Horizontal Transfer Of Antimicrobial Resistance Genes Research Articles

Antibiotic resistance patterns in soils across the Scottish landscape

The environment disseminates antimicrobial-resistance genes; however, it remains challenging to distinguish whether human activities exacerbate antimicrobial resistance or what is natural. Here, we quantified ~300 resistance-related genes in 200+ Scottish soil samples. Location or land use does not explain gene differences, but nutrient levels reduce gene richness. Elevated levels of metals increased gene richness, and selenium increased transposase levels. Rainfall and persistent organic pollutants also increased transposase relative abundance, possibly promoting conditions conducive to the horizontal transfer of antimicrobial-resistance genes. Selenium and polychlorinated biphenyls were primary factors in gene abundance, while polychlorinated biphenyls, polycyclic aromatic hydrocarbons, and pH influenced gene diversity. Polychlorinated biphenyls are derived from anthropogenic activities, highlighting human activities’ potential impact on gene prevalence. This is the first national-scale, high spatial resolution dataset of antimicrobial-resistance genes in Scottish soils and provides a novel resource on which to build future studies.

A global survey of Salmonella plasmids and their associations with antimicrobial resistance.

Plasmids are the primary vector for horizontal transfer of antimicrobial resistance (AMR) within bacterial populations. We applied the MOB-suite, a toolset for reconstructing and typing plasmids, to 150 767 publicly available Salmonella whole-genome sequencing samples covering 1204 distinct serovars to produce a large-scale population survey of plasmids based on the MOB-suite plasmid nomenclature. Reconstruction yielded 183 017 plasmids representing 1044 primary MOB-clusters and 830 potentially novel MOB-clusters. Replicon and relaxase typing were able to type 83.4 and 58 % of plasmids, respectively, compared to 99.9 % for MOB-clusters. Within this work, we developed an approach to characterize the horizonal transfer of MOB-clusters and AMR genes across different serotypes, as well as the diversity of MOB-cluster associations with AMR genes. Aggregating conjugative mobility predictions provided by the MOB-suite and their corresponding serovar entropy demonstrated that non-mobilizable plasmids were associated with fewer serotypes compared to mobilizable or conjugative MOB-clusters. The host-range predictions for MOB-clusters also showed differences between the mobility classes, with mobilizable MOB-clusters accounting for 88.3 % of the multi-phyla (broad-host-range) predictions compared to 3 and 8.6 % for conjugative and non-mobilizable, respectively. A total of 296 (22 %) of identified MOB-clusters were associated with at least one resistance gene, indicating that the majority of Salmonella plasmids are not involved in AMR dissemination. Shannon entropy analysis of horizontal transfer of AMR genes across serovars and MOB-clusters demonstrated that horizonal transfer of genes is higher between serovars compared to transfer between different MOB-clusters. In addition to the population structure characterization based on primary MOB-clusters, we characterized a multi-plasmid outbreak responsible for the global dissemination of bla CMY-2 across different serotypes using higher resolution MOB-suite secondary cluster codes. The plasmid characterization approach developed here can be applied to different organisms to identify plasmids and genes which pose high risks for horizontal transfer.

Deciphering environmental resistome and mobilome risks on the stone monument: A reservoir of antimicrobial resistance genes

Antimicrobial resistance (AMR) in the environment has attracted increasing attention as an emerging global threat to public health. Stone is an essential ecosystem in nature and also an important material for human society, having architectural and aesthetic values. However, little is known about the AMR in stone ecosystems, particularly in the stone monument, where antimicrobials are often applied against biodeterioration. Here, we provide the first detailed metagenomic study of AMR genes across different types of biodeteriorated stone monuments, which revealed abundant and diverse AMR genes conferring resistance to drugs (antibiotics), biocides, and metals. Totally, 132 AMR subtypes belonging to 27 AMR types were detected including copper-, rifampin-, and aminocoumarins-resistance genes, of which diversity was mainly explained by the spatial turnover (replacement of genes between samples) rather than nestedness (loss of nested genes between samples). Source track analysis confirms that stone resistomes are likely driven by anthropogenic activities across stone heritage areas. We also detected various mobile genetic elements (namely mobilome, e.g., prophages, plasmids, and insertion sequences) that could accelerate replication and horizontal transfer of AMR genes. Host-tracking analysis further identified multiple biodeterioration-related bacterial genera such as Pseudonocardia, Sphingmonas, and Streptomyces as the major hosts of resistome. Taken together, these findings highlight that stone microbiota is one of the natural reservoirs of antimicrobial-resistant hazards, and the diverse resistome and mobilome carried by active biodeteriogens may improve their adaptation on stone and even deactivate the antimicrobials applied against biodeterioration. This enhanced knowledge may also provide novel and specific avenues for environmental management and stone heritage protection.

Whole-Genome Sequences of Vibrio Species from Warm-Water Shrimps Imported into Canada: Detection of Genetic Elements Associated with Antimicrobial Resistance and Potential Mobilizing Capacities.

ABSTRACTWe present draft genome sequences of Vibrio species (Vibrio alginolyticus, Vibrio cholerae, and two Vibrio parahaemolyticus strains) that were isolated from warm-water shrimps imported into Canada. All four isolates harbor genetic elements associated with antimicrobial resistance (AMR), including mobile genetic elements that can promote horizontal transfer of AMR genes.

Trans-Regional and Cross-Host Spread of mcr-Carrying Plasmids Revealed by Complete Plasmid Sequences - 44 Countries, 1998-2020.

BackgroundThe surveillance of antimicrobial resistance genes (ARGs) and bacteria is one critical approach to prevent and control antimicrobial resistance (AMR). Next-generation sequencing (NGS) is a powerful tool in monitoring the emergence and spread of ARGs and resistant bacteria. The horizontal transfer of ARGs across host bacteria mediated by plasmids is a challenge in NGS surveillance for resistance because short-read sequencing can hardly generate the complete plasmid genome sequence, and the correlation between ARGs and plasmids are difficult to determine.MethodsThe complete genome sequences of 455 mcr-carrying plasmids (pMCRs), and the data of their host bacteria and isolation regions were collected from the NCBI database. Genes of Inc types and ARGs were searched for each plasmid. The genome similarity of these plasmids was analyzed by pangenome clustering and genome alignment. ResultsA total of 52 Inc types, including a variety of fusion plasmids containing 2 or more Inc types were identified in these pMCRs and carried by complex host bacteria. The cooccurrence of ARGs in pMCRs was generally observed, with an average of 3.9 ARGs per plasmid. Twenty-two clusters with consistent or highly similar sequences and gene compositions were identified by the pangenome clustering, which were characterized with distributions in different countries/regions, years or host bacteria in each cluster.DiscussionBased on the complete plasmid sequences, distribution of mcr genes in different Inc type plasmids, their co-existence with other AMRs, and transmission of one pMCR across regions and host bacteria can be revealed definitively. Complete plasmid genomes and comparisons in the laboratory network are necessary for spread tracing of ARG-carrying plasmids and risk assessment in AMR surveillance.

Antimicrobial resistance phenotypes and genotypes of Streptococcus suis isolated from clinically healthy pigs from 2017 to 2019 in Jiangxi Province, China.

This study aimed to investigate the antimicrobial resistance (AMR) profiles and genotypes of Streptococcus suis from Jiangxi Province, China. A total of 314 nasal swab samples were collected from clinically healthy pigs, with a positive isolation rate of S. suis of 34·08%. Antimicrobial susceptibility testing showed that more than 80% of the isolates were susceptible to vancomycin, penicillin, minocycline and chloramphenicol. A high frequency of resistance to clindamycin, tetracycline, clarithromycin and erythromycin was observed. All of the isolates were resistant to three or more categories of antimicrobials. The erm(B) and tet(O) served as the most frequent genotypes that contributed to lincosamide, macrolide and tetracycline resistances. A part of macrolide-resistant genotypes could not exhibit specific phenotypes. Finally, integrative and conjugative elements (ICEs) were identified in 28·97% of the isolates. The multidrug resistance of S. suis has widely emerged in Jiangxi Province. The most prevalent resistance genes and genotypes were similar to those in other regions or countries. The presence of ICEs is increasing the risk of horizontal transfer of AMR genes. The findings could provide guidance for the rational use of antimicrobial drugs and be helpful for monitoring the AMR information of S. suis in China.

Mathematical modelling to study the horizontal transfer of antimicrobial resistance genes in bacteria: current state of the field and recommendations.

Antimicrobial resistance (AMR) is one of the greatest public health challenges we are currently facing. To develop effective interventions against this, it is essential to understand the processes behind the spread of AMR. These are partly dependent on the dynamics of horizontal transfer of resistance genes between bacteria, which can occur by conjugation (direct contact), transformation (uptake from the environment) or transduction (mediated by bacteriophages). Mathematical modelling is a powerful tool to investigate the dynamics of AMR; however, the extent of its use to study the horizontal transfer of AMR genes is currently unclear. In this systematic review, we searched for mathematical modelling studies that focused on horizontal transfer of AMR genes. We compared their aims and methods using a list of predetermined criteria and used our results to assess the current state of this research field. Of the 43 studies we identified, most focused on the transfer of single genes by conjugation in Escherichia coli in culture and its impact on the bacterial evolutionary dynamics. Our findings highlight the existence of an important research gap in the dynamics of transformation and transduction and the overall public health implications of horizontal transfer of AMR genes. To further develop this field and improve our ability to control AMR, it is essential that we clarify the structural complexity required to study the dynamics of horizontal gene transfer, which will require cooperation between microbiologists and modellers.

Petrol and diesel exhaust particles accelerate the horizontal transfer of plasmid-mediated antimicrobial resistance genes

Particles exhausted from petrol and diesel consumptions are major components of urban air pollution that can be exposed to human via direct inhalation or other routes due to atmospheric deposition into water and soil. Antimicrobial resistance is one of the most serious threats to modern health care. However, how the petrol and diesel exhaust particles affect the development and spread of antimicrobial resistance genes (ARGs) in various environments remain largely unknown. This study investigated the effects and potential mechanisms of four representative petrol and diesel exhaust particles, namely 97 octane petrol, 93 octane petrol, light diesel oil, and marine heavy diesel oil, on the horizontal transfer of ARGs between two opportunistic Escherichia coli (E. coli) strains, E. coli S17-1 (donor) and E. coli K12 (recipient). The results demonstrated that these four representative types of nano-scale particles induced concentration-dependent increases in conjugative transfer rates compared with the controls. The underlying mechanisms involved in the accelerated transfer of ARGs were also identified, including the generation of intracellular reactive oxygen species (ROS) and the consequent induction of oxidative stress, SOS response, changes in cell morphology, and the altered mRNA expression of membrane protein genes and those involved in the promotion of conjugative transfer. The findings provide new evidences and mechanistic insights into the antimicrobial resistance risks posed by petrol and diesel exhaust particles, and highlight the implications and need for stringent strategies on alternative fuels to mitigate air pollution and health risks.

Metagenomic Evidence of the Prevalence and Distribution Patterns of Antimicrobial Resistance Genes in Dairy Agroecosystems.

Antimicrobial resistance (AR) is a global problem with serious implications for public health. AR genes are frequently detected on animal farms, but little is known about their origin and distribution patterns. We hypothesized that AR genes can transfer from animal feces to the environment through manure, and to this end, we characterized and compared the resistomes (collections of AR genes) of animal feces, manure, and soil samples collected from five dairy farms using a metagenomics approach. Resistomes constituted only up to 1% of the total gene content, but were variable by sector and also farm. Broadly, the identified AR genes were associated with 18 antibiotic resistances classes across all samples; however, the most abundant genes were classified under multidrug transporters (44.75%), followed by resistance to vancomycin (12.48%), tetracycline (10.52%), bacitracin (10.43%), beta-lactam resistance (7.12%), and MLS efflux pump (6.86%) antimicrobials. The AR gene profiles were variable between farms. Farm 09 was categorized as a high risk farm, as a greater proportion of AR genes were common to at least three sectors, suggesting possible horizontal transfer of AR genes. Taxonomic characterization of AR genes revealed that a majority of AR genes were associated with the phylum Proteobacteria. Nonetheless, there were several members of Bacteroidetes, particularly Bacteroides genus and several lineages from Firmicutes that carried similar AR genes in different sectors, suggesting a strong potential for horizontal transfer of AR genes between unrelated bacterial hosts in different sectors of the farms. Further studies are required to affirm the horizontal gene transfer mechanisms between microbiomes of different sectors in animal agroecosystems.

Horizontal Transfer of Plasmid-Mediated Cephalosporin Resistance Genes in the Intestine of Houseflies (Musca domestica)

Houseflies are a mechanical vector for various types of bacteria, including antimicrobial-resistant bacteria (ARB). If the intestine of houseflies is a suitable site for the transfer of antimicrobial resistance genes (ARGs), houseflies could also serve as a biological vector for ARB. To clarify whether cephalosporin resistance genes are transferred efficiently in the housefly intestine, we compared with conjugation experiments in vivo (in the intestine) and in vitro by using Escherichia coli with eight combinations of four donor and two recipient strains harboring plasmid-mediated cephalosporin resistance genes and chromosomal-encoded rifampicin resistance genes, respectively. In the in vivo conjugation experiment, houseflies ingested donor strains for 6 hr and then recipient strains for 3 hr, and 24 hr later, the houseflies were surface sterilized and analyzed. In vitro conjugation experiments were conducted using the broth-mating method. In 3/8 combinations, the in vitro transfer frequency (Transconjugants/Donor) was ≥1.3 × 10(-4); the in vivo transfer rates of cephalosporin resistance genes ranged from 2.0 × 10(-4) to 5.7 × 10(-5). Moreover, cephalosporin resistance genes were transferred to other species of enteric bacteria of houseflies such as Achromobacter sp. and Pseudomonas fluorescens. These results suggest that houseflies are not only a mechanical vector for ARB but also a biological vector for the occurrence of new ARB through the horizontal transfer of ARGs in their intestine.