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

Large-scale network analysis captures biological features of bacterial plasmids

Many bacteria can exchange genetic material through horizontal gene transfer (HGT) mediated by plasmids and plasmid-borne transposable elements. Here, we study the population structure and dynamics of over 10,000 bacterial plasmids, by quantifying their genetic similarities and reconstructing a network based on their shared k-mer content. We use a community detection algorithm to assign plasmids into cliques, which correlate with plasmid gene content, bacterial host range, GC content, and existing classifications based on replicon and mobility (MOB) types. Further analysis of plasmid population structure allows us to uncover candidates for yet undescribed replicon genes, and to identify transposable elements as the main drivers of HGT at broad phylogenetic scales. Our work illustrates the potential of network-based analyses of the bacterial 'mobilome' and opens up the prospect of a natural, exhaustive classification framework for bacterial plasmids.

Occurrence of integrons and antibiotic resistance genes in cryoconite and ice of Svalbard, Greenland, and the Caucasus glaciers

The prevalence of integrons and antibiotic resistance genes (ARGs) is a serious threat for public health in the new millennium. Although commonly detected in sites affected by strong anthropogenic pressure, in remote areas their occurrence, dissemination, and transfer to other ecosystems is poorly recognized. Remote sites are considered as a benchmark for human-induced contamination on Earth. For years glaciers were considered pristine, now they are regarded as reservoirs of contaminants, thus studies on contamination of glaciers, which may be released to other ecosystems, are highly needed. Therefore, in this study we evaluated the occurrence and frequency of clinically relevant ARGs and resistance integrons in the genomes of culturable bacteria and class 1 integron-integrase gene copy number in the metagenome of cryoconite, ice and supraglacial gravel collected on two Arctic (South-West Greenland and Svalbard) and two High Mountain (the Caucasus) glaciers. Altogether, 36 strains with intI1 integron-integrase gene were isolated. Presence of class 1 integron-integrase gene was also recorded in metagenomic DNA from all sampling localities. The mean values of relative abundance of intI1 gene varied among samples and ranged from 0.7% in cryoconite from Adishi Glacier (the Caucasus) to 16.3% in cryoconite from Greenland. Moreover, antibiotic-resistant strains were isolated from all regions. Genes conferring resistance to β-lactams (bla_SHV, bla_TEM, bla_OXA, bla_CMY), fluoroquinolones (qepA, qnrC), and chloramphenicol (cat, cmr) were detected in the genomes of bacterial isolates.

Mobile genetic elements associated with carbapenemase genes in South American Enterobacterales

Introduction

Carbapenem resistance in members of order Enterobacterales is a growing public health problem causing high mortality in developing and industrialized countries. Its emergence and rapid propagation worldwide was due to both intercontinental spread of pandemic strains and horizontal dissemination via mobile genetic elements (MGE) such as plasmids and transposons.

Objective

To describe MGE carrying carbapenem resistance genes in Enterobacterales which have been reported in South America.

Search strategy and selection criteria

A search of the literature in English or Spanish published until 2019 in PubMed, Google Scholar, LILACS and SciELO databases was performed for studies of MGE in Enterobacterales reported in South American countries.

Results

Seven South American countries reported MGE related to carbapenemases. Carbapenemase-producing Klebsiella pneumoniae belonging to clonal complex 258 were the most prevalent pathogens reported; others carbapenemase-producing Enterobacterales such as Escherichia coli, Serratia marcescens, and Providencia rettgeri also have been reported. The MGE implicated in the spread of the most prevalent carbapenemase genes are Tn4401 and non-Tn4401 elements for bla_KPC and ISAba125 for bla_NDM, located in different plasmid incompatibility groups, i.e. L/M, A/C, FII and bacterial clones.

Conclusion

This review indicates that, like in other parts of the world, the most commonly reported carbapenemases in Enterobacterales from South America are being disseminated through clones, plasmids, and transposons which have been previously reported in other parts of the world.

Factors Obscuring the Role of E. coli from Domestic Animals in the Global Antimicrobial Resistance Crisis: An Evidence-Based Review

Recent studies have found limited associations between antimicrobial resistance (AMR) in domestic animals (and animal products), and AMR in human clinical settings. These studies have primarily used Escherichia coli, a critically important bacterial species associated with significant human morbidity and mortality. E. coli is found in domestic animals and the environment, and it can be easily transmitted between these compartments. Additionally, the World Health Organization has highlighted E. coli as a "highly relevant and representative indicator of the magnitude and the leading edge of the global antimicrobial resistance (AMR) problem". In this paper, we discuss the weaknesses of current research that aims to link E. coli from domestic animals to the current AMR crisis in humans. Fundamental gaps remain in our understanding the complexities of E. coli population genetics and the magnitude of phenomena such as horizontal gene transfer (HGT) or DNA rearrangements (transposition and recombination). The dynamic and intricate interplay between bacterial clones, plasmids, transposons, and genes likely blur the evidence of AMR transmission from E. coli in domestic animals to human microbiota and vice versa. We describe key factors that are frequently neglected when carrying out studies of AMR sources and transmission dynamics.

Genomic Characterization of Escherichia coli Isolates Belonging to a New Hybrid aEPEC/ExPEC Pathotype O153:H10-A-ST10 eae-beta1 Occurred in Meat, Poultry, Wildlife and Human Diarrheagenic Samples

Different surveillance studies (2005–2015) in northwest Spain revealed the presence of eae-positive isolates of Escherichia coli O153:H10 in meat for human consumption, poultry farm, wildlife and human diarrheagenic samples. The aim of this study was to explore the genetic and genomic relatedness between human and animal/meat isolates, as well as the mechanism of its persistence. We also wanted to know whether it was a geographically restricted lineage, or whether it was also reported elsewhere. Conventional typing showed that 32 isolates were O153:H10-A-ST10 fimH54, fimAv_MT78, traT and eae-beta1. Amongst these, 21 were CTX-M-32 or SHV-12 producers. The PFGE XbaI-macrorestriction comparison showed high similarity (>85%). The plasmidome analysis revealed a stable combination of IncF (F2:A-:B-), IncI1 (STunknown) and IncX1 plasmid types, together with non-conjugative Col-like plasmids. The core genome investigation based on the cgMLST scheme from EnteroBase proved close relatedness between isolates of human and animal origin. Our results demonstrate that a hybrid MDR aEPEC/ExPEC of the clonal group O153:H10-A-ST10 (CH11-54) is circulating in our region within different hosts, including wildlife. It seems implicated in human diarrhea via meat transmission, and in the spreading of ESBL genes (mainly of CTX-M-32 type). We found genomic evidence of a related hybrid aEPEC/ExPEC in at least one other country.

Behavior of last resort antibiotic resistance genes (mcr-1 and blaNDM-1) in a drinking water supply system and their possible acquisition by the mouse gut flora

Mcr-1 and bla_NDM-1 antibiotic resistance genes (ARGs) confer resistance to colistins and carbapenems, which are often antibiotics used as a last resort in tertiary care hospitals. Dissemination of these two ARGs in drinking water supply systems and their effect on healthy gut bacteria are poorly studied. In this study, the dissemination of mcr-1 and bla_NDM-1 in a drinking water supply system, and their effect on the antibiotic resistance of mouse gut bacteria are explored. Metagenome analysis revealed that source water (Taipu river and Jinze reservoir) was polluted with ARGs. Mcr-1 and bla_NDM-1 can be disseminated through the water distribution system. Even advanced water treatments (ozone and biological activated carbon (BAC)) could not effectively remove mcr-1 and bla_NDM-1. Low concentrations of chloramine disinfectants in the water distribution system were not effective at limiting ARG abundance. Mobile genetic elements were also found to play a major role in the dissemination of ARGs via horizontal gene transfer (HGT) throughout the water supply system. Statistical analysis revealed that there was no effect of temperature on the abundance of mcr-1 and bla_NDM-1 throughout the water supply system. A last resort ARG, mcr-1 can disseminate from drinking water to the healthy mouse gut. The presence of mcr-1 in a strain belonging to Enterococcus hirae, which is different from the strain belonging to the Bacillus cereus group isolated from drinking water, strongly supports the phenomena of HGT inside the gut. This research provides novel insights into the role of drinking water in disseminating ARGs to the gut and strongly suggests that drinking water may also play a major role apart from other factors known to be involved in the prevalence of last resort ARGs in the gut.

Resident microbial communities inhibit growth and antibiotic-resistance evolution of Escherichia coli in human gut microbiome samples

Countering the rise of antibiotic-resistant pathogens requires improved understanding of how resistance emerges and spreads in individual species, which are often embedded in complex microbial communities such as the human gut microbiome. Interactions with other microorganisms in such communities might suppress growth and resistance evolution of individual species (e.g., via resource competition) but could also potentially accelerate resistance evolution via horizontal transfer of resistance genes. It remains unclear how these different effects balance out, partly because it is difficult to observe them directly. Here, we used a gut microcosm approach to quantify the effect of three human gut microbiome communities on growth and resistance evolution of a focal strain of Escherichia coli. We found the resident microbial communities not only suppressed growth and colonisation by focal E. coli but also prevented it from evolving antibiotic resistance upon exposure to a beta-lactam antibiotic. With samples from all three human donors, our focal E. coli strain only evolved antibiotic resistance in the absence of the resident microbial community, even though we found resistance genes, including a highly effective resistance plasmid, in resident microbial communities. We identified physical constraints on plasmid transfer that can explain why our focal strain failed to acquire some of these beneficial resistance genes, and we found some chromosomal resistance mutations were only beneficial in the absence of the resident microbiota. This suggests, depending on in situ gene transfer dynamics, interactions with resident microbiota can inhibit antibiotic-resistance evolution of individual species.

Temporal dynamics of antibiotic resistant genes and their association with the bacterial community in a water-sediment mesocosm under selection by 14 antibiotics

Antibiotics in aquatic environments at high concentrations and sub-inhibitory concentrations potentially select for the evolution of antibiotic resistant genes (ARGs), posing a potential risk to aquatic ecological safety. Our knowledge of the temporal and successive dynamics of ARGs and bacterial community under the selective pressure of antibiotics in natural water-sediment system was limited. This study used a 120-d operating hydrodynamic mesocosm to explore the temporal dynamics of ARGs in water-sediment systems, and the main selective mechanisms following the attenuation and transport of 14 commonly used antibiotics. Under the selective pressures by antibiotics, ARGs propagated transiently, and persisted after antibiotic removal; the bacterial community structures likewise changed. Mantel test and network analysis indicated that ARGs significantly correlated with the bacterial community in the water and surface sediments. Structural equation model (SEM) further revealed that the evolution of ARGs was mainly due to the direct effect of the change in bacterial community and horizontal gene transfer (HGT) via the class 1 integron-integrase gene (intI1), but antibiotics indirectly influenced ARG profiles. The migration of ARGs in deep layer sediments was not related to the bacterial community and intI1, but may be explained by antibiotic selective effects and ARG transformation.

Evolution and distribution of resistance genes and bacterial community in water and biofilm of a simulated fish-duck integrated pond with stress

Integrated fish-duck pond is a common circular farming model in South China, besides, it is also hot-spot for the co-selection of antibiotic resistance genes (ARGs). The aim of this study was to investigate the effects of duck manure, As and cefotaxime on the bacterial community, and the evolution and distribution of ARGs and metal(loid) resistance genes (MRGs) in water and biofilm. Five groups of fish tanks included a control and four test groups. The experimental period lasted for 100 days. Six ARGs (CIT, DHA, EBC, FOX, MOX, TEM), two MRGs (arsB, arsC), and two integron genes (intI1, intI2) were tracked and detected in water and biofilm. The results showed that duck manure brought ARGs and MRGs into fish tanks. Stress factors (cefotaxime, As) increased the relative abundance of resistance genes, and this was positively correlated with stress concentrations. The biofilm was visible significantly at the end of stage 3, and the total relative abundance of resistance genes in biofilm was higher than water from stage 5 onwards. Evolution of AmpC β-lactamase resistance genes was more obvious than MRGs, especially for MOX, which increased by 3 orders of magnitude. The abundance of Flavobacterium was higher in biofilm than in water. Moreover, correlation analysis showed that both arsB and MOX were significantly correlated with intI1 (p < 0.05), which suggested a potentially dissemination risk of resistance genes. This study provides a reference for health risk assessment in integrated aquaculture environment contaminated with duck manure, antibiotics and metalloids.

Antimicrobial Resistance in Veterinary Medicine: An Overview

Antimicrobial resistance (AMR) represents one of the most important human- and animal health-threatening issues worldwide. Bacterial capability to face antimicrobial compounds is an ancient feature, enabling bacterial survival over time and the dynamic surrounding. Moreover, bacteria make use of their evolutionary machinery to adapt to the selective pressure exerted by antibiotic treatments, resulting in reduced efficacy of the therapeutic intervention against human and animal infections. The mechanisms responsible for both innate and acquired AMR are thoroughly investigated. Commonly, AMR traits are included in mobilizable genetic elements enabling the homogeneous diffusion of the AMR traits pool between the ecosystems of diverse sectors, such as human medicine, veterinary medicine, and the environment. Thus, a coordinated multisectoral approach, such as One-Health, provides a detailed comprehensive picture of the AMR onset and diffusion. Following a general revision of the molecular mechanisms responsible for both innate and acquired AMR, the present manuscript focuses on reviewing the contribution of veterinary medicine to the overall issue of AMR. The main sources of AMR amenable to veterinary medicine are described, driving the attention towards the indissoluble cross-talk existing between the diverse ecosystems and sectors and their cumulative cooperation to this warning phenomenon.

Occurrence and fate of antibiotic residues and antibiotic resistance genes in a reservoir with ecological purification facilities for drinking water sources

Antibiotics and antibiotic resistance genes (ARGs) are emerging contaminants in surface waters, especially drinking water sources, where they can pose a risk to human health and aquatic ecology. The ecological purification facilities constructed in the drinking water reservoirs are intended to safeguard water quality. However, their ability to remove antibiotics and ARGs from the water and the presence of ARGs in such river-reservoir systems have not been comprehensively characterized yet. The occurrence, distribution and spatiotemporal variations in antibiotics, ARGs, and mobile genetic elements (MGEs) were investigated in a representative river-reservoir system in Shanghai, China. A total of 283 ARGs and 12 MGEs were detected in the water using high- throughput quantitative PCR analysis. Antibiotic residues and the absolute abundance of total ARGs and MGEs in reservoir inflow were significantly reduced when water from the river passed through the ecological purification processes in the reservoir. Antibiotics in this river-reservoir system posed only limited risks to the aquatic ecosystem and human health. No significant correlation was observed between the distribution pattern of ARGs and spatiotemporal factors. The dominant ARGs were strongly and significantly correlated with integrons. Through redundancy analysis and variation partitioning analysis, we determined that MGEs were the major driver shifting the distribution of ARGs, and the effects of environmental factors and antibiotic residues were reflected in the joint effects with MGEs. The small ecological reservoir was verified as an effective engineering to mitigate ecological risk in the drinking water source.

Metadata Analysis of mcr-1-Bearing Plasmids Inspired by the Sequencing Evidence for Horizontal Transfer of Antibiotic Resistance Genes Between Polluted River and Wild Birds

We sequenced the whole genomes of three mcr-1-positive multidrug-resistant E. coli strains, which were previously isolated from the environment of egret habitat (polluted river) and egret feces. The results exhibit high correlation between antibiotic-resistant phenotype and genotype among the three strains. Most of the mobilized antibiotic resistance genes (ARGs) are distributed on plasmids in the forms of transposons or integrons. Multidrug-resistant (MDR) regions of high homology are detected on plasmids of different E. coli isolates. Therefore, horizontal transfer of resistance genes has facilitated the transmission of antibiotic resistance between the environmental and avian bacteria, and the transfer of ARGs have involved multiple embedded genetic levels (transposons, integrons, plasmids, and bacterial lineages). Inspired by this, systematic metadata analysis was performed for the available sequences of mcr-1-bearing plasmids. Among these plasmids, IncHI2 plasmids carry the most additional ARGs. The composition of these additional ARGs varies according to their geographical distribution. The phylogenetic reconstruction of IncI2 and IncX4 plasmids provides the evidence for their multiregional evolution. Phylogenetic analysis at the level of mobile genetic element (plasmid) provides important epidemiological information for the global dissemination of mcr-1 gene. Highly homologous mcr-1-bearing IncI2 plasmids have been isolated from different regions along the East Asian-Australasian Flyway, suggesting that migratory birds may mediate the intercontinental transportation of ARGs.

Bacterial Transformation Buffers Environmental Fluctuations through the Reversible Integration of Mobile Genetic Elements

Horizontal gene transfer (HGT) promotes the spread of genes within bacterial communities. Among the HGT mechanisms, natural transformation stands out as being encoded by the bacterial core genome. Natural transformation is often viewed as a way to acquire new genes and to generate genetic mixing within bacterial populations. Another recently proposed function is the curing of bacterial genomes of their infectious parasitic mobile genetic elements (MGEs). Here, we propose that these seemingly opposing theoretical points of view can be unified. Although costly for bacterial cells, MGEs can carry functions that are at points in time beneficial to bacteria under stressful conditions (e.g., antibiotic resistance genes). Using computational modeling, we show that, in stochastic environments, an intermediate transformation rate maximizes bacterial fitness by allowing the reversible integration of MGEs carrying resistance genes, although these MGEs are costly for host cell replication. Based on this dual function (MGE acquisition and removal), transformation would be a key mechanism for stabilizing the bacterial genome in the long term, and this would explain its striking conservation.IMPORTANCE Natural transformation is the acquisition, controlled by bacteria, of extracellular DNA and is one of the most common mechanisms of horizontal gene transfer, promoting the spread of resistance genes. However, its evolutionary function remains elusive, and two main roles have been proposed: (i) the new gene acquisition and genetic mixing within bacterial populations and (ii) the removal of infectious parasitic mobile genetic elements (MGEs). While the first one promotes genetic diversification, the other one promotes the removal of foreign DNA and thus genome stability, making these two functions apparently antagonistic. Using a computational model, we show that intermediate transformation rates, commonly observed in bacteria, allow the acquisition then removal of MGEs. The transient acquisition of costly MGEs with resistance genes maximizes bacterial fitness in environments with stochastic stress exposure. Thus, transformation would ensure both a strong dynamic of the bacterial genome in the short term and its long-term stabilization.

Constructing and deconstructing the bacterial cell wall

The history of modern medicine cannot be written apart from the history of the antibiotics. Antibiotics are cytotoxic secondary metabolites that are isolated from Nature. The antibacterial antibiotics disproportionately target bacterial protein structure that is distinct from eukaryotic protein structure, notably within the ribosome and within the pathways for bacterial cell-wall biosynthesis (for which there is not a eukaryotic counterpart). This review focuses on a pre-eminent class of antibiotics-the β-lactams, exemplified by the penicillins and cephalosporins-from the perspective of the evolving mechanisms for bacterial resistance. The mechanism of action of the β-lactams is bacterial cell-wall destruction. In the monoderm (single membrane, Gram-positive staining) pathogen Staphylococcus aureus the dominant resistance mechanism is expression of a β-lactam-unreactive transpeptidase enzyme that functions in cell-wall construction. In the diderm (dual membrane, Gram-negative staining) pathogen Pseudomonas aeruginosa a dominant resistance mechanism (among several) is expression of a hydrolytic enzyme that destroys the critical β-lactam ring of the antibiotic. The key sensing mechanism used by P. aeruginosa is monitoring the molecular difference between cell-wall construction and cell-wall deconstruction. In both bacteria, the resistance pathways are manifested only when the bacteria detect the presence of β-lactams. This review summarizes how the β-lactams are sensed and how the resistance mechanisms are manifested, with the expectation that preventing these processes will be critical to future chemotherapeutic control of multidrug resistant bacteria.

Probiotic Supplements: Hope or Hype?

Probiotic bacteria have been associated with various health benefits and included in overwhelming number of foods. Today, probiotic supplements are consumed with increasing regularity and record a rapidly growing economic value. With billions of heterogeneous populations of probiotics per serving, probiotic supplements contain the largest quantity of probiotics across all functional foods. They often carry antibiotic-resistant determinants that can be transferred to and accumulate in resident bacteria of the gastrointestinal tract and risk their acquisitions by opportunistic pathogens. While the health benefits of probiotics have been widely publicized, this health risk, however, is underrepresented in both scientific studies and public awareness. On the other hand, the human gut presents conditions that are unfavorable for bacteria, including probiotics. It remains uncertain if probiotics from supplements can tolerate acids and bile salts that may undermine their effectiveness in conferring health benefits. Here, we put into perspective the perceived health benefits and the long-term safety of consuming probiotic supplements, specifically bringing intolerance to acids and bile salts, and the long-standing issue of antibiotic-resistant gene transfer into sharp focus. We report that probiotics from supplements examined in this study have poor tolerance to acids and bile salts while also displaying resistance to multiple antibiotics. They could also adapt and gain resistance to streptomycin in vitro. In an environment where consuming supplements is considered a norm, our results and that of others will put in perspective the persisting concerns surrounding probiotic supplements so that the current hype does not overpower the hope.

New insight into fates of sulfonamide and tetracycline resistance genes and resistant bacteria during anaerobic digestion of manure at thermophilic and mesophilic temperatures

This study investigated the variations in antibiotic (sulfonamide and tetracycline) resistance genes (ARGs) and resistant bacteria (ARB) during manure anaerobic digestion (AD) at 35 ℃ and 55 ℃, and discussed the mechanisms of variations in ARGs. The AD lasted for 60 days, five ARGs and intI1 each decreased in abundance after AD at the thermophilic temperature, while only half decreased at the mesophilic temperature. On days 10, 30, and 60, sulfonamide and tetracycline ARB were screened on selective media. During thermophilic AD, ARB numbers reduced by 4-log CFUs per gram dry manure, but only by approximately 1-log CFU at the mesophilic temperature. However, ARB composition analysis showed that at either temperature, no significant reduction in identified ARB species was observed. Furthermore, 72 ARB clones were randomly selected to detect the ARGs they harbored, and the results showed that each ARG was harbored by various hosts, and no definitive link existed between ARGs and bacterial species. In addition, by comparison with the identified host by culture method, the host prediction results based on the correlation analysis between ARGs and the bacterial community was proven to be unreliable. Overall, these findings indicated that relationships between ARB and ARGs were intricate.

Molecular characterisation of an Acinetobacter baumannii outbreak

Background

Acinetobacter baumannii are problematic hospital pathogens, and the increased incidence of multi drug resistance has significantly limited treatment options. The global epidemiology is not fully characterised due to large data gaps from low- and middle-income countries. This study characterised the molecular epidemiology of an A. baumanniii outbreak in Egypt.

Methods

Fifty-four A. baumannii isolates were recovered from a 4-month-outbreak at Tanta University Hospitals (TUH). Associated clinical and demographic data, and the antibiograms were analysed, and Carbapenem resistant isolates were screened for acquired carbapenemase genes by PCR and sequencing. Epidemiological typing was performed by single-locus sequencing of bla_OXA-51-like and Multi Locus Sequence Typing (MLST), and sequence types (STs) were analysed based on maximum-likelihood phylogeny (PhyML) to identify relatedness.

Findings

Immune suppression and ICU admission were the most common co-morbidity and risk factor. Carbapenem resistance accounted for 81%, and correlated with the presence of OXA-23, NDM-1 and -2, and VIM-1 and -2 carbapenemases. Nine different bla_OXA-51-like genes were identified which corresponded to 22 different Sequence Types (STs), including 10 novel. International clone (IC2) was the predominant clone. PhyML analysis revealed the presence of 2 distinct clones with multiple sub-lineages.

Conclusion

Given the short duration of the study, there was a rare heterogeneous population in the hospital. Carbapenem resistance is mediated by acquired carbapenemases in diverse lineages indicating the possibility of horizontal gene transfer. The diversity indicates the influx of multiple lineages of IC2 into TUH from unknown sources. Molecular epidemiological studies are essential for infection prevention and control measures.

Fifteen-Year Application of Manure and Chemical Fertilizers Differently Impacts Soil ARGs and Microbial Community Structure

Manure, which contains large amounts of antibiotics and antibiotic resistance genes (ARGs), is widely used in agricultural soils and may lead to the evolution and dispersal of ARGs in the soil environment. In the present study, soils that received manure or chemical fertilizers for 15 years were sampled on the North China Plain (NCP), which is one of the primary areas of intensive agriculture in China. High-throughput quantitative PCR and sequencing technologies were employed to assess the effects of long-term manure or chemical fertilizer application on the distribution of ARGs and microbial communities. A total of 114 unique ARGs were successfully amplified from all soil samples. Manure application markedly increased the relative abundance and detectable numbers of ARGs, with up to 0.23 copies/16S rRNA gene and 81 unique ARGs. The increased abundance of ARGs in manure-fertilized soil was mainly due to the manure increasing the abundance of indigenous soil ARGs. In contrast, chemical fertilizers only moderately affected the diversity of ARGs and had no significant effect on the relative abundance of the total ARGs. In addition, manure application increased the abundance of mobile genetic elements (MGEs), which were significantly and positively correlated with most types of ARGs, indicating that horizontal gene transfer via MGEs may play an important role in the spread of ARGs. Furthermore, the application of manure and chemical fertilizers significantly affected microbial community structure, and variation partitioning analysis showed that microbial community shifts represented the major driver shaping the antibiotic resistome. Taken together, our results provide insight into the long-term effects of manure and chemical fertilization on the dissemination of ARGs in intensive agricultural ecosystems.

Clinical class 1 integron-integrase gene - A promising indicator to monitor the abundance and elimination of antibiotic resistance genes in an urban wastewater treatment plant

In this study, 295 antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) from the influent, activated sludge (AS), and membrane bioreactor (MBR) permeate were primarily examined in the wastewater treatment plant (WWTP) biweekly over 13 months. The absolute concentrations of ARGs and MGEs respectively ranged from 1.27 × 10¹⁰ to 1.94 × 10¹¹ and 8.00 × 10⁹ to 1.24 × 10¹¹ copies/L in the influent, of which were reduced by 2 to 3 orders of magnitude in the permeate. No significant seasonal variation of ARGs and MGEs was found in the WWTP, except that the absolute abundance of ARGs and MGEs in the AS was peaked during spring. The antibiotics affected neither ARGs nor MGEs significantly, suggesting their concentrations may be not high enough to pose a selective pressure. In contrast, the bacterial community had direct effect on the MGEs variation, meanwhile the MGEs influenced the ARG abundance directly. Class 1 integron-integrase gene (intI1), clinical intI1, and Tn21 associated more frequently with ARGs in the AS over long-term, suggesting the potential of them involved in horizontal gene transfer. Both intI1 and clinical intI1 had significantly positive associations with the overall abundance of ARGs, as well as significantly negative relationships with the overall removal rates of ARGs in the MBR. However, the abundances between intI1 and clinical intI1 were significantly different. Meanwhile, clinical intI1 remained rather consistent proportion with the ARG abundance in the AS and permeate, was stronger correlated with human pathogens, and was associated with greater number of ARGs over time. Moreover, clinical intI1 was significantly associated with the removal efficiency of ARGs from all classes. Taken together, clinical intI1 can be adopted as an indicator for the abundance and removal efficiency of ARGs in the WWTP.

Pathogenomic Analysis of a Novel Extensively Drug-Resistant Citrobacter freundii Isolate Carrying a blaNDM-1 Carbapenemase in South Africa

Pathogenomic analysis was performed on a novel carbapenem-resistant Citrobacter freundii isolate (H2730R) from a rectal swab of an adult male patient admitted to a tertiary hospital, Durban, South Africa. H2730R was identified using selective media and API 20e kit. Confirmatory identification and antibiotic susceptibility testing were performed using the VITEK II. H2730R was whole-genome sequenced on the Illumina MiSeq platform. H2730R was resistant to all tested antibiotics except tigecycline and was defined as ST498 by the C. freundii multilocus sequence typing (MLST) database. The estimated pathogenic potential predicted a higher probability (P_score ≈ 0.875), supporting H2730R as a human pathogen. H2730R harbored 25 putative acquired resistance genes, 4 plasmid replicons, 4 intact prophages, a class 1 integron (IntI1), 2 predominant insertion sequences (IS3 and IS5), numerous efflux genes, and virulome. BLASTn analysis of the bla_NDM-1 encoding contig (00022) and its flanking sequences revealed the bla_NDM-1 was located on a plasmid similar to the multireplicon p18-43_01 plasmid reported for the spread of carbapenem resistance in South Africa. Phylogenomic analysis showed clustering of H2730R with CF003/CF004 strains in the same clade, suggesting a possible association between C. freundii strains/clones. Acquiring the p18-43_01 plasmid containing bla_NDM-1, the diversity, and complex resistome, virulome, and mobilome of this pathogen makes its incidence very worrying regarding mobilized resistance. This study presents the background genomic information for future surveillance and tracking of the spread of carbapenem-resistant Enterobacteriaceae in South Africa.

Mouse Genetic Background Affects Transfer of an Antibiotic Resistance Plasmid in the Gastrointestinal Tract

Dissemination of antibiotic resistance (AR) genes, often on plasmids, leads to antibiotic-resistant bacterial infections, which is a major problem for animal and public health. Bacterial conjugation is the primary route of AR gene transfer in the mammalian gastrointestinal tract. Significant gaps in knowledge about which gastrointestinal communities and host factors promote plasmid transfer remain. Here, we used Salmonella enterica serovar Kentucky strain CVM29188 carrying plasmid pCVM29188_146 (harboring streptomycin and tetracycline resistance genes) to assess plasmid transfer to Escherichia coli under in vitro conditions and in various mouse strains with a conventional or defined microbiota. As an initial test, the transfer of pCVM29188_146 to the E. coli strains was confirmed in vitro Colonization resistance and, therefore, a lack of plasmid transfer were found in wild-type mice harboring a conventional microbiota. Thus, mice harboring the altered Schaedler flora (ASF), or ASF mice, were used to probe for host factors in the context of a defined microbiota. To assess the influence of inflammation on plasmid transfer, we compared interleukin-10 gene-deficient 129S6/SvEv ASF mice (proinflammatory environment) to wild-type 129S6/SvEv ASF mice and found no difference in transconjugant yields. In contrast, the mouse strain influenced plasmid transfer, as C3H/HeN ASF mice had significantly lower levels of transconjugants than 129S6/SvEv ASF mice. Although gastrointestinal members were identical between the ASF mouse strains, a few differences from C3H/HeN ASF mice were detected, with C3H/HeN ASF mice having significantly lower abundances of ASF members 356 (Clostridium sp.), 492 (Eubacterium plexicaudatum), and 502 (Clostridium sp.) than 129S6/SvEv ASF mice. Overall, we demonstrate that microbiota complexity and mouse genetic background influence in vivo plasmid transfer.IMPORTANCE Antibiotic resistance is a threat to public health. Many clinically relevant antibiotic resistance genes are carried on plasmids that can be transferred to other bacterial members in the gastrointestinal tract. The current study used a murine model to study the transfer of a large antibiotic resistance plasmid from a foodborne Salmonella strain to a gut commensal E. coli strain in the gastrointestinal tract. We found that different mouse genetic backgrounds and a different diversity of microbial communities influenced the level of Escherichia coli that acquired the plasmid in the gastrointestinal tract. This study suggests that the complexity of the microbial community and host genetics influence plasmid transfer from donor to recipient bacteria.

Pathogenomics and Evolutionary Epidemiology of Multi-Drug Resistant Clinical Klebsiella pneumoniae Isolated from Pretoria, South Africa

Antibiotic-resistant Klebsiella pneumoniae is increasingly being implicated in invasive infections worldwide with high mortalities. Forty-two multidrug resistant (MDR) K. pneumoniae isolates were collected over a 4-month period. Antimicrobial susceptibility was determined using Microscan. The evolutionary epidemiology, resistome, virulome and mobilome of the isolates were characterised using whole-genome sequencing and bioinformatics analysis. All isolates contained the bla_CTX-M gene, whilst 41/42(97%) contained bla_TEM, 36/42(86%) contained bla_OXA and 35/42(83%) harboured bla_SHV genes. Other resistance genes found included bla_LEN, aac(6′)-lb-cr, qnrA, qnrB, qnrS, oqxAB, aad, aph, dfr, sul1, sul2, fosA, and cat genes. Fluoroquinolone and colistin resistance-conferring mutations in parC, gyrAB, pmrAB, phoPQ and kpnEF were identified. The bla_LEN gene, rarely described worldwide, was identified in four isolates. The isolates comprised diverse sequence types, the most common being ST152 in 7/42(17%) isolates; clone-specific O and K capsule types were identified. Diverse virulence genes that were not clone-specific were identified in all but one isolate. IncF, IncH and IncI plasmid replicons and two novel integrons were present. The bla_CTX-M-15 and bla_TEM-1 genes were bracketed by Tn3 transposons, ISEc9, a resolvase and IS91 insertion sequence. There were 20 gene cassettes in 14 different cassette arrays, with the dfrA and aadA gene cassettes being the most frequent. Phylogenetic analysis demonstrated that the isolates were evolutionarily associated with strains from both South Africa and abroad. These findings depict the rich resistome, mobilome and virulome repertoire in clinical K. pneumoniae strains, which are mainly transmitted by clonal, multiclonal and horizontal means in South Africa.

A newly developed Escherichia coli isolate panel from a cross section of U.S. animal production systems reveals geographic and commodity-based differences in antibiotic resistance gene carriage

There are limited numbers of Escherichia coli isolate panels that represent United States food animal production. The majority of existing Escherichia coli isolate panels are typically designed: (i) to optimize genetic and/or phenotypic diversity; or (ii) focus on human isolates. To address this shortfall in agriculturally-related resources, we have assembled a publicly-available isolate panel (AgEc) from the four major animal production commodities in the United States, including beef, dairy, poultry, and swine, as well as isolates from agriculturally-impacted environments, and other commodity groups. Diversity analyses by phylotyping and Pulsed-field Gel Electrophoresis revealed a highly diverse composition, with the 300 isolates clustered into 71 PFGE sub-types based upon an 80% similarity cutoff. To demonstrate the panel's utility, tetracycline and sulfonamide resistance genes were assayed, which identified 131 isolates harboring genes involved in tetracycline resistance, and 41 isolates containing sulfonamide resistance genes. There was strong overlap in the two pools of isolates, 38 of the 41 isolates harboring sulfonamide resistance genes also contained tetracycline resistance genes. Analysis of antimicrobial resistance gene patterns revealed significant differences along commodity and geographical lines. This panel therefore provides the research community an E. coli isolate panel for study of issues pertinent to U.S. food animal production.

A Bioinformatic Analysis of Integrative Mobile Genetic Elements Highlights Their Role in Bacterial Adaptation

Mobile genetic elements (MGEs) contribute to bacterial adaptation and evolution; however, high-throughput, unbiased MGE detection remains challenging. We describe MGEfinder, a bioinformatic toolbox that identifies integrative MGEs and their insertion sites by using short-read sequencing data. MGEfinder identifies the genomic site of each MGE insertion and infers the identity of the inserted sequence. We apply MGEfinder to 12,374 sequenced isolates of 9 prevalent bacterial pathogens, including Mycobacterium tuberculosis, Staphylococcus aureus, and Escherichia coli, and identify thousands of MGEs, including candidate insertion sequences, conjugative transposons, and prophage elements. The MGE repertoire and insertion rates vary across species, and integration sites often cluster near genes related to antibiotic resistance, virulence, and pathogenicity. MGE insertions likely contribute to antibiotic resistance in laboratory experiments and clinical isolates. Additionally, we identified thousands of mobility genes, a subset of which have unknown function opening avenues for exploration. Future application of MGEfinder to commensal bacteria will further illuminate bacterial adaptation and evolution.

Nationwide Stepwise Emergence and Evolution of Multidrug-Resistant Campylobacter jejuni Sequence Type 5136, United Kingdom

We examined whole-genome–sequenced Campylobacter jejuni and C. coli from 2012–2015 isolated from birds and human stool samples in North East Scotland for the presence of antimicrobial resistance genes. We found that sequence type (ST) 5136 (clonal complex 464) was the most prevalent multidrug-resistant strain of C. jejuni exclusively associated with poultry host reservoirs and recovered from human cases of campylobacteriosis. Tetracycline resistance in ST5136 isolates was due to a tet(O/32/O) mosaic gene, ampicillin resistance was conferred by G → T transversion in the −10 promoter region of bla_OXA-193, fluoroquinolone resistance was due to C257T change in gyrA, and aminoglycoside resistance was conferred by aac. Whole-genome analysis showed that the strain ST5136 evolved from ST464. The nationwide emergence of ST5136 was probably due to stepwise acquisition of antimicrobial resistance genes selected by high use of β-lactam, tetracycline, fluoroquinolone, and aminoglycoside classes of drugs in the poultry industry.

Multidrug resistance genes are associated with a 42-kb island TGI1 carrying a complex class 1 integron in Trueperella pyogenes

OBJECTIVES

This research was conducted to ascertain the context and location of the antibiotic resistance determinants in a multiple antibiotic-resistant Trueperella pyogenes isolate TP1.

METHODS

The genome was sequenced using PacBio RS II, and the filtered data were assembled using Canu. Sequences were annotated on the basis of those in GenBank, and the genomic island (GI) of the TP1 was predicted by IslandPath-DIMOB.

RESULTS

TP1 as a multiple antibiotic-resistant isolate was recovered at Jilin Province (China) in 2017 from a dairy cow with pneumonia. TP1 exhibited resistance to aminoglycosides (gentamicin and amikacin), macrolides (erythromycin), lincosamides (clindamycin), sulfonamides (sulfamonomethoxine), tetracyclines (tetracycline and doxycycline) and chloramphenicols (chloramphenicol and florfenicol). An antibiotic resistance gene clustered together with the aadB, aadA1, cmlA5 and cmlA6 resistance genes located on a 7-kilobase (kb) multidrug-resistant (MDR) region, constituting a complex class 1 integron. The MDR region was located at one end of a 42-kb GI, and IS6100Δ1 mediated a genetic rearrangement with the complex class 1 integron-like SGI1 and formed a composite transposon. Furthermore, the tetW gene was located outside the four GIs consistent with tetracycline and doxycycline resistance. The ermD gene positioned in the front end of the 42-kb GI played an important role in mediating acquired erythromycin and clindamycin resistance.

CONCLUSIONS

Multiple resistance genes are located in a complex class 1 integron within a 42-kb T. pyogenes genomic island (TGI1), leading to TP1 multiple drug resistance. In comparison with SG1 families, TGI1 possesses versatile gene distribution and specific gene context for it upstream and downstream, and it represents a new lineage of genomic resistance islands.

Development of a multi-locus sequence typing system helps reveal the evolution of Cardinium hertigii, a reproductive manipulator symbiont of insects

Background

Cardinium is an intracellular bacterial symbiont in the phylum Bacteroidetes that is found in many different species of arthropods and some nematodes. This symbiont is known to be able to induce three reproductive manipulation phenotypes, including cytoplasmic incompatibility. Placing individual strains of Cardinium within a larger evolutionary context has been challenging because only two, relatively slowly evolving genes, 16S rRNA gene and Gyrase B, have been used to generate phylogenetic trees, and consequently, the relationship of different strains has been elucidated in only its roughest form.

Results

We developed a Multi Locus Sequence Typing (MLST) system that provides researchers with three new genes in addition to Gyrase B for inferring phylogenies and delineating Cardinium strains. From our Cardinium phylogeny, we confirmed the presence of a new group D, a Cardinium clade that resides in the arachnid order harvestmen (Opiliones). Many Cardinium clades appear to display a high degree of host affinity, while some show evidence of host shifts to phylogenetically distant hosts, likely associated with ecological opportunity. Like the unrelated reproductive manipulator Wolbachia, the Cardinium phylogeny also shows no clear phylogenetic signal associated with particular reproductive manipulations.

Conclusions

The Cardinium phylogeny shows evidence of diversification within particular host lineages, and also of host shifts among trophic levels within parasitoid-host communities. Like Wolbachia, the relatedness of Cardinium strains does not necessarily predict their reproductive phenotypes. Lastly, the genetic tools proposed in this study may help future authors to characterize new strains and add to our understanding of Cardinium evolution.

Mobile Genetic Elements in Pseudomonas stutzeri

Mobile genetic elements (MGE) play a large role in the plasticity of genomes, participating in several phenomena which involve genes acquisition. Pseudomonas stutzeri is an environmental widely distributed bacteria. This bacteria has a very large genomic plasticity, which would explain its occurrence in several different environments. NCBI data bank and online programs were used to build an inventory to investigate diversity and structure of MGE in Pseudomonas stutzeri, searching for insertion sequences (IS), integrases/transposases, plasmids and prophages. Five hundred and forty-eight ISs, 62 integrases, 166 transposases, five plasmids and eight complete prophages were found. MGE location and adjacent genes were investigated. Possible implications of the presence of these mobile elements explaining phenotypic diversity of Pseudomonas stutzeri were discussed. The study showed that MGEs might be good clues to understand the dynamics of genomes and their phenotypic plasticity, although they are not the only elements responsible for these characteristics.

Selective enrichment of bacterial pathogens by microplastic biofilm

Microplastics have been found to be ubiquitous in freshwater ecosystems, providing a novel substrate for biofilm formation. Here, we incubated biofilm on microplastics and two natural substrates (rock and leaf) under a controlled environment to investigate the differences of microbial community structure, antibiotic resistance gene (ARG) profiles, and ARG microbial hosts between biofilms on three types of substrates. Results from high-throughput sequencing of 16S rRNA gene revealed that microplastic biofilm had a distinctive community structure. Network analyses suggested that microplastic biofilm possessed the highest node connected community, but with lower average path length, network diameter and modularity compared with biofilm on two natural particles. Metagenomic analyses further revealed microplastic biofilm with broad-spectrum and distinctive resistome. Specifically, according to taxonomic annotation of ARG microbial hosts, two opportunisitic human pathogens (Pseudomonas monteilii, Pseudomonas mendocina) and one plant pathogen (Pseudomonas syringae) were detected only in the microplastic biofilm, but not in biofilms formed on natural substrates. Our findings suggest that microplastic is a novel microbial niche and may serve as a vector for ARGs and pathogens to new environment in river water, generating freshwater environmental risk and exerting adverse impacts on human health.

The Resistome, Mobilome, Virulome and Phylogenomics of Multidrug-Resistant Escherichia coli Clinical Isolates from Pretoria, South Africa

Antibiotic-resistant Escherichia coli is a common occurrence in food, clinical, community and environmental settings worldwide. The resistome, mobilome, virulome and phylogenomics of 20 multidrug resistant (MDR) clinical E. coli isolates collected in 2013 from Pretoria, South Africa, were characterised. The isolates were all extended-spectrum β-lactamase producers, harbouring CTX-M (n = 16; 80%), TEM-1B (n = 10; 50%) and OXA (n = 12, 60%) β-lactamases alongside genes mediating resistance to fluoroquinolones, aminoglycosides, tetracyclines etc. Most resistance determinants were found on contigs containing IncF plasmid replicons and bracketed by composite transposons (Tn3), diverse ISs and class 1 integrons (In13, In54, In369, and In467). Gene cassettes such as bla_OXA,dfrA5-psp-aadA2-cmlA1a-aadA1-qac and estX3-psp-aadA2-cmlA1a-aadA1a-qac were encompassed by Tn3 and ISs; several isolates had same or highly similar genomic antibiotic resistance islands. ST131 (n = 10), ST617 (n = 2) and singletons of ST10, ST73, ST95, ST410, ST648, ST665, ST744 and ST998 clones were phylogenetically related to clinical (human and animal) strains from Egypt, Kenya, Niger, Nigeria, Tanzania, and UK. A rich repertoire of virulence genes, including iss, gad and iha were identified. MDR E. coli harbouring chromosomal and plasmid-borne resistance genes in same and multiple clones exist in South Africa, which is very worrying for clinical epidemiology and infectious diseases management.

One Aeromonas salmonicida subsp. salmonicida isolate with a pAsa5 variant bearing antibiotic resistance and a pRAS3 variant making a link with a swine pathogen

The Gram-negative bacterium Aeromonas salmonicida subsp. salmonicida is an aquatic pathogen which causes furunculosis to salmonids, especially in fish farms. The emergence of strains of this bacterium exhibiting antibiotic resistance is increasing, limiting the effectiveness of antibiotherapy as a treatment against this worldwide disease. In the present study, we discovered an isolate of A. salmonicida subsp. salmonicida that harbors two novel plasmids variants carrying antibiotic resistance genes. The use of long-read sequencing (PacBio) allowed us to fully characterize those variants, named pAsa5-3432 and pRAS3-3432, which both differ from their classic counterpart through their content in mobile genetic elements. The plasmid pAsa5-3432 carries a new multidrug region composed of multiple mobile genetic elements, including a Class 1 integron similar to an integrated element of Salmonella enterica. With this new region, probably acquired through plasmid recombination, pAsa5-3432 is the first reported plasmid of this bacterium that bears both an essential virulence factor (the type three secretion system) and multiple antibiotic resistance genes. As for pRAS3-3432, compared to the classic pRAS3, it carries a new mobile element that has only been identified in Chlamydia suis. Hence, with the identification of those two novel plasmids harboring mobile genetic elements that are normally encountered in other bacterial species, the present study puts emphasis on the important impact of mobile genetic elements in the genomic plasticity of A. salmonicida subsp. salmonicida and suggests that this aquatic bacterium could be an important reservoir of antibiotic resistance genes that can be exchanged with other bacteria, including human and animal pathogens.

Determining the Virulence Properties of Escherichia coli ST131 Containing Bacteriocin-Encoding Plasmids Using Short- and Long-Read Sequencing and Comparing Them with Those of Other E. coli Lineages

Escherichia coli ST131 is a clinical challenge due to its multidrug resistant profile and successful global spread. They are often associated with complicated infections, particularly urinary tract infections (UTIs). Bacteriocins play an important role to outcompete other microorganisms present in the human gut. Here, we characterized bacteriocin-encoding plasmids found in ST131 isolates of patients suffering from a UTI using both short- and long-read sequencing. Colicins Ia, Ib and E1, and microcin V, were identified among plasmids that also contained resistance and virulence genes. To investigate if the potential transmission range of the colicin E1 plasmid is influenced by the presence of a resistance gene, we constructed a strain containing a plasmid which had both the colicin E1 and blaCMY-2 genes. No difference in transmission range was found between transformant and wild-type strains. However, a statistically significantly difference was found in adhesion and invasion ability. Bacteriocin-producing isolates from both ST131 and non-ST131 lineages were able to inhibit the growth of other E. coli isolates, including other ST131. In summary, plasmids harboring bacteriocins give additional advantages for highly virulent and resistant ST131 isolates, improving the ability of these isolates to compete with other microbiota for a niche and thereby increasing the risk of infection.

Contamination of antibiotic resistance genes (ARGs) in a typical marine aquaculture farm: source tracking of ARGs in reared aquatic organisms

Although the prevalence and concentrations of antibiotic resistance genes (ARGs) in aquaculture is receiving increasing scientific interest, there is little understanding of the direct sources and dissemination pathways of ARGs in marine aquaculture-reared organisms. This study investigated the dynamics of ARGs and the bacterial community throughout the rearing period in a typical marine aquaculture farm in South China. The results demonstrated that sul1 and qnrD were predominant in the sediment, and qnrD and qnrA were predominant in the intestinal tracts of shrimps. Network analysis showed that the chemical oxygen demand, total organic carbon, dissolved organic carbon, suspended solids, and total phosphorus were positively correlated with the predominant ARGs. The results of the network and source tracking analyses indicate that environmental factors and the bacterial community may drive the dissemination of ARGs dissemination in the environment and in shrimp reared by marine aquaculture, and sediment is the most direct and important medium in this dissemination. These results aid in improving our understanding of the sources, level, and dissemination of ARGs in marine aquaculture.

Freshwater environments as reservoirs of antibiotic resistant bacteria and their role in the dissemination of antibiotic resistance genes

Freshwater environments are susceptible to possible contamination by residual antibiotics that are released through different sources, such as agricultural runoffs, sewage discharges and leaching from nearby farms. Freshwater environment can thus become reservoirs where an antibiotic impact microorganisms, and is an important public health concern. Degradation and dilution processes are fundamental for predicting the actual risk of antibiotic resistance dissemination from freshwater reservoirs. This study reviews major approaches for detecting and quantifying antibiotic resistance bacteria (ARBs) and genes (ARGs) in freshwater and their prevalence in these environments. Finally, the role of dilution, degradation, transmission and the persistence and fate of ARB/ARG in these environments are also reviewed. Culture-based single strain approaches and molecular techniques that include polymerase chain reaction (PCR), quantitative polymerase chain reaction (qPCR) and metagenomics are techniques for quantifying ARB and ARGs in freshwater environments. The level of ARBs is extremely high in most of the river systems (up to 98% of the total detected bacteria), followed by lakes (up to 77% of the total detected bacteria), compared to dam, pond, and spring (<1%). Of most concern is the occurrence of extended-spectrum β-lactamase producing Enterobacteriaceae, methicillin resistant Staphylococcus aureus (MRSA) and vancomycin resistant Enterococcus (VRE), which cause highly epidemic infections. Dilution and natural degradation do not completely eradicate ARBs and ARGs in the freshwater environment. Even if the ARBs in freshwater are effectively inactivated by sunlight, their ARG-containing DNA can still be intact and capable of transferring resistance to non-resistant strains. Antibiotic resistance persists and is preserved in freshwater bodies polluted with high concentrations of antibiotics. Direct transmission of indigenous freshwater ARBs to humans as well as their transitory insertion in the microbiota can occur. These findings are disturbing especially for people that rely on freshwater resources for drinking, crop irrigation, and food in form of fish.

Functional Traits Co-Occurring with Mobile Genetic Elements in the Microbiome of the Atacama Desert

Mobile genetic elements (MGEs) play an essential role in bacterial adaptation and evolution. These elements are enriched within bacterial communities from extreme environments. However, very little is known if specific genes co-occur with MGEs in extreme environments and, if so, what their function is. We used shotgun-sequencing to analyse the metagenomes of 12 soil samples and characterized the composition of MGEs and the genes co-occurring with them. The samples ranged from less arid coastal sites to the inland hyperarid core of the Atacama Desert, as well as from sediments below boulders, protected from UV-irradiation. MGEs were enriched at the hyperarid sites compared with sediments from below boulders and less arid sites. MGEs were mostly co-occurring with genes belonging to the Cluster Orthologous Group (COG) categories “replication, recombination and repair,” “transcription” and “signal transduction mechanisms.” In general, genes coding for transcriptional regulators and histidine kinases were the most abundant genes proximal to MGEs. Genes involved in energy production were significantly enriched close to MGEs at the hyperarid sites. For example, dehydrogenases, reductases, hydrolases and chlorite dismutase and other enzymes linked to nitrogen metabolism such as nitrite- and nitro-reductase. Stress response genes, including genes involved in antimicrobial and heavy metal resistance genes, were rarely found near MGEs. The present study suggests that MGEs could play an essential role in the adaptation of the soil microbiome in hyperarid desert soils by the modulation of housekeeping genes such as those involved in energy production.

Exploring the persistence and spreading of antibiotic resistance from manure to biocompost, soils and vegetables

The main avenue in which antibiotic resistance enters soils is through the application of livestock manure. However, whether antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) persist and spread to vegetables with the application of manure and manure products is still unclear. This study assessed seven kinds of cultured ARB, 221 ARGs subtypes and three transposon genes in the vegetable production chain (from manure to biocompost, soils and vegetables). Results showed that at least 80% of ARB, ARGs and transposon genes were removed after aerobic composting. However, aerobic composting did not reduce the diversity of ARGs in pig and chicken manure. A total of 19 ARGs subtypes still persisted during aerobic composting. Compared to the temperature-thermophilic stage, the number of bacteria resistant to erythromycin, the relative abundance of ARGs and IS613 increased 1.7-4.9 times at the temperature-decreasing stage. Direct application of biocompost introduced 11 ARGs subtypes to pakchoi, but these ARGs did not present in biocompost-amended soil. A transposon gene tnpA was also detected in the biocompost-amended soil, but surprisingly was found in the control vegetable. This demonstrated that the transposon gene is intrinsic in pakchoi. Bacterial community analysis and network analysis revealed that a specific genus Terrisporobacter carrying tetO, tetW ermB and tnpA persisted in the vegetable production chain, which may generate a potential risk in the following production. Our study illuminates the persistence and spreading of antibiotic resistance in the vegetable production chain which could help manage the ecological risks arising from antibiotic resistance in manure sources.

State of the art of tertiary treatment technologies for controlling antibiotic resistance in wastewater treatment plants

Antibiotic resistance genes (ARGs) have been considered as emerging contaminants of concern nowadays. There are no special technologies designed to directly remove ARGs in wastewater treatment plants (WWTPs). In order to reduce the risk of ARGs, it is vital to understand the efficiency of advanced treatment technologies in removing antibiotic resistance genes in WWTPs. This review highlights the application and efficiency of tertiary treatment technologies on the elimination of ARGs, s, based on an understanding of their occurrence and fate in WWTPs. These technologies include chemical-based processes such as chlorination, ozonation, ultraviolet, and advanced oxidation technology, as well as physical separation processes, biological processes such as constructed wetland and membrane bioreactor, and soil aquifer treatment. The merits, limitations and ameliorative measures of these processes are discussed, with the view to optimizing future treatment strategies and identifying new research directions.

Higher functionality of bacterial plasmid DNA in water after peracetic acid disinfection compared with chlorination

Peracetic acid (PAA) is an emerging disinfectant with a low disinfection by-product formation potential, but how PAA destroys gene function after killing bacteria remains to be studied. Bacterial plasmid DNA is a mobile genetic element that often harbors undesirable genes encoding antibiotic resistance and virulence factors. Even though PAA efficiently kills bacteria, bacterial plasmids and other mobile genetic elements might still be intact and functional after PAA disinfection, posing potential public health and environmental risks. This study evaluated the impact of PAA disinfection on the functionality of plasmid DNA in vivo and compared the results with those from chlorination. We delivered a plasmid DNA harboring two antibiotic resistance genes to Escherichia coli TOP10 to form an antibiotic-resistant bacterium (ARB). The planktonic ARB was treated with PAA and chlorine to find the minimum doses inhibiting the regrowth of the strain. PAA and chlorine stopped the regrowth at 8 ± 1 mg PAA·L^-1 and 20 ± 9 mg Cl₂·L^-1, respectively. The functionality of the plasmid DNA after PAA and chlorine disinfection was then determined at higher doses in vivo. Neither PAA nor chlorine completely destroyed the plasmid DNA. However, chlorine was more efficient than PAA in eliminating the plasmid DNA. PAA at 25 mg PAA·L^-1 reduced the transforming activity of the plasmid DNA by less than 0.3 log₁₀ units, whereas chlorine at 25 mg Cl₂·L^-1 reduced the transforming activity by approximately 1.7 log₁₀ units. Chlorine had a more pronounced impact on the functionality of the plasmid DNA because it oxidizes or destroys bacterial components including plasmid DNA faster than PAA. In addition, environmental scanning electron microscopy shows that chlorination desiccated the cells resulting in the flat cellular structure and possibly more complete loss of plasmid DNA, whereas PAA disinfection had a less impact on cell structure and morphology. This study demonstrates that more plasmid DNA remains functional in water after PAA disinfection than after chlorination. These functional genetic elements could be acquired by other microorganisms via horizontal gene transfer to pose potential public health and environmental risks.

Knowledge, attitudes and practices of livestock and aquaculture producers regarding antimicrobial use and resistance in Vietnam

The use of antibiotics in livestock production is considered a major driver of antibiotic resistance on a global scale. In Vietnam, small- and medium-scale livestock producers dominate the domestic market and regulatory pushes have done little to decrease antibiotic use. In order to inform future policy directions, this study aims to explore knowledge, attitudes, and practices amongst livestock producers to identify their perspectives on antibiotic use and resistance. A total of 392 small- and medium-scale producers specialized in pig, poultry and aquaculture production participated in the study. The results showed that the primary reason for antibiotic use reported by producers was for the treatment of infections (69%). However, prophylactic use was also evident, with farmers reporting other reasons for antibiotic use such as “animals display abnormal symptoms or behaviour” (55%), the “weather is about to change” (25%), or “animals on neighboring farms fall ill” (27%). Only one-fifth of producers demonstrated favorable attitudes towards antibiotic use and preventing antibiotic resistance. Moreover, administering antibiotics remained the preferred countermeasure directly applied by farmers at the first indication of disease (17%), compared to enacting hygiene (10%) or quarantine (5%) measures. The results showed divergent trends amongst producers, with pig producers demonstrating higher levels of knowledge, more favorable attitudes, and higher self-reported utilization of good practice. Better knowledge, attitudes, and practices were also associated with producers who engaged in efforts to explore information on antibiotic use and resistance, which improved incrementally with the number of sources consulted and hours invested. However, there were some areas where increased knowledge or more favorable attitude scores did not translate into better practices. For instance, producers with higher levels of formal education performed significantly better than those with lower education in terms of knowledge and attitude, though both groups reported similar practices. The findings of this study may support future interventions to prevent both antibiotic misuse and the development of antimicrobial resistance.

Genomic analysis of a multidrug-resistant clinical Providencia rettgeri (PR002) strain with the novel integron ln1483 and an A/C plasmid replicon

Whole-genome sequence analysis was performed on a multidrug-resistant Providencia rettgeri PR002 clinical strain isolated from the urine of a hospitalized patient in Pretoria, South Africa, in 2013. The resistome, mobilome, pathogenicity island(s), as well as virulence and heavy-metal resistance genes of the isolate, were characterized using whole-genome sequencing and bioinformatic analysis. PR002 had a genome assembly size of 4,832,624 bp with a GC content of 40.7%, an A/C₂ plasmid replicase gene, four integrons/gene cassettes, 17 resistance genes, and several virulence and heavy metal resistance genes, confirming PR002 as a human pathogen. A novel integron, In1483, harboring the gene bla_OXA-2 , was identified, with other uncharacterized class 1 integrons harboring aacA4cr and dfrA1. Aac(3')-IIa and bla_SCO-1 , as well as bla_PER-7 , sul2, and tet(B), were found bracketed by composite Tn3 transposons, and IS91, IS91, and IS4 family insertion sequences, respectively. PR002 was resistant to all antibiotics tested except amikacin, carbapenems, cefotaxime-clavulanate, ceftazidime-clavulanate, cefoxitin, and fosfomycin. PR002 was closely related to PR1 (USA), PRET_2032 (SPAIN), DSM_1131, and NCTC7477 clinical P. rettgeri strains, but not close enough to suggest it was imported into South Africa from other countries. Multidrug resistance in P. rettgeri is rare, particularly in clinical settings, making this case an important incident requiring urgent attention. This is also the first report of an A/C plasmid in P. rettgeri. The array, multiplicity, and diversity of resistance and virulence genes in this strain are concerning, necessitating stringent infection control, antibiotic stewardship, and periodic resistance surveillance/monitoring policies to preempt further horizontal and vertical spread of these resistance genes.

Characterization of the Microbial Resistome in Conventional and "Raised Without Antibiotics" Beef and Dairy Production Systems

Metagenomic investigations have the potential to provide unprecedented insights into microbial ecologies, such as those relating to antimicrobial resistance (AMR). We characterized the microbial resistome in livestock operations raising cattle conventionally (CONV) or without antibiotic exposures (RWA) using shotgun metagenomics. Samples of feces, wastewater from catchment basins, and soil where wastewater was applied were collected from CONV and RWA feedlot and dairy farms. After DNA extraction and sequencing, shotgun metagenomic reads were aligned to reference databases for identification of bacteria (Kraken) and antibiotic resistance genes (ARGs) accessions (MEGARes). Differences in microbial resistomes were found across farms with different production practices (CONV vs. RWA), types of cattle (beef vs. dairy), and types of sample (feces vs. wastewater vs. soil). Feces had the greatest number of ARGs per sample (mean = 118 and 79 in CONV and RWA, respectively), with tetracycline efflux pumps, macrolide phosphotransferases, and aminoglycoside nucleotidyltransferases mechanisms of resistance more abundant in CONV than in RWA feces. Tetracycline and macrolide–lincosamide–streptogramin classes of resistance were more abundant in feedlot cattle than in dairy cow feces, whereas the β-lactam class was more abundant in dairy cow feces. Lack of congruence between ARGs and microbial communities (procrustes analysis) suggested that other factors (e.g., location of farms, cattle source, management practices, diet, horizontal ARGs transfer, and co-selection of resistance), in addition to antimicrobial use, could have impacted resistome profiles. For that reason, we could not establish a cause–effect relationship between antimicrobial use and AMR, although ARGs in feces and effluents were associated with drug classes used to treat animals according to farms’ records (tetracyclines and macrolides in feedlots, β-lactams in dairies), whereas ARGs in soil were dominated by multidrug resistance. Characterization of the “resistance potential” of animal-derived and environmental samples is the first step toward incorporating metagenomic approaches into AMR surveillance in agricultural systems. Further research is needed to assess the public-health risk associated with different microbial resistomes.

Evaluation of The Pathogenic Potential of Insecticidal Serratia marcescens Strains to Humans

We observed the death of insect caterpillars of Spodoptera exigua in the laboratory culture line and identified Serratia marcescens as the bacterial causative agent of the insect death. We confirmed that S. marcescens had insecticidal activity against S. exigua and caused high mortality of larvae. The LC₅₀ values of S. marcescens CFU per 1 cm² of insect diet surface were similar for all isolates. Our research reports novel strains with high pesticidal activity as candidates for future research on a new bioinsecticide. As bioinsecticides cannot be harmful to non-target organisms, we determined the pathogenic properties of S. marcescens to humans. We proved the ability of S. marcescens to damage mammalian epithelial cells. All strains had cytopathic effects to Vero cells with a cytotoxic index ranging from 51.2% ± 3.8% to 79.2% ± 4.1%. We found that all of the strains excreted catecholate siderophore - enterobactin. All isolates were resistant to sulfamethoxazole, tobramycin, gentamicin, cefepime, and aztreonam. We did not observe the ESBL phenotype and the integrons' integrase genes. Resistance to sulfamethoxazole was due to the presence of the sul1 or sul2 gene. The use of resistant S. marcescens strains that are pathogenic to humans in plant protection may cause infections difficult to cure and lead to the spread of resistance genes. The results of our study emphasize the necessity of determination of the safety to vertebrates of the bacteria that are proposed to serve as biocontrol agents. The novelty of our study lies in the demonstration of the indispensability of the bacteria verification towards the lack of hazardous properties to humans.

We observed the death of insect caterpillars of Spodoptera exigua in the laboratory culture line and identified Serratia marcescens as the bacterial causative agent of the insect death. We confirmed that S. marcescens had insecticidal activity against S. exigua and caused high mortality of larvae. The LC₅₀ values of S. marcescens CFU per 1 cm² of insect diet surface were similar for all isolates. Our research reports novel strains with high pesticidal activity as candidates for future research on a new bioinsecticide. As bioinsecticides cannot be harmful to non-target organisms, we determined the pathogenic properties of S. marcescens to humans. We proved the ability of S. marcescens to damage mammalian epithelial cells. All strains had cytopathic effects to Vero cells with a cytotoxic index ranging from 51.2% ± 3.8% to 79.2% ± 4.1%. We found that all of the strains excreted catecholate siderophore – enterobactin. All isolates were resistant to sulfamethoxazole, tobramycin, gentamicin, cefepime, and aztreonam. We did not observe the ESBL phenotype and the integrons’ integrase genes. Resistance to sulfamethoxazole was due to the presence of the sul1 or sul2 gene. The use of resistant S. marcescens strains that are pathogenic to humans in plant protection may cause infections difficult to cure and lead to the spread of resistance genes. The results of our study emphasize the necessity of determination of the safety to vertebrates of the bacteria that are proposed to serve as biocontrol agents. The novelty of our study lies in the demonstration of the indispensability of the bacteria verification towards the lack of hazardous properties to humans.

Evaluation of The Pathogenic Potential of Insecticidal Serratia marcescens Strains to Humans

We observed the death of insect caterpillars of Spodoptera exigua in the laboratory culture line and identified Serratia marcescens as the bacterial causative agent of the insect death. We confirmed that S. marcescens had insecticidal activity against S. exigua and caused high mortality of larvae. The LC₅₀ values of S. marcescens CFU per 1 cm² of insect diet surface were similar for all isolates. Our research reports novel strains with high pesticidal activity as candidates for future research on a new bioinsecticide. As bioinsecticides cannot be harmful to non-target organisms, we determined the pathogenic properties of S. marcescens to humans. We proved the ability of S. marcescens to damage mammalian epithelial cells. All strains had cytopathic effects to Vero cells with a cytotoxic index ranging from 51.2% ± 3.8% to 79.2% ± 4.1%. We found that all of the strains excreted catecholate siderophore – enterobactin. All isolates were resistant to sulfamethoxazole, tobramycin, gentamicin, cefepime, and aztreonam. We did not observe the ESBL phenotype and the integrons’ integrase genes. Resistance to sulfamethoxazole was due to the presence of the sul1 or sul2 gene. The use of resistant S. marcescens strains that are pathogenic to humans in plant protection may cause infections difficult to cure and lead to the spread of resistance genes. The results of our study emphasize the necessity of determination of the safety to vertebrates of the bacteria that are proposed to serve as biocontrol agents. The novelty of our study lies in the demonstration of the indispensability of the bacteria verification towards the lack of hazardous properties to humans.

Host bacterial community of MGEs determines the risk of horizontal gene transfer during composting of different animal manures

Mobile genetic elements (MGEs) play critical roles in transferring antibiotic resistance genes (ARGs) among different microorganisms in the environment. This study aimed to explore the fate of MGEs during chicken manure (CM) and bovine manure (BM) composting to assess horizontal transfer risks of ARGs. The results showed that the removal efficiency of MGEs during CM composting was significantly higher than that during BM composting, because the potential host bacteria of MGEs were eliminated largely during CM composting. Meanwhile, these potential host bacterial communities are significantly influenced by pH, NH₄⁺, NO₃^- and total N, which can be used to regulate host bacterial communities to remove MGEs during composting. Projection pursuit regression further confirmed that composting can effectively reduce the horizontal transfer risk of ARGs, especially for CM composting. These results identified the critical roles of host bacterial communities in MGEs removal during composting of different animal manures.

NanoARG: a web service for detecting and contextualizing antimicrobial resistance genes from nanopore-derived metagenomes

BACKGROUND

Direct and indirect selection pressures imposed by antibiotics and co-selective agents and horizontal gene transfer are fundamental drivers of the evolution and spread of antibiotic resistance. Therefore, effective environmental monitoring tools should ideally capture not only antibiotic resistance genes (ARGs), but also mobile genetic elements (MGEs) and indicators of co-selective forces, such as metal resistance genes (MRGs). A major challenge towards characterizing the potential human health risk of antibiotic resistance is the ability to identify ARG-carrying microorganisms, of which human pathogens are arguably of greatest risk. Historically, short reads produced by next-generation sequencing technologies have hampered confidence in assemblies for achieving these purposes.

RESULTS

Here, we introduce NanoARG, an online computational resource that takes advantage of the long reads produced by nanopore sequencing technology. Specifically, long nanopore reads enable identification of ARGs in the context of relevant neighboring genes, thus providing valuable insight into mobility, co-selection, and pathogenicity. NanoARG was applied to study a variety of nanopore sequencing data to demonstrate its functionality. NanoARG was further validated through characterizing its ability to correctly identify ARGs in sequences of varying lengths and a range of sequencing error rates.

CONCLUSIONS

NanoARG allows users to upload sequence data online and provides various means to analyze and visualize the data, including quantitative and simultaneous profiling of ARGs, MRGs, MGEs, and putative pathogens. A user-friendly interface allows users the analysis of long DNA sequences (including assembled contigs), facilitating data processing, analysis, and visualization. NanoARG is publicly available and freely accessible at https://bench.cs.vt.edu/nanoarg .

Antibiotic resistance in urban runoff

Aquatic ecosystems subjected to anthropogenic pressures are places of rapid evolution of microbial communities and likely hotspots for selection and emergence of antibiotic resistant bacteria. In urban settings, water quality and the risk of infection are generally assessed in sewers and in effluents of wastewater treatment plants. Physical and chemical parameters as well as the presence of antibiotics, antibiotic-resistant bacteria and genes of resistance are driven by urban activities, with adverse effects on aquatic ecosystems. In this paper we review the environmental pressures exerted on bacterial communities in urban runoff waters and discuss the impact of these settings on antibiotic resistance. Considering the worrisome epidemiology of infectious diseases and estimated mortality due to antimicrobial resistance in the coming decades, there is an urgent need to identify all environmental reservoirs of resistant bacteria and resistance genes to complete our knowledge of the epidemiological cycle and of the dynamics of urban antibiotic resistance.

Diverse Commensal Escherichia coli Clones and Plasmids Disseminate Antimicrobial Resistance Genes in Domestic Animals and Children in a Semirural Community in Ecuador

The increased prevalence of antimicrobial resistance (AMR) among Enterobacteriaceae has had major clinical and economic impacts on human medicine. Many of the multidrug-resistant (multiresistant) Enterobacteriaceae found in humans are community acquired, and some of them are possibly linked to food animals (i.e., livestock raised for meat and dairy products). In this study, we examined whether numerically dominant commensal Escherichia coli strains from humans (n = 63 isolates) and domestic animals (n = 174 isolates) in the same community and with matching phenotypic AMR patterns were clonally related or shared the same plasmids. We identified 25 multiresistant isolates (i.e., isolates resistant to more than one antimicrobial) that shared identical phenotypic resistance patterns. We then investigated the diversity of E. coli clones, AMR genes, and plasmids carrying the AMR genes using conjugation, replicon typing, and whole-genome sequencing. All of the multiresistant E. coli isolates (from children and domestic animals) analyzed had at least 90 or more whole-genome SNP differences between one another, suggesting that none of the strains was recently transferred. While the majority of isolates shared the same antimicrobial resistance genes and replicons, DNA sequencing indicated that these genes and replicons were found on different plasmid structures. We did not find evidence of the clonal spread of AMR in this community: instead, AMR genes were carried on diverse clones and plasmids. This presents a significant challenge for understanding the movement of AMR in a community.IMPORTANCE Even though Escherichia coli strains may share nearly identical phenotypic AMR profiles and AMR genes and overlap in space and time, the diversity of clones and plasmids challenges research that aims to identify sources of AMR. Horizontal gene transfer appears to play a more significant role than clonal expansion in the spread of AMR in this community.