Lateral Antimicrobial Resistance Genetic Transfer is active in the open environment

Comprehensive profiling and risk assessment of antibiotic resistance genes in a drinking water watershed by integrated analysis of air-water-soil

The prevalence of antibiotic resistance genes (ARGs) in diverse habitats threatens public health. Watersheds represent critical freshwater ecosystems that interact with both the soil and atmosphere. However, a holistic understanding of ARGs distribution across these environmental media is currently inadequate. We profiled ARGs and bacterial communities in air-water-soil in the same watershed area during four seasons using high-throughput qPCR and 16S rRNA gene sequencing. Our findings demonstrated that aminoglycoside resistance genes (58.5%) were dominant in water, and multidrug resistance genes (55.2% and 54.2%) were dominant in soil and air. Five ARGs and nineteen bacterial genera were consistently detected in all samples, were named as shared genes or bacteria. Co-occurrence Network analysis revealed the co-occurrence module of resistance genes, mobile genetic elements (MGEs), and potential bacterial hosts, indicating that shared genes and bacteria may persist and co-spread across different environmental media. The risk assessment framework, based on ARGs' abundance, detection rate, and mobility, identified 33 high-risk ARGs. This is essential to evaluate the health risks of ARGs and to develop strategies to limit the threat of antibiotic resistance. Our study offers new insights into the risks associated with ARGs in the environment and suggests that ARGs may depend on specific bacterial cohabitants that co-exist with MGEs to facilitate their spread across environmental interfaces.

Exchange of Carbapenem-Resistant Escherichia coli Sequence Type 38 Intercontinentally and among Wild Bird, Human, and Environmental Niches

Carbapenem-resistant Enterobacteriaceae (CRE) are a global threat to human health and are increasingly being isolated from nonclinical settings. OXA-48-producing Escherichia coli sequence type 38 (ST38) is the most frequently reported CRE type in wild birds and has been detected in gulls or storks in North America, Europe, Asia, and Africa. The epidemiology and evolution of CRE in wildlife and human niches, however, remains unclear. We compared wild bird origin E. coli ST38 genome sequences generated by our research group and publicly available genomic data derived from other hosts and environments to (i) understand the frequency of intercontinental dispersal of E. coli ST38 clones isolated from wild birds, (ii) more thoroughly measure the genomic relatedness of carbapenem-resistant isolates from gulls sampled in Turkey and Alaska, USA, using long-read whole-genome sequencing and assess the spatial dissemination of this clone among different hosts, and (iii) determine whether ST38 isolates from humans, environmental water, and wild birds have different core or accessory genomes (e.g., antimicrobial resistance genes, virulence genes, plasmids) which might elucidate bacterial or gene exchange among niches. Our results suggest that E. coli ST38 strains, including those resistant to carbapenems, are exchanged between humans and wild birds, rather than separately maintained populations within each niche. Furthermore, despite close genetic similarity among OXA-48-producing E. coli ST38 clones from gulls in Alaska and Turkey, intercontinental dispersal of ST38 clones among wild birds is uncommon. Interventions to mitigate the dissemination of antimicrobial resistance throughout the environment (e.g., as exemplified by the acquisition of carbapenem resistance by birds) may be warranted. IMPORTANCE Carbapenem-resistant bacteria are a threat to public health globally and have been found in the environment as well as the clinic. Some bacterial clones are associated with carbapenem resistance genes, such as Escherichia coli sequence type 38 (ST38) and the carbapenemase gene blaOXA-48. This is the most frequently reported carbapenem-resistant clone in wild birds, though it was unclear if it circulated within wild bird populations or was exchanged among other niches. The results from this study suggest that E. coli ST38 strains, including those resistant to carbapenems, are frequently exchanged among wild birds, humans, and the environment. Carbapenem-resistant E. coli ST38 clones in wild birds are likely acquired from the local environment and do not constitute an independent dissemination pathway within wild bird populations. Management actions aimed at preventing the environmental dissemination and acquisition of antimicrobial resistance by wild birds may be warranted.

A systematic review and meta-analysis on prevalence and antimicrobial resistance profile of Escherichia coli isolated from water in africa (2000-2021)

Water is essential for the survival of humans, animals and plants. Numerous research has been conducted on the prevalence and antibiotic resistance of Escherichia coli (E. coli) in water from various African countries, however, there is lack of comprehensive analysis of published literature. We conducted a systematic review and meta-analysis following the PRISMA guidelines where articles published in English language between January 2000 and March 2022 were searched from ScienceDirect, PubMed, Google Scholar, Scopus, African Journal Online (AJO), and Africa Index Medicus (AIM). Comprehensive Meta-Analysis (CMA) Ver 3.0 software was used to analyze the data. The pooled prevalence estimate (PPE) with 95% confidence interval was calculated using the random-effects model (CI). The overall PPE and antimicrobial resistance trends of E. coli isolated from water was screened from 4009 isolates which were isolated from 2586 samples. We extracted data from 17 studies including drinking water (n = 6), rivers (n = 5), wastewaters (n = 4) and wastewater/river (n = 1) which are all covering 27 countries in Africa with 3438 isolates. The PPE of E. coli in water was 71.7% (0.717; 95% CI: 0.562-0.833). The highest PPE antibiotic resistance was against penicillin followed by erythromycin, and ampicilin with resistance rates of 93.4%, 92.3%, and 69.4%, respectively. This systematic review provides critical evidence of E. coli consolidated prevalence and antibiotic resistance profiles, as well as regions where future studies and enhanced reporting could be beneficial in the African continent.

Prevalence of Antibiotic-Resistant Seafood-Borne Pathogens in Retail Seafood Sold in Malaysia: A Systematic Review and Meta-Analysis

The objective of this study was to examine the frequency and extent of antibiotic-resistant pathogens in seafood sold in Malaysia, using a systematic review and meta-analysis approach to analyze primary research studies. Four bibliographic databases were systematically searched for primary studies on occurrence. Meta-analysis using a random-effect model was used to understand the prevalence of antibiotic-resistant bacteria in retail seafood sold in Malaysia. A total of 1938 primary studies were initially identified, among which 13 met the inclusion criteria. In the included primary studies, a total of 2281 seafoods were analyzed for the presence of antibiotic-resistant seafood-borne pathogens. It was observed that 51% (1168/2281) of the seafood was contaminated with pathogens. Overall, the prevalence of antibiotic-resistant seafood-borne pathogens in retail seafood was 55.7% (95% CI: 0.46-0.65). Antibiotic-resistant Salmonella species had an overall prevalence of 59.9% (95% CI: 0.32-0.82) in fish, Vibrio species had an overall prevalence of 67.2% (95% CI: 0.22-0.94) in cephalopods, and MRSA had an overall prevalence of 70.9% (95% CI: 0.36-0.92) in mollusks. It could be concluded that there is a high prevalence of antibiotic-resistant seafood-borne pathogens in the retail seafood sold in Malaysia, which could be of public health importance. Therefore, there is a need for proactive steps to be taken by all stakeholders to reduce the widespread transmission of antibiotic-resistant pathogens from seafood to humans.

Reduction of metronidazole in municipal wastewater and protection of activated sludge system using a novel immobilized Aspergillus tabacinus LZ-M

Metronidazole (MNZ) accumulation inhibits municipal wastewater treatment bio-systems, and an effective solution to augment anaerobic activated sludge (AAS) is required. This research discovered that Aspergillus tabacinus LZ-M could degrade 77.39% of MNZ at 5 mg/L. MNZ was metabolized into urea, and the enzymes involved in its degradation were aminotransferase, methyltransferase, monooxygenase, and CN cleavage hydrolase. The strain was immobilized in polyurethane foam and used in AAS for the treatment of MNZ-containing municipal wastewater. The results showed that, using immobilized LZ-M, MNZ was completely removed, and the degradation efficiency of wastewater's chemical oxygen demand (COD) was increased from 11.7% to 83.31%. The extracellular polymer and ROS levels indicated that MNZ's toxicity on AAS was reduced. Furthermore, bioaugmentation stabilized its microbial community, and decreased MNZ resistance genes. These observations confirm that the immobilized fungi are effective in protecting AAS against antibiotic contamination in the treatment process of municipal wastewater.

Comparative genome analysis of the genus Shewanella unravels the association of key genetic traits with known and potential pathogenic lineages

Shewanella spp. are Gram-negative rods widely disseminated in aquatic niches that can also be found in human-associated environments. In recent years, reports of infections caused by these bacteria have increased significantly. Mobilome and resistome analysis of a few species showed that they are versatile; however, comprehensive comparative studies in the genus are lacking. Here, we analyzed the genetic traits of 144 genomes from Shewanella spp. isolates focusing on the mobilome, resistome, and virulome to establish their evolutionary relationship and detect unique features based on their genome content and habitat. Shewanella spp. showed a great diversity of mobile genetic elements (MGEs), most of them associated with monophyletic lineages of clinical isolates. Furthermore, 79/144 genomes encoded at least one antimicrobial resistant gene with their highest occurrence in clinical-related lineages. CRISPR-Cas systems, which confer immunity against MGEs, were found in 41 genomes being I-E and I-F the more frequent ones. Virulome analysis showed that all Shewanella spp. encoded different virulence genes (motility, quorum sensing, biofilm, adherence, etc.) that may confer adaptive advantages for survival against hosts. Our data revealed that key accessory genes are frequently found in two major clinical-related groups, which encompass the opportunistic pathogens Shewanella algae and Shewanella xiamenensis together with several other species. This work highlights the evolutionary nature of Shewanella spp. genomes, capable of acquiring different key genetic traits that contribute to their adaptation to different niches and facilitate the emergence of more resistant and virulent isolates that impact directly on human and animal health.

Antibiotic resistant bacteria: A bibliometric review of literature

Antibiotic-resistant bacteria (ARB) are a serious threat to the health of people and the ecological environment. With this problem becoming more and more serious, more countries made research on the ARB, and the research number has been sharply increased particularly over the past decade. Therefore, it is quite necessary to globally retrace relevant researches on the ARB published from 2010 to 2020. This will help researchers to understand the current research situation, research trends and research hotspots in this field. This paper uses bibliometrics to examine publications in the field of ARB from 2010 to 2020 that were retrieved from the Web of Science (WOS). Our study performed a statistical analysis of the countries, institutions, journals, authors, research areas, author keywords, Essential Science Indicators (ESI) highly cited papers, and ESI hotspots papers to provide an overview of the ARB field as well as research trends, research hotspots, and future research directions in the field. The results showed that the number of related studies is increasing year by year; the USA is most published in the field of ARB; China is the most active in this field in the recent years; the Chinese Acad Sci published the most articles; Sci. Total Environ. published the greatest number of articles; CM Manaia has the most contributions; Environmental Sciences and Ecology is the most popular research area; and "antibiotic resistance," "antibiotics," and "antibiotic resistance genes" were the most frequently occurring author keywords. A citation analysis showed that aquatic environment-related antibiotic resistance is a key research area in this field, while antimicrobial nanomaterial-related research is a recent popular topic.

Carbapenem-resistant Escherichia coli from shrimp and salmon available for purchase by consumers in Canada: a risk profile using the Codex framework

Resistance to carbapenems in human pathogens is a growing clinical and public health concern. The carbapenems are in an antimicrobial class considered last-resort, they are used to treat human infections caused by multidrug-resistant Enterobacterales, and they are classified by the World Health Organization as 'High Priority Critically Important Antimicrobials'. The presence of carbapenem-resistant Enterobacterales (CREs) of animal-origin is of concern because targeted studies of Canadian retail seafood revealed the presence of carbapenem resistance in a small number of Enterobacterales isolates. To further investigate this issue, a risk profile was developed examining shrimp and salmon, the two most important seafood commodities consumed by Canadians and Escherichia coli, a member of the Enterobacterales order. Carbapenem-resistant E. coli (CREc) isolates have been identified in shrimp and other seafood products. Although carbapenem use in aquaculture has not been reported, several classes of antimicrobials are utilised globally and co-selection of antimicrobial-resistant microorganisms in an aquaculture setting is also of concern. CREs have been identified in retail seafood purchased in Canada and are currently thought to be uncommon. However, data concerning CRE or CREc occurrence and distribution in seafood are limited, and argue for implementation of ongoing or periodic surveillance.

Prevalence of Escherichia coli strains in horticultural farms from Argentina: antibiotic resistance, biofilm formation, and phylogenetic affiliation

Escherichia coli is the bacteria most commonly used as an indicator of fecal contamination in agricultural environments. Moreover, E. coli is categorized as a priority pathogen due to its widespread antibiotic resistance. This study aimed to characterize E. coli strains isolated from 10 horticultural farms. Isolates were obtained from samples of vegetable crops (n = 62), the surrounding soil (n = 62), poultry litter (n = 8), and groundwater (n = 6). Phyllo-grouping assignment was performed on the total of E. coli isolates. Antibiograms and quantification of the minimal inhibitory concentration (MIC) were performed with antibiotics commonly used in humans. Biofilm formation capacity was studied by quantifying cells attached to culture tubes. Overall, 21 E. coli isolates were obtained. Three phylogenetic groups (A, B1, and C) and two Escherichia clade IV and IV-V were identified in the collection by polymerase chain reaction. Sixty-seven percent of the E. coli isolates were resistant to amoxicillin-clavulanic acid and/or ampicillin. Amoxicillin MIC values ranged from 11.9 to >190.5 µg/mL and ampicillin MIC values ranged from 3 to >190.5 µg/mL. All the E. coli isolates, resistant and non-resistant, had biofilm forming capacity. The presence of phenotypic resistance on fresh produce and environmental matrices could present significant opportunities for contamination that result in health risks for consumers. To the authors' best knowledge, this is the first environmental assessment of resistant E. coli occurrence in horticultural farms in South America.

High Prevalence of Antimicrobial Resistance and Integron Gene Cassettes in Multi-Drug-Resistant Klebsiella pneumoniae Isolates From Captive Giant Pandas (Ailuropoda melanoleuca)

Multi-drug-resistant Klebsiella pneumoniae (MDR K. pneumonia) is increasingly being reported with corresponding increase in morbidity and mortality all over the world. However, limited information is available concerning MDR K. pneumonia in giant pandas. The objective of this study was to grasp the drug resistance profile of MDR K. pneumonia isolated from giant pandas. A total of 182 K. pneumoniae isolates were collected from fresh feces of 94 captive giant pandas of different ages and sex and separated by season. We performed a standard disk diffusion antimicrobial susceptibility test with the isolates and further evaluated the antibiotic resistance genes (ARGs) of multi-drug-resistant strains by high-throughput quantitative PCR. In addition, we then analyzed mobile genetic elements (MGEs), integron gene cassettes, and the multi-locus sequence typing of multi-drug-resistant strains by PCR. Antimicrobial susceptibility testing results demonstrated that a total of 30 (16.5%) K. pneumoniae isolates showed multiple drug resistances. The thirty MDR K. pneumonia isolates were mainly resistant to amoxicillin (100.0%), doxycycline (86.7%), chloramphenicol (60.0%), compound trimethoprim (60.0%) and trimethoprim (56.7%). Fifty different types of antibiotic resistance genes were found, which included a total of 671 antibiotic resistance genes, in the 30 multi-drug-resistant isolates. The top ten resistance genes were: vanTC-02, aacC, blaCTX-M-04, blaSHV-01, blaSHV-02, ampC-04, blaOXY, tetD, blaTEM and tetA-02. Thirteen mobile genetic elements were detected, of which IS26 (96.67%) and intI1 (96.67%) had the highest frequency. The thirty MDR K. pneumonia isolates were negative for the traA, traF, tnsA, IS1133, ISpa7, ISkpn6, intI2 and intI3 genes. Moreover, a further investigation of integrons revealed that two types of specific gene cassettes (dfrA12 + orfF + aadA2 and dfrA12 + orfF) were identified in class 1 integrons. Multi-locus sequence typing results showed that 22 STs in the thirty MDR K. pneumonia isolates were identified, the main type was ST37 (5/30). Our results illustrate that effective surveillance and strict biosecurity strategies should be taken to prevent the spread of multi-drug-resistant bacteria, and monitor the emergence of mobile genetic elements and integrons.

Anthropogenic Activities and the Problem of Antibiotic Resistance in Latin America: A Water Issue

Antibiotics revolutionized modern medicine and have been an excellent tool to fight infections. However, their overuse and misuse in different human activities such as health care, food production and agriculture has resulted in a global antimicrobial resistance crisis. Some regions such as Latin America present a more complex scenario because of the lack of resources, systematic studies and legislation to control the use of antimicrobials, thus increasing the spread of antibiotic resistance. This review aims to summarize the state of environmental antibiotic resistance in Latin America, focusing on water resources. Three databases were searched to identify publications on antimicrobial resistance and anthropogenic activities in relation to natural and artificial water ecosystems. We found that antibiotic resistant bacteria, mainly against beta lactam antibiotics, have been reported in several Latin American countries, and that resistant bacteria as well as resistant genes can be isolated from a wide variety of aquatic environments, including drinking, surface, irrigation, sea and wastewater. It is urgent to establish policies and regulations for antibiotic use to prevent the increase of multi-drug resistant microorganisms in the environment.

Evidence for continental-scale dispersal of antimicrobial resistant bacteria by landfill-foraging gulls

Anthropogenic inputs into the environment may serve as sources of antimicrobial resistant bacteria and alter the ecology and population dynamics of synanthropic wild animals by providing supplemental forage. In this study, we used a combination of phenotypic and genomic approaches to characterize antimicrobial resistant indicator bacteria, animal telemetry to describe host movement patterns, and a novel modeling approach to combine information from these diverse data streams to investigate the acquisition and long-distance dispersal of antimicrobial resistant bacteria by landfill-foraging gulls. Our results provide evidence that gulls acquire antimicrobial resistant bacteria from anthropogenic sources, which they may subsequently disperse across and between continents via migratory movements. Furthermore, we introduce a flexible modeling framework to estimate the relative dispersal risk of antimicrobial resistant bacteria in western North America and adjacent areas within East Asia, which may be adapted to provide information on the risk of dissemination of other organisms and pathogens maintained by wildlife through space and time.

Plant Species-Dependent Increased Abundance and Diversity of IncP-1 Plasmids in the Rhizosphere: New Insights Into Their Role and Ecology

IncP-1 plasmids, first isolated from clinical specimens (R751, RP4), are recognized as important vectors spreading antibiotic resistance genes. The abundance of IncP-1 plasmids in the environment, previously reported, suggested a correlation with anthropogenic pollution. Unexpectedly, qPCR-based detection of IncP-1 plasmids revealed also an increased relative abundance of IncP-1 plasmids in total community DNA from the rhizosphere of lettuce and tomato plants grown in non-polluted soil along with plant age. Here we report the successful isolation of IncP-1 plasmids by exploiting their ability to mobilize plasmid pSM1890. IncP-1 plasmids were captured from the rhizosphere but not from bulk soil, and a high diversity was revealed by sequencing 14 different plasmids that were assigned to IncP-1β, δ, and ε subgroups. Although backbone genes were highly conserved and mobile elements or remnants as Tn501, IS1071, Tn402, or class 1 integron were carried by 13 of the sequenced IncP-1 plasmids, no antibiotic resistance genes were found. Instead, seven plasmids had a mer operon with Tn501-like transposon and five plasmids contained putative metabolic gene clusters linked to these mobile elements. In-depth sequence comparisons with previously known plasmids indicate that the IncP-1 plasmids captured from the rhizosphere are archetypes of those found in clinical isolates. Our findings that IncP-1 plasmids do not always carry accessory genes in unpolluted rhizospheres are important to understand the ecology and role of the IncP-1 plasmids in the natural environment.

Antibiotic-contaminated wastewater irrigated vegetables pose resistance selection risks to the gut microbiome

Wastewater reuse in food crop irrigation has led to agroecosystem pollution concerns and human health risks. However, there is limited attention on the relationship of sub-lethal antibiotic levels in vegetables and resistance selection. Most risk assessment studies show non-significant toxicity, but overlook the link between antibiotics in crops and propagation of gut microbiome resistance selection. The review highlights the risk of antibiotics in treated water used for irrigation, uptake, and accumulation in edible vegetable parts. Moreover, it elucidates the risks to the adaptive resistance selection of the gut microbiome from sub-lethal antibiotic levels, as a result of dietary contaminated vegetables. Experiments have reported that bacterial resistance selection is possible at concentrations that are several hundred-folds lower than lethal effect levels on susceptible cells. Consequently, mutants selected at low antibiotic levels, such as those from vegetables, are fitter and more resistant compared to those selected at high concentrations. Necessary standardization, such as the development of minimum acceptable antibiotic limits allowable in food crop irrigation water, with a focus on minimum selection concentration, and not only toxicity, has been proposed. Wastewater irrigation offers environmental benefits and can contribute to food security, but it has non-addressed risks. Research gaps, future perspectives, and frameworks of mitigating the potential risks are discussed.

Environmental fate of Bacteroidetes, with particular emphasis on Bacteroides fragilis group bacteria and their specific antibiotic resistance genes, in activated sludge wastewater treatment plants

The aim of this study was to determine the effect of the activated sludge process on the abundance of anaerobic bacteria of the phylum Bacteroidetes, with special emphasis on Bacteroides fragilis group (BFG) bacteria, in twelve full-scale wastewater treatment plants. The composition of bacterial phyla and classes in wastewater samples were analyzed by next-generation sequencing. The presence of specific to BFG bacteria genes and the abundance of ARGs and genes encoding class 1 integrase in wastewater samples were determined by qPCR. Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes were dominant bacterial phyla in wastewater samples. Next-generation sequencing revealed similar proportions of Bacteroidia (<1.0-8.2 % of all bacteria) in wastewater influents and effluents, which suggest that these microorganisms are not completely eliminated in the activated sludge process. The average copy numbers of specific to BFG bacteria gene, were 10⁶, and 10⁴ copies in 1 mL of wastewater influents and effluents, respectively. The results revealed a correlation between the abundance of BFG bacteria and BFG-specific genes encoding resistance to antibiotics. The observed changes in the prevalence of BFG-specific genes and ARGs in untreated and treated wastewater indicate that the activated sludge process decreases the number of gene copies in the effluent evacuated to the environment.

High prevalence of multi-drug resistances and diversity of mobile genetic elements in Escherichia coli isolates from captive giant pandas

The purpose of this study was to characterize the antimicrobial resistance produced by mobile genetic elements and integron gene cassettes in Escherichia coli isolated from the feces of captive giant pandas. We performed a standard disk diffusion antimicrobial susceptibility test with 84 E. coli isolates and further evaluated the mobile genetic elements and integron gene cassettes. The antimicrobial susceptibility test demonstrated that 43.37% (36/84) of the isolates showed multiple drug resistances. The E. coli isolates mainly showed resistance to aztreonam (86.90%, 73/84) and amoxicillin/clavulanic acid (80.95%, 68/84). The most frequently observed resistance patterns were ampicillin/amoxicillin-clavulanic acid (13.10%, n = 11), and doxycycline/amoxicillin-clavulanic acid (4.76%, n = 4). Further analyses detected 11 mobile genetic elements, of which merA (54/84, 64.30%) had the highest frequency. All isolates were negative for intI3, traA, tnpU, traF, tnp513, tnsA, ISkpn7, ISpa7, ISkpn6, and ISCR1. We further analyzed antimicrobial resistance-related integrons among 30 E. coli isolates (the 27 intI1-positive isolates and the 3 intI2-positive isolates); six gene cassette profiles (dfrA17+aadA5, aadA2, dfrA12+aadA2, dfrA1+aadA1, dfrA1, and aadA1) were identified in the 27 intI1-positive isolates, but not in the three intI2-positive ones. Our study sheds light on the prevalence of multiple drug resistances and the diversity of mobile genetic elements in E. coli isolates, and highlights the necessity to monitor antibiotic resistance in more E. coli strains from captive giant pandas.

Prevalence of class 1 integron in Escherichia coli isolated from animal sources in Iran: a systematic review and meta-analysis

Background

Among the genetic elements, integrons may contribute to the widespread incidence and spreading of antibiotic resistance among Escherichia coli isolates. Accordingly, this review aims to investigate the prevalence of class 1 integron in E. coli isolated from animal sources in Iran.

Methods

This systematic literature search was performed from January 1, 2000 to the end of May 1, 2019.

Then, publications that met our inclusion criteria were selected for data extraction and analysis. Also, the quality of included studies was independently assessed by two researchers based on the Joanna Briggs Institute. Meta-analysis was performed by the Comprehensive Meta-Analysis (CMA) software using the random effects model, Cochran’s Q, and I² tests. Publication bias was estimated by funnel plot and Egger’s linear regression test.

Results

Based on inclusion criteria, five studies were included to meta-analysis. From those studies, the pooled prevalence of integrons was 33% (95% CI, 23.8–43.7%) ranging from 23.8 to 52.4%. There was a significant heterogeneity among the 5 studies (χ² = 11.73; p < 0.019; I² = 65.91%). Additionally, Begg’s and Egger’s tests were performed to quantitatively evaluate the publication biases. According to the results of Begg’s test (z = 1.22, p = 0.22) and Egger’s test (t = 3.03, p = 0.056), a significant publication bias was not observed.

Conclusions

Our finding revealed the relatively high prevalence of class 1 integrons among E. coli isolates. Moreover, there was a significant heterogeneity among studies and subgroup analysis also showed that there was no difference about prevalence of class 1 integrons among different sample source.

A triclosan-resistance protein from the soil metagenome is a novel enoyl-acyl carrier protein reductase: Structure-guided functional analysis

The synthetic biocide triclosan targets enoyl-acyl carrier protein reductase(s) (ENR) in bacterial type II fatty acid biosynthesis. Screening and sequence analyses of the triclosan resistome from the soil metagenome identified a variety of triclosan-resistance ENRs. Interestingly, the mode of triclosan resistance by one hypothetical protein was elusive, mainly due to a lack of sequence similarity with other proteins that mediate triclosan resistance. Here, we carried out a structure-based function prediction of the hypothetical protein, herein referred to as FabMG, and in vivo and in vitro functional analyses. The crystal structure of FabMG showed limited structural homology with FabG and FabI, which are also involved in type II fatty acid synthesis. In vivo complementation and in vitro activity assays indicated that FabMG is functionally a FabI-type ENR that employs NADH as a coenzyme. Variations in the sequence and structure of FabMG are likely responsible for inefficient binding of triclosan, resulting in triclosan resistance. These data unravel a previously uncharacterized FabMG, which is prevalent in various microbes in triclosan-contaminated environments and provide mechanistic insight into triclosan resistance.

Bacteria From the Multi-Contaminated Tinto River Estuary (SW, Spain) Show High Multi-Resistance to Antibiotics and Point to Paenibacillus spp. as Antibiotic-Resistance-Dissemination Players

Bacterial resistance to antibiotics is an ever-increasing phenomenon that, besides clinical settings, is generally assumed to be prevalent in environmental soils and waters. The analysis of bacteria resistant to each one of 11 antibiotics in waters and sediments of the Huelva’s estuary, a multi-contaminated environment, showed high levels of bacteria resistant mainly to Tm, among others. To further gain knowledge on the fate of multi-drug resistance (MDR) in environmental bacteria, 579 ampicillin-resistant bacteria were isolated tested for resistance to 10 antibiotics. 92.7% of the isolates were resistant to four or more antibiotic classes, indicating a high level of multi-resistance. 143 resistance profiles were found. The isolates with different MDR profiles and/or colony morphologies were phylogenetically ascribed based on 16S rDNA to phyla Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes, including 48 genera. Putative intrinsic resistance was detected in different phylogenetic groups including genera Altererythrobacter, Bacillus, Brevundimonas, Erythrobacter, Mesonia, Ochrobactrum, and Ponticaulis. Correlation of the presence of pairs of the non-intrinsic-resistances in phylogenetic groups based on the kappa index (κ) highlighted the co-habitation of some of the tested pairs at different phylogenetic levels. Maximum correlation (κ = 1.000) was found for pairs Cz^R/Tc^R in Betaproteobacteria, and Cc^R/Tc^R and Em^R/Sm^R in Sphingobacteriia at the class level, while at the genus level, was found for Cc^R/Tc^R and Nx^R/Tm^R in Mesonia, Cz^R/Tm^R and Em^R/Km^R in Paenibacillus, and Cc^R/Em^R and Rp^R/Tc^R in Pseudomonas. These results could suggest the existence of intra-class and intra-genus-transmissible genetic elements containing determinants for both members of each pair. Network analysis based on κ values higher than 0.4 indicated the sharing of paired resistances among several genera, many of them centered on the Paenibacillus node and raising the hypothesis of inter-genera transmission of resistances interconnected through members of this genus. This is the first time that a possible hotspot of resistance interchange in a particular environment may have been detected, opening up the possibility that one, or a few, bacterial members of the community could be important promoters of antibiotic resistance (AR) dissemination in this environment’s bacterial population. Further studies using the available isolates will likely give insights of the possible mechanisms and genetic elements involved.

Urban beaches are environmental hotspots for antibiotic resistance following rainfall

To reveal the occurrence and mechanisms for dispersal of antibiotic resistance (AbR) among the microbial assemblages inhabiting impacted coastal environments, we performed a weekly, two-year duration time-series study at two urban beaches between 2014 and 2016. We combined quantitative PCR and multiplex PCR/reverse line blot techniques to track patterns in the occurrence of 31 AbR genes, including genes that confer resistance to antibiotics that are critically important antimicrobials for human medicine. Patterns in the abundance of these genes were linked to specific microbial groups and environmental parameters by coupling qPCR and 16S rRNA amplicon sequencing data with network analysis. Up to 100-fold increases in the abundance of several AbR genes, including genes conferring resistance to quinolones, trimethoprim, sulfonamides, tetracycline, vancomycin and carbapenems, occurred following storm-water and modelled wet-weather sewer overflow events. The abundance of AbR genes strongly and significantly correlated with several potentially pathogenic bacterial OTUs regularly associated with wastewater infrastructure, such as Arcobacter, Acinetobacter, Aeromonas and Cloacibacterium. These high-resolution observations provide clear links between storm-water discharge and sewer overflow events and the occurrence of AbR in the coastal microbial assemblages inhabiting urban beaches, highlighting a direct mechanism for potentially significant AbR exposure risks to humans.

Class 1 integrons as predominant carriers in Escherichia coli isolates from waterfowls in Hainan, China

This study was conducted to determine the prevalence of integrons and associated gene cassettes in Escherichia coli (E. coli) isolates from waterfowls in Hainan, China. The antimicrobial resistance profile of the isolates was examined by using disc diffusion test. In addition, PCR, RFLP, plasmid replicon typing and DNA sequencing analyses were used for the characterization of integrase genes (class 1, 2 and 3) and associated gene cassettes. Approximatively, 90% of the isolates were positive for the integrase genes by PCR. Specifically, class 1 and class 2 integrons were found in 252 (81%) and 7 (2.3%) strains, respectively. While 21 (6.7%) isolates were positive for both class 1 and class 2 integrons. However, none of the isolate was positive for the class 3 integrons. In addition, 5 various cassette arrays, dfrA1-orfC, aadA2, aadA1, dfrA1-aadA1, and dfrA1-orfC- aadA1, were found within the variable regions (VRs) of class 1 integron isolates. While only single cassette array, dfrA1-sat2- aadA1, was identified within VRs of class 2 integron isolates. We identified incF plasmid as the most common plasmid type, which was detected in 81 of 243 VRs containing isolates. This study is the first report showing the baseline characteristics of integrons in E. coli isolates from waterfowls in Hainan, China. Our results provide evidence of the waterfowl birds as a reservoir of class 1 and class 2 integrons carrying antibiotic resistance gene cassettes. Therefore, strict preventive measures should be taken to avoid the spread of mobile genetic resistance elements in waterfowls in China.

Recent advances in dairy goat products

Goat population world-wide is increasing, and the dairy goat sector is developing accordingly. Although the new technology applied to the goat industry is being introduced slowly because the weight of traditional subsector in the dairy sector, considerable advances have been made in the last decade. Present review focuses on the emerging topics in the dairy goat sector. Research and development of traditional and new dairy goat products are reviewed, including the new research in the use of goat milk in infant formula. The research in alternatives to brine, production of skimmed goat cheeses and the use of different modified atmosphere packaging are also addressed. Special attention is given to antibiotic residues and their determination in goat milk. Functional foods for human benefits are a trending topic. Health properties recently discovered in dairy goat products are included in the paper, with special attention to the antioxidant activity. The dual-purpose use of goats by humankind is affecting the way of how new technology is being incorporated in the dairy goat sector and will certainly affect the future development of dairy goat products.

Antibiotic resistance in drinking water systems: Occurrence, removal, and human health risks

In recent years, there has been a growing interest on the occurrence of antibiotic-resistant bacteria (ARB) and antibiotic resistant genes (ARGs) in treated and untreated drinking water. ARB and ARGs pose a public health concern when they transfer antibiotic resistance (AR) to human pathogens. However, it is still unclear whether the presence of environmental ARB and ARGs in source water, drinking water treatment plants, and drinking water distribution systems has any significant impact on human exposure to pathogenic ARB. In this review, we critically examine the occurrence of AR in groundwater, surface water, and treated distributed water. This offered a new perspective on the human health threat posed by AR in drinking water and helped in crafting a strategy for monitoring AR effectively. Using existing data on removal of ARB and ARGs in drinking water treatment plants, presence and proliferation of AR in drinking water distribution systems, and mechanisms and pathways of AR transfer in drinking water treatment plants, we conclude that combining UV-irradiation with advanced oxidative processes (such as UV/chlorine, UV/H₂O₂, and H₂O₂/UV/TiO₂) may enhance the removal of ARB and ARGs, while disinfection may promote horizontal gene transfer from environmental ARB to pathogens. The potential human health risks of AR were determined by examining human exposure to antibiotic resistant human pathogens and re-evaluating waterborne disease outbreaks and their links to environmental AR. We concluded that integrating disease outbreak analysis, human exposure modelling, and clinical data could provide critical information that can be used to estimate the dose-response relationships of pathogenic ARB in drinking water, which is required for accurate risk assessments.

Modelling environmental antibiotic-resistance gene abundance: A meta-analysis

The successful treatment of infectious diseases heavily relies on the therapeutic usage of antibiotics. However, the high use of antibiotics in humans and animals leads to increasing pressure on bacterial populations in favour of resistant phenotypes. Antibiotics reach the environment from a variety of emission sources and are being detected at relatively low concentrations. Given the possibility of selective pressure to occur at sub-inhibitory concentrations, the ecological impact of environmental antibiotic levels on microbial communities and resistance levels is vastly unknown. Quantification of antibiotic-resistance genes (ARG) and of antibiotic concentrations is becoming commonplace. Yet, these two parameters are often assessed separately and in a specific spatiotemporal context, thus missing the opportunity to investigate how antibiotics and ARGs relate. Furthermore, antibiotic (multi)resistance has been receiving ever growing attention from researchers, policy-makers, businesses and civil society. Our aim was to collect the limited data on antibiotic concentrations and ARG abundance currently available to explore if a relationship could be defined in surface waters, sediments and wastewaters. A metric of antibiotic selective pressure, i.e. the sum of concentrations corrected for microbial inhibition potency, was used to correlate the presence of antibiotics in the environment to total relative abundance of ARG while controlling for basic sources of non-independent variability, such as country, year, study, sample and antibiotic class. The results of this meta-analysis show a significant statistical effect of antibiotic pressure and type of environmental compartment on the increase of ARG abundance even at very low levels. If global environmental antibiotic pollution continues, ARG abundance is expected to continue as well. Moreover, our analysis emphasizes the importance of integrating existing information particularly when attempting to describe complex relationships with limited mechanistic understanding.

Relationship between modification of activated sludge wastewater treatment and changes in antibiotic resistance of bacteria

Biological treatment processes at wastewater treatment plants (WWTPs), which are the most common methods of sewage treatment, could cause selective elimination and/or changes in the proportions of phenotypes/genotypes within bacterial populations in effluent. Therefore, WWTPs based on activated sludge used in sewage treatment constitute an important reservoir of enteric bacteria which harbour potentially transferable resistance genes. Together with treated wastewater, these microorganisms can penetrate the soil, surface water, rural groundwater supplies and drinking water. Because of this, the aim of this study was to determine the impact of various modification of sewage treatment (the conventional anaerobic/anoxic/oxic (A2/O) process, mechanical-biological (MB) system, sequencing batch reactors (SBR), mechanical-biological system with elevated removal of nutrients (MB-ERN)) on the amount of antibiotic resistant bacteria (ARB) (including E. coli) and antibiotic resistance genes (ARGs) in sewage flowing out of the 13 treatment plants using activated sludge technology. There were no significant differences in ARB and ARGs regardless of time of sampling and type of treated wastewater (p > 0.05). The highest percentage of reduction (up to 99.9%) in the amount of ARB and ARGs was observed in WWTPs with MB and MB-ERN systems. The lowest reduction was detected in WWTPs with SBR. A significant increase (p < 0.05) in the percentage of bacteria resistant to the new generation antibiotics (CTX and DOX) in total counts of microorganisms was observed in effluents (EFF) from WWTPs with A2/O system and with SBR. Among all ARGs analyzed, the highest prevalence of ARGs copies in EFF samples was observed for sul1, tet(A) and qepA, the lowest for bla_TEM and bla_SHV. Although, the results of presented study demonstrate high efficiency of ARB and ARGs removal during the wastewater treatment processes, especially by WWTPs with MB and MB-ERN systems, EFF is still an important reservoir of ARGs which can be transferred to other microorganisms.

Critical knowledge gaps and research needs related to the environmental dimensions of antibiotic resistance

There is growing understanding that the environment plays an important role both in the transmission of antibiotic resistant pathogens and in their evolution. Accordingly, researchers and stakeholders world-wide seek to further explore the mechanisms and drivers involved, quantify risks and identify suitable interventions. There is a clear value in establishing research needs and coordinating efforts within and across nations in order to best tackle this global challenge. At an international workshop in late September 2017, scientists from 14 countries with expertise on the environmental dimensions of antibiotic resistance gathered to define critical knowledge gaps. Four key areas were identified where research is urgently needed: 1) the relative contributions of different sources of antibiotics and antibiotic resistant bacteria into the environment; 2) the role of the environment, and particularly anthropogenic inputs, in the evolution of resistance; 3) the overall human and animal health impacts caused by exposure to environmental resistant bacteria; and 4) the efficacy and feasibility of different technological, social, economic and behavioral interventions to mitigate environmental antibiotic resistance.1.