Discovery of Highly Trimethoprim-Resistant DfrB Dihydrofolate Reductases in Diverse Environmental Settings Suggests an Evolutionary Advantage Unrelated to Antibiotic Resistance

Type B dihydrofolate reductases (DfrB) are intrinsically highly resistant to the widely used antibiotic trimethoprim, posing a threat to global public health. The ten known DfrB family members have been strongly associated with genetic material related to the application of antibiotics. Several dfrB genes were associated with multidrug resistance contexts and mobile genetic elements, integrated both in chromosomes and plasmids. However, little is known regarding their presence in other environments. Here, we investigated the presence of dfrB beyond the traditional areas of enquiry by conducting metagenomic database searches from environmental settings where antibiotics are not prevalent. Thirty putative DfrB homologues that share 62 to 95% identity with characterized DfrB were identified. Expression of ten representative homologues verified trimethoprim resistance in all and dihydrofolate reductase activity in most. Contrary to samples associated with the use of antibiotics, the newly identified dfrB were rarely associated with mobile genetic elements or antibiotic resistance genes. Instead, association with metabolic enzymes was observed, suggesting an evolutionary advantage unrelated to antibiotic resistance. Our results are consistent with the hypothesis that multiple dfrB exist in diverse environments from which dfrB were mobilized into the clinically relevant resistome. Our observations reinforce the need to closely monitor their progression.

Impact of Anthropogenic Activities on the Dissemination of ARGs in the Environment-A Review

Over the past few decades, due to the excessive consumption of drugs in human and veterinary medicine, the antimicrobial resistance (AR) of microorganisms has risen considerably across the world, and this trend is predicted to intensify. Many worrying research results indicate the occurrence of pools of AR, both directly related to human activity and environmental factors. The increase of AR in the natural environment is mainly associated with the anthropogenic activity. The dissemination of AR is significantly stimulated by the operation of municipal facilities, such as wastewater treatment plants (WWTPs) or landfills, as well as biogas plants, agriculture and farming practices, including animal production and land application of manure. These activities entail a risk to public health by spreading bacteria resistant to antimicrobial products (ARB) and antibiotic resistance genes (ARGs). Furthermore, subinhibitory concentrations of antimicrobial substances additionally predispose microbial consortia and resistomes to changes in particular environments that are permeated by these micropollutants. The current state of knowledge on the fate of ARGs, their dissemination and the complexity of the AR phenomenon in relation to anthropogenic activity is inadequate. This review summarizes the state-of-the-art knowledge on AR in the environment, in particular focusing on AR spread in an anthropogenically altered environment and related environmental consequences.

Novel Mobile Integrons and Strain-Specific Integrase Genes within Shewanella spp. Unveil Multiple Lateral Genetic Transfer Events within The Genus

Shewanella spp. are Gram-negative bacteria that thrive in aquatic niches and also can cause infectious diseases as opportunistic pathogens. Chromosomal (CI) and mobile integrons (MI) were previously described in some Shewanella isolates. Here, we evaluated the occurrence of integrase genes, the integron systems and their genetic surroundings in the genus. We identified 22 integrase gene types, 17 of which were newly described, showing traits of multiple events of lateral genetic transfer (LGT). Phylogenetic analysis showed that most of them were strain-specific, except for Shewanella algae, where SonIntIA-like may have co-evolved within the host as typical CIs. It is noteworthy that co-existence of up to five different integrase genes within a strain, as well as their wide dissemination to Alteromonadales, Vibrionales, Chromatiales, Oceanospirillales and Enterobacterales was observed. In addition, identification of two novel MIs suggests that continuous LGT events may have occurred resembling the behavior of class 1 integrons. The constant emergence of determinants associated to antimicrobial resistance worldwide, concomitantly with novel MIs in strains capable to harbor several types of integrons, may be an alarming threat for the recruitment of novel antimicrobial resistance gene cassettes in the genus Shewanella, with its consequent contribution towards multidrug resistance in clinical isolates.

Existing evidence on antibiotic resistance exposure and transmission to humans from the environment: a systematic map

BACKGROUND

Antimicrobial resistance (AMR) is predicted to become the leading cause of death by 2050 with antibiotic resistance being an important component. Anthropogenic pollution introduces antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) to the natural environment. Currently, there is limited empirical evidence demonstrating whether humans are exposed to environmental AMR and whether this exposure can result in measurable human health outcomes. In recent years there has been increasing interest in the role of the environment and disparate evidence on transmission of AMR to humans has been generated but there has been no systematic attempt to summarise this. We aim to create two systematic maps that will collate the evidence for (1) the transmission of antibiotic resistance from the natural environment to humans on a global scale and (2) the state of antibiotic resistance in the environment in the United Kingdom.

METHODS

Search strategies were developed for each map. Searches were undertaken in 13 bibliographic databases. Key websites were searched and experts consulted for grey literature. Search results were managed using EndNote X8. Titles and abstracts were screened, followed by the full texts. Articles were double screened at a minimum of 10% at both stages with consistency checking and discussion when disagreements arose. Data extraction occurred in Excel with bespoke forms designed. Data extracted from each selected study included: bibliographic information; study site location; exposure source; exposure route; human health outcome (Map 1); prevalence/percentage/abundance of ARB/antibiotic resistance elements (Map 2) and study design. EviAtlas was used to visualise outputs.

RESULTS

For Map 1, 40 articles were included, from 11,016 unique articles identified in searches, which investigated transmission of AMR from the environment to humans. Results from Map 1 showed that consumption/ingestion was the most studied transmission route. Exposure (n = 17), infection (n = 16) and colonisation (n = 11) being studied as an outcome a similar number of times, with mortality studied infrequently (n = 2). In addition, E. coli was the most highly studied bacterium (n = 16). For Map 2, we included 62 studies quantifying ARB or resistance elements in the environment in the UK, from 6874 unique articles were identified in the searches. The most highly researched species was mixed communities (n = 32). The most common methodology employed in this research question was phenotypic testing (n = 37). The most commonly reported outcome was the characterisation of ARBs (n = 40), followed by characterisation of ARGs (n = 35). Other genetic elements, such as screening for intI1 (n = 15) (which encodes a Class 1 integron which is used as a proxy for environmental ARGs) and point mutations (n = 1) were less frequently reported. Both maps showed that research was focused towards aquatic environments.

CONCLUSIONS

Both maps can be used by policy makers to show the global (Map 1) and UK (Map 2) research landscapes and provide an overview of the state of AMR in the environment and human health impacts of interacting with the environment. We have also identified (1) clusters of research which may be used to perform meta-analyses and (2) gaps in the evidence base where future primary research should focus.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1186/s13750-022-00262-2.

Metagenomic profiles of the resistome in subtropical estuaries: Co-occurrence patterns, indicative genes, and driving factors

Estuaries are resistome hotspots owing to resistome accumulation and propagation at these locations from surrounding rivers, yet the large-scale biogeographic pattern of resistome, especially biocide and metal resistance genes (BMRGs) and its driving mechanisms in estuarine waters remains to be elucidated. Here, a metagenomics-based approach was firstly used to investigate resistome and mobilome profiles in waters from 30 subtropical estuaries, South China. The Pearl River estuaries had a higher diversity and abundance of antibiotic resistance genes (ARGs), BMRGs, and mobile genetic elements (MGEs) when compared with estuaries from east and west regions. Genes resistant to multiple antibiotics, metals, and biocides were the most abundant gene types in the resistome. The abundance of MGEs (e.g., intI1, IS91, and tnpA) was highly associated with the total abundance of resistance genes, suggesting their utility as potential indicators for quantitative estimations of the resistome contamination. Further, MGEs contributed more than bacterial communities in shaping the resistome in subtropical estuaries. Physicochemical factors (e.g., pH) regulated MGE composition and stochastic assembly, which mediated the co-selection of ARGs and BMRGs via horizontal gene transfer. Our findings have important implications and provide a reference on the management of ARGs and BMRGs in subtropical estuarine ecosystems.

Environmental integrons: the dark side of the integron world

Integrons are bacterial genetic elements notorious for their role in spreading antibiotic resistance in clinical settings. In the natural environment, integrons present a wide and hidden diversity, raising questions as to their broader role in bacterial adaptation. From the One Health perspective, they must be considered a threatening pool of resistance determinants.

Microbial and chemical pollutants on the manure-crops pathway in the perspective of "One Health" holistic approach

This study determined the impact of poultry and bovine manure fertilization on the content of antibiotics, heavy metals (HMs), and the quantitative and qualitative composition of integrase and antibiotic resistance genes in soil, groundwater, and crops cultivated on manure-amended plots. Antibiotic concentration levels were analyzed using the HPLC-MS/MS, heavy metal concentration level were measured by HGAAS and ICP-OES, while the integrase genes and ARGs were quantified using Real-Time PCR (qPCR) method. Manure, soil, and crops samples contained the highest concentration of Zn (10⁴-10⁵ ng g_dm^-1) and Cu (10³-10⁵ ng g_dm^-1) of all HMs tested. Manure-supplemented soil was characterised by a high concentration of doxycycline and enrofloxacin. A high abundance of integrase genes was noted in samples of manure (10⁹-10¹⁰ copies g_dm^-1) and soil (10⁷-10⁸ copies g_dm^-1). Among all the analyzed genes, sul1, sul2, bla_TEM, and integrase genes were the most common. Results of the study demonstrate the selective character of ARGs transfer from poultry and bovine manure to plants. The only gene to occur in all studied environmental compartments was sul1 (from 10² - groundwater to 10¹¹ - poultry manure). It was also found that animal manure may cause an increase in the HMs concentration in soil and their accumulation in crops, which may influence the health of humans and animals consuming crops grown on manure-amended soil. The high abundance of integrase genes and ARGs and their reciprocal correlations with HMs pose a serious risk of the rapid spread of antibiotic resistance in the environment. Moreover, unusual dependencies between integrase genes and selected ARGs indicate the possibility of changes in the mobility nature of genetic elements.

Effect of Urban Wastewater Discharge on the Abundance of Antibiotic Resistance Genes and Antibiotic-Resistant Escherichia coli in Two Italian Rivers

Background: Wastewater treatment plants (WWTPs) are microbial factories aimed to reduce the amount of nutrients and pathogenic microorganisms in the treated wastewater before its discharge into the environment. We studied the impact of urban WWTP effluents on the abundance of antibiotic resistance genes (ARGs) and antibiotic-resistant Escherichia coli (AR-E. coli) in the last stretch of two rivers (Arrone and Tiber) in Central Italy that differ in size and flow volume. Methods: Water samples were collected in three seasons upstream and downstream of the WWTP, at the WWTP outlet, and at sea sites near the river mouth, and analyzed for the abundance of ARGs by qPCR and AR-E. coli using cultivation followed by disk diffusion assays. Results: For all studied genes (16S rRNA, intI1, sul1, ermB, blaTEM, tetW and qnrS), absolute concentrations were significantly higher in the Tiber than in the Arrone at all sampling sites, despite their collection date, but the prevalence of target ARGs within bacterial communities in both rivers was similar. The absolute concentrations of most ARGs were also generally higher in the WWTP effluent with median levels between log 4 and log 6 copies per ml but did not show differences along the studied stretches of rivers. Statistically significant site effect was found for E. coli phenotypic resistance to tetracycline and ciprofloxacin in the Arrone but not in the Tiber. Conclusions: In both rivers, diffuse or point pollution sources other than the studied WWTP effluents may account for the observed resistance pattern, although the Arrone appears as more sensitive to the wastewater impact considering its lower flow volume.

Evolution of antibiotic resistance at low antibiotic concentrations including selection below the minimal selective concentration

Determining the selective potential of antibiotics at environmental concentrations is critical for designing effective strategies to limit selection for antibiotic resistance. This study determined the minimal selective concentrations (MSCs) for macrolide and fluoroquinolone antibiotics included on the European Commissionʼs Water Framework Directive’s priority hazardous substances Watch List. The macrolides demonstrated positive selection for ermF at concentrations 1–2 orders of magnitude greater (>500 and <750 µg/L) than measured environmental concentrations (MECs). Ciprofloxacin illustrated positive selection for intI1 at concentrations similar to current MECs (>7.8 and <15.6 µg/L). This highlights the need for compound specific assessment of selective potential. In addition, a sub-MSC selective window defined by the minimal increased persistence concentration (MIPC) is described. Differential rates of negative selection (or persistence) were associated with elevated prevalence relative to the no antibiotic control below the MSC. This increased persistence leads to opportunities for further selection over time and risk of human exposure and environmental transmission.

Stanton et al. determine the minimal selective concentrations for macrolide and fluoroquinolone antibiotics and describe a selective window defined by the minimal increased persistence concentration. These assessments and thresholds allow for better assessment of potential selection for antibiotic resistance and the risks of human exposure and environmental transmission.

The legacy of industrial pollution in estuarine sediments: spatial and temporal variability implications for ecosystem stress

The direct impacts of anthropogenic pollution are widely known public and environmental health concerns, and details on the indirect impact of these are starting to emerge, for example affecting the environmental microbiome. Anthropogenic activities throughout history with associated pollution burdens are notable contributors. Focusing on the historically heavily industrialised River Clyde, Scotland, we investigate spatial and temporal contributions to stressful/hostile environments using a geochemical framework, e.g. pH, EC, total organic carbon and potentially toxic elements: As, Co, Cr, Cu, Ni, Pb and Zn and enrichment indicators. With regular breaches of the sediment quality standards in the estuarine system we focused on PTE correlations instead. Multivariate statistical analysis (principle component analysis) identifies two dominant components, PC1: As, Cr, Cu, Pb and Zn, as well as PC2: Ni, Co and total organic carbon. Our assessment confirms hot spots in the Clyde Estuary indicative of localised inputs. In addition, there are sites with high variability indicative of excessive mixing. We demonstrate that industrialised areas are dynamic environmental sites dependant on historical anthropogenic activity with short-scale variation. This work supports the development of 'contamination' mapping to enable an assessment of the impact of historical anthropogenic pollution, identifying specific 'stressors' that can impact the microbiome, neglecting in estuarine recovery dynamics and potentially supporting the emergence of antimicrobial resistance in the environment.

The Peril and Promise of Integrons: Beyond Antibiotic Resistance

Integrons are bacterial genetic elements that can capture, rearrange, and express mobile gene cassettes. They are best known for their role in disseminating antibiotic-resistance genes among pathogens. Their ability to rapidly spread resistance phenotypes makes it important to consider what other integron-mediated traits might impact human health in the future, such as increased virulence, pathogenicity, or resistance to novel antimicrobial strategies. Exploring the functional diversity of cassettes and understanding their de novo creation will allow better pre-emptive management of bacterial growth, while also facilitating development of technologies that could harness integron activity. If we can control integrons and cassette formation, we could use integrons as a platform for enzyme discovery and to construct novel biochemical pathways, with applications in bioremediation or biosynthesis of industrial and therapeutic molecules. Integron activity thus holds both peril and promise for humans.

High diversity and rapid spatial turnover of integron gene cassettes in soil

Integrons are genetic elements that promote rapid adaptation in bacteria by capturing exogenous, mobile gene cassettes. Recently, a subset of gene cassettes has facilitated the global spread of antibiotic resistance. However, outside clinical settings, very little is known about their diversity and spatial ecology. To address this question, we sequenced integron gene cassettes from soils sampled across Australia and Antarctica. We recovered 44 970 open reading frames that encoded 27 215 unique proteins, representing an order of magnitude more cassettes than previous sequencing efforts. We found that cassettes have extremely high local richness, significantly greater than previously predicted, with estimates ranging from 4000 to 18 000 unique cassettes per 0.3 g of soil. We show that cassettes have a heterogeneous distribution across space, and that they exhibit rapid turnover with distance. Similarity between samples drops to between 0.1% and 10% at distances of as little as 100 m. Together, these data provide key insights into the ecology and size of the gene cassette metagenome.

Co-selection of multi-antibiotic resistance in bacterial pathogens in metal and microplastic contaminated environments: An emerging health threat

Misuse/over use of antibiotics increases the threats to human health since this is a main reason behind evolution of antibiotic resistant bacterial pathogens. However, metals such as mercury, lead, zinc, copper and cadmium are accumulating to critical concentration in the environment and triggering co-selection of antibiotic resistance in bacteria. The co-selection of metal driven antibiotic resistance in bacteria is achieved through co-resistance or cross resistance. Metal driven antibiotic resistant determinants evolved in bacteria and present on same mobile genetic elements are horizontally transferred to distantly related bacterial human pathogens. Additionally, in marine environment persistent pollutants like microplastics is recognized as a vector for the proliferation of metal/antibiotics and human pathogens. Recently published research confirmed that horizontal gene transfer between phylogenetically distinct microbes present on microplastics is much faster than free living microbes. Therefore, microplastics act as an emerging hotspot for metal driven co-selection of multidrug resistant human pathogens and pose serious threat to humans which do recreational activities in marine environment and ingest marine derived foods. Therefore, marine environment co-polluted with metal, antibiotics, human pathogens and microplastics pose an emerging health threat globally.

Long-Term Nickel Contamination Increases the Occurrence of Antibiotic Resistance Genes in Agricultural Soils

Heavy metal contamination is assumed to be a selection pressure on antibiotic resistance, but to our knowledge, evidence of the heavy metal-induced changes of antibiotic resistance is lacking on a long-term basis. Using quantitative PCR array and Illumina sequencing, we investigated the changes of a wide spectrum of soil antibiotic resistance genes (ARGs) following 4-5 year nickel exposure (0-800 mg kg^-1) in two long-term experimental sites. A total of 149 unique ARGs were detected, with multidrug and β-lactam resistance as the most prevailing ARG types. The frequencies and abundance of ARGs tended to increase along the gradient of increasing nickel concentrations, with the highest values recorded in the treatments amended with 400 mg nickel kg^-1 soil. The abundance of mobile genetic elements (MGEs) was significantly associated with ARGs, suggesting that nickel exposure might enhance the potential for horizontal transfer of ARGs. Network analysis demonstrated significant associations between ARGs and MGEs, with the integrase intI1 gene having the most frequent interactions with other co-occurring ARGs. The changes of ARGs were mainly driven by nickel bioavailability and MGEs as revealed by structural equation models. Taken together, long-term nickel exposure significantly increased the diversity, abundance, and horizontal transfer potential of soil ARGs.

Relationship between antibiotic resistance genes and metals in residential soil samples from Western Australia

Increasing drug-resistant infections have drawn research interest towards examining environmental bacteria and the discovery that many factors, including elevated metal conditions, contribute to proliferation of antibiotic resistance (AR). This study examined 90 garden soils from Western Australia to evaluate predictions of antibiotic resistance genes from total metal conditions by comparing the concentrations of 12 metals and 13 genes related to tetracycline, beta-lactam and sulphonamide resistance. Relationships existed between metals and genes, but trends varied. All metals, except Se and Co, were related to at least one AR gene in terms of absolute gene numbers, but only Al, Mn and Pb were associated with a higher percentage of soil bacteria exhibiting resistance, which is a possible indicator of population selection. Correlations improved when multiple factors were considered simultaneously in a multiple linear regression model, suggesting the possibility of additive effects occurring. Soil-metal concentrations must be considered when determining risks of AR in the environment and the proliferation of resistance.

Field-based evidence for copper contamination induced changes of antibiotic resistance in agricultural soils

Bacterial resistance to antibiotics and heavy metals are frequently linked, suggesting that exposure to heavy metals might select for bacterial assemblages conferring resistance to antibiotics. However, there is a lack of clear evidence for the heavy metal-induced changes of antibiotic resistance in a long-term basis. Here, we used high-capacity quantitative PCR array to investigate the responses of a broad spectrum of antibiotic resistance genes (ARGs) to 4-5 year copper contamination (0-800 mg kg^-1 ) in two contrasting agricultural soils. In total, 157 and 149 unique ARGs were detected in the red and fluvo-aquic soil, respectively, with multidrug and β-lactam as the most dominant ARG types. The highest diversity and abundance of ARGs were observed in medium copper concentrations (100-200 mg kg^-1 ) of the red soil and in high copper concentrations (400-800 mg kg^-1 ) of the fluvo-aquic soil. The abundances of total ARGs and several ARG types had significantly positive correlations with mobile genetic elements (MGEs), suggesting mobility potential of ARGs in copper-contaminated soils. Network analysis revealed significant co-occurrence patterns between ARGs and microbial taxa, indicating strong associations between ARGs and bacterial communities. Structural equation models showed that the significant impacts of copper contamination on ARG patterns were mainly driven by changes in bacterial community compositions and MGEs. Our results provide field-based evidence that long-term Cu contamination significantly changed the diversity, abundance and mobility potential of environmental antibiotic resistance, and caution the un-perceived risk of the ARG dissemination in heavy metal polluted environments.