Gene flow, mobile genetic elements and the recruitment of antibiotic resistance genes into Gram-negative pathogens

From genome structure to function: insights into structural variation in microbiology

Structural variation in bacterial genomes is an important evolutionary driver. Genomic rearrangements, such as inversions, duplications, and insertions, can regulate gene expression and promote niche adaptation. Importantly, many of these variations are reversible and preprogrammed to generate heterogeneity. While many tools have been developed to detect structural variation in eukaryotic genomes, variation in bacterial genomes and metagenomes remains understudied. However, recent advances in genome sequencing technology and the development of new bioinformatic pipelines hold promise in further understanding microbial genomics.

Exploration of the presence and abundance of multidrug resistance efflux genes in oil and gas environments

As sequencing technology improves and the cost of metagenome sequencing decreases, the number of sequenced environments increases. These metagenomes provide a wealth of data in the form of annotated and unannotated genes. The role of multidrug resistance efflux pumps (MDREPs) is the removal of antibiotics, biocides and toxic metabolites created during aromatic hydrocarbon metabolism. Due to their naturally occurring role in hydrocarbon metabolism and their role in biocide tolerance, MDREP genes are of particular importance for the protection of pipeline assets. However, the heterogeneity of MDREP genes creates a challenge during annotation and detection. Here we use a selection of primers designed to target MDREPs in six pure species and apply them to publicly available metagenomes associated with oil and gas environments. Using in silico PCR with relaxed primer binding conditions we probed the metagenomes of a shale reservoir, a heavy oil tailings pond, a civil wastewater treatment, two marine sediments exposed to hydrocarbons following the Deepwater Horizon oil spill and a non-exposed marine sediment to assess the presence and abundance of MDREP genes. Through relaxed primer binding conditions during in silico PCR, the prevalence of MDREPs was determined. The percentage of nucleotide sequences identified by the MDREP primers was partially augmented by exposure to hydrocarbons in marine sediment and in shale reservoir compared to hydrocarbon-free marine sediments while tailings ponds and wastewater had the highest percentages. We believe this approach lays the groundwork for a supervised method of identifying poorly conserved genes within metagenomes.

Characterization of toxin-antitoxin systems from public sequencing data: A case study in Pseudomonas aeruginosa

The toxin-antitoxin (TA) system is a widely distributed group of genetic modules that play important roles in the life of prokaryotes, with mobile genetic elements (MGEs) contributing to the dissemination of antibiotic resistance gene (ARG). The diversity and richness of TA systems in Pseudomonas aeruginosa, as one of the bacterial species with ARGs, have not yet been completely demonstrated. In this study, we explored the TA systems from the public genomic sequencing data and genome sequences. A small scale of genomic sequencing data in 281 isolates was selected from the NCBI SRA database, reassembling the genomes of these isolates led to the findings of abundant TA homologs. Furthermore, remapping these identified TA modules on 5,437 genome/draft genomes uncovers a great diversity of TA modules in P. aeruginosa. Moreover, manual inspection revealed several TA systems that were not yet reported in P. aeruginosa including the hok-sok, cptA-cptB, cbeA-cbtA, tomB-hha, and ryeA-sdsR. Additional annotation revealed that a large number of MGEs were closely distributed with TA. Also, 16% of ARGs are located relatively close to TA. Our work confirmed a wealth of TA genes in the unexplored P. aeruginosa pan-genomes, expanded the knowledge on P. aeruginosa, and provided methodological tips on large-scale data mining for future studies. The co-occurrence of MGE, ARG, and TA may indicate a potential interaction in their dissemination.

High Prevalence of Beta-Lactam-Resistant Escherichia coli in South Australian Grey-Headed Flying Fox Pups (Pteropus poliocephalus)

The emergence of antimicrobial-resistant Escherichia coli in wildlife is concerning-especially resistance to clinically important beta-lactam antibiotics. Wildlife in closer proximity to humans, including in captivity and in rescue/rehabilitation centres, typically have a higher prevalence of antimicrobial-resistant E. coli compared to their free-living counterparts. Each year, several thousand Australian fruit bat pups, including the grey-headed flying fox (GHFF; Pteropus poliocephalus), require rescuing and are taken into care by wildlife rescue and rehabilitation groups. To determine the prevalence of beta-lactam-resistant E. coli in rescued GHFF pups from South Australia, faecal samples were collected from 53 pups in care. A combination of selective culture, PCR, antimicrobial susceptibility testing, whole-genome sequencing, and phylogenetic analysis was used to identify and genetically characterise beta-lactam-resistant E. coli isolates. The prevalence of amoxicillin-, amoxicillin-plus-clavulanic-acid-, and cephalosporin-resistant E. coli in the 53 pups was 77.4% (n = 41), 24.5% (n = 13), and 11.3% (n = 6), respectively. GHFF beta-lactam-resistant E. coli also carried resistance genes to aminoglycosides, trimethoprim plus sulphonamide, and tetracyclines in 37.7% (n = 20), 35.8% (n = 19), and 26.4% (n = 14) of the 53 GHFF pups, respectively, and 50.9% (n = 27) of pups carried multidrug-resistant E. coli. Twelve E. coli strain types were identified from the 53 pups, with six strains having extraintestinal pathogenic traits, indicating that they have the potential to cause blood, lung, or wound infections in GHFFs. Two lineages-E. coli ST963 and ST58 O8:H25-were associated with human extraintestinal infections. Phylogenetic analyses determined that all 12 strains were lineages associated with humans and/or domestic animals. This study demonstrates high transmission of anthropogenic-associated beta-lactam-resistant E. coli to GHFF pups entering care. Importantly, we identified potential health risks to GHFF pups and zoonotic risks for their carers, highlighting the need for improved antibiotic stewardship and biosafety measures for GHFF pups entering care.

Dispersal of antibiotic resistance genes in an agricultural influenced multi-branch river network

Rivers in agricultural regions serve as an important sink for livestock and poultry farm runoff, fertilizer runoff, and country living sewage, which could bring antibiotic resistance genes (ARGs) contaminations. However, the diversity and distribution of ARGs has not been well documented in the agricultural influenced river. Here, the diversity of ARGs, and their relationship with biochemical factors were determined in the surface water in an agricultural region of the Jialing River and its five rural branches. The 218 unique ARGs encoding resistance to eight major antibiotic classes have been detected using high-throughput quantitative PCR. The branches of the river had a remarkably higher abundance of ARGs than the mainstream. The aminoglycoside, beta_Lactamase, MLSB, and Multidrug resistance genes were significantly enriched in the branches compared to the mainstream. Compared with the mainstream, the ARGs profiles in the branches showed obvious higher spatial variability. Significant correlation between ARGs profiles and bacterial community structures were observed, and network analysis further showed that the ARGs were associated with their potential hosts, such as Ottowia and Novosphingobium. Redundancy discrimination analysis revealed that Cu content has a significant contribution to the increase of ARGs in the river. The microbial diversity index was negatively correlated with the abundance of the ARGs. These results provide evidence for the enrichment of ARGs in the agricultural influenced river and branches due to the joint influence of chemical and microbial variables.

Antimicrobial Resistance Monitoring of Water Environments: A Framework for Standardized Methods and Quality Control

Antimicrobial resistance (AMR) is a grand societal challenge with important dimensions in the water environment that contribute to its evolution and spread. Environmental monitoring could provide vital information for mitigating the spread of AMR; this includes assessing antibiotic resistance genes (ARGs) circulating among human populations, identifying key hotspots for evolution and dissemination of resistance, informing epidemiological and human health risk assessment models, and quantifying removal efficiencies by domestic wastewater infrastructure. However, standardized methods for monitoring AMR in the water environment will be vital to producing the comparable data sets needed to address such questions. Here we sought to establish scientific consensus on a framework for such standardization, evaluating the state of the science and practice of AMR monitoring of wastewater, recycled water, and surface water, through a literature review, survey, and workshop leveraging the expertise of academic, governmental, consulting, and water utility professionals.

Host gut resistome in Gulf War chronic multisymptom illness correlates with persistent inflammation

Chronic multisymptom illness (CMI) affects a subsection of elderly and war Veterans and is associated with systemic inflammation. Here, using a mouse model of CMI and a group of Gulf War (GW) Veterans' with CMI we show the presence of an altered host resistome. Results show that antibiotic resistance genes (ARGs) are significantly altered in the CMI group in both mice and GW Veterans when compared to control. Fecal samples from GW Veterans with persistent CMI show a significant increase of resistance to a wide class of antibiotics and exhibited an array of mobile genetic elements (MGEs) distinct from normal healthy controls. The altered resistome and gene signature is correlated with mouse serum IL-6 levels. Altered resistome in mice also is correlated strongly with intestinal inflammation, decreased synaptic plasticity, reversible with fecal microbiota transplant (FMT). The results reported might help in understanding the risks to treating hospital acquired infections in this population.

Structure-Based Ligand Design Targeting Pseudomonas aeruginosa LpxA in Lipid A Biosynthesis

Enzymes involved in lipid A biosynthesis are promising antibacterial drug targets in Gram-negative bacteria. In this study, we use a structure-based design approach to develop a series of novel tetrazole ligands with low μM affinity for LpxA, the first enzyme in the lipid A pathway. Aided by previous structural data, X-ray crystallography, and surface plasmon resonance bioanalysis, we identify 17 hit compounds. Two of these hits were subsequently modified to optimize interactions with three regions of the LpxA active site. This strategy ultimately led to the discovery of ligand L13, which had a K_D of 3.0 μM. The results reveal new chemical scaffolds as potential LpxA inhibitors, important binding features for ligand optimization, and protein conformational changes in response to ligand binding. Specifically, they show that a tetrazole ring is well-accommodated in a small cleft formed between Met169, the "hydrophobic-ruler" and His156, both of which demonstrate significant conformational flexibility. Furthermore, we find that the acyl-chain binding pocket is the most tractable region of the active site for realizing affinity gains and, along with a neighboring patch of hydrophobic residues, preferentially binds aliphatic and aromatic groups. The results presented herein provide valuable chemical and structural information for future inhibitor discovery against this important antibacterial drug target.

Accelerated Evolution by Diversity-Generating Retroelements

Diversity-generating retroelements (DGRs) create vast amounts of targeted, functional diversity by facilitating the rapid evolution of ligand-binding protein domains. Thousands of DGRs have been identified in bacteria, archaea, and their respective viruses. They are broadly distributed throughout the microbial world, with enrichment observed in certain taxa and environments. The diversification machinery works through a novel mechanism termed mutagenic retrohoming, whereby nucleotide sequence information is copied from an invariant DNA template repeat (TR) into an RNA intermediate, selectively mutagenized at TR adenines during cDNA synthesis by a DGR-encoded reverse transcriptase, and transferred to a variable repeat (VR) region within a variable-protein gene (54). This unidirectional flow of information leaves TR-DNA sequences unmodified, allowing for repeated rounds of mutagenic retrohoming to optimize variable-protein function. DGR target genes are often modular and can encode one or more of a wide variety of discrete functional domains appended to a diversifiable ligand-binding motif. Bacterial variable proteins often localize to cell surfaces, although a subset appear to be cytoplasmic, while phage-encoded DGRs commonly diversify tail fiber-associated receptor-binding proteins. Here, we provide a comprehensive review of the mechanism and consequences of accelerated protein evolution by these unique and beneficial genetic elements. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Plantaricin A, Derived from Lactiplantibacillus plantarum, Reduces the Intrinsic Resistance of Gram-Negative Bacteria to Hydrophobic Antibiotics

The outer membrane of Gram-negative bacteria is one of the major factors contributing to the development of antibiotic resistance, resulting in a lack of effectiveness of several hydrophobic antibiotics. Plantaricin A (PlnA) intensifies the potency of antibiotics by increasing the permeability of the bacterial outer membrane. Moreover, it has been proven to bind to the lipopolysaccharide of Escherichia coli via electrostatic and hydrophobic interactions and to interfere with the integrity of the bacterial outer membrane. Based on this mechanism, we designed a series of PlnA1 analogs by changing the structure, hydrophobicity, and charge to enhance their membrane-permeabilizing ability. Subsequent analyses revealed that among the PlnA1 analogs, OP4 demonstrated the highest penetrating ability, weaker cytotoxicity, and a higher therapeutic index. In addition, it decelerated the development of antibiotic resistance when the E. coli cells were continuously exposed to sublethal concentrations of erythromycin and ciprofloxacin for 30 generations. Further in vivo studies in mice with sepsis showed that OP4 heightens the potency of erythromycin against E. coli and relieves inflammation. In summary, our results showed that the PlnA1 analogs investigated in the present study, especially OP4, reduce the intrinsic antibiotic resistance of Gram-negative pathogens and expand the antibiotic sensitivity spectrum of hydrophobic antibiotics in Gram-negative bacteria. IMPORTANCE Antibiotic resistance is a global health concern due to indiscriminate use of antibiotics, resistance transfer, and intrinsic resistance of certain Gram-negative bacteria. The asymmetric bacterial outer membrane prevents the entry of hydrophobic antibiotics and renders them ineffective. Consequently, these antibiotics could be employed to treat infections caused by Gram-negative bacteria, after increasing their outer membrane permeability. As PlnA reportedly penetrates outer membranes, we designed a series of PlnA1 analogs and proved that OP4, one of these antimicrobial peptides, effectively augmented the permeability of the bacterial outer membrane. Furthermore, OP4 effectively improved the potency of erythromycin and alleviated inflammatory responses caused by Escherichia coli infection. Likewise, OP4 curtailed antibiotic resistance development in E. coli, thereby prolonging exposure to sublethal antibiotic concentrations. Thus, the combined use of hydrophobic antibiotics and OP4 could be used to treat infections caused by Gram-negative bacteria by decreasing their intrinsic antibiotic resistance.

Microbial Resistance to Antibiotics and Effective Antibiotherapy

Currently, the efficacy of antibiotics is severely affected by the emergence of the antimicrobial resistance phenomenon, leading to increased morbidity and mortality worldwide. Multidrug-resistant pathogens are found not only in hospital settings, but also in the community, and are considered one of the biggest public health concerns. The main mechanisms by which bacteria develop resistance to antibiotics include changes in the drug target, prevention of entering the cell, elimination through efflux pumps or inactivation of drugs. A better understanding and prediction of resistance patterns of a pathogen will lead to a better selection of active antibiotics for the treatment of multidrug-resistant infections.

Deciphering the extracellular and intracellular antibiotic resistance genes in multiple environments reveals the persistence of extracellular ones

The extracellular and intracellular antibiotic resistance genes (eARGs and iARGs) together constitute the entire resistome in environments. However, the systematic analysis of eARGs and iARGs was still inadequate. Three kinds of environments, i.e., livestock manure, sewage sludge, and lake sediment, were analyzed to reveal the comprehensive characteristics of eARGs and iARGs. Based on the metagenomic data, the diversities, relative abundances, and compositions of eARGs and iARGs were similar. The extracellular and intracellular integrons and insertion sequences (ISs) also did not show any significant differences. However, the degree and significance of the correlation between total relative abundances of integrons/ISs and ARGs were lower outside than inside the cells. Gene cassettes carried by class 1 integron were amplified in manure and sludge samples, and sequencing results showed that the identified ARGs extracellularly and intracellularly were distinct. By analyzing the genetic contexts, most ARGs were found located on chromosomes. Nevertheless, the proportion of ARGs carried by plasmids increased extracellularly. qPCR was employed to quantify the absolute abundances of sul1, sul2, tetO, and tetW, and their extracellular proportions were found highest in sludge samples. These findings together raised the requirements of considering eARGs and iARGs separately in terms of risk evaluation and removal management.

Intra- and interpopulation transposition of mobile genetic elements driven by antibiotic selection

The spread of genes encoding antibiotic resistance is often mediated by horizontal gene transfer (HGT). Many of these genes are associated with transposons, a type of mobile genetic element that can translocate between the chromosome and plasmids. It is widely accepted that the translocation of antibiotic resistance genes onto plasmids potentiates their spread by HGT. However, it is unclear how this process is modulated by environmental factors, especially antibiotic treatment. To address this issue, we asked whether antibiotic exposure would select for the transposition of resistance genes from chromosomes onto plasmids and, if so, whether antibiotic concentration could tune the distribution of resistance genes between chromosomes and plasmids. We addressed these questions by analysing the transposition dynamics of synthetic and natural transposons that encode resistance to different antibiotics. We found that stronger antibiotic selection leads to a higher fraction of cells carrying the resistance on plasmids because the increased copy number of resistance genes on multicopy plasmids leads to higher expression of those genes and thus higher cell survival when facing antibiotic selection. Once they have transposed to plasmids, antibiotic resistance genes are primed for rapid spread by HGT. Our results provide quantitative evidence for a mechanism by which antibiotic selection accelerates the spread of antibiotic resistance in microbial communities.

HopE and HopD Porin-Mediated Drug Influx Contributes to Intrinsic Antimicrobial Susceptibility and Inhibits Streptomycin Resistance Acquisition by Natural Transformation in Helicobacter pylori

Helicobacter pylori is a human pathogen competent for natural transformation. Intrinsic and acquired antibiotic resistance contribute to the survival and multiplication of H. pylori under antibiotics. While drug-resistance dissemination by natural transformation (NT)-mediated horizontal gene transfer remains poorly understood in H. pylori. The purpose of the study was to investigate the role of H. pylori porins (HopA, HopB, HopC, HopD, and HopE) in the intrinsic antibiotic resistance and to preliminarily reveal the potential effect of HopE and HopD porins in streptomycin resistance acquisition after NT in the presence of antibiotics. Using traditional antibiotic susceptibility tests and growth curve analysis, we found the MIC values of metronidazole, clarithromycin, levofloxacin, tetracycline, rifampin, and streptomycin in mutants lacking HopE and/or HopD were significantly elevated compare to those in wild-type strain. The quantitative analysis of the tetramethyl rhodamine isothiocyanate (TRITC)-labeled streptomycin accumulation at the single-cell level showed reduced streptomycin intracellular fluorescence in ΔhopE and ΔhopD mutant cells. Furthermore, in the presence of translation-inhibiting antibiotic streptomycin, the resistance acquisition frequency was decreased in the wild-type strain, which could be reversed by mutants lacking HopE and HopD that restored relatively high resistance acquisition frequencies. By transforming a pUC19-rpsLmut-sfgfp linear plasmid carrying a streptomycin conferring mutation, we observed that the impaired ability of rpsLmut synthesis in the wild-type strain was restored in the ΔhopE and ΔhopD mutant transformants. Our study revealed that in the presence of streptomycin, resistance acquisition at least partially relied on the deletion of the hopE and hopD genes, because their loss reduced streptomycin concentration in the cell and thus restored the expression of the resistance-conferring gene, which was inhibited by streptomycin in wild-type strain. The loss of HopE and HopD influx activity may also preserve resistance acquisition by transformation in the presence of antibiotics with other modes of action. IMPORTANCE Helicobacter pylori is constitutively competent for natural transformation (NT) and possesses an efficient system for homologous recombination, which could be utilized to study the NT-mediated horizontal gene transfer induced antibiotic resistance acquisition. Bacterial porins have drawn renewed attention because of their crucial role in antibiotic susceptibility. From the perspective of porin-mediated influx in H. pylori, our study preliminarily revealed the important role of HopE and HopD porins not only in preserving the intrinsic susceptibility to specific antibiotic but also in evading acquired antibiotic resistance by NT in the presence of translation-inhibiting antimicrobial. Therefore, the loss of HopE or HopD porin in H. pylori genomes, combined with the large number of secreted or cell-free genetic elements carrying mutations conferring antibiotic resistance, may raise the possibility that this mechanism plays a potential role in the propagation of antibiotic resistance within H. pylori communities.

The High Risk of Bivalve Farming in Coastal Areas With Heavy Metal Pollution and Antibiotic-Resistant Bacteria: A Chilean Perspective

Anthropogenic pollution has a huge impact on the water quality of marine ecosystems. Heavy metals and antibiotics are anthropogenic stressors that have a major effect on the health of the marine organisms. Although heavy metals are also associate with volcanic eruptions, wind erosion or evaporation, most of them come from industrial and urban waste. Such contamination, coupled to the use and subsequent misuse of antimicrobials in aquatic environments, is an important stress factor capable of affecting the marine communities in the ecosystem. Bivalves are important ecological components of the oceanic environments and can bioaccumulate pollutants during their feeding through water filtration, acting as environmental sentinels. However, heavy metals and antibiotics pollution can affect several of their physiologic and immunological processes, including their microbiome. In fact, heavy metals and antibiotics have the potential to select resistance genes in bacteria, including those that are part of the microbiota of bivalves, such as Vibrio spp. Worryingly, antibiotic-resistant phenotypes have been shown to be more tolerant to heavy metals, and vice versa, which probably occurs through co- and cross-resistance pathways. In this regard, a crucial role of heavy metal resistance genes in the spread of mobile element-mediated antibiotic resistance has been suggested. Thus, it might be expected that antibiotic resistance of Vibrio spp. associated with bivalves would be higher in contaminated environments. In this review, we focused on co-occurrence of heavy metal and antibiotic resistance in Vibrio spp. In addition, we explore the Chilean situation with respect to the contaminants described above, focusing on the main bivalves-producing region for human consumption, considering bivalves as potential vehicles of antibiotic resistance genes to humans through the ingestion of contaminated seafood.

Prevalent and highly mobile antibiotic resistance genes in commercial organic fertilizers

Compost-based organic fertilizers made from animal manures may contain high levels of antibiotic resistance genes (ARGs). However, the factors affecting the abundance and profile of ARGs in organic fertilizers remain unclear. We conducted a national-wide survey in China to investigate the effect of material type and composting process on ARG abundance in commercial organic fertilizers and quantified the contributions of bacterial composition and mobile genetic elements (MGEs) to the structuring of ARGs, using quantitative PCR and Illumina sequencing of 16S rRNA gene amplicons. The tetracycline, sulfonamide, aminoglycoside and macrolide resistance genes were present at high levels in all organic fertilizers. Seven ARGs that confer resistance to clinically important antibiotics, including three β-lactam resistance genes, three quinolone resistance genes and the colistin resistance gene mcr-1, were detected in 8 - 50% the compost samples, whereas the vancomycin resistance gene vanC was not detected. Raw material type had a significant (p < 0.001) effect on the ARG abundance, with composts made from animal feces except some cattle feces generally having higher loads of ARGs than those from non-animal raw materials. Composting process type showed no significant (p > 0.05) effect on ARG abundance in the organic fertilizers. MGEs exerted a greater influence on ARG composition than bacterial community, suggesting a strong mobility of ARGs in the organic fertilizers. Our study highlights the need to manage the risk of ARG dissemination from agricultural wastes.

HAM-ART: An optimised culture-free Hi-C metagenomics pipeline for tracking antimicrobial resistance genes in complex microbial communities

Shotgun metagenomics is a powerful tool to identify antimicrobial resistance (AMR) genes in microbiomes but has the limitation that extrachromosomal DNA, such as plasmids, cannot be linked with the host bacterial chromosome. Here we present a comprehensive laboratory and bioinformatics pipeline HAM-ART (Hi-C Assisted Metagenomics for Antimicrobial Resistance Tracking) optimised for the generation of metagenome-assembled genomes including both chromosomal and extrachromosomal AMR genes. We demonstrate the performance of the pipeline in a study comparing 100 pig faecal microbiomes from low- and high-antimicrobial use pig farms (organic and conventional farms). We found significant differences in the distribution of AMR genes between low- and high-antimicrobial use farms including a plasmid-borne lincosamide resistance gene exclusive to high-antimicrobial use farms in three species of Lactobacilli. The bioinformatics pipeline code is available at https://github.com/lkalmar/HAM-ART.

Enrofloxacin Promotes Plasmid-Mediated Conjugation Transfer of Fluoroquinolone-Resistance Gene qnrS

This study aimed to determine the effect of enrofloxacin (ENR) on the transfer of the plasmid-mediated quinolone resistance (PMQR) gene qnrS from opportunistic pathogen Escherichia coli (E2) to Salmonella Enteritidis (SE211) and to analyze the resistance characteristics of SE211-qnrS isolates. The plasmid carrying qnrS gene of E2 was sequenced by Oxford Nanopore technology. The plasmid carrying qnrS gene belonged to incompatibility group IncY. In vitro, the transfer experiment of IncY plasmid was performed by the liquid medium conjugation method. The conjugation transfer frequency of the IncY plasmid was 0.008 ± 0.0006 in the absence of ENR, 0.012 ± 0.003 in 1/32 MIC_ENR, 0.01 ± 0.008 in 1/8 MIC_ENR, and 0.03 ± 0.015 (Mean±SD) in 1/2 MIC_ENR, respectively. After inoculation of E. coli E2 and SE211, chickens were treated with different doses of ENR (3.03, 10, and 50 mg/kg b.w.) for 7 days consecutively. To screen the SE211-qnrS strains from intestinal tract of chickens, the resistance genes and susceptibility of isolates were identified. The amount of E. coli E2 and the copy number of qnrS gene in the chicken intestinal tract were determined by colony counting and qPCR, respectively. In vivo, more SE211-qnrS strains were isolated from the treated group compared with the untreated group. SE211-qnrS strains not only obtained IncY plasmid, but also showed similar resistance phenotype as E2. In conclusion, ENR treatment can promote the spread of a IncY-resistance plasmid carrying the qnrS fluoroquinolone-resistance gene in Escherichia coli and the development of drug-resistant bacteria.

Whole-genome sequencing and gene sharing network analysis powered by machine learning identifies antibiotic resistance sharing between animals, humans and environment in livestock farming

Anthropogenic environments such as those created by intensive farming of livestock, have been proposed to provide ideal selection pressure for the emergence of antimicrobial-resistant Escherichia coli bacteria and antimicrobial resistance genes (ARGs) and spread to humans. Here, we performed a longitudinal study in a large-scale commercial poultry farm in China, collecting E. coli isolates from both farm and slaughterhouse; targeting animals, carcasses, workers and their households and environment. By using whole-genome phylogenetic analysis and network analysis based on single nucleotide polymorphisms (SNPs), we found highly interrelated non-pathogenic and pathogenic E. coli strains with phylogenetic intermixing, and a high prevalence of shared multidrug resistance profiles amongst livestock, human and environment. Through an original data processing pipeline which combines omics, machine learning, gene sharing network and mobile genetic elements analysis, we investigated the resistance to 26 different antimicrobials and identified 361 genes associated to antimicrobial resistance (AMR) phenotypes; 58 of these were known AMR-associated genes and 35 were associated to multidrug resistance. We uncovered an extensive network of genes, correlated to AMR phenotypes, shared among livestock, humans, farm and slaughterhouse environments. We also found several human, livestock and environmental isolates sharing closely related mobile genetic elements carrying ARGs across host species and environments. In a scenario where no consensus exists on how antibiotic use in the livestock may affect antibiotic resistance in the human population, our findings provide novel insights into the broader epidemiology of antimicrobial resistance in livestock farming. Moreover, our original data analysis method has the potential to uncover AMR transmission pathways when applied to the study of other pathogens active in other anthropogenic environments characterised by complex interconnections between host species.

Livestock have been suggested as an important source of antimicrobial-resistant (AMR) Escherichia coli, capable of infecting humans and carrying resistance to drugs used in human medicine. China has a large intensive livestock farming industry, poultry being the second most important source of meat in the country, and is the largest user of antibiotics for food production in the world. Here we studied antimicrobial resistance gene overlap between E. coli isolates collected from humans, livestock and their shared environments in a large-scale Chinese poultry farm and associated slaughterhouse. By using a computational approach that integrates machine learning, whole-genome sequencing, gene sharing network and mobile genetic elements analysis we characterized the E. coli community structure, antimicrobial resistance phenotypes and the genetic relatedness of non-pathogenic and pathogenic E. coli strains. We uncovered the network of genes, associated with AMR, shared across host species (animals and workers) and environments (farm and slaughterhouse). Our approach opens up new avenues for the development of a fast, affordable and effective computational solutions that provide novel insights into the broader epidemiology of antimicrobial resistance in livestock farming.

The fate and behavior mechanism of antibiotic resistance genes and microbial communities in anaerobic reactors treating oxytetracycline manufacturing wastewater

In this study, two parallel-operated expanded granular sludge bed (EGSB) reactors, one used to treat oxytetracycline (OTC) manufacturing wastewater with gradual increase of OTC concentration as experimental reactor and the other fed with the same wastewater without OTC as control reactor, were operated to investigate the behavior of antibiotics resistance genes (ARGs) and mobile genetic elements (MGEs) and their possible relationships with bacterial community among influent, sludge and effluent environments. Though the average absolute abundance of ARGs slightly decreased (0.26 - log), the ARGs' relative abundance normalized to 16S-rRNA gene copy numbers showed a significant upward trend in effluent (2 multiples - increase) and the absolute and relative abundances both extremely increased in anaerobic sludge, indicating that anaerobic treatment process cannot reduce ARGs efficiently, inversely can increase the risk of ARGs through the proliferation of antibiotics resistance bacteria (ARB) under the suppression of OTC. MGEs, bacterial communities and OTC concentration mainly impacted the ARGs profiles, which contributed 88.4% to the variation of ARGs. The differences and correlations of hosts in influent, effluent and sludge were further confirmed by network analysis. Overall, this study enhanced the understanding of the prevalence and transfer of ARGs in OTC production effluents during anaerobic treatment.

Comprehensive Analysis of Imipenemase (IMP)-Type Metallo-β-Lactamase: A Global Distribution Threatening Asia

Antibiotic resistance, particularly beta-lactam resistance, is a major problem worldwide. Imipenemase or IMP-type metallo-β-lactamase (MBL) has become a more prominent enzyme, especially in Asia, since it was discovered in the 1990s in Japan. There are currently 88 variants of IMP-type enzymes. The most commonly identified variant of IMP-type enzymes is IMP−1 variant. IMP-type MBLs have been detected in more than ten species in Enterobacterales. Pseudomonas aeruginosa is the most frequent carrier of IMP-type enzymes worldwide. In Asia, IMP-type MBLs have been distributed in many countries. This work investigated a variety of currently available IMP-type MBLs at both a global level and a regional level. Out of 88 variants of IMP-type MBLs reported worldwide, only 32 variants were found to have susceptibility profiles. Most of the bacterial isolates carrying IMP-type MBLs were resistant to Carbapenems, especially Imipenem and Meropenem, followed by the 3rd-generation cephalosporins, and interestingly, monobactams. Our results comprehensively indicated the distribution of IMP-type MBLs in Asia and raised the awareness of the situation of antimicrobial resistance in the region.

Straw return promoted the simultaneous elimination of sulfamethoxazole and related antibiotic resistance genes in the paddy soil

Straw return could provide a natural available carbon source for the soil microorganisms, which might affect the environmental behaviours of organic pollutants. In this study, microcosm system was constructed to investigate the effect of rice straw return on the fate of sulfamethoxazole (SMX) and related antibiotic resistance genes (ARGs). The results showed that straw return (1% of soil dry mass) could accelerate the degradation of SMX via co-metabolism. In the treatment group with rice straw, SMX was rapidly decomposed into small molecular compounds (e.g., (Z)-1-amino-3-oxobut-1-en-1-aminium and benzenesulfinic acid) within the first six days, and SMX was undetectable after 60 days; while for the SMX group without rice straw, 1.3 mg kg^-1 of SMX still remained at the 60th day. Straw return could enhance the relative abundances of Proteobacteria involved in SMX degradation, including Microvirga and Ramlibacter, which co-metabolized SMX via the degradation pathways of mineralizable components and aromatic compound. Furthermore, straw return significantly eliminated the ARGs. After 60 days, the int1 and sul1 abundances of the treatment group with rice straw were less than one-tenth of the SMX group without rice straw. The redundancy and network analysis of bacterial community and environmental factors showed that dissolved organic carbon and bacteria belonged to Proteobacteria and Actinobacteria might play positive roles in eliminating ARGs. Our results demonstrate that straw return could promote the simultaneous elimination of SMX and corresponding ARGs, which provides a promising approach to effectively treat antibiotics and ARGs in the farmland.

Carriage of antibiotic resistant bacteria in endangered and declining Australian pinniped pups

The rapid emergence of antimicrobial resistance (AMR) is a major concern for wildlife and ecosystem health globally. Genetic determinants of AMR have become indicators of anthropogenic pollution due to their greater association with humans and rarer presence in environments less affected by humans. The objective of this study was to determine the distribution and frequency of the class 1 integron, a genetic determinant of AMR, in both the faecal microbiome and in Escherichia coli isolated from neonates of three pinniped species. Australian sea lion (Neophoca cinerea), Australian fur seal (Arctocephalus pusillus doriferus) and long-nosed fur seal (Arctocephalus forsteri) pups from eight breeding colonies along the Southern Australian coast were sampled between 2016-2019. DNA from faecal samples (n = 309) and from E. coli (n = 795) isolated from 884 faecal samples were analysed for class 1 integrons using PCRs targeting the conserved integrase gene (intI) and the gene cassette array. Class 1 integrons were detected in A. p. doriferus and N. cinerea pups sampled at seven of the eight breeding colonies investigated in 4.85% of faecal samples (n = 15) and 4.52% of E. coli isolates (n = 36). Integrons were not detected in any A. forsteri samples. DNA sequencing of the class 1 integron gene cassette array identified diverse genes conferring resistance to four antibiotic classes. The relationship between class 1 integron carriage and the concentration of five trace elements and heavy metals was also investigated, finding no significant association. The results of this study add to the growing evidence of the extent to which antimicrobial resistant bacteria are polluting the marine environment. As AMR determinants are frequently associated with bacterial pathogens, their occurrence suggests that these pinniped species are vulnerable to potential health risks. The implications for individual and population health as a consequence of AMR carriage is a critical component of ongoing health investigations.

Profiling the antibiotic resistome in soils between pristine and human-affected sites on the Tibetan Plateau

With increasing pressure from anthropogenic activity in pristine environments, the comprehensive profiling of antibiotic resistance genes (ARGs) is essential to evaluate the potential risks from human-induced antibiotic resistance in these under-studied places. Here, we characterized the microbial resistome in relatively pristine soil samples collected from four distinct habitats on the Tibetan Plateau, using a Smart chip based high-throughput qPCR approach. We compared these to soils from the same habitats that had been subjected to various anthropogenic activities, including residential sewage discharge, animal farming, atmospheric deposition, and tourism activity. Compared to pristine samples, an average of 23.7% more ARGs were detected in the human-affected soils, and the ARGs enriched in these soils mainly encoded resistances to aminoglycoside and beta-lactam. Of the four habitats studied, soils subjected to animal farming showed the highest risks of ARG enrichment and dissemination. As shown, the number of ARGs enriched (a total of 42), their fold changes (17.6 fold on average), and the co-occurrence complexity between ARGs and mobile genetic elements were all the highest in fecal-polluted soils. As well as antibiotics themselves, heavy metals also influenced ARG distributional patterns in Tibetan environments. However, compared to urban areas, the Tibetan Plateau had a low potential for ARG selection and exhibited low carriage of ARGs by mobile genetic elements, even in environments impacted by humans, suggesting that these ARGs have a limited capacity to disseminate. The present study examined the effects of multiple anthropogenic activities on the soil resistomes in relatively pristine environments.

High prevalence of plasmid-mediated quinolone resistance (PMQR) among E. coli from aquatic environments in Bangladesh

Fluro(quinolones) is an important class of antibiotic used widely in both human and veterinary medicine. Resistance to fluro(quinolones) can be acquired by either chromosomal point mutations or plasmid-mediated quinolone resistance (PMQR). There is a lack of studies on the prevalence of PMQR in organisms from environmental sources in Bangladesh. In this study, we investigated the occurrence of PMQR genes in E. coli from various water sources and analysed associations between multi-drug resistance (MDR) and resistance to extended spectrum β-lactam antibiotics. We analysed 300 E. coli isolates from wastewaters of urban live-bird markets (n = 74) and rural households (n = 80), rural ponds (n = 71) and river water samples (n = 75) during 2017–2018. We isolated E. coli by filtering 100 ml of water samples through a 0.2μm cellulose membrane and incubating on mTEC agar media followed by identification of isolated colonies using biochemical tests. We selected one isolate per sample for detection of PMQR genes by multiplex PCR and tested for antibiotic susceptibility by disc diffusion. Clonal relatedness of PMQR-positive isolates was evaluated by enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR). About 66% (n = 199) of E. coli isolates harbored PMQR-genes, predominantly qnrS (82%, n = 164) followed by aac(6’)-lb-cr (9%, n = 17), oqxAB (7%, n = 13), qnrB (6%, n = 11) and qepA (4%, n = 8). Around 68% (n = 135) of PMQR-positive isolates were MDR and 92% (n = 183) were extended spectrum β-lactamase (ESBL)-producing of which the proportion of positive samples was 87% (n = 159) for bla_CTX-M-1’ 34% (n = 62) for bla_TEM, 9% (n = 16) for bla_OXA-1,bla_OXA-47 and bla_CMY-2, and 2% (n = 4) for bla_SHV. Further, 16% (n = 32) of PMQR-positive isolates were resistant to carbapenems of which 20 isolates carried bla_NDM-1. Class 1 integron (int1) was found in 36% (n = 72) of PMQR-positive E. coli isolates. PMQR genes were significantly associated with ESBL phenotypes (p≤0.001). The presence of several PMQR genes were positively associated with ESBL and carbapenemase encoding genes such as qnrS with bla_CTXM-1 (p<0.001), qnrB with bla_TEM (p<0.001) and bla_OXA-1 (p = 0.005), oqxAB and aac(6’)-lb-cr with bla_SHV and bla_OXA-1 (p<0.001), qnrB with bla_NDM-1 (p<0.001), aac(6’)-lb-cr with bla_OXA-47 (p<0.001) and bla_NDM-1 (p = 0.002). Further, int1 was found to correlate with qnrB (p<0.001) and qepA (p = 0.011). ERIC-PCR profiles allowed identification of 84 of 199 isolates with 85% matching profiles which were further grouped into 33 clusters. Only 5 clusters had isolates (n = 11) with identical ERIC-PCR profiles suggesting that PMQR-positive E. coli isolates are genetically heterogeneous. Overall, PMQR-positive MDR E. coli were widely distributed in aquatic environments of Bangladesh indicating poor wastewater treatment and highlighting the risk of transmission to humans and animals.

Challenges and opportunities for cheat therapy in the control of bacterial infections

Covering: 1999 to 2021Bacterial pathogens can be highly social, communicating and cooperating within multi-cellular groups to make us sick. The requirement for collective action in pathogens presents novel therapeutic avenues that seek to undermine cooperative behavior, what we call here 'cheat therapies'. We review two broad avenues of cheat therapy: first, the introduction of genetically engineered 'cheat' strains (bio-control cheats), and second the chemical induction of 'cheat' behavior in the infecting pathogens (chemical-control cheats). Both genetically engineered and chemically induced cheats can socially exploit the cooperative wildtype infection, reducing pathogen burden and the severity of disease. We review the costs and benefits of cheat therapies, highlighting advantages of evolutionary robustness and also the challenges of low to moderate efficacy, compared to conventional antibiotic treatments. We end with a summary of what we see as the most valuable next steps, focusing on adjuvant treatments and use as alternate therapies for mild, self-resolving infections - allowing the reservation of current and highly effective antibiotics for more critical patient needs.

Increase in antimicrobial resistance in Escherichia coli in food animals between 1980 and 2018 assessed using genomes from public databases

BACKGROUND

Next-generation sequencing has considerably increased the number of genomes available in the public domain. However, efforts to use these genomes for surveillance of antimicrobial resistance have thus far been limited and geographically heterogeneous. We inferred global resistance trends in Escherichia coli in food animals using genomes from public databases.

METHODS

We retrieved 7632 E. coli genomes from public databases (NCBI, PATRIC and EnteroBase) and screened for antimicrobial resistance genes (ARGs) using ResFinder. Selection bias towards resistance, virulence or specific strains was accounted for by screening BioProject descriptions. Temporal trends for MDR, resistance to antimicrobial classes and ARG prevalence were inferred using generalized linear models for all genomes, including those not subjected to selection bias.

RESULTS

MDR increased by 1.6 times between 1980 and 2018, as genomes carried, on average, ARGs conferring resistance to 2.65 antimicrobials in swine, 2.22 in poultry and 1.58 in bovines. Highest resistance levels were observed for tetracyclines (42.2%-69.1%), penicillins (19.4%-47.5%) and streptomycin (28.6%-56.6%). Resistance trends were consistent after accounting for selection bias, although lower mean absolute resistance estimates were associated with genomes not subjected to selection bias (difference of 3.16%±3.58% across years, hosts and antimicrobial classes). We observed an increase in extended-spectrum cephalosporin ARG blaCMY-2 and a progressive substitution of tetB by tetA. Estimates of resistance prevalence inferred from genomes in the public domain were in good agreement with reports from systematic phenotypic surveillance.

CONCLUSIONS

Our analysis illustrates the potential of using the growing volume of genomes in public databases to track AMR trends globally.

Antimicrobial-induced horizontal transfer of antimicrobial resistance genes in bacteria: a mini-review

The emergence and spread of antimicrobial resistance (AMR) among pathogenic bacteria constitute an accelerating crisis for public health. The selective pressures caused by increased use and misuse of antimicrobials in medicine and livestock production have accelerated the overall selection of resistant bacteria. In addition, horizontal gene transfer (HGT) plays an important role in the spread of resistance genes, for example mobilizing reservoirs of AMR from commensal bacteria into pathogenic ones. Antimicrobials, besides antibacterial function, also result in undesirable effects in the microbial populations, including the stimulation of HGT. The main aim of this narrative review was to present an overview of the current knowledge of the impact of antimicrobials on HGT in bacteria, including the effects of transformation, transduction and conjugation, as well as other less well-studied mechanisms of HGT. It is widely accepted that conjugation plays a major role in the spread of AMR in bacteria, and the focus of this review is therefore mainly on the evidence provided that antimicrobial treatment affects this process. Other mechanisms of HGT have so far been deemed less important in this respect; however, recent discoveries suggest their role may be larger than previously thought, and the review provides an update on the rather limited knowledge currently available regarding the impact of antimicrobial treatment on these processes as well. A conclusion from the review is that there is an urgent need to investigate the mechanisms of antimicrobial-induced HGT, since this will be critical for developing new strategies to combat the spread of AMR.

Sourcing Antibiotic-Resistant Escherichia coli in Aquatic Ecosystems: A Combined Laboratory and Field Module

The emergence of antibiotic-resistant bacteria represents a growing threat in aquatic ecosystems. In this combined field and laboratory activity, students will determine whether Escherichia coli, an indicator bacteria species commonly found in aquatic ecosystems, shows signs of resistance to common antibiotics. In addition, students will use molecular biology techniques to identify whether Escherichia coli cells sourced from different hosts (i.e., phylogroups) show different patterns of antibiotic resistance. This activity will help students to gain experience in environmental microbiology, environmental science, molecular biology, and public health. This module is also designed to provide instructors with flexibility to pick and choose activities that best meet the needs of their class or research program.

Microplastics deteriorate the removal efficiency of antibiotic resistance genes during aerobic sludge digestion

Sludge from wastewater treatment plants (WWTPs) is considered to be reservoirs of antibiotic resistance genes (ARGs), which can be efficiently removed by sludge treatment processes, e.g., aerobic sludge digestion. However, recent studies report microplastics, which also accumulate in sludge, may serve as carriers for ARGs. In the presence of microplastics, whether ARGs can still be efficiently destroyed by aerobic sludge digestion remains to be urgently investigated. In this study, the fate of ARGs during aerobic digestion was investigated with and without the addition of three prevalent categories of (i.e., polyvinyl chloride (PVC), polyethylene (PE), and polyethylene terephthalate (PET)). Nine ARGs and class 1 integron-integrase gene (intI1) that represents the horizontal transfer potential of ARGs were tested in this study. Compared with the control, the ARGs removal efficiency decreased by 129.6%, 137.0%, and 227.6% with the presence of PVC, PE, and PET, respectively, although a negligible difference was observed with their solids reduction efficiencies. The abundance of potential bacterial hosts of ARGs and intI1 increased in the reactors with the addition of microplastics, suggesting that microplastics potentially selectively enriched bacterial hosts and promoted the horizontal transfer of ARGs during aerobic sludge digestion. These may have contributed to the deteriorated ARGs removal efficiency. This study demonstrated that microplastics in sludge would decrease the ARGs removal efficiency in aerobic digestion process, potentially leading to more ARGs entering the local environment during sludge disposal or utilization.

Susceptibility to Nisin, Bactofencin, Pediocin and Reuterin of Multidrug Resistant Staphylococcus aureus, Streptococcus dysgalactiae and Streptococcus uberis Causing Bovine Mastitis

Antibiotics are the most effective strategy to prevent and treat intramammary infections. However, their misuse has led to the dissemination of multidrug resistant bacteria (MDR) for both animals and humans. Efforts to develop new alternative strategies to control bacterial infections related to MDR are continuously on the rise. The objective of this study was to evaluate the antimicrobial activity of different bacteriocins and reuterin against MDR Staphylococcus and Streptococcus clinical isolates involved in bovine mastitis. A bacterial collection including S. aureus (n = 19), S. dysgalactiae (n = 17) and S. uberis (n = 19) was assembled for this study. Antibiotic resistance profiles were determined by the disk diffusion method. In addition, sensitivity to bacteriocins and reuterin was evaluated by determining minimum inhibitory concentrations (MIC). A total of 21 strains (37.5%) were MDR. MICs ranged from ≤1.0 μg/mL to ≥100 μg/mL for nisin and 2.0 to ≥250 μg/mL for bactofencin. Reuterin was active against all tested bacteria, and MICs vary between 70 and 560 μg/mL. Interestingly, 20 MDR strains were inhibited by bactofencin at a concentration of ≤250 μg/mL, while 14 were inhibited by nisin at an MIC of ≤100 μg/mL. Pediocin did not show an inhibitory effect.

Characterization and comparison of the microbiomes and resistomes of colostrum from selectively treated dry cows

Professionals in animal agriculture promote prudent use of antimicrobials to address public and animal health concerns, such as reduction of antimicrobial residues and antimicrobial resistance (AMR) in products. Few studies evaluate the effect of selective dry-cow therapy on preservation of the milk microbiome or the profile of AMR genes (the resistome) present at freshening. Our objectives were to characterize and compare the microbiomes and resistomes in the colostrum of cows with low somatic cell count that were treated or not treated with intramammary cephapirin benzathine at dry-off. From a larger parent study, cows on a New York dairy farm eligible for dry-off and with histories of somatic cell counts ≤200,000 cells/mL were enrolled to this study (n = 307). Cows were randomly assigned to receive an intramammary antimicrobial and external teat sealant (ABXTS) or sealant only (TS) at dry-off. Composite colostrum samples taken within 4 h of freshening, and quarter milk samples taken at 1 to 7 d in milk were subjected to aerobic culture. The DNA extraction was performed on colostrum from cows with culture-negative samples (ABXTS = 43; TS = 33). The DNA from cows of the same treatment group and parity were pooled (26 pools; ABXTS = 12; TS = 14) for 16S rRNA metagenomic sequencing. Separately, the resistome was captured using a custom RNA bait library for target-enriched sequencing. Sequencing reads were aligned to taxonomic and AMR databases to characterize the microbiome and resistome, respectively. The R statistical program was used to tabulate abundances and to analyze differences in diversity measures and in composition between treatment groups. In the microbiome, the most abundant phyla were Firmicutes (68%), Proteobacteria (23%), Actinobacteria (4%), and Bacteroidetes (3%). Shannon and richness diversity means were 0.93 and 14.7 for ABXTS and 0.94 and 13.1 for TS, respectively. Using analysis of similarities (ANOSIM), overall microbiome composition was found to be similar between treatment groups at the phylum (ANOSIM R = 0.005), class (ANOSIM R = 0.04), and order (ANOSIM R = -0.04) levels. In the resistome, we identified AMR gene accessions associated with 14 unique mechanisms of resistance across 9 different drug classes in 14 samples (TS = 9, ABXTS = 5). The majority of reads aligned to gene accessions that confer resistance to aminoglycoside (TS = ABXTS each 35% abundance), tetracycline (TS = 22%, ABXTS = 54%), and β-lactam classes (TS = 15%, ABXTS = 12%). Shannon diversity means for AMR class and mechanism, respectively, were 0.66 and 0.69 for TS and 0.19 and 0.19 for ABXTS. Resistome richness diversity means for class and mechanism were 3.1 and 3.4 for TS and 1.4 and 1.4 for ABXTS. Finally, resistome composition was similar between groups at the class (ANOSIM R = -0.20) and mechanism levels (ANOSIM R = 0.01). Although no critical differences were found between treatment groups regarding their microbiome or resistome composition in this study, a larger sample size, deeper sequencing, and additional methodology is needed to identify more subtle differences, such as between lower-abundance features.

Dynamics of integron structures across a wastewater network - Implications to resistance gene transfer

Class 1 and other integrons are common in wastewater networks, often being associated with antibiotic resistance genes (ARGs). However, the importance of different integron structures in ARG transfer within wastewater systems has only been implied, especially between community and hospital sources, among wastewater treatment plant compartments, and in receiving waters. This uncertainty is partly because current clinical class 1 integron qPCR assays (i.e., that target human-impacted structures, i.e., clintI1) poorly delineate clintI1 from non-impacted class 1 integron structures. They also say nothing about their ARG content. To fill these technical gaps, new real-time qPCR assays were developed for "impacted" class 1 structures (called aint1; i.e., anthropogenic class 1 integrons) and empty aint1 structures (i.e., carry no ARGs; called eaint1). The new assays and other integron assays then were used to examine integron dynamics across a wastewater network. 16S metagenomic sequencing also was performed to characterise associated microbiomes. aint1 abundances per bacterial cell were about 10 times greater in hospital wastewaters compared with other compartments, suggesting aint1 enrichment with ARGs in hospital sources. Conversely, the relative abundance of eaint1 structures were over double in recycled activated sludge compared with other compartments, except receiving waters (RAS; ∼30% of RAS class 1 structures did not carry ARGs). Microbiome analysis showed that human-associated bacterial taxa with mobile integrons also differed in RAS and river sediments. Further, class 1 integrons in RAS bacteria appear to have released ARGs, whereas hospital bacteria have accumulated ARGs. Results show that quantifying integron dynamics can help explain where ARG transfer occurs in wastewater networks, and should be considered in future studies on antibiotic resistance in the environment.

Ubiquitous Conjugative Mega-Plasmids of Acinetobacter Species and Their Role in Horizontal Transfer of Multi-Drug Resistance

Conjugative mega-plasmids play a special role in adaptation since they carry a huge number of accessory genes, often allowing the host to develop in new niches. In addition, due to conjugation they are able to effectively spread themselves and participate in the transfer of small mobilizable plasmids. In this work, we present a detailed characterization of a recently discovered family of multiple-drug resistance mega-plasmids of Acinetobacter species, termed group III-4a. We describe the structure of the plasmid backbone region, identify the rep gene and the origin of plasmid replication, and show that plasmids from this group are able not only to move between different Acinetobacter species but also to efficiently mobilize small plasmids containing different mob genes. Furthermore, we show that the population of natural Acinetobacter strains contains a significant number of mega-plasmids and reveal a clear correlation between the living conditions of Acinetobacter strains and the structure of their mega-plasmids. In particular, comparison of the plasmids from environmental and clinical strains shows that the genes for resistance to heavy metals were eliminated in the latter, with the simultaneous accumulation of antibiotic resistance genes by incorporation of transposons and integrons carrying these genes. The results demonstrate that this group of mega-plasmids plays a key role in the dissemination of multi-drug resistance among Acinetobacter species.

Removal of antimicrobial prophylaxis and its effect on swine carriage of antimicrobial-resistant coliforms

The use of antimicrobials in the food animal industry has caused an increased prevalence of antimicrobial-resistant bacteria and antimicrobial resistance genes, which can be transferred to the microbiota of humans through the food chain or the environment. To reduce the development and spread of antimicrobial resistance, restrictions on antimicrobial use in food animals have been implemented in different countries. We investigated the impact of an antimicrobial restriction intervention during two generations of pigs. Fecal samples were collected in five growth phases. The frequency of antimicrobial-resistant coliforms and antimicrobial-resistant bacteria or antimicrobial resistance genes was analyzed. No differences in the richness or abundance of antimicrobial-resistant coliforms or antimicrobial resistance genes were found when animals fed with or without prophylactic antimicrobials were compared. Withholding antimicrobial supplementation did not negatively affect weight gain in pigs. Withdrawal of prophylactic antimicrobial consumption during two generations of pigs was not enough to reduce the prevalence of antimicrobial resistance genes, as measured by richness and abundance markers. This study indicates that the fitness costs associated with bacterial carriage of some antimicrobial resistance genes are low.

Nanopore-based metagenomics analysis reveals prevalence of mobile antibiotic and heavy metal resistome in wastewater

In-depth studies of the microbiome and mobile resistome profile of different environments is central to understanding the role of the environment in antimicrobial resistance (AMR), which is one of the urgent threats to global public health. In this study, we demonstrated the use of a rapid (and easily portable) sequencing approach coupled with user-friendly bioinformatics tools, the MinION (Oxford Nanopore Technologies), on the evaluation of the microbial as well as mobile metal and antibiotic resistome profile of semi-rural wastewater. A total of 20 unique phyla, 43 classes, 227 genera, and 469 species were identified in samples collected from the Amherst Wastewater Treatment Plant, both from primary and secondary treated wastewater. Alpha diversity indices indicated that primary samples were significantly richer and more microbially diverse than secondary samples. A total of 1041 ARGs, 68 MRGs, and 17 MGEs were detected in this study. There were more classes of AMR genes in primary than secondary wastewater, but in both cases multidrug, beta-lactam and peptide AMR predominated. Of note, OXA β-lactamases, some of which are also carbapenemases, were enriched in secondary samples. Metal resistance genes against arsenic, copper, zinc and molybdenum were the dominant MRGs in the majority of the samples. A larger proportion of resistome genes were located in chromosome-derived sequences except for mobilome genes, which were predominantly located in plasmid-derived sequences. Genetic elements related to transposase were the most common MGEs in all samples. Mobile or MGE/plasmid-associated resistome genes that confer resistance to last resort antimicrobials such as carbapenems and colistin were detected in most samples. Worryingly, several of these potentially transferable genes were found to be carried by clinically-relevant hosts including pathogenic bacterial species in the orders Aeromonadales, Clostridiales, Enterobacterales and Pseudomonadales. This study demonstrated that the MinION can be used as a metagenomics approach to evaluate the microbiome, resistome, and mobilome profile of primary and secondary wastewater.

Antibiotics and fecal transfaunation differentially affect microbiota recovery, associations, and antibiotic resistance in lemur guts

BACKGROUND

Antibiotics alter the diversity, structure, and dynamics of host-associated microbial consortia, including via development of antibiotic resistance; however, patterns of recovery from microbial imbalances and methods to mitigate associated negative effects remain poorly understood, particularly outside of human-clinical and model-rodent studies that focus on outcome over process. To improve conceptual understanding of host-microbe symbiosis in more naturalistic contexts, we applied an ecological framework to a non-traditional, strepsirrhine primate model via long-term, multi-faceted study of microbial community structure before, during, and following two experimental manipulations. Specifically, we administered a broad-spectrum antibiotic, either alone or with subsequent fecal transfaunation, to healthy, male ring-tailed lemurs (Lemur catta), then used 16S rRNA and shotgun metagenomic sequencing to longitudinally track the diversity, composition, associations, and resistomes of their gut microbiota both within and across baseline, treatment, and recovery phases.

RESULTS

Antibiotic treatment resulted in a drastic decline in microbial diversity and a dramatic alteration in community composition. Whereas microbial diversity recovered rapidly regardless of experimental group, patterns of microbial community composition reflected long-term instability following treatment with antibiotics alone, a pattern that was attenuated by fecal transfaunation. Covariation analysis revealed that certain taxa dominated bacterial associations, representing potential keystone species in lemur gut microbiota. Antibiotic resistance genes, which were universally present, including in lemurs that had never been administered antibiotics, varied across individuals and treatment groups.

CONCLUSIONS

Long-term, integrated study post antibiotic-induced microbial imbalance revealed differential, metric-dependent evidence of recovery, with beneficial effects of fecal transfaunation on recovering community composition, and potentially negative consequences to lemur resistomes. Beyond providing new perspectives on the dynamics that govern host-associated communities, particularly in the Anthropocene era, our holistic study in an endangered species is a first step in addressing the recent, interdisciplinary calls for greater integration of microbiome science into animal care and conservation.

Water volume influences antibiotic resistomes and microbiomes during fish corpse decomposition

Corpse decomposition may cause serious pollution (e.g., releasing antibiotic resistance genes) to the water environment, thereby threatening public health. However, whether antibiotic resistance genes (ARGs) and microbiomes are affected by different water volumes during carcass decomposition remains unknown. Here, we investigated the effects of large/small water volumes on microbial communities and ARGs during fish cadaver decomposition by 16S rRNA high-throughput sequencing and high-throughput quantitative PCR. The results showed that the large water volume almost eliminated the effects of corpse decomposition on pH, total organic carbon (TOC), and total nitrogen (TN). When the water volume enlarged by 62.5 fold, the relative abundances of some ARGs resisting tetracycline and sulfonamide during carcass decomposition decreased by 217 fold on average, while there was also a mean 5267 fold increase of vancomycin resistance genes. Compared with the control group, the enriched types of ARGs varied between the large and small volume. Water volume, mobile genetic elements, and carcass decomposition were the most important factors affecting ARG profiles. Many opportunistic pathogens (like Bacteroides and Comamonas) were enriched in the corpse group. Bacteroides and Comamonas may be potential hosts of ARGs, indicating the potential for the spread of ARGs to humans by water pathogenic bacteria. This research highlights that the "dilution effect" can contribute to eliminating this adverse effect during corpse decomposition to a certain extent. It may provide references for environmental governance and public health.

High frequency of multidrug-resistant (MDR) Klebsiella pneumoniae harboring several β-lactamase and integron genes collected from several hospitals in the north of Iran

Background

Klebsiella pneumoniae is one of the leading causes of hospital outbreaks worldwide. Also, antibiotic-resistant K. pneumoniae is progressively being involved in invasive infections with high morbidity and mortality. The aim of the current study was to determine antimicrobial susceptibility patterns and the incidence of resistance genes (integron types and β-lactamase-encoded genes) among clinical isolates of K. pneumoniae.

Methods

In this cross-sectional study, a total of 100 clinical samples were obtained from hospitalized patients in three teaching hospitals in the north of Iran, from November 2018 and October 2019. Antimicrobial susceptibility testing was performed using disk agar diffusion test in line with CLSI recommendations. For colistin, minimum inhibitory concentration (MIC) was determined using broth microdilution. Based on antibiogram, multi-drug resistant (MDR) and extensive-drug resistant (XDR) strains were detected. Finally, integron types and β-lactamase resistance genes were identified using polymerase chain reaction technique.

Results

The most and least clinical samples were related to the urine and bronchoalveolar lavage, respectively. Based on the antibiogram results, amikacin and gentamicin exhibited good activity against K. pneumoniae strains in vitro. The high resistance rate (93%) to ampicillin/sulbactam predicts the limited efficacy of this antibiotic, in the hospitals studied. Among all the 100 isolates, the frequency of MDR and XDR phenotypes were 58% and 13%, respectively, while no pan-drug resistant (PDR) strains were found. In the MDR K. pneumoniae strains, the prevalence of bla_SHV, bla_TEM, bla_CTX-M-15, bla_KPC, bla_OXA-48, bla_NDM β-lactamase genes were 91.4%, 82.7%, 79.3%, 29.3%, 36.2% and 6.9%, respectively, however 91.4% of the isolates were carrying intI gene. Class II and III integrons were not detected in any isolates.

Conclusion

The MDR K. pneumoniae is becoming a serious problem in hospitals, with many strains developing resistance to most available antimicrobials. Our results indicate co-presence of a series of β-lactamase and integron types on the MDR strains recovered from hospitalized patients. The increasing rate of these isolates emphasizes the importance of choosing an appropriate antimicrobial regimen based on antibiotic susceptibility pattern.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12941-021-00476-1.

Animal manures application increases the abundances of antibiotic resistance genes in soil-lettuce system associated with shared bacterial distributions

An increasing amount of animal manures is being used in agriculture, and the effect of animal manures application on the abundance of antibiotics resistance genes (ARGs) in soil-plant system has attracted widespread attention. However, the impacts of animal manures application on the various types of bacterial distribution that occur in soil-lettuce system are unclear. To address this topic, the effects of poultry manure, swine manure or chemical fertilizer application on ARG abundance and the distribution of shared bacteria were investigated in this study. In a lettuce pot experiment, 13 ARGs and 2 MGEs were quantified by qPCR, and bacterial communities in the soil, lettuce endosphere and lettuce phyllosphere were analysed by 16S rRNA sequence analysis. The results showed that the application of poultry or swine manure significantly increased ARG abundance in the soil, a result attributed mainly to increases in the abundances of tetG and tetC. The application of poultry manure, swine manure and chemical fertilizer significantly increased ARG abundance in the lettuce endosphere, and tetG abundance was significantly increased in the poultry and swine manure groups. However, animal manures application did not significantly increase ARG abundance in the lettuce phyllosphere. Flavobacteriaceae, Sphingomonadaceae and 11 other bacterial families were the shared bacteria in the soil, lettuce endosphere, and phyllosphere. The Streptomycetaceae and Methylobacteriaceae were significantly positively correlated with intI1 in both the soil and endosphere. Chemical fertilizer application increased both the proportions of Sphingomonadaceae and tetX abundance, which were positively correlated in the endosphere. Comamonadaceae and Flavobacteriaceae were not detected in the lettuce endosphere under swine manure application. Cu was related to Flavobacteriaceae in the lettuce endosphere. Overall, poultry and swine manure application significantly increased ARG abundance in the soil-lettuce system, which might be due to the shared bacterial distribution.

Novel strains of Klebsiella africana and Klebsiella pneumoniae in Australian fruit bats (Pteropus poliocephalus)

Over the past decade human associated multidrug resistant (MDR) and hypervirulent Klebsiella pneumoniae lineages have been increasingly detected in wildlife. This study investigated the occurrence of K. pneumoniae species complex (KpSC) in grey-headed flying foxes (GHFF), an Australian fruit bat. Thirty-nine KpSC isolates were cultured from 275 GHFF faecal samples (14.2%), comprising K. pneumoniae (n = 30), Klebsiella africana (n = 8) and Klebsiella variicola subsp. variicola (n = 1). The majority (79.5%) of isolates belonged to novel sequence types (ST), including two novel K. africana STs. This is the first report of K. africana outside of Africa and in a non-human host. A minority (15.4%) of GHFF KpSC isolates shared STs with human clinical K. pneumoniae strains, of which, none belonged to MDR clonal lineages that cause frequent nosocomial outbreaks, and no isolates were characterised as hypervirulent. The occurrence of KpSC isolates carrying acquired antimicrobial resistance genes in GHFF was low (1.1%), with three K. pneumoniae isolates harbouring both fluoroquinolone and trimethoprim resistance genes. This study indicates that GHFF are not reservoirs for MDR and hypervirulent KpSC strains, but they do carry novel K. africana lineages. Health risks associated with KpSC carriage by GHFF are deemed low for the public and GHFF.

A Preliminary Study of Antibiotic Resistance Genes in Domestic Honey Produced in China

Antibiotic resistance genes (ARGs) are emerging contaminants that pose a health risk to humans worldwide. Little information on ARGs in bee honey is available. This study profiles ARGs in bee honey samples produced in China, the biggest producer in the world. Of 317 known ARGs encoding resistance to 8 classes of antibiotics, 212 were found in collected honey samples by a real-time quantitative polymerase chain reaction approach. Occurrence frequencies of genes providing resistance to FCA (fluoroquinolone, quinolone, florfenicol, chloramphenicol, and amphenicol) and aminoglycosides were 21.0% and 18.5%, respectively. Frequencies of genes encoding efflux pumps were 42.5% and those of destructase genes 36.6%, indicating that these two mechanisms were predominant for resistance. Nine plasmid-mediated quinolone resistance genes were detected. Of the nine transposase genes known to be involved in antibiotic resistance, eight were found in the samples examined, with tnpA-4, tnpA-5, and tnpA-6 being more abundant. The abundance of the transposase genes was associated with genes conferring resistance to tetracyclines (r = 0.648, p < 0.01), macrolide-lincosamide-streptogramin B (r = 0.642, p < 0.01), FCA (r = 0.517, p < 0.01), and aminoglycosides (r = 0.401, 0.01 < p < 0.05). This is the first study on the abundance and diversity of ARGs in Chinese bee honey products. These findings suggest that bee honey may be a significant source of ARGs that might pose threat to public health. Further research is required to collect more samples in diverse geographic regions in China to make a more comprehensive judgment of ARG in bee honey.

Short-term cold stress can reduce the abundance of antibiotic resistance genes in the cecum and feces in a pig model

Comprehensive studies on the effects of cold stress on antibiotic resistance genes (ARGs) in the intestines and feces remain scarce. In this study, pigs were selected as the animal model and divided into a normal temperature group and a 48-h short-term cold stress group. The ARG profiles in fecal, cecal content and cecal mucosa samples were analyzed. The results showed that the normalized abundance of ARGs in the cecal mucosa samples in the cold stress group was significantly higher than that in the normal temperature group, while the normalized ARG abundances in the fecal and cecal content samples were significantly lower than those in the normal temperature group (P < 0.05). The bacterial community composition (especially Firmicutes) was the major driver impacting the ARG profile and accounted for 32.2% of the variation in the ARG profile, followed by metabolites (especially creatinine and oxypurinol) and mobile genetic elements (MGEs) (especially plasmids and insertion elements). And it was found that creatinine and oxypurinol can reduce the abundance of ARGs and Firmicutes in the in vitro experiment. The results indicate that short-term cold stress can reduce the abundance of ARGs in the cecum and feces of pigs, providing reference data for environmental safety.

Antimicrobial Resistance Phenotypes and Genotypes of Escherichia coli Isolates from Broiler Chickens Fed Encapsulated Cinnamaldehyde and Citral

ABSTRACT

This study was conducted to investigate the effects of in-feed encapsulated cinnamaldehyde (CIN) and citral (CIT) alone or in combination on antimicrobial resistance (AMR) phenotypes and genotypes of Escherichia coli isolates recovered from feces of 6-, 16-, 23-, and 27-day-old broiler chickens. The five dietary treatments including the basal diet (negative control [NC]) and the basal diet supplemented with 55 ppm of bacitracin (BAC), 100 ppm of encapsulated CIN, 100 ppm of encapsulated CIT, or 100 ppm each of encapsulated CIN and encapsulated CIT (CIN+CIT). Antimicrobial susceptibility testing of 240 E. coli isolates revealed that the most common resistance was to β-lactams, aminoglycosides, sulfonamides, and tetracycline; however, the prevalence of AMR decreased (P < 0.05) as birds aged. The prevalence of resistance to amoxicillin-clavulanic acid, ceftiofur, ceftriaxone, cefoxitin, gentamicin, and sulfonamide was lower (P < 0.05) in isolates from the CIN or CIN+CIT groups than in isolates from the NC or BAC groups. Whole genome sequencing of 227 of the 240 isolates revealed 26 AMR genes and 19 plasmids, but the prevalence of some AMR genes and the number of plasmids were lower (P < 0.05) in E. coli isolated from CIN or CIN+CIT birds than in isolates from NC or BAC birds. The most prevalent resistance genes were tet(A) (108 isolates), aac(3)-VIa (91 isolates), aadA1 (86 isolates), blaCMY-2 (78 isolates), sul1 (77 isolates), aph(3)-Ib (58 isolates), aph(6)-Id (58 isolates), and sul2 (24 isolates). The numbers of most virulence genes carried by isolates increased (P < 0.05) in chickens from 6 to 27 days of age. The prevalence of E. coli O21:H16 isolates was lower (P < 0.05) in CIN and CIN+CIT, and the colibacillosis-associated multilocus sequence type (ST117) was most prevalent in isolates from 23-day-old chickens. A phylogenetic tree of whole genome sequences revealed a close relationship between 25 of the 227 isolates and human or broiler extraintestinal pathogenic E. coli strains. These findings indicate that AMR and virulence genotypes of E. coli could be modulated by providing encapsulated CIN or CIN+CIT feed supplements, but further investigation is needed to determine the mechanisms of the effects of these supplements.

HIGHLIGHTS

Azithromycin and Ciprofloxacin Can Promote Antibiotic Resistance in Biosolids and Biosolids-Amended Soils

Spread of biosolids-borne antibiotic resistance is a growing public and environmental health concern. Herein, we conducted incubation experiments involving biosolids, which are byproducts of sewage treatment processes, and biosolids-amended soil. Quantitative reverse transcription-PCR (RT-qPCR) was employed to assess responses of select antibiotic resistance genes (ARGs) and mobile elements to environmentally relevant concentrations of two biosolids-borne antibiotics, azithromycin (AZ) and ciprofloxacin (CIP). Additionally, we examined sequence distribution of gyrA (encoding DNA gyrase; site of action of CIP) to assess potential shifts in genotype. Increasing antibiotic concentrations generally increased the transcriptional activities of qnrS (encoding CIP resistance) and ermB and mefE (encoding AZ resistance). The transcriptional activity of intl1, a marker of class 1 integrons, was unaffected by CIP or AZ concentrations, but biosolids amendment increased intl1 activity in the soil by 4 to 5 times, which persisted throughout incubation. While the dominant gyrA sequences found herein were unrelated to known CIP-resistant genotypes, the increasing CIP concentrations significantly decreased the diversity of genes encoding the DNA gyrase A subunit, suggesting changes in microbial community structures. This study suggests that biosolids harbor transcriptionally active ARGs and mobile elements that could survive and spread in biosolids-amended soils. However, more research is warranted to investigate these trends under field conditions. IMPORTANCE Although previous studies have indicated that biosolids may be important spreaders of antibiotics and antibiotic resistance genes (ARGs) in environments, the potential activities of ARGs or their responses to environmental parameters have been understudied. This study highlights that certain biosolids-borne antibiotics can induce transcriptional activities of ARGs and mobile genetic elements in biosolids and biosolids-amended soil, even when present at environmentally relevant concentrations. Furthermore, these antibiotics can alter the structure of microbial populations expressing ARGs. Our findings indicate the bioavailability of the antibiotics in biosolids and provide evidence that biosolids can promote the activities and dissemination of ARGs and mobile genes in biosolids and soils that receive contaminated biosolids, thus, underscoring the importance of investigating anthropogenically induced antibiotic resistance in the environment under real-world scenarios.

Predicting plasmid persistence in microbial communities by coarse-grained modeling

Plasmids are a major type of mobile genetic elements (MGEs) that mediate horizontal gene transfer. The stable maintenance of plasmids plays a critical role in the functions and survival for microbial populations. However, predicting and controlling plasmid persistence and abundance in complex microbial communities remain challenging. Computationally, this challenge arises from the combinatorial explosion associated with the conventional modeling framework. Recently, a plasmid-centric framework (PCF) has been developed to overcome this computational bottleneck. This framework enables the derivation of a simple metric, the persistence potential, to predict plasmid persistence and abundance. Here, we discuss how PCF can be extended to account for plasmid interactions. We also discuss how such model-guided predictions of plasmid fates can benefit from the development of new experimental tools and data-driven computational methods.

Reversing Antibiotic Resistance Caused by Mobile Resistance Genes of High Fitness Cost

The reversibility of antibiotic resistance is theoretically attractive due to the prospect of restoring the clinical potency of antibiotics. It is important to find out the factors that affect the reversibility of antibiotic resistance. Here, an mcr-1-positive multidrug-resistant (MDR) environmental Escherichia coli isolate was successively passaged under four antibiotic-free culture conditions. The relative abundances of multiple antibiotic resistance genes (ARGs) kept decreasing during the successive passages. The linear correlations between abundances of ARGs on the same MDR plasmid reflected that the decay of antibiotic resistance during the passage was mainly due to the elimination of the MDR plasmid (pMCR_W5-6). Colistin-susceptible strains were isolated at the end of the passage. The whole-genome sequencing of two susceptible isolates detected the elimination of the MDR plasmid and deletion of the mcr-1 gene. Deletions of DNA fragments from chromosome and plasmid were closely related to a variety of insertion sequences (ISs). The results of coculture of resistant and susceptible strains at different antibiotic concentrations indicated that the high fitness cost led to the poor stability of mobile ARGs. Strict control of the use of antibiotics can at least reverse the severe antibiotic resistance caused by mobile ARGs of high fitness cost.

IMPORTANCE The dissemination of bacterial antibiotic resistance is a serious threat to human health. The development of new antibiotics faces both economic and technological challenges. The reversibility of antibiotic resistance has become an important issue causing wide concern due to the prospect of restoring the clinical potency of antibiotics. Our study suggests that the high mobility of ARGs of high fitness cost may just reflect their poor stability. Therefore, strict control of the use of antibiotics can at least reverse the severe antibiotic resistance caused by mobile ARGs of high fitness cost. This study brings hope for the possibility of curbing the dissemination of antibiotic resistance.

Black Soldier Fly Larvae Can Effectively Degrade Oxytetracycline Bacterial Residue by Means of the Gut Bacterial Community

Antibiotic bacterial residue is a unique hazardous waste, and its safe and effective disposal has always been a concern of pharmaceutical enterprises. This report presents the effective treatment of hazardous waste-antibiotic bacterial residue-by black soldier fly larvae (larvae), oxytetracycline bacterial residue (OBR), and soya meal with mass ratios of 0:1 (soya), 1:20 (OBRlow), and 1:2 (OBRhigh), which were used as substrates for larval bioconversion. Degradation of OBR and oxytetracycline, the bacterial community, the incidence of antibiotic resistance genes (ARGs) and the bacterial function in the gut were examined. When the larvae were harvested, 70.8, 59.3, and 54.5% of the substrates had been consumed for soya, OBRlow and OBRhigh; 65.9 and 63.3% of the oxytetracycline was degraded effectively in OBRlow and OBRhigh, respectively. The larval bacterial communities were affected by OBR, abundant and various ARGs were discovered in the gut, and metabolism was the major predicted function of the gut. These findings show that OBR can be digested and converted by larvae with gut bacteria, and the larvae can be used as a bioremediation tool for the treatment of hazardous waste. Finally, the abundant ARGs in the gut deserve further attention and consideration in environmental health risk assessments.