in food animals' feces under a special environment.

Degradation and transformation of carbamazepine in aqueous medium under non-thermal plasma oxidation process

Carbamazepine (CBZ) is a pharmaceutical compound detected in various water resources. With a view to removing this contaminant, the applicability of non-thermal plasma (NTP) oxidation process has been widely tested in recent years. This study utilized NTP from a dielectric barrier discharge reactor in the treatment of CBZ. NTP on the surface of a water sample containing 25 mg.L-1 of CBZ resulted in a removal efficiency of over 90% with an energy yield of 0.19 g. (kWh)-1. On the other hand, a rapid reduction in pH and an increase of conductivity and nitrate/nitrite ions concentration were observed during the degradation. The applied voltage amplitude significantly affected the removal efficiency and the energy yield as the degradation efficiency was 55%, 70%, and 72% respectively with an applied voltage of 8, 10, and 12 kV. The water matrices containing inorganic anions such as chloride and carbonate ions reduced the removal efficiency by scavenging the reactive species. Accordingly, a reduction in the removal efficiency was observed in tap water. The high-resolution mass spectrometry (HRMS) results revealed that both reactive oxygen and nitrogen species take part in the reaction process which yields many intermediate products including aromatic nitro-products. This study concluded that NTP can effectively degrade CBZ in both pure and tap water, but special attention must be paid to changes in the water quality parameters (pH, conductivity, and nitrate/nitrite ions) and the fate of nitro products.

Impact of contrasting poultry exposures on human, poultry, and wastewater antibiotic resistomes in Bangladesh

IMPORTANCE

Through the use of DNA sequencing, our study shows that there is no significant difference in the antibiotic resistance genes found in stool samples taken from individuals with high exposure to poultry routinely fed antibiotics and those without such exposure. This finding is significant as it suggests limited transmission of antibiotic resistance genes between poultry and humans in these circumstances. However, our research also demonstrates that commercially reared poultry are more likely to possess resistance genes to antibiotics commonly administered on medium-sized farms. Additionally, our study highlights the under-explored potential of wastewater as a source of various antibiotic resistance genes, some of which are clinically relevant.

Livestock wastes from family-operated farms are potential important sources of potentially toxic elements, antibiotics, and estrogens in rural areas in North China

The open-air storage and disposal of livestock waste from family-operated livestock farms can be a potential health threat to rural residents. In this study, the occurrence and seasonal distribution of 8 potentially toxic elements, 24 antibiotics, and 4 estrogens were investigated in 44 waste samples from 11 rural farms in North China. The results showed that these micropollutants were ubiquitous in livestock waste, with concentration ranges of 238.9-4555 mg/kg for potentially toxic elements, not detected (ND) to 286,672 μg/kg for antibiotics and ND to 229.5 μg/kg for estrogens. The pollutants in animal wastes showed seasonal variation. Since these wastes are directly applicable to nearby farmland without treatment, the risks those wastes pose to farmland soils were also evaluated. Risk assessment results showed that Zn, Cd, Hg, FF and DC in swine manures were at high risk, while total estrogens in chicken and dairy cattle manures were at high risk. The results will provide important data for the regulation of animal wastes produced by small-scale livestock farms in rural areas of China.

The resistomes of rural and urban pigs and poultry in Ghana

IMPORTANCE

To the best of our knowledge, this is the first report on the resistomes that are measured using metagenomics in livestock from Sub-Saharan Africa. We find notable differences in the microbiomes between both pigs and poultry, and those also varied markedly compared to similar samples from Europe. However, for both animal species, the same bacterial taxa drove such differences. In pigs and urban free-range poultry, we find a very low abundance of antimicrobial resistance genes (ARGs), whereas rural free-range poultry displayed similarity to the European average, and industrialized poultry exhibited higher levels. These findings show how different African livestock bacterial communities and resistomes are from their European counterparts. They also underscore the importance of continued surveillance and investigation into antimicrobial resistance across diverse ecosystems, contributing significantly to global efforts toward combating the threat of antibiotic resistance.

Effects of Short- and Medium-Chain Fatty Acids on Production, Meat Quality, and Microbial Attributes-A Review

The non-therapeutic use of antimicrobials in poultry production contributes to the spread of drug-resistant pathogens in both birds and humans. Antibiotics are known to enhance feed efficiency and promote the growth and weight gain of poultry. New regulatory requirements and consumer preferences have led to a reduced use of antibiotics in poultry production and to the discovery of natural alternatives to antibiotic growth promoters. This interest is not only focused on the direct removal or inhibition of causative microorganisms but also on the prevention of diseases caused by enteric pathogens using a range of feed additives. A group of promising feed additives is composed of short- and medium-chain fatty acids (SCFAs and MCFAs) and their derivatives. MCFAs possess antibacterial, anticoccidial, and antiviral effects. In addition, it has been proven that these acids act in synergy if they are used together with organic acids, essential oils, or probiotics. These fatty acids also benefit intestinal health integrity and homeostasis in broilers. Other effects have been documented as well, such as an increase in intestinal angiogenesis and the gene expression of tight junctions. The aim of this review is to provide an overview of SCFAs and MCFAs as alternatives to antibiotic growth promoters and to summarize the current findings in the literature to show their possible benefits on production, meat quality, and gut health in poultry.

Molecular mechanism of antimicrobial co-resistance Colistin (mcr-1) and ESBLs genes among Escherichia coli isolates from commercial chickens in Pakistan

Emergence of plasmid mediated colistin and extended spectrum β-lactamases (ESBL) resistant genes has been impacted the efficacy of colistin and β-lactams drugs like 3rd, 4th generation cephalosporin. Current study was aimed to investigate antimicrobial resistance genes (ARGs) among Escherichia coli isolates from meat producing commercial broilers in Pakistan. Two hundred (n=200) fecal samples were collected during January-2018 to August-2019. For isolation of E. coli, pink colonies on MacConkey agar were transferred to EMB agar. Metallic sheen color colonies were tested biochemically using API-20E kit. The molecular identification of E. coli (n=153) was targeted by amplification of uid gene through polymerase chain reaction (PCR) and different ARGs i.e. gentamicin, streptomycin, tetracycline, colistin, β-lactams drugs, quinolone and ampicillin followed by sequence analysis. Genotypically, followed by phenotypically of resistant ARGs of isolated PCR-confirmed E. coli (153) shoed resistant against gentamicin (aac(3)-IV), streptomycin (aadA1), tetracycline (tetA), colistine (mcr-1), ampicillin (bla-TEM) and bla-CTX-M were 86%, 88%, 86%, 88%, 83% & 77% respectively. 33/38 (86%) of the isolate was positive for quinolone resistance. Colistine (mcr-1), ESBLs (bla-TEM) and (bla-CTX-M) resistance genes were 88%, 83% and 77% respectively. About 33 isolated E. coli harbored the both mcr-1 and ESBLs genes. All of E. coli isolates were found sensitive to ceftriaxone (CTX-30) and imipenem (IMP-10). The Isolated E. coli showed single or multi clade decadency. The E. coli and ARGs sequences showed single or multi clade decadency. This is first comprehensive study from Pakistan that described the molecular evidences of ARGs and their co-existence in single isolates originated from commercial poultry. Commercial chicken (Broilers) can act as melting pot of antibiotic resistance genes for human being. It is alarming situation for surveillance of antibiotic resistance program because of more regulated prescription of antimicrobial agents in Pakistan.

Effects of carbamazepine on gut microbiota, ARGs and intestinal health in zebrafish

Carbamazepine (CBZ) in the aquatic environment is recognized as a potential threat to aquatic organisms and public health. However, the response of organism intestinal health, resistome, microbiota, and their relationship after CBZ exposure has been rarely reported. This study aimed to explore the impacts of CBZ on gut microbiota, antibiotic resistance genes (ARGs) and the expression of intestinal health related genes as well as their interaction using the zebrafish model. 16 S ribosomal RNA sequencing indicated CBZ altered the composition of gut microbiota. Using high-throughput quantitative polymerase chain reaction (HT-qPCR), we found the number and abundance of ARGs were impacted by CBZ levels and exposure duration. We also observed the upregulated expression of the pro-inflammatory gene IL6 and downregulated expression of toll-like receptor gene TLR2 and intestinal barrier gene TJP2a at different exposure times. Correlation analyses revealed that Geobacillus, Rhodococcus, Ralstonia, Delftia, Luteolibacter and Escherichia-Shigella might be the main bacterial genera carrying ARGs. Meanwhile, Cetobacterium and Aeromonas could be the dominant bacteria affecting intestinal health related genes. Our results could contribute to understanding the health risks of CBZ to the intestinal microecology of aquatic animals.

Characterization of the gut microbiome and resistome of Galapagos marine iguanas (Amblyrhynchus cristatus) from uninhabited islands

BACKGROUND

Understanding the natural microbiome and resistome of wildlife from remote places is necessary to monitor the human footprint on the environment including antimicrobial use (AU). Marine iguanas are endemic species from the Galapagos Islands where they are highly affected by anthropogenic factors that can alter their microbiota as well as their abundance and diversity of antimicrobial-resistant genes (ARGs). Thus, this study aims to apply culture-independent approaches to characterize the marine iguana's gut metagenomic composition of samples collected from the uninhabited islands Rabida (n = 8) and Fernandina (Cabo Douglas, n = 30; Punta Espinoza, n = 30). Fresh feces from marine iguanas were analyzed through SmartChip RT-PCR, 16S rRNA, and metagenomic next-generation sequencing (mNGS) to identify their microbiome, microbial-metabolic pathways, resistome, mobilome, and virulome.

RESULTS

The marine iguana's gut microbiome composition was highly conserved despite differences in ecological niches, where 86% of taxa were shared in the three locations. However, site-specific differences were mainly identified in resistome, mobilome, virulorome, and metabolic pathway composition, highlighting the existence of factors that induce microbial adaptations in each location. Functional gut microbiome analyses revealed its role in the biosynthesis and degradation of vitamins, cofactors, proteinogenic amino acids, carbohydrates, nucleosides and nucleotides, fatty acids, lipids, and other compounds necessary for the marine iguanas. The overall bacterial ARG abundance was relatively low (0.006%); nevertheless, the presence of genes encoding resistance to 22 drug classes was identified in the iguana's gut metagenome. ARG-carrying contig and co-occurrence network analyses revealed that commensal bacteria are the main hosts of ARGs. Taxa of public health interest such as Salmonella, Vibrio, and Klebsiella also carried multidrug-resistance genes associated with MGEs which can influence the dissemination of ARGs through horizontal gene transfer.

CONCLUSION

Marine iguanas depend on the gut microbiome for the biosynthesis and degradation of several compounds through a symbiotic relationship. Niche-specific adaptations were evidenced in the pool of microbial accessory genes (i.e., ARGs, MGEs, and virulence) and metabolic pathways, but not in the microbiome composition. Culture-independent approaches outlined the presence of a diverse resistome composition in the Galapagos marine iguanas from remote islands. The presence of AR pathogens in marine iguanas raises concerns about the dispersion of microbial-resistant threats in pristine areas, highlighting wildlife as sentinel species to identify the impact of AU.

An exhaustive investigation on antibiotics contamination from livestock farms within sensitive reservoir water area: Spatial density, source apportionment and risk assessment

Although the studies on antibiotic contamination are common at present, large-scale sampling studies drawing highly representative conclusions are still scarce. This study conducted a comprehensive investigation on a total of 1183 samples from 70 livestock farms within a sensitive area around reservoir waters. 45 types of antibiotics belonging to 5 different classes were monitored. This is the first analysis to comprehensively investigate the density distribution, source apportionment, ecological and health risk of antibiotics in an entire area of sensitive waters. The results showed that the layer manure samples had highest detection rate of antibiotics (0.0 %-96.1 %, average value = 30.7 %) followed by pig manure samples. Oxytetracycline had the highest concentration of 712.16 mg/kg in a pig manure sample. Different from using antibiotic concentration as a proxy for pollution level, the spatial density was calculated by averaging antibiotic concentration to area and converting different livestock to pig equivalent. The spatial density of pig equivalent can more realistically reflect the pollution caused by different breeds of livestocks. It was shown that the pig farms contributed higher to total antibiotic density than the layer and cattle farms did. After assessed, a few antibiotics (oxytetracycline, chlorotetracycline and tetracycline) have posed high ecological risks to soil around the farms. However, none of them caused hazard quotient (HQ) risk and carcinogenic risk (CR) to human health in the water of reservoir. Children were more likely to be at hazard risk than adults. Antibiotic mass fluctuation rules were analyzed along the chain (feed → livestock waste → soil → surface water). Feed, livestock waste and soil had similar diversity, but the antibiotic concentrations continued to decline, implying the possible sources of antibiotic residues were similar. Thus, it is important to reduce unnecessary antibiotic use to prevent the potential long-term risk of antibiotics.

Characteristics of Wild Bird Resistomes and Dissemination of Antibiotic Resistance Genes in Interconnected Bird-Habitat Systems Revealed by Similarity of blaTEM Polymorphic Sequences

Wild birds are known to harbor and discharge antibiotic-resistant bacteria (ARB) and their associated antibiotic resistance genes (ARGs). However, assessments of their contribution to the dissemination of antibiotic resistance in the environment are limited to culture-dependent bacterial snapshots. Here, we present a high-throughput sequencing study that corroborates extensive ARG exchange between wild bird feces and their habitats and implies the need to scrutinize high-mobility birds as potential vectors for global propagation of ARGs. We characterized the resistome (281 ARGs) and microbiome of seven wild bird species and their terrestrial and aquatic habitats. The resistomes of bird feces were influenced by the microbial community structure, mobile genetic elements (MGEs), and residual antibiotics. We designated 33 ARGs found in more than 90% of the bird fecal samples as core ARGs of wild bird feces, among which 16 ARGs were shared as core ARGs in both wild bird feces and their habitats; these genes represent a large proportion of both the bird feces (35.0 ± 15.9%) and the environmental resistome (29.9 ± 21.4%). One of the most detected β-lactam resistance genes (bla_TEM, commonly harbored by multidrug resistant "superbugs") was used as molecular marker to demonstrate the high interconnectivity of ARGs between the microbiomes of wild birds and their habitats. Overall, this work provides a comprehensive analysis of the wild bird resistome and underscores the importance to consider genetic exchange between animals and the environment in the One Health approach.

Dose-dependent impact of enrofloxacin on broiler chicken gut resistome is mitigated by synbiotic application

Fluoroquinolone agents are considered critical for human medicine by the World Health Organization (WHO). However, they are often used for the treatment of avian colibacillosis in poultry production, creating considerable concern regarding the potential spread of fluoroquinolone resistance genes from commensals to pathogens. Therefore, there is a need to understand the impact of fluoroquinolone application on the reservoir of ARGs in poultry gut and devise means to circumvent potential resistome expansion. Building upon a recent dose optimization effort, we used shotgun metagenomics to investigate the time-course change in the cecal microbiome and resistome of broiler chickens receiving an optimized dosage [12.5 mg/kg body weight (bw)/day], with or without synbiotic supplementation (PoultryStar^®, BIOMIN GmbH), and a high dosage of enrofloxacin (50 mg/kg bw/day). Compared to the high dose treatment, the low (optimized) dose of enrofloxacin caused the most significant perturbations in the cecal microbiota and resistome of the broiler chickens, demonstrated by a lower cecal microbiota diversity while substantially increasing the antibiotic resistance genes (ARGs) resistome diversity. Withdrawal of antibiotics resulted in a pronounced reduction in ARG diversity. Chickens receiving the synbiotic treatment had the lowest diversity and number of enriched ARGs, suggesting an alleviating impact on the burden of the gut resistome. Some Proteobacteria were significantly increased in the cecal metagenome of chickens receiving enrofloxacin and showed a positive association with increased ARG burden. Differential abundance (DA) analysis revealed a significant increase in the abundance of ARGs encoding resistance to macrolides-lincosamides-streptogramins (MLS), aminoglycosides, and tetracyclines over the period of enrofloxacin application, with the optimized dosage application resulting in a twofold higher number of affected ARG compared to high dosage application. Our results provide novel insights into the dose-dependent effects of clinically important enrofloxacin application in shaping the broiler gut resistome, which was mitigated by a synbiotic application. The contribution to ameliorating the adverse effects of antimicrobial agents, that is, lowering the spread of antimicrobial resistance genes, on the poultry and potentially other livestock gastrointestinal microbiomes and resistomes merits further study.

Nitrogen Regulates the Distribution of Antibiotic Resistance Genes in the Soil-Vegetable System

The increasing antibiotic resistance genes (ARGs) in fertilizer-amended soils can potentially enter food chains through their transfer in a soil-vegetable system, thus, posing threats to human health. As nitrogen is an essential nutrient in agricultural production, the effect of nitrogen (in the forms NH₄ ⁺-N and NO₃ ^--N) on the distribution of ARGs (blaTEM-1, sul1, cmlA, str, and tetO) and a mobile genetic element (MGE; tnpA-4) in a soil-Chinese cabbage system was investigated. Not all the tested genes could transfer from soil to vegetable. For transferable ones (blaTEM-1, sul1, and tnpA-4), nitrogen application influenced their abundances in soil and vegetable but did not impact their distribution patterns (i.e., preference to either leaf or root tissues). For ARGs in soil, effects of nitrogen on their abundances varied over time, and the positive effect of NH₄ ⁺-N was more significant than that of NO₃ ^--N. The ARG accumulation to vegetables was affected by nitrogen application, and the nitrogen form was no longer a key influencing factor. In most cases, ARGs were found to prefer being enriched in roots, and nitrogen application may slightly affect their migration from root to leaf. The calculated estimated human intake values indicated that both children and adults could intake 10⁶-10⁷ copies of ARGs per day from Chinese cabbage consumption, and nitrogen application affected ARG intake to varying degrees. These results provided a new understanding of ARG distribution in vegetables under the agronomic measures such as nitrogen application, which may offer knowledge for healthy vegetable cultivation in future.

Fate of Antibiotic Resistance Genes and Changes in Bacterial Community With Increasing Breeding Scale of Layer Manure

The use of antimicrobials in intensive poultry production is becoming increasingly common because of its high throughput of meat and egg products. However, the profile of antibiotic resistance genes (ARGs) and the underlying mechanisms in different breeding scale farms were not fully explored. The study examined the profiles of ARGs in layer manure from three free-range and 12 intensive layer farms with different scales (N500, N5000, N10000, and N20000). A quantitative PCR (qPCR) array was used to quantify ARGs, and microbial community structure was analyzed by 16S rRNA gene sequencing. A total of 48 ARGs, belonging to seven major types, were identified in the layer manure samples, with sul2, tetM-01, and ermB being the predominant ones. The abundance, diversity, and mobility potential of ARGs in layer manure changed significantly with the increasing of the breeding scale. The abundances of total ARGs had significantly positive correlations with mobile genetic elements (MGEs), suggesting the mobility potential of ARGs in layer manure samples. Bacterial abundance did not show significant differences among the five group manure samples. However, bacterial diversity showed an increasing trend along the breeding scale. Pathogenic Bacteroidetes increased in the largest-scale layer manure samples and showed significant positive correlations with most ARGs. Network analysis revealed significant co-occurrence patterns between ARGs and microbial taxa, indicating ARGs had a wide range of bacterial hosts. Proteobacteria and Firmicutes were potential hosts for tetracycline and macrolide-lincosamide-streptogramin B (MLSB) resistant genes. Our results indicated that the expansion of the breeding scale of a farm promotes the abundance, diversity, and mobility potential of ARGs in layer manure.

Multi-generational effects of enrofloxacin on lifespan and reproduction of Caenorhabditis elegans with SKN-1-mediated antioxidant responses and lipid metabolism disturbances

Antibiotics are ubiquitous environmental pollutants and they can provoke multi-generational impacts due to their pseudo-persistence. However, their multi-generational effects and potential mechanisms remained poorly studied. Presently, effects of enrofloxacin (ENR) were studied on Caenorhabditis elegans with a continuous exposure over 9 generations (from F1 to F9) at an environmentally realistic level. Regarding reproduction, ENR showed stimulation in F1 (1.18-fold of the control) and F2 (1.08), inhibition in F3 (0.70), stimulation in F4 (1.86), F5 (3.18) and F6 (1.53), inhibition in F7 (0.73) and F8 (0.69) and stimulation again in F9 (1.89). That is to say, ENR provoked multi-generational oscillatory effects on the reproduction. Such oscillation was also observed in effects on lifespan with much less magnitudes than those on reproduction. Biochemical assays were performed in F1, F3, F4 and F9 which represented the oscillation over generations. Results showed more antioxidants (e.g., superoxide dismutase and glutathione), mild oxidative stress (e.g., reactive oxygen species) and less oxidative damage (i.e., protein carbonyl) underlying the generation-dependent stimulation. Moreover, ENR provoked multi-generational oscillation on the enzymes that regulate the lipogenesis (e.g., fatty acid synthase and acetyl-CoA carboxylase) and lipolysis (e.g., acyl-CoA synthetase), with similarities to the effects on the oxidative stress and damage. Further analysis on SKN-1 and its activating PMK-1 and GSK-3 demonstrated their involvement in regulating both antioxidant detoxification and lipid metabolism.

Inhibition of AI-2 Quorum Sensing and Biofilm Formation in Campylobacter jejuni by Decanoic and Lauric Acids

Campylobacter jejuni is a major bacterial cause of human diarrheal diseases worldwide. Despite its sensitivity to environmental stresses, C. jejuni ubiquitously distributes throughout poultry production chains. Biofilm formation mediated by quorum sensing is suggested to be critical to the survival of C. jejuni in agroecosystem. C. jejuni possesses LuxS, the enzyme involved in the production of autoinducer-2 (AI-2) signaling molecules. In this study, two fatty acids, namely decanoic acid and lauric acid, were identified to be effective in inhibiting AI-2 activity of C. jejuni. Both decanoic acid and lauric acid at 100 ppm inhibited ∼90% AI-2 activity (P < 0.05) of C. jejuni without bacterial inactivation. The biofilm biomass of two C. jejuni strains was reduced by 10-50% (P < 0.05) after treatment by both fatty acids, while increased biofilm formation was observed for one C. jejuni strain. In addition, both fatty acids effectively reduced the motility of all tested C. jejuni strains. These findings can aid in developing alternative C. jejuni control strategies in agri-food and clinical settings.

Distribution of antimicrobial resistance across the overall environment of dairy farms - A case study

The environmental implications of antimicrobial resistance arising from food animal farm practice are still a knowledge gap. This study investigates the fate and transport of antimicrobial resistance genes related to the use of antibiotics on a dairy farm in Michigan. Manure, soil, animal feed, animal drinking water, surface and groundwater samples were taken and the abundance of antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) were subsequently measured using high parallel quantitative PCR targeting 136 genes. The total abundance and detected numbers of ARGs were found to be highest in the stagnant lagoon. Up to 44 ARG subtypes with high abundance were found in drinking water in pen which was very close to those in manure compost. The ARGs pattern clustered by soil depth although they were treated by different manure. ARGs and MGEs were detected in surface and groundwater surrounded by dairy farmlands, with the occurrence of carbapenemase-encoding KPC gene in two waters, which may be due to transport of ARGs through runoff or other sources. Overall, the results of the study suggest high prevalence of ARGs both inside and outside the animal raising area and their potential contribution to environmental ARGs.

"Chicken dumping": Motivations and perceptions in shifting poultry production practices

Non-governmental organizations (NGOs) often implement overseas development aid through intensive small-scale animal agriculture to alleviate food insecurity in low- and middle-income countries. Intensive animal farming can pose unclear outcomes to households engaged in the practice because of the reliance on industrial animal breeds that are reared with antibiotics and raised in higher densities compared to traditional scavenging husbandry systems. As a result, intensive small-scale farming operations that lack proper infrastructure, training, and financial resources could facilitate the spread of antimicrobial resistance and infectious diseases. We applied a mixed-methods framework towards analyzing the effectiveness of small-scale broiler chicken farming in northern Ecuador. First, from May 2016 – May 2017, our observational surveys indicated that intensive small-scale poultry farming follows a boom-and-bust cycle that is extremely vulnerable to environmental stressors. Second, in May 2016, we followed a cohort of households enrolled in a poultry development project led by an NGO. We observed a substantial decline in chicken survivorship from Survey period 1 to 2 (mean chicken count decrease from 50 to 35 corresponding to a 70% survivorship) and from Survey period 2 to 3 (mean chicken count decrease from 35 to 20.3 corresponding to a 58% survivorship). Heads of households were self-reporting broiler chicken survivorship substantially higher than our recorded observations during survey period two (46 compared to 35 respectively) and three (44.3 compared to 20.3 respectively). We speculate that if households continue to inaccurately report poultry demographics, then it could perpetuate a negative feedback loop where NGOs continue to conduct the same intervention practices without receiving accurate outcome metrics. Third, we used semi-structured questionnaires to determine that access to financial resources was the major motivation for determining when to farm broiler chickens. Intensive small-scale poultry farming can be unreliable and disease-enhancing, yet also associated with dubious self-reports of success.

Spatial Exposure of Agricultural Antimicrobial Resistance in Relation to Free-Ranging Domestic Chicken Movement Patterns among Agricultural Communities in Ecuador

The use of antimicrobial growth promoters in chicken farming has been commonly associated with high levels of antimicrobial resistance (AMR) in humans. Most of this work, however, has been focused on intensive large-scale operations. Intensive small-scale farming that regularly uses antibiotics is increasing worldwide and has different exposure pathways compared with large-scale farming, most notably the spatial connection between chickens and households. In these communities, free-ranging backyard chickens (not fed antibiotics) can roam freely, whereas broiler chickens (fed antibiotics) are reared in the same husbandry environment but confined to coops. We conducted an observational field study to better understand the spatial distribution of AMR in communities that conduct small-scale farming in northwestern Ecuador. We analyzed phenotypic resistance of Escherichia coli sampled from humans and backyard chickens to 12 antibiotics in relation to the distance to the nearest small-scale farming operation within their community. We did not find a statistically significant relationship between the distance of a household to small-scale farming and antibiotic-resistant E. coli isolated from chicken or human samples. To help explain this result, we monitored the movement of backyard chickens and found they were on average 17 m (min-max: 0-59 m) from their household at any given time. These backyard chickens on average ranged further than the average distance from any study household to its closest neighbor. This level of connectivity provides a viable mechanism for the spread of antimicrobial-resistant bacteria and genes throughout the community.

Comparison of microbiota, antimicrobial resistance genes and mobile genetic elements in flies and the feces of sympatric animals

Flies are well-known vectors of bacterial pathogens, but there are little data on their role in spreading microbial community and antimicrobial resistance. In this study, we compared the bacterial community, antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) in flies with those in the feces of sympatric animals. A 16S rRNA-based microbial analysis identified 23 bacterial phyla in fecal samples and 25 phyla in flies; all the phyla identified in the fecal samples were also found in the flies. Bray-Curtis dissimilarity analysis showed that the microbiota of the flies were more similar to the microbiota of the feces of their sympatric animals than those of the feces from the three other animal species studied. The qPCR array amplified 276 ARGs/MGEs in fecal samples, and 216 ARGs/MGEs in the flies, while 198 of these genes were identified in both flies and feces. Long-term studies with larger sample numbers from more geospatially distinct populations and infection trials are indicated to further evaluate the possibility of flies as sentinels for antimicrobial resistance.

Occurrence of antibiotic resistance genes and microbial source tracking markers in the water of a karst spring in Germany

The emergence of antimicrobial resistances causes serious public health concerns worldwide. In recent years, the aquatic ecosystem has been recognized as a reservoir for antibiotic-resistant bacteria and antibiotic resistance genes (ARGs). The prevalence of 11 ARGs, active against six antibiotic classes (β-lactams, aminoglycosides, tetracycline, macrolides, trimethoprim, and sulfonamides), was evaluated at a karst spring (Gallusquelle) in Germany, using molecular biological methods. In addition, fecal indicator bacteria (FIB), turbidity, electrical conductivity, spring discharge, and microbial source tracking markers specific for human, horse, chicken, and cow were determined. The ARGs most frequently detected were ermB (42.1%), tet(C) (40.8%), sul2 (39.5%), and sul1 (36.8%), which code for resistance to macrolides, tetracycline and sulfonamides, respectively. After a heavy rain event, the increase in FIB in the spring water was associated with the increase in ARGs and human-specific microbial source tracking (MST) markers. The determined correlations of the microbiological parameters, the observed overflow of a combined sewer overflow basin a few days before the increase of these parameters, and the findings of previous studies indicate that the overflow of this undersized basin located 9 km away from the spring could be a factor affecting the water quality of the karst spring. Our results provide a scientific basis for minimization of the input of fecal pollution and thus ARGs into the karst spring.

High levels of antibiotic resistance genes and opportunistic pathogenic bacteria indicators in urban wild bird feces

This study analyzed fresh feces from three common bird species that live in urban environments and interact with human communities. Antibiotic resistance genes (ARGs) encoding resistance to three major classes of antibiotics (i.e., tetracyclines, β-lactams, and sulfonamides) and the mobile genetic element integrase gene (intI1) were abundant (up to 10⁹, 10⁸, 10⁹, and 10¹⁰ copies/g dry feces for tetW, bla_TEM, sul1, and intI1, respectively), with relative concentrations surprisingly comparable to that in poultry and livestock that are occasionally fed antibiotics. Biomarkers for opportunistic pathogens were also abundant (up to 10⁷ copies/g dry feces) and the dominant isolates (i.e., Enterococcus spp. and Pseudomonas aeruginosa) harbored both ARGs and virulence genes. ARGs in bird feces followed first-order attenuation with half-lives ranging from 1.3 to 11.1 days in impacted soil. Although residual antibiotics were detected in the feces, no significant correlation was observed between fecal antibiotic concentrations and ARG relative abundance. Thus, other unaccounted factors likely contributed selective pressure for ARG maintenance. These findings highlight the contribution of wild urban bird feces to the maintenance and dissemination of ARGs, and the associated health risks.

Incorporating the plasmidome into antibiotic resistance surveillance in animal agriculture

Mobile genetic elements (MGE) carrying resistance genes represent a unique challenge to risk assessment and surveillance of antimicrobial resistance (AMR). Yet determining the mobility of resistance genes within animal microbiomes is essential to evaluating the potential dissemination from livestock to potential human pathogens, as well as evaluating co-selection mechanisms that may impact persistence of resistance genes with changing antibiotic use patterns. Current surveillance efforts utilize phenotypic testing and sequencing of individual isolates for tracking of AMR in livestock. In this work, we investigated the utility of using long-read sequencing of the plasmids from mixed Enterobacterales enrichments of swine fecal samples as a surveillance strategy for AMR plasmids. Enrichments were performed in either MacConkey broth without selection or with selection by addition of tetracycline or ceftriaxone, and plasmids were extracted and sequenced in order to evaluate the diversity of plasmids enriched by each method. Intact resistance plasmids were successfully assembled, as well as complex resistance transposons carrying multiple repeated elements that would interfere with assembly by short read sequencing technologies. Comparison of the assembled plasmids with representatives from public databases confirmed the quality of the assemblies and also revealed the occurrence of IncI2 plasmids carrying bla_CMY-2 in Ontario swine samples, which have not been found in previous studies.

Occurrence and distribution of antibiotic resistance genes in various rural environmental media

Antibiotic resistance genes (ARGs) in rural environments have been poorly characterized in the literature. In this study, the diversity, abundance, and distribution of ARGs in surface waters, soils, and sediments of a typical hilly rural area in the Upper Yangtze River watershed were investigated using the high-throughput quantitative polymerase chain reaction, and their relationships with chemical properties of the samples were analyzed. No significant differences in the diversity and abundance of ARGs were observed among the three medium types while the ARG distribution pattern in the sediments was obviously different from that of the surface waters. According to the co-occurrence pattern of ARGs subtypes obtained by network analysis, blaOXA10-02, blaPSE, lnuB-02, and qacEΔ1-01 can be used to estimate the relative abundance of total ARGs for the study area. It appeared that the prevalence of ARGs in the sediments was promoted by the horizontal gene transfer (HGT) and vertical gene transfer together, while their spread in the surface waters and soils were facilitated by the supply of biogenic elements and HGT, respectively. Mobile genetic elements (MGEs) were abundant and detected in all samples, and their abundance was significantly and positively correlated with that of ARGs, implying that the potential horizontal transfer of ARGs to other bacteria and pathogens in rural environments should not be overlooked.

A Review of Antimicrobial Resistance in Poultry Farming within Low-Resource Settings

The emergence, spread, and persistence of antimicrobial resistance (AMR) remain a pressing global health issue. Animal husbandry, in particular poultry, makes up a substantial portion of the global antimicrobial use. Despite the growing body of research evaluating the AMR within industrial farming systems, there is a gap in understanding the emergence of bacterial resistance originating from poultry within resource-limited environments. As countries continue to transition from low- to middle income countries (LMICs), there will be an increased demand for quality sources of animal protein. Further promotion of intensive poultry farming could address issues of food security, but it may also increase risks of AMR exposure to poultry, other domestic animals, wildlife, and human populations. Given that intensively raised poultry can function as animal reservoirs for AMR, surveillance is needed to evaluate the impacts on humans, other animals, and the environment. Here, we provide a comprehensive review of poultry production within low-resource settings in order to inform future small-scale poultry farming development. Future research is needed in order to understand the full extent of the epidemiology and ecology of AMR in poultry within low-resource settings.

Genotyping and molecular characterization of antimicrobial resistance in thermophilic Campylobacter isolated from poultry breeders and their progeny in Eastern Spain

Thermophilic Campylobacter spp. are recognized as a major cause of acute bacterial diarrhea in humans, with broiler meat being the most common source of human infection. Antibiotic therapy is usually necessary for severe or prolonged infections, especially in immunocompromised populations such as young or elderly individuals. However, different studies have demonstrated a close association between antibiotic use in animal production and antimicrobial resistance (AMR) in humans. In this sense, there is social pressure to reduce antibiotic administration and find adequate alternatives to control the presence of bacterial infections in farms. However, there is a lack of information related to Campylobacter AMR dynamics through the entire production system from breeders to their progeny. It is unknown if resistance genes are a result of adaptation through chromosomal mutation or through horizontal gene transfer, instead of vertical transmission of DNA from the parent to their progeny. Thus, the main objectives of this study were to assess the main AMR rates present in a poultry production system, to study the relationship between Campylobacter AMR profiles from breeders and their progeny, and to study the presence and distribution of antibiotic resistance genes in poultry production. Regarding AMR rates, ciprofloxacin was classified as extremely high, followed by nalidixic acid and tetracyclines that were classified as very high. Moreover, this study demonstrated a relationship between the AMR patterns and genes found from Campylobacter strains isolated in breeders and those present in their progeny.

Perinatal risk factors for fecal antibiotic resistance gene patterns in pregnant women and their infants

Perinatal factors can shape fecal microbiome patterns among pregnant women and their infants. However, there is scarce information about the effect of maternal demographics and perinatal exposures on antibiotic resistance genes (ARG) and mobile genetic element (MGE) patterns in pregnant women and infants. We examined fecal samples from pregnant women during their third trimester of pregnancy (n = 51) and 6-month-old infants (n = 40). Of the 91 participants, 72 represented 36 maternal-infant dyads, 15 were additional pregnant women, and 4 were additional infants. We assessed the effects of demographics, pre-pregnancy BMI, smoking and parity in the pregnancy resistome and the effects of demographics, delivery mode, feeding habits and prenatal antibiotic treatment on the infancy resistome. ARG and MGE richness and abundance were assessed using a SmartChip qPCR-array. Alpha diversity (Shannon and Inverse Simpson index) and beta diversity (Sorensen and Bray-Curtis index) were calculated. The Wilcoxon and the Kruskal non-parametric test were used for comparisons. There is a high variability in shared resistome patterns between pregnant women and their infants. An average of 29% of ARG and 24% of MGE were shared within dyads. Infants had significantly greater abundance and higher diversity of ARG and MGE compared to pregnant women. Pregnancy and infancy samples differed in ARG and MGE gene composition and structure. Composition of the fecal resistome was significantly associated with race in pregnant women, with non-white women having different patterns than white women, and, in infants, with extent of solid food consumption. Our data showed that the pregnancy and infancy resistome had different structure and composition patterns, with maternal race and infant solid food consumption as possible contributors to ARG. By characterizing resistome patterns, our results can inform the mechanism of antibiotic resistome development in pregnant women and their infants.

Antibiotic Resistance Genes in Antibiotic-Free Chicken Farms

Rising concern about the use of antibiotics in food production has resulted in many studies on the occurrence of antibiotic resistance genes (ARGs) in animal-associated bacterial communities. There are few baseline data on the abundance of ARGs on farms where chickens are intensively raised with little or no use of antibiotics. This study used a high-throughput quantitative PCR array to survey two antibiotic-free chicken farms for the occurrence of ARGs and mobile genetic elements known to enhance the spread of ARGs. No antibiotics had been used on the study farms for five years prior to this study. The results provide a baseline for the occurrence of resistance genes in the chicken production system without direct selective pressure.

The dynamic of antibiotic resistance in commensal Escherichia coli throughout the growing period in broiler chickens: fast-growing vs. slow-growing breeds

Antimicrobial resistance (AMR) is an important threat to public health worldwide. Furthermore, different studies have demonstrated a close association between antibiotic use in animal production and AMR in humans. It is well known that it is necessary to reduce antibiotic administration in farms by finding effective alternative treatments, using more resistant breeds and improving animal welfare. However, to be able to assess the alternatives proposed, it is essential to study the epidemiology of AMR under production conditions. Hence, the aim of this study was to investigate the AMR dynamic in 2 genetic poultry breeds during the growing period. The study was performed in 2 experimental poultry houses to simulate real production conditions, and no antibiotics were administered during the growing period. In addition, 2 poultry breeds were used, fast-growing and slow-growing. To evaluate AMR evolution, Escherichia coli was selected as indicator bacterium. To this end, animals from each experimental group were sampled at different times: on day of arrival, at mid-period, and at slaughter day. In the laboratory, cecal content was removed and inoculated in selective media. Then, biochemical tests were performed to confirm E. coli. Finally, antibiotic susceptibility was assessed according to Decision 2013/653. At the onset of the cycle, significant differences were observed between breeds, as the E. coli strains isolated from fast-growing 1-day-old-chicks showed higher AMR rates. However, at the end of the period, no significant differences were found between breeds and their presence of resistant bacteria (above 95%). Therefore, although no antibiotics were administered during the growing period, a high level of AMR at slaughter day was demonstrated. Further studies are necessary to determine the main risk factors that increase the level of AMR throughout the productive cycle in broiler chickens. In conclusion, it is important to highlight that although it is crucial to control both antibiotic use and animal welfare during the growing period, measures should be taken at all levels of the production chain.

Multi-generational obesogenic effects of sulfomethoxazole on Caenorhabditis elegans through epigenetic regulation

Increasing concerns are earned on the multigenerational hazards of antibiotics due to the connection between their mother-children transfer via cord blood and breast milk and obesity in the children. Currently, Caenorhabditis elegans was exposed to sulfamethoxazole (SMX) over 11 generations (F0-F10). Indicators of obesogenic effects and gene expressions were measured in each generation and also in T11 to T13 that were the offspring of F10. Biochemical analysis results showed that SMX stimulated fatty acids in most generations including T13. The stimulation was resulted from the balance between enzymes for fatty acid synthesis (e.g., fatty acid synthetase) and those for its consumption (e.g., fatty acid transport protein). Gene expression analysis demonstrated that the obesogenic effects of SMX involved peroxisome proliferator activated receptors (PPARs, e.g., nhr-49) and insulin/insulin-like signaling (IIS) pathways (e.g., ins-1, daf-2 and daf-16). Further epigenetic analysis demonstrated that SMX caused 3-fold more H3K4me3 binding genes than the control in F10 and T13. In F10, the most significantly activated genes were in metabolic and biosynthetic processes of various lipids, nervous system and development. The different gene expressions in T13 from those in F10 involved development, growth, reproduction and responses to chemicals in addition to metabolic processes.

Translating 'big data': better understanding of host-pathogen interactions to control bacterial foodborne pathogens in poultry

Recent technological advances has led to the generation, storage, and sharing of colossal sets of information ('big data'), and the expansion of 'omics' in science. To date, genomics/metagenomics, transcriptomics, proteomics, and metabolomics are arguably the most ground breaking approaches in food and public safety. Here we review some of the recent studies of foodborne pathogens (Campylobacter spp., Salmonella spp., and Escherichia coli) in poultry using big data. Genomic/metagenomic approaches have reveal the importance of the gut microbiota in health and disease. They have also been used to identify, monitor, and understand the epidemiology of antibiotic-resistance mechanisms and provide concrete evidence about the role of poultry in human infections. Transcriptomics studies have increased our understanding of the pathophysiology and immunopathology of foodborne pathogens in poultry and have led to the identification of host-resistance mechanisms. Proteomic/metabolomic approaches have aided in identifying biomarkers and the rapid detection of low levels of foodborne pathogens. Overall, 'omics' approaches complement each other and may provide, at least in part, a solution to our current food-safety issues by facilitating the development of new rapid diagnostics, therapeutic drugs, and vaccines to control foodborne pathogens in poultry. However, at this time most 'omics' approaches still remain underutilized due to their high cost and the high level of technical skills required.

High Prevalence of Extended-Spectrum Beta-Lactamase CTX-M-Producing Escherichia coli in Small-Scale Poultry Farming in Rural Ecuador

Small-scale farming may have large impacts on the selection and spread of antimicrobial resistance to humans. We conducted an observational study to evaluate antibiotic-resistant Escherichia coli populations from poultry and humans in rural northwestern Esmeraldas, Ecuador. Our study site is a remote region with historically low resistance levels of third-generation antibiotics such cefotaxime (CTX), a clinically relevant antibiotic, in both poultry and humans. Our study revealed 1) high CTX resistance (66.1%) in farmed broiler chickens, 2) an increase in CTX resistance over time in backyard chicken not fed antibiotics (2.3-17.9%), and 3) identical bla _CTX-M sequences from human and chicken bacteria, suggesting a spillover event. These findings provide evidence that small-scale meat production operations have direct impacts on the spread and selection of clinically important antibiotics among underdeveloped settings.

Impacts of small-scale chicken farming activity on antimicrobial-resistant Escherichia coli carriage in backyard chickens and children in rural Ecuador

The emergence, spread, and persistence of antimicrobial resistance (AMR) remains a pressing global concern. Increased promotion of commercial small-scale agriculture within low-resource settings has facilitated an increased use in antimicrobials as growth promoters globally, creating antimicrobial-resistant animal reservoirs. We conducted a longitudinal field study in rural Ecuador to monitor the AMR of Escherichia coli populations from backyard chickens and children at three sample periods with approximately 2-month intervals (February, April, and June 2017). We assessed AMR to 12 antibiotics using generalized linear mixed effects models (GLMM). We also sampled and assessed AMR to the same 12 antibiotics in one-day-old broiler chickens purchased from local venders. One-day-old broiler chickens showed lower AMR at sample period 1 compared to sample period 2 (for 9 of the 12 antibiotics tested); increases in AMR between sample periods 2 and 3 were minimal. Two months prior to the first sample period (December 2016) there was no broiler farming activity due to a regional collapse followed by a peak in annual farming in February 2017. Between sample periods 1 and 2, we observed significant increases in AMR to 6 of the 12 antibiotics in children and to 4 of the 12 antibiotics in backyard chickens. These findings suggest that the recent increase in farming, and the observed increase of AMR in the one-day old broilers, may have caused the increase in AMR in backyard chickens and children. Small-scale farming dynamics could play an important role in the spread of AMR in low- and middle-income countries.

Antibiotic resistance genes and bacterial communities in cornfield and pasture soils receiving swine and dairy manures

Land application of animal manure could change the profiles of antibiotic resistant bacteria (ARB), antibiotic resistance genes (ARGs) and bacterial communities in receiving soils. Using high-throughput real-time quantitative PCR and 16S rRNA amplicon sequencing techniques, this study investigated the ARGs and bacterial communities in field soils under various crop (corn and pasture) and manure (swine and dairy) managements, which were compared with those of two non-manured reference soils from adjacent golf course and grassland. In total 89 unique ARG subtypes were found in the soil samples and they conferred resistance via efflux pump, cellular protection and antibiotic deactivation. Compared to the ARGs in the golf course and grassland soils (28 and 34 subtypes respectively), manured soils generally had greater ARG diversity (36-55 subtypes). Cornfield soil frequently receiving raw swine manure had the greatest ARG abundance. The short-term (one week) application of composted and liquid swine manures increased the diversity and total abundance of ARGs in cornfield soils. Intriguingly the composted swine manure only marginally increased the total abundance of ARGs, but substantially increased the number of ARG subtypes in the cornfield soils. The network analysis revealed three major network modules in the co-occurrence patterns of ARG subtypes, and the hubs of these major modules (intl1-1, vanC, and pncA) may be candidates for selecting indicator genes for surveillance of ARGs in manured soils. The network analyses between ARGs and bacteria taxa revealed the potential host bacteria for the detected ARGs (e.g., aminoglycoside resistance gene aacC4 may be mainly carried by Acidobacteriaceae). Overall, this study highlighted the potentially varying impact of various manure management on antibiotic resistome and microbiome in cornfield and pasture soils.