Urban informal settlements as hotspots of antimicrobial resistance and the need to curb environmental transmission

Pollution by antimicrobials and antibiotic resistance genes in East Africa: Occurrence, sources, and potential environmental implications

The escalating burden of antimicrobial pollution in East Africa poses severe threats to public health, environmental integrity, and economic stability. Environmental compartments such as soil and water serve as reservoirs for these pollutants such as antimicrobials and antibiotic resistance genes, creating selective pressure that accelerates the emergence of antimicrobial resistance (AMR). These dynamic fosters the proliferation of multidrug-resistant pathogens, or "superbugs," complicating infection management and amplifying health risks in a region already challenged by inadequate healthcare and sanitation infrastructure. Furthermore, pollution by antimicrobials and antibiotic resistance genes critically disrupts ecological processes, such as nutrient cycling and organic matter degradation, diminishing soil fertility, water quality, and agricultural productivity, thereby threatening food security and overall ecological health. Current surveillance efforts, including the Global Antimicrobial Resistance and Use Surveillance System (GLASS) and the East Africa Public Health Laboratory Networking Project (EAPHLNP), have made strides in tracking AMR trends and guiding policy decisions. However, these efforts remain insufficient to address the growing crisis. This study highlights the urgent need for integrated strategies, including stringent antibiotic usage regulations, advanced wastewater treatment technologies, and comprehensive environmental surveillance. Therefore, there is a need to address the intersections of health, agriculture, and environment, to mitigate AMR and its far-reaching consequences to ensure public health safety and sustainability.

Molecular-Level Strategy from Bottom-Up to Acquire High-Efficiency Antimicrobial Peptides

The escalating threat of multidrug-resistant pathogens necessitates efficient antimicrobial development, in which antimicrobial peptides (AMPs) have been extensively studied due to their broad-spectrum antibiotic activity. Combining sum frequency generation and molecular dynamics simulation, we rationally designed AMPs by identifying two structural principles. Simply increasing the number of basic amino acids does not reliably improve antimicrobial efficacy; terminal (N' and C') phenylalanine residues can enhance AMP's membrane interfacial activity via the hydrophobic effect. After two rounds of sequence optimization, among the derivatives we designed, an artificial AMP named GF demonstrated superior membrane binding (especially insertion) and spatial conformation stability. In vitro and in vivo evaluations revealed GF's potential broad-spectrum efficacy against common bacteria and drug-resistant bacteria. Notably, GF exhibited enhanced antimicrobial potency over conventional antibiotics at lower concentrations. Our study established a bottom-up (mechanism-driven) design framework and provided a template for developing precision antimicrobials against resistant infections.

Transmissible antimicrobial resistance in Escherichia coli isolated from household drinking water in Ibadan, Nigeria

Contaminated household water in peri-urban communities is a reservoir for virulent Escherichia coli, but its role in the environmental transmission of antibiotic resistance genes (ARGs) remains poorly understood. This study characterized E. coli from household water and additionally aimed to investigate the transmissibility of ARGs from drug-resistant isolates. Twenty-five E. coli isolates from thirteen household well water sources were tested for resistance to 14 antibiotics by disc diffusion and whole-genome sequenced using the Illumina platform. The ARGs and plasmid replicon types were respectively predicted using ResFinder and PlasmidFinder. Multidrug-resistant strains carrying plasmid replicons found in unrelated strains were conjugated with nalidixic acid-resistant (NALR) E. coli C600 using the solid plate method. Fifteen isolates displayed a multi-drug resistance (MDR) phenotype, with 18 possessing ARGs that confer resistance to trimethoprim-sulfamethoxazole, macrolide, sulphonamide, aminoglycoside, chloramphenicol, β-lactams, and tetracycline. Fifteen of the 25 isolates belonged to sequence type detected more than once, and fourteen of these were multidrug resistant. Through solid plate mating, beta-lactam-resistant qnrS1-tet-dfrA14-positive strains bearing IncFI-, IncHI2, and IncHI2A successfully transferred ampicillin resistance to a nalidixic acid-resistant derivative of E. coli-C600. This research highlights the urgent need to safeguard household water sources against fecal contamination to curb the dissemination of ARGs among bacterial populations in this environment.

Gender differences in global antimicrobial resistance

Antimicrobial resistance is one of the leading causes of mortality globally. However, little is known about the distribution of antibiotic resistance genes (ARGs) in human gut metagenomes, collectively referred to as the resistome, across socio-demographic gradients. In particular, limited evidence exists on gender-based differences. We investigated how the resistomes differ between women and men in a global dataset of 14,641 publicly available human gut metagenomes encompassing countries with widely variable economic statuses. We observed a 9% higher total ARG load in women than in men in high-income countries. However, in low- and middle-income countries, the difference between genders was reversed in univariate models, but not significant after adjusting for covariates. Interestingly, the differences in ARG load between genders emerged in adulthood, suggesting resistomes differentiate between genders after childhood. Collectively, our data-driven analyses shed light on global, gendered antibiotic resistance patterns, which may help guide further research and targeted interventions.

Potential environmental transmission of antibiotic-resistant Escherichia coli and Enterococcus faecium harbouring multiple antibiotic resistance genes and mobile genetic elements in surface waters close to informal settlements: A tale of two cities

Aquatic environments, including wastewater and surface water (rivers and streams), increasingly harbour third-generation cephalosporin-resistant Escherichia coli and drug-resistant Enterococcus faecium, presenting a transmission risk to humans, animals, and plants. We investigated the resistome, mobilome, and phylogenetic relationships of antibiotic-resistant E. coli and E. faecium in surface water from two cities using whole genome sequencing (WGS). Water samples (500 mL) from streams near informal settlements in Durban and Pietermaritzburg were filtered through 0.45 μm membrane filters. E. faecium and E. coli were identified on selective media and tested for antibiotic susceptibility using the VITEK® 2 platform. DNA was extracted from isolates for WGS to delineate the resistome, mobilome, multi-locus strain types (STs) and phylogenetic relationships using the open-source CARD, CGE, RAST, BV-BRC and PubMLST tools. Eleven E. faecium and 12 E. coli isolates were molecularly identified. Antibiotic resistance was observed in seven E. coli belonging to two STs and seven E. faecium belonging to five STs. Third and fourth-generation cephalosporin-resistant E. coli (3/7) were found in Durban. These isolates did not harbour extended-spectrum β-lactamase genes conferring cephalosporin resistance but had the AcrAB-TolC efflux pump for multiple antibiotic resistance. E. coli harboured blaTEM-1, sul1, sul3, and dfrA12, conferring resistance to amoxicillin-clavulanic acid, piperacillin-tazobactam and cotrimoxazole, respectively. Also, E. faecium harboured qnrB19, qnrS1, tet(A), cmlA1, aadA1 and aadA2. tet(M), tet(L), msr(C) and erm(B) conferring resistance to tetracycline and erythromycin, respectively. ARGs and MGEs in E. faecium were mostly chromosome-borne. Plasmid-carried ARGs were associated with IS1, IS1B, IS6, IS256 and ISKpn19, and the Tn3 transposons in E. coli. Phylogenetic analysis revealed close relationships with other South African human, animal and environmental isolates. These ARGs, associated with MGEs, present possible transmission routes of these resistance genes within and across bacterial species in aquatic environments, making these surface waters potential reservoirs for antibiotic resistance transmission.

Contaminated drinking water facilitates Escherichia coli strain-sharing within households in urban informal settlements

Identifying bacterial transmission pathways is crucial to inform strategies that limit the spread of pathogenic and antibiotic-resistant bacteria. Here we assessed Escherichia coli strain-sharing and overlap of antibiotic resistance genes (ARGs) across humans, poultry, canines, soil, and drinking water within and between households in urban informal settlements in Nairobi, Kenya. We collected 321 samples from 50 households with half having access to chlorinated water. We performed Pooling Isolated Colonies-seq, which sequences pools of up to five E. coli colonies per sample to capture strain diversity. Pooling Isolated Colonies-seq captured 1,516 colonies and identified 154 strain-sharing events, overcoming limitations of single-isolate sequencing and metagenomics. Within households, strain-sharing rates and resistome similarities across sample types were strongly correlated, suggesting clonal transmission of ARGs. E. coli isolated from the environment carried clinically relevant ARGs. Strain-sharing was rare between animals and humans but frequent between humans and drinking water. E. coli-contaminated stored drinking water was associated with higher human-human strain-sharing within households. These results suggest that contaminated drinking water facilitates human to human strain-sharing, and water treatment can disrupt transmission.

Environmental concentrations of copper and iron can alter the evolution of antimicrobial resistance of E. coli against ciprofloxacin and doxycycline

Antimicrobial resistance (AMR) is a global health challenge and there is increasing recognition of the role of the environment, particularly wastewater, in the development and spread of AMR. Although trace metals are common contaminants in wastewater, the quantitative effects of trace metals on AMR in wastewater settings remain understudied. We experimentally determined the interactions between common antibiotic residues and metal ions found in wastewater and investigated their effects on the development of antibiotic resistance in Escherichia coli over time. These data were then used to expand on a previously developed computational model of antibiotic resistance development in continuous flow settings to incorporate the effects of trace metals acting in combination with multiple antibiotic residues. We found that copper and iron, interact with both ciprofloxacin and doxycycline at wastewater relevant concentrations. This can significantly affect resistance development due to antibiotic chelation of the metal ions causing a reduction in the antibiotics' bioactivity. Furthermore, modeling the effect of these interactions in wastewater systems showed the potential for metal ions in wastewater to significantly increase the development of antibiotic resistant E. coli populations. These results demonstrate the need to quantitatively understand the effects of trace metal-antibiotic interactions on AMR development in wastewater.

Antihistamine drug loratadine at environmentally relevant concentrations promotes conjugative transfer of antibiotic resistance genes: Coeffect of oxidative stress and ion transport

Due to the widespread use of loratadine (LOR) as an antihistamine, it is widely distributed in the environment as an emerging contaminant. However, its impact on the dissemination of antibiotic resistance genes (ARGs) remains unclear. This study investigated the effect of LOR on the conjugative transfer of ARGs and elucidated the potential mechanisms through transcriptome analysis. The results showed that LOR significantly promoted the frequency of conjugative transfer up to 1.5- to 8.6-fold higher compared with the control group. Exposure to LOR increased reactive oxidative species (ROS) and intracellular Ca2+ concentrations, leading to the upregulation of expression of genes related to transmembrane transport and SOS response. Meanwhile, it stimulated the increase of cell membrane permeability. Moreover, LOR exposure could enhance H+ efflux in donor bacteria, resulting in the decrease of intracellular pH and the elevation of transmembrane potential, which could induce the increase of ion transport, thereby promoting plasmid efflux from the cell membrane. Based on this, we inferred that LOR can induce an increase in ROS level and intracellular Ca2+ concentrations, and promoted the efflux of intracellular H+. This, in turn, triggered the intensification of various ion transport processes on the cell membrane, thereby increasing membrane permeability and accelerating plasmid efflux. Ultimately, the coeffect of oxidative stress response and ion transport promoted conjugative transfer. This study demonstrated that LOR significantly promotes plasmid-mediated conjugative transfer of ARGs, providing novel insights into the mechanisms underlying this process.

Flash optimization of drug combinations for Acinetobacter baumannii with IDentif.AI-AMR

Antimicrobial resistance (AMR) is an emerging threat to global public health. Specifically, Acinetobacter baumannii (A. baumannii), one of the main pathogens driving the rise of nosocomial infections, is a Gram-negative bacillus that displays intrinsic resistance mechanisms and can also develop resistance by acquiring AMR genes from other bacteria. More importantly, it is resistant to nearly 90% of standard of care (SOC) antimicrobial treatments, resulting in unsatisfactory clinical outcomes and a high infection-associated mortality rate of over 30%. Currently, there is a growing challenge to sustainably develop novel antimicrobials in this ever-expanding arms race against AMR. Therefore, a sustainable workflow that properly manages healthcare resources to ultra-rapidly design optimal drug combinations for effective treatment is needed. In this study, the IDentif.AI-AMR platform was harnessed to pinpoint effective regimens against four A. baumannii clinical isolates from a pool of nine US FDA-approved drugs. Notably, IDentif.AI-pinpointed ampicillin-sulbactam/cefiderocol and cefiderocol/polymyxin B/rifampicin combinations were able to achieve 93.89 ± 5.95% and 92.23 ± 11.89% inhibition against the bacteria, respectively, and they may diversify the reservoir of treatment options for the indication. In addition, polymyxin B in combination with rifampicin exhibited broadly applicable efficacy and strong synergy across all tested clinical isolates, representing a potential treatment strategy for A. baumannii. IDentif.AI-pinpointed combinations may potentially serve as alternative treatment strategies for A. baumannii.

Urban waste piles are reservoirs for human pathogenic bacteria with high levels of multidrug resistance against last resort antibiotics: A comprehensive temporal and geographic field analysis

Inadequate waste management and poor sanitation practices in Low- and Middle-Income Countries (LMICs) leads to waste accumulation in urban and peri-urban residential areas. This increases human exposure to hazardous waste, including plastics, which can harbour pathogenic bacteria. Although lab-based studies demonstrate how plastic pollution can increase the persistence and dissemination of dangerous pathogens, empirical data on pathogen association with plastic in real-world settings are limited. We conducted a year-long spatiotemporal sampling survey in a densely populated informal settlement in Malawi, quantifying enteric bacterial pathogens including ESBL-producing E. coli, Klebsiella pneumoniae, Salmonella spp., Shigella spp., and Vibrio cholerae. Culture-based screening and molecular approaches were used to quantify the presence of each pathogen, together with the distribution and frequency of resistance to antibiotics. Our data indicate that these pathogens commonly associate with urban waste materials. Elevated levels of these pathogens precede typical infection outbreaks, suggesting that urban waste piles may be an important source of community transmission. Notably, many pathogens displayed increased levels of AMR, including against several 'last resort' antibiotics. These findings highlight urban waste piles as potential hotspots for the dissemination of infectious diseases and AMR and underscores the need for urgent waste management interventions to mitigate public health risks.

Water, sanitation, handwashing, and nutritional interventions can reduce child antibiotic use: evidence from Bangladesh and Kenya

Antibiotics can trigger antimicrobial resistance and microbiome alterations. Reducing pathogen exposure and undernutrition can reduce infections and antibiotic use. We assess effects of water, sanitation, handwashing (WSH) and nutrition interventions on caregiver-reported antibiotic use in Bangladesh and Kenya, longitudinally measured at three timepoints among birth cohorts (ages 3-28 months) in a cluster-randomized trial. Over 50% of children used antibiotics at least once in the 90 days preceding data collection. In Bangladesh, the prevalence of antibiotic use was 10-14% lower in groups receiving WSH (prevalence ratio [PR] = 0.90 (0.82-0.99)), nutrition (PR = 0.86 (0.78-0.94)), and nutrition+WSH (PR = 0.86 (0.79-0.93)) interventions. The prevalence of using antibiotics multiple times was 26-35% lower in intervention arms. Reductions were largest when the birth cohort was younger. In Kenya, interventions did not affect antibiotic use. In this work, we show that improving WSH and nutrition can reduce antibiotic use. Studies should assess whether such reductions translate to reduced antimicrobial resistance.

Prevalence and determinants of faecal carriage of carbapenem- and third-generation cephalosporin-resistant Enterobacterales: a cross-sectional household survey in northern Vietnam

Background

Antimicrobial resistance (AMR) is a silent pandemic causing 1.27 million deaths in 2019, disproportionately affecting low- and middle-income countries, but resistance among commensal microbiota and the determinants of carriage have not been widely reported. This cross-sectional household study aimed to determine the prevalence of carbapenem-resistant (CRE) and third-generation cephalosporin-resistant Enterobacterales (C3GRE) in a rural community in Ha Nam northern Vietnam, as well as the socio-demographic, behavioural, and environmental determinants of carriage.

Methods

1502 individuals across 324 households were surveyed between July 2018 and April 2019. Faecal samples were cultured on meropenem and ceftazidime supplemented media to identify CRE and C3GRE, respectively. Logistic regression models were used to explore risk factors for CRE and C3GRE carriage compared to susceptible strains.

Findings

Colonisation with C3GRE and CRE was 94.0% (95% Confidence Interval (CI) 93.5%-94.4%) and 1.9% (1.6%-2.2%), respectively. The CRE prevalence was too low to explore determinants. Antibiotic use in the last month (adjusted OR 1.22 [95% CI 0.45-3.31]) and recent illness (aOR 1.48 [0.34-6.51]) were not associated with C3GRE carriage. Variables associated with C3GRE carriage were high-income (OR 0.29 [0.12-0.74]), worse sanitary conditions (aOR 4.35 [1.07-17.43]), and frequent beef consumption (aOR 6.56 [2.16-19.98]). A protective association between C3GRE carriage and animal husbandry was observed in children under 5-years (aOR 0.27 [0.09-0.84]). For participants 5-years and older, chicken consumption was associated with increased likelihood of C3GRE carriage (aOR 3.45 [1.45-8.22]), while a protective association was observed for regular tofu (aOR 0.32 [0.14-0.74]) and fermented food consumption (aOR 0.55 [0.31-0.96]).

Interpretation

In this high-prevalence setting, colonisation with C3GRE was not associated with individual antibiotic use, while environmental exposures, including food and sanitary conditions, were associated with C3GRE colonisation. Further research is required to understand the mechanisms behind these associations.

Funding

This work was supported by Oxford University Clinical Research Unit internal grants in Vietnam from the Wellcome Trust Africa Asia Programme core grants (2015-2022-106680/Z/14/Z, and 2022-2029-225167/Z/22/Z).

Dynamics of antibiotic resistance genes and bacterial community structure within substrate biofilms

Biofilms that develop on the surface of substrates are critical for treating wastewater. The accumulation of antibiotic resistance genes (ARGs) within these biofilms is particularly noteworthy. Despite their importance, studies that focus on biofilms attached to substrate surfaces remain scarce. This investigation explored the prevalence and succession of ARGs and microbial dynamics in biofilms on different substrates (ceramic, biomass filter, and steel slag) versus water biofilms over a year. Results showed distinct differences in ARG profiles between water and substrate biofilms. Multidrug ARGs constituted 39.14-46.73% of all ARGs in the substrate biofilms, with macrolide ARGs making up 11.98-14.52%. Seasonal variations influenced the diversity of the ARGs, notably increasing during the spring. The neutral community model suggested that the ARG assembly was dominantly driven by stochastic process. Proteobacteria, Actinobacteria and Campylobacter emerged as the predominant phyla within these biofilms. The microbial community distribution was predominantly influenced by ammonium nitrogen (NH4+-N) (R2 = 0.4113), temperature and total nitrogen (TN). Notably, temperature exerted a critical impact on the microbial community distribution (P = 0.001), identifying it as the principal factor for spatial arrangement. Furthermore, the structural variations of ARGs were primarily driven by total organic carbon (TOC) (R2 = 0.3988), temperature, oxidation-reduction potential (ORP) and NH4+-N. Our findings provided new insights into the optimization of substrate selection and ecological management to manage ARG enrichment, offering a promising strategy for aquatic ecological restoration and pollution control.

Antibiotic resistance in urban soils: Dynamics and mitigation strategies

Antibiotic resistance (AR) is a critical global health issue with significant clinical and economic implications. AR occurs when microorganisms develop mechanisms to withstand the effects of antibiotics, reducing treatment efficacy and increasing the risk of mortality and healthcare costs. While the connection between antibiotic use in clinical and agricultural settings and the emergence of AR is well-established, the role of urban soils as reservoirs and spreaders of AR is underexplored. This review examines the complex dynamics of AR in urban soils, highlighting the various sources of antibiotics, including domestic wastewater, industrial effluents, urban agricultural practices, but also microplastics and domestic animal excrements. The selective pressure exerted by these anthropogenic sources promotes the proliferation of antibiotic-resistant bacteria, particularly through horizontal gene transfer, which facilitates the transmission of resistance genes among soil microorganisms in urban environments. About that, the presence of antibiotics in urban soils poses a significant threat to public health by potentially transferring resistance genes to human pathogens through multiple pathways, including direct contact, food consumption, and water ingestion. Furthermore, AR in urban soils disrupts microbial community dynamics, impacting soil fertility, plant growth, and overall environmental quality. Therefore, this review aims to address gaps in understanding AR in urban soils, offering insights into its implications for human health and ecosystem integrity. By identifying these gaps and suggesting evidence-based strategies, this review proposes valid and sustainable solutions to mitigate and counteract the spread of AR in urban environments.

Dairy farm waste: A potential reservoir of diverse antibiotic resistance and virulence genes in aminoglycoside- and beta-lactam-resistant Escherichia coli in Gansu Province, China

Aminoglycosides (AGs) and beta-lactams are the most commonly used antimicrobials in animal settings, particularly on dairy farms. Dairy farm waste is an important reservoir of antibiotic resistance genes (ARGs) and virulence genes (VGs) in environmental Escherichia coli, which is an important indicator of environmental contamination and foodborne pathogen that potentially threaten human and animal health. In the present study, we aimed to characterize the ARGs and VGs in AG- and beta-lactam-resistant E. coli from dairy farm waste in Gansu Province, China. The dairy farm waste consisted of fecal (n = 265) and sewage (n = 54) samples processed using standard microbiological techniques and the Clinical & Laboratory Standards Institute guidelines. The total DNA of AG- and beta-lactam-resistant E. coli was extracted, and whole-genome sequencing (WGS) was performed using the Illumina NovaSeq platform and analyzed using various bioinformatics tools. In this study, among 84.3% (269/319) of the E. coli strains, 23.8% (64/269) were identified as AG- and beta-lactam-resistant E. coli. WGS analysis revealed a large pool of ARGs belonging to multiple classes such as AGs, beta-lactams, aminocoumarins, fluoroquinolones, macrolides, phenicol, tetracyclines, phosphonic acid, disinfecting and antiseptic agents, elfamycin, rifamycin, and multidrug resistance genes. Furthermore, virulome analysis of 64 E. coli strains revealed clinically important virulence factors associated with adherence, biofilm, invasion, auto-transportation, siderophores, secretion systems, toxins, anti-phagocytosis, quorum sensing, regulation, metabolism, and motility. We identified dairy farm feces and sewage waste as important reservoirs of antimicrobial resistance and virulence determinants in E. coli in Gansu, China, which can threaten human and animal health through ecological exposure and contamination of food and water. We recommend continuous large-scale surveillance in dairy farm settings to formulate protective guidelines for public health safety.

Effects of commonly used antibiotics on children's developing gut microbiomes and resistomes in peri-urban Lima, Peru

Background

The effects of antibiotic use on children's gut microbiomes and resistomes are not well characterized in middle-income countries, where pediatric antibiotic consumption is exceptionally common. We characterized the effects of antibiotics commonly used by Peruvian children (i.e., amoxicillin, azithromycin, cefalexin, sulfa-trimethoprim) on gut diversity, genera, and antibiotic resistance gene (ARG) abundance from 3-16 months.

Methods

This study included 54 children from a prospective cohort of enteric infections in peri-urban Lima, 2016-2019. Stool collected at 3, 6, 7, 9, 12, and 16 months underwent DNA extraction and short-read metagenomic sequencing. We profiled the taxonomy of stool metagenomes and assessed ARG abundance by aligning reads to the ResFinder database. We used daily surveillance data (40,662 observations) to tabulate the number of antibiotic courses consumed in the 30 days prior to stool sampling. Using linear mixed models, the association of recent antibiotic use with species richness, diversity, gut genera, and ARG abundance over time was examined.

Results

Most children were vaginally delivered (73%), received breastmilk almost daily over the study period, and belonged to socioeconomically diverse households. Amoxicillin, azithromycin, cefalexin, and sulfa-trimethoprim did not impact gut diversity or genera abundance. Azithromycin use significantly impacted ARGs from the macrolide, aminoglycoside, and folate pathway antagonist classes. Amoxicillin use significantly increased total ARGs. Antibiotics' effects on ARGs appeared to be independent of gut microbiome changes.

Conclusion

Common antibiotics like amoxicillin and azithromycin may be key drivers of the gut resistome but not the microbiome during early childhood in this setting with frequent breastfeeding.

Hot spots of resistance: Transit centers as breeding grounds for airborne ARG-carrying bacteriophages

The presence of pathogenic bacteria and antibiotic resistance genes (ARGs) in urban air poses a significant threat to public health. While prevailing research predominantly focuses on the airborne transmission of ARGs by bacteria, the potential influence of other vectors, such as bacteriophages, is often overlooked. This study aims to investigate the characteristics of phages and ARGs in aerosols originating from hospitals, public transit centers, wastewater treatment plants, and landfill sites. The average abundance of ARGs carried by phages in the public transit centers was 8.81 ppm, which was 2 to 3 times higher than that at the other three sites. Additionally, the abundance of ARGs across different risk levels at this site was also significantly higher than at the other three sites. The assembled phage communities bearing ARGs in public transit centers are chiefly governed by homogeneous selection processes, likely influenced by human movement. Furthermore, observations at public transit sites revealed that the average abundance ratio of virulent phages to their hosts was 1.01, and the correlation coefficient between their auxiliary metabolic genes and hosts' metabolic genes was 0.59, which were 20 times and 3 times higher, respectively, than those of temperate phages. This suggests that virulent phages may enhance their survival by altering host metabolism, thereby aiding the dispersion of ARGs and bacterial resistance. These revelations furnish fresh insights into phage-mediated ARG transmission, offering scientific substantiation for strategies aimed at preventing and controlling resistance within aerosols.

Antimicrobial resistance profile of Escherichia coli in drinking water from one health perspective in low and middle income countries

Introduction

Antimicrobial resistance is a major global public health concern, especially in low-resource settings. In low- and middle-income countries, the existing evidence about antimicrobial resistance in drinking water is inconsistence and not comprehensive. Therefore, this study aimed to estimate the pooled prevalence of antimicrobial resistance profiles of Escherichia coli from drinking water in low- and middle-income countries.

Methods

This study was conducted using comprehensive literature searches using various databases such as PubMed, Scientific Direct, HINARI, and Google Scholar. Data extraction was performed using Microsoft Excel and exported to STATA 14/SE software for analysis. We used the Joanna Briggs Institute's quality appraisal tool to ensure the quality of the included studies. A random effects model was employed to estimate the pooled prevalence. Publication bias was evaluated using funnel plots and Egger's regression test. Subgroup and sensitivity analysis were also conducted in this study.

Results

The study found that the pooled prevalence of Escherichia coli isolates in drinking water was 37.94% (95% CI: 26.73-49.13). The prevalence of multidrug resistance was 43.65% (95% CI: 31.15-56.15). Regarding specific antimicrobials, the pooled resistance levels of Escherichia coli were 54.65% (95% CI: 41.35-67.96) against contrimoxazole, followed by 48.64% (95% CI: -3.6-101) against amoxicillin and 48% (95% CI: -18.1-114.2) against cefuroxime.

Conclusion

The findings indicated a significant prevalence of antimicrobial resistance of Escherichia coli isolated from drinking water and its multidrug resistance. To address this issue, it recommends focusing on improving basic hygiene and sanitation practices and enhancing water and wastewater treatment systems.

Systematic review registration

Identifier CRD42024533592.

Is there a role for intestinal sporobiota in the antimicrobial resistance crisis?

Antimicrobial resistance (AMR) is a complex issue requiring specific, multi-sectoral measures to slow its spread. When people are exposed to antimicrobial agents, it can cause resistant bacteria to increase. This means that the use, misuse, and excessive use of antimicrobial agents exert selective pressure on bacteria, which can lead to the development of "silent" reservoirs of antimicrobial resistance genes. These genes can later be mobilized into pathogenic bacteria and contribute to the spread of AMR. Many socioeconomic and environmental factors influence the transmission and dissemination of resistance genes, such as the quality of healthcare systems, water sanitation, hygiene infrastructure, and pollution. The sporobiota is an essential part of the gut microbiota that plays a role in maintaining gut homeostasis. However, because spores are highly transmissible and can spread easily, they can be a vector for AMR. The sporobiota resistome, particularly the mobile resistome, is important for tracking, managing, and limiting the spread of antimicrobial resistance genes among pathogenic and commensal bacterial species.

SIL-IS LC-ESI-MS/MS method for simultaneous quick detection of amoxicillin and clavulanic acid in human plasma: Development, validation and its application to a pharmacokinetics study

A liquid chromatography electrospray ionization tandem mass spectrometry method with amoxicillin-d4 as the stable isotope-labeled internal standard for simultaneous quick detection of amoxicillin and clavulanic acid in human plasma was developed and validated. Chromatographic separations were performed on a Hedera ODS-2 column (2.1 × 150 mm, 5 μm). The mobile phases for gradient elution were aqueous solution containing 0.2% acetic acid (AA) (mobile phase A) together with organic phase solution (acetonitrile and methanol mixed solution, mobile phase B). Mass spectrometry was performed using negative electrospray ionization in multiple reaction monitoring mode. The target fragment ion pairs of amoxicillin, clavulanic acid and amoxicillin-d4 were m/z 364.1 → 223.1, 198.1 → 135.9 and 368.1 → 227.1, respectively. The linear ranges of this method were 40-5,000 ng/ml for amoxicillin and 30-2,500 ng/ml for clavulanic acid, with coefficient of determination > 0.9900. This method validation included selectivity, standard curve, lower limit of quantitation, accuracy, precision, recovery, matrix effect (hemolytic matrix and hyperlipidemic matrix), carryover, stability, dilution reliability and incurred sample reanalysis study. A successful application of this method was realized in a pharmacokinetic study after administration of amoxicillin-clavulanic acid potassium granules.

Integrative metagenomic dissection of last-resort antibiotic resistance genes and mobile genetic elements in hospital wastewaters

Hospital wastewater is a critical source of antimicrobial resistance (AMR), which facilitates the proliferation and spread of clinically significant antimicrobial resistance genes (ARGs) and pathogenic bacteria. This study utilized metagenomic approaches, including advanced binning techniques, such as MetaBAT2, MaxBin2, and CONCOCT, which offer significant improvements in accuracy and completeness over traditional binning methods. These methods were used to comprehensively assess the dynamics and composition of resistomes and mobilomes in untreated wastewater samples taken from two general hospitals and one cancer hospital. This study revealed a diverse bacterial landscape, largely consisting of Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria, with notable variations in microbial composition among hospitals. Analysis of the top 15 genera showed unique microbial pattern distribution in each hospital: Aeromonas was predominant in 1stHWTS (49.39 %), Acidovorax in the CAHWTS at 16.85 %, and Escherichia and Bacteroides in the 2ndHWTS at 11.44 % and 11.33 %, respectively. A total of 114 pathogenic bacteria were identified, with drug-resistant Aeromonas caviae and Escherichia coli being the most prevalent. The study identified 34 types and 1660 subtypes of ARGs, including important last-resort antibiotic resistance genes (LARGs), such as blaNDM, mcr, and tet(X). Using metagenomic binning, this study uncovered distinct patterns of host-resistance associations, particularly with Proteobacteria and Firmicutes. Network analysis highlighted the complex interactions among ARGs, mobile genetic elements (MGEs), and bacterial species, all contributing to the dissemination of AMR. These findings emphasize the intricate nature of AMR in hospital wastewater and the influence of hospital-specific factors on microbial resistance patterns. This study provides support for implementing integrated management strategies, including robust surveillance, advanced wastewater treatment, and strict antibiotic stewardship, to control the dissemination of AMR. Understanding the interplay among bacterial communities, ARGs, and MGEs is important for developing effective public health measures against AMR.

Nanoscale Multipatterning Zn,Co-ZIF@FeOOH for Eradication of Multidrug-Resistant Bacteria and Antibacterial Treatment of Wounds

The rising incidence of infections caused by multidrug-resistant bacteria highlights the urgent need for innovative bacterial eradication strategies. Metal ions, such as Zn2+ and Co2+, have bactericidal effects by disrupting bacterial cell membranes and interfering with essential cellular processes. This has led to increased attention toward metal-organic frameworks (MOFs) as potential nonantibiotic bactericidal agents. However, the uniform and enhanced localized release of bactericidal metal ions remains a challenge. Herein, we introduce a nanoscale multipatterned Zn,Co-ZIF@FeOOH, featuring a multipod-like morphology with spiky corners, and dual-bactericidal metal ions. Compared to pure Zn,Co-ZIF, the multipod-like morphology of Zn,Co-ZIF@FeOOH exhibits enhanced adhesion toward bacterial surfaces via topological and multiple interactions of electrostatic interaction, significantly increasing the local release of Zn2+ and Co2+. Additionally, the spiky corners of the spindle-shaped FeOOH nanorods physically penetrate bacterial membranes, causing damage and further enhancing adhesion to bacteria. Nine Gram-negative and one Gram-positive bacteria were selected for in vitro test. Notably, the nanoscale multipatterned Zn,Co-ZIF@FeOOH exhibited high bactericidal efficacy against various multidrug-resistant bacteria, including extended-spectrum β-lactamase-producing (ESBL+) bacteria and carbapenem-resistant bacteria, performing well in both acidic and neutral environments. The wound healing activity of Zn,Co-ZIF@FeOOH was further demonstrated using female Balb/c mouse models infected with bacteria, where the materials show robust antibacterial efficacy and commendable biocompatibility. This study showcases the assembly of metal oxide/MOF composites for nanoscale multipatterning, aims at synergistic bacterial eradication and offers insights into developing nanomaterial-based strategies against multidrug-resistant bacteria.

Characterization of antibiotic resistance development of E. coli in synthetic and real wastewater

Antimicrobial resistance (AMR) is a major threat to global health and resistant bacterial populations have been observed to develop and spread in and around wastewater. However, in vitro studies on AMR development are typically conducted in ideal media conditions which can differ in composition and nutrient density from wastewater. In this study, we compare the growth and AMR development of E. coli in standard LB broth to a synthetic wastewater recipe and autoclaved wastewater samples from the Massachusetts Water Resources Authority (MWRA). We found that synthetic wastewater and real wastewater samples both supported less bacterial growth compared to LB. Additionally, bacteria grown in synthetic wastewater and real wastewater samples had differing susceptibility to antibiotic pressure from Doxycycline, Ciprofloxacin, and Streptomycin. However, AMR development over time during continuous passaging under subinhibitory antibiotic pressure was similar in fold change across all media types. Thus, we find that while LB can act as a proxy for wastewater for AMR studies in E. coli, synthetic wastewater is a more accurate predictor of both E.coli growth and antibiotic resistance development. Moreover, we also show that antibiotic resistance can develop in real wastewater samples and components within wastewater likely have synergistic and antagonistic interactions with antibiotics.

Discovery and optimization of thiazole-based quorum sensing inhibitors as potent blockers of Pseudomonas aeruginosa pathogenicity

Pseudomonas aeruginosa causes life-threatening infections especially in hospitalized patients and shows an increasing resistance to established antibiotics. A process known as quorum sensing (QS) enables the pathogen to collectively adapt to various environmental conditions. Disrupting this cell-to-cell communication machinery by small-molecular entities leads to a blockade of bacterial pathogenicity. We aim to devise QS inhibitors acting on the PA-specific PQS QS system via the signal-molecule receptor and transcriptional regulator PqsR (MvfR). In this manuscript, we describe the further optimization of PqsR inverse agonists by broadening the structural space of a previously described triazole-bearing lead compound and arriving at highly potent thiazole derivatives with activities against P. aeruginosa virulence factor pyocyanin in the nanomolar range. All new derivatives were profiled regarding biological activity as well as in vitro ADMET parameters. Additionally, we assessed safety-pharmacology characteristics of the two most promising compounds both bearing a 3-chloro-4-isopropoxyphenyl motive. Demonstrating an overall favorable profile, our new PqsR inverse agonists represent a valuable addition as optimized lead compounds, enabling preclinical development of P. aeruginosa-specific pathoblockers.

The perfluorooctanoic acid accumulation and release from pipelines promoted growth of bacterial communities and opportunistic pathogens with different antibiotic resistance genes in drinking water

The spread of opportunistic pathogens (OPs) and antibiotic resistance genes (ARGs) through drinking water has already caused serious human health issues. There is also an urgent need to know the effects of perfluorooctanoic acid (PFOA) on OPs with different ARGs in drinking water. Our results suggested that PFOA accumulation and release from the pipelines induced its concentration in pipelines effluents increase from 0.03 ± 0.01 μg/L to 0.70 ± 0.01 μg/L after 6 months accumulation. The PFOA also promoted the growth of Hyphomicrobium, Microbacterium, and Bradyrhizobium. In addition, PFOA accumulation and release from the pipelines enhanced the metabolism and tricarboxylic acid (TCA) cycle processes, resulting in more extracellular polymeric substances (EPS) production. Due to EPS protection, Pseudomonas aeruginosa and Legionella pneumophila increased to (7.20 ± 0.09) × 104 gene copies/mL, and (8.85 ± 0.11) × 102 gene copies/mL, respectively. Moreover, PFOA also enhanced the transfer potential of different ARGs, including emrB, mdtB, mdtC, mexF, and macB. The main bacterial community composition and the main OPs positively correlated with the main ARGs and mobile genetic elements (MGE)-ARGs significantly. Therefore, PFOA promoted the propagation of OPs with different ARGs. These results are meaningful for controlling the microbial risk caused by the OPs with ARGs and MGE-ARGs in drinking water.

Key environmental exposure pathways to antimicrobial resistant bacteria in southern Malawi: A SaniPath approach

Antimicrobial resistance (AMR) poses a severe global health threat, yet the transmission pathways of AMR within communal public environments, where humans and animals interact, remain poorly explored. This study investigated AMR risk pathways, prevalence, and seasonality of extended-spectrum β-lactamase (ESBL) producing E. coli and K. pneumoniae, and observed practices contributing to environmental contamination within urban, peri-urban, and rural Malawi. Using the SaniPath tool, in August 2020, transect walks across three Malawian study sites identified potential AMR exposure pathways, including drains, standing water, soil, and areas of communal hand contact. Subsequently, from September-2020 to August-2021, 1440 environmental samples were collected at critical points along exposure routes (n = 40/month from each site). These underwent microbiological analysis using chromogenic agar techniques to detect the presence of ESBL E. coli and ESBL K. pneumoniae. Results showed the highest ESBL prevalence in urban environments (68.1 %, 95%CI = 0.64-0.72, p < 0.001) with a higher ESBL presence seen in drains (58.8 %, 95%CI = 055-0.62, p < 0.001) and soil (54.1 %, 95%CI = 0.46-0.62, p < 0.001) compared to other pathways. Environmental contamination was attributed to unavailability and poor condition of sanitation and hygiene infrastructure based on key informant interviews with community leaders (n = 9) and confirmed by independent observation. ESBL prevalence varied between seasons (χ2 (2,N = 1440) = 10.89, p = 0.004), with the highest in the hot-dry period (55.8 % (n = 201)). Prevalence also increased with increased rainfall (for ESBL E.coli). We highlight that community environments are likely to be a crucial component in AMR transmission, evident in the abundance of ESBL bacteria in identified exposure pathways. Additionally, poor sanitation infrastructure and practices coupled with seasonal dynamics further affect the presence of ESBLs in communal environments. Therefore, a context appropriate whole system approach that tackles infrastructure and behavioural factors, supported by effective surveillance is required to impact AMR and a range of aligned development challenges in these settings.

Effects of Organic Soil Amendments on Antimicrobial-Resistant Bacteria in Urban Agriculture Environments

Biological soil amendments of animal origin (BSAAOs) are widely used in urban agriculture to improve soil quality. Although BSAAO use is regulated due to risks for introducing foodborne pathogens, effects on antimicrobial-resistant (AMR) bacteria are not well established. Here, we aimed to explore the impacts of BSAAOs on levels of resident AMR bacteria in leafy vegetable production environments (i.e., kale, lettuce, chard, cabbage) across urban farms and community gardens in the greater Washington D.C. area (n = 7 sites). Leaf tissue (LT), root zone soil (RZS; amended soil in crop beds), and bulk soil (BS; site perimeter) were collected and analyzed for concentrations of total heterotrophic bacteria (THB), ampicillin (Amp) or tetracycline (Tet) resistant THB, and coliforms. As expected, amended plots harbored significantly higher concentrations of THB than bulk soil (P < 0.001). The increases in total bacteria associated with reduced fractions of Tet-resistant bacteria (P = 0.008), as well as case-specific trends for reduced fractions of Amp-resistant bacteria and coliforms. Site-to-site variation in concentrations of AMR bacteria in soil and vegetable samples reflected differences in land history and crop management, while within-site variation was associated with specific amendment sources, as well as vegetable type and cultivar. Representative isolates of the AMR bacteria and coliforms were further screened for multidrug resistance (MDR) phenotypes, and a high frequency was observed for the former. In amended soils, as the soil pH (range 6.56-7.80) positively correlated with the fraction of Tet-resistant bacteria (rho = 0.529; P < 0.001), crop management strategies targeting pH may have applications to control related risks. Overall, our findings demonstrate that soil amendments promote soil bacteria concentrations and have important implications for limiting the spread of AMR bacteria, at least in the urban landscape.

Towards integrated cross-sectoral surveillance of pathogens and antimicrobial resistance: Needs, approaches, and considerations for linking surveillance to action

Pathogenic and antimicrobial-resistant (AMR) microorganisms are continually transmitted between human, animal, and environmental reservoirs, contributing to the high burden of infectious disease and driving the growing global AMR crisis. The sheer diversity of pathogens, AMR mechanisms, and transmission pathways connecting these reservoirs create the need for comprehensive cross-sectoral surveillance to effectively monitor risks. Current approaches are often siloed by discipline and sector, focusing independently on parts of the whole. Here we advocate that integrated surveillance approaches, developed through transdisciplinary cross-sector collaboration, are key to addressing the dual crises of infectious diseases and AMR. We first review the areas of need, challenges, and benefits of cross-sectoral surveillance, then summarise and evaluate the major detection methods already available to achieve this (culture, quantitative PCR, and metagenomic sequencing). Finally, we outline how cross-sectoral surveillance initiatives can be fostered at multiple scales of action, and present key considerations for implementation and the development of effective systems to manage and integrate this information for the benefit of multiple sectors. While methods and technologies are increasingly available and affordable for comprehensive pathogen and AMR surveillance across different reservoirs, it is imperative that systems are strengthened to effectively manage and integrate this information.

Context-Seq: CRISPR-Cas9 Targeted Nanopore Sequencing for Transmission Dynamics of Antimicrobial Resistance

Antimicrobial resistance (AMR) aligns with a One Health framework in that resistant bacteria and antibiotic resistance genes (ARGs) can be transmitted between humans, animals, and the environment. However, there is a critical need to more precisely understand how and to what extent AMR is exchanged between animals and humans. Metagenomic sequencing has low detection for rare targets such as ARGs, while whole genome sequencing of isolates is burdensome and misses exchange between uncultured bacterial species. We developed a novel, targeted sequencing assay using CRISPR-Cas9 to selectively sequence ARGs and their genomic context with long-read sequencing. Using this method, termed Context-Seq, we investigated overlapping AMR elements containing the ARGs bla CTX-M and bla TEM between adults, children, poultry, and dogs in animal-owning households in Nairobi, Kenya. We identified 22 genetically distinct clusters (> 80%ID over ≥ 3000 bp) containing bla TEM and one cluster containing bla CTX-M that were shared within and between households. Half of the clusters were shared between humans and animals, while the other half were shared only between animals (poultry-poultry, dog-dog, and dog-poultry). We identified potentially pathogenic hosts of ARGs including Escherichia coli, Klebsiella pneumonia, and Haemophilus influenzae across sample types. Context-Seq complements conventional methods to obtain an additional view of bacterial and mammalian hosts in the proliferation of AMR.

High-throughput microfluidic quantitative PCR system for the simultaneous detection of antibiotic resistance genes and bacterial and viral pathogens in wastewater

Comprehensive data on bacterial and viral pathogens of diarrhea and studies applying culture-independent methods for examining antibiotic resistance in wastewater are lacking. This study aimed to simultaneously quantify antibiotic resistance genes (ARGs), class 1 integron-integrase (int1), bacterial and viral pathogens of diarrhea, 16S rRNA, and other indicators using a high-throughput quantitative PCR (HT-qPCR) system. Thirty-six grab wastewater samples from a wastewater treatment plant in Japan, collected three times a month between August 2022 and July 2023, were centrifuged, followed by nucleic acid extraction, reverse transcription, and HT-qPCR. Fourteen targets were included, and HT-qPCR was performed on the Biomark X9™ System (Standard BioTools). For all qPCR assays, R2 was ≥0.978 and the efficiencies ranged from 90.5% to 117.7%, exhibiting high performance. Of the 36 samples, 20 (56%) were positive for Norovirus genogroup II (NoV-GII), whereas Salmonella spp. and Campylobacter jejuni were detected in 24 (67%) and Campylobacter coli in 13 (36%) samples, with mean concentrations ranging from 3.2 ± 0.8 to 4.7 ± 0.3 log10 copies/L. NoV-GII detection ratios and concentrations were higher in winter and spring. None of the pathogens of diarrhea correlated with acute gastroenteritis cases, except for NoV-GII, suggesting the need for data on specific bacterial infections to validate bacterial wastewater-based epidemiology (WBE). All samples tested positive for sul1, int1, and blaCTX-M, irrespective of season. The less explored blaNDM-1 showed a wide prevalence (>83%) and consistent abundance ranging from 4.3 ± 1.0 to 4.9 ± 0.2 log10 copies/L in all seasons. sul1 was the predominant ARG, whereas absolute abundances of 16S rRNA, int1, and blaCTX-M varied seasonally. int1 was significantly correlated with blaCTX-M in autumn and spring, whereas it showed no correlation with blaNDM-1, questioning the applicability of int1 as a sole indicator of overall resistance determinants. This study exhibited that the HT-qPCR system is pivotal for WBE.

Bacterial strain sharing between humans, animals, and the environment among urban households

Identifying bacterial transmission pathways is crucial to inform strategies aimed at curbing the spread of pathogenic and antibiotic-resistant bacteria, especially in rapidly urbanizing low- and middle-income countries. In this study, we assessed bacterial strain-sharing and dissemination of antibiotic resistance across humans, domesticated poultry, canines, household soil, and drinking water in urban informal settlements in Nairobi, Kenya. We collected 321 samples from 50 households and performed Pooling Isolated Colonies-seq (PIC-seq) by sequencing pools of up to five Escherichia coli colonies per sample to capture strain diversity, strain-sharing patterns, and overlap of antibiotic-resistant genes (ARGs). Bacterial strains isolated from the household environment carried clinically relevant ARGs, reinforcing the role of the environment in antibiotic resistance dissemination. Strain-sharing rates and resistome similarities across sample types were strongly correlated within households, suggesting clonal spread of bacteria is a main driver of dissemination of ARGs in the domestic urban environment. Within households, E. coli strain-sharing was rare between humans and animals but more frequent between humans and drinking water. E. coli contamination in stored drinking water was also associated with higher strain-sharing between humans in the same household. Our study demonstrates that contaminated drinking water facilitates human to human strain sharing and water treatment can disrupt transmission.

Disinfection and post-disinfection conditions drive bacterial and viral evolution across the environment and host

Water disinfection practices have long been established as a critical engineering intervention for controlling pathogen transmission and safeguarding individual and public health. However, recent discoveries have unveiled the significant role disinfection and post-disinfection play in accelerating the development of resistance to disinfectants and antimicrobial drugs within bacterial and viral communities in the environment. This phenomenon, in turn, may facilitate the emergence of persistent microbes and those with new genetic characteristics. These microbes may thrive in host environments with increased infectivity and resistance, posing challenges to current medical treatments and jeopardizing human health. In this perspective, we illuminate the intricate interplay between aquatic environments, microbes, and hosts and how microbial virulence evolves across the environment and host under the pressure of disinfection and post-disinfection conditions. We aim to draw attention to the previously overlooked potential risks associated with disinfection in driving the virulence evolution of bacteria and viruses, establish connections between pathogens in diverse environments and hosts within the overarching framework of the One Health concept, and ultimately provide guidelines for advancing future water disinfection technologies to effectively curb the spread of infectious diseases.

Indicators to complement global monitoring of safely managed on-site sanitation to understand health risks

Halfway through the Sustainable Development Goal (SDG) period, there has been little research on the criteria for monitoring safely managed sanitation under SDG target 6.2. For reporting against SDGs, global indicators are necessarily limited and exclude many safety aspects from a public health perspective. Primary survey data from 31,784 households in seven countries in Asia and Africa were analysed, comparing estimates of safely managed on-site sanitation based on global indicators with five complementary indicators of safety: animal access to excreta, groundwater contamination, overdue emptying, entering containments to empty and inadequate protection during emptying. Application of additional criteria reduced the population with safely managed sanitation by 0.4-35% for specific indicators, with the largest impact due to the risk of groundwater contamination, animal access, and containments overdue for emptying. Combining these indicators across the service chain, excluding transport and treatment, found almost three-quarters of on-site systems currently assessed as safely managed with global indicators were considered unsafe based on complementary indicators. A more comprehensive assessment of safety of on-site sanitation can be achieved through these indicators, which could be integrated into national monitoring systems and used to inform sanitation investments that address local health-related risks.

Polymyxins: recent advances and challenges

Antibiotic resistance is a pressing global health challenge, and polymyxins have emerged as the last line of defense against multidrug-resistant Gram-negative (MDR-GRN) bacterial infections. Despite the longstanding utility of colistin, the complexities surrounding polymyxins in terms of resistance mechanisms and pharmacological properties warrant critical attention. This review consolidates current literature, focusing on polymyxins antibacterial mechanisms, resistance pathways, and innovative strategies to mitigate resistance. We are also investigating the pharmacokinetics of polymyxins to elucidate factors that influence their in vivo behavior. A comprehensive understanding of these aspects is pivotal for developing next-generation antimicrobials and optimizing therapeutic regimens. We underscore the urgent need for advancing research on polymyxins to ensure their continued efficacy against formidable bacterial challenges.

Environment, animals, and food as reservoirs of antibiotic-resistant bacteria for humans: One health or more?

Antimicrobial resistance (AMR) is a major public health challenge. For several years, AMR has been addressed through a One Health approach that links human health, animal health, and environmental quality. In this review, we discuss AMR in different reservoirs with a focus on the environment. Anthropogenic activities produce effluents (sewage, manure, and industrial wastes) that contaminate soils and aquatic environments with antibiotic-resistant bacteria (ARB), antibiotic-resistant genes (ARGs), and selective agents such as antibiotics, biocides, and heavy metals. Livestock treated with antibiotics can also contaminate food with ARB. In high-income countries (HICs), effective sanitation infrastructure and limited pharmaceutical industries result in more controlled discharges associated with human activities. Hence, studies using genome-based typing methods have revealed that, although rare inter-reservoir transmission events have been reported, human acquisition in HICs occurs primarily through person-to-person transmission. The situation is different in low- and middle-income countries (LMICs) where high population density, poorer sanitation and animal farming practices are more conducive to inter-reservoir transmissions. In addition, environmental bacteria can be a source of ARGs that, when transferred to pathogenic species under antibiotic selection pressure in environmental hotspots, produce new antibiotic-resistant strains that can potentially spread in the human community through human-to-human transmission. The keys to reducing AMR in the environment are (i) better treatment of human waste by improving wastewater treatment plants (WWTPs) in HICs and improving sanitation infrastructure in LMICs, (ii) reducing the use of antibiotics by humans and animals, (iii) prioritizing the use of less environmentally harmful antibiotics, and (iv) better control of pharmaceutical industry waste.

The urban political ecology of antimicrobial resistance: A critical lens on integrative governance

The objective of this paper is to integrate Urban Political Ecology (UPE) as a theory for identifying under-exposed urban dimensions of Antimicrobial Resistance (AMR). A UPE lens allows us to conceptualize urbanization as a ubiquitous socio-ecological process and an interpretive frame that could inform AMR governance strategies across related contexts by: a) situating AMR risks in relation to urbanization processes shaping social and political co-determinants of such systemic threats as climate change; b) aligning UPE scholarship with One Health (OH) approaches that address AMR to reveal the under-exposed link of AMR to environmental threats and broader structural dimensions that influence these threats; and c) identifying shared AMR and environmental governance pathways that inform the rationale for more equitable governance arrangements. We delineate a context in which the speed and scale of human activity in the larger context of urbanization, driven by global market integration strategies, impacts human-animal-environmental health threats such as AMR. We demonstrate how UPE scholarship can be leveraged to offer theoretical depth to approaches considering the interdependencies of AMR and climate change threats. We then propose a strategic approach focused on identifying shared governance pathways and intersectoral accountability frameworks to address upstream structural drivers of AM-Environmental threats. The co-benefits of a UPE-informed framework to human-animal-environmental health that leverages enabling policy environments to foster a more collaborative, equitable and sustainable approach to address systemic global health threats are clarified. Just as the concept of "health in all policies" emphasized taking health implications into account in all public policy development, the integration of UPE in AMR governance arrangements would emphasize the need to take other sectors into account through an intersectoral whole-of-government approach that fosters shared AMR - climate change governance pathways.

Unraveling Multicopper [Cu3] and [Cu6] Clusters with Rare μ3-Sulfato and Linear μ2-Oxido-Bridges as Potent Antibiofilm Agents against Multidrug-Resistant Staphylococcus aureus

In this research article, two multicopper [Cu3] and [Cu6] clusters, [Cu3(cpdp)(μ3-SO4)(Cl)(H2O)2]·3H2O (1) and [Cu6(cpdp)2(μ2-O)(Cl)2(H2O)4]·2Cl (2) (H3cpdp = N,N'-bis[2-carboxybenzomethyl]-N,N'-bis[2-pyridylmethyl]-1,3-diaminopropan-2-ol), have been explored as potent antibacterial and antibiofilm agents. Their molecular structures have been determined by a single-crystal X-ray diffraction study, and the compositions have been established by thermal and elemental analyses, including electrospray ionization mass spectrometry. Structural analysis shows that the metallic core of 1 is composed of a trinuclear [Cu3] assembly encapsulating a μ3-SO42- group, whereas the structure of 2 represents a hexanuclear [Cu6] assembly in which two trinuclear [Cu3] motifs are exclusively bridged by a linear μ2-O2- group. The most striking feature of the structure of 2 is the occurrence of an unusual linear oxido-bridge, with the Cu3-O6-Cu3' bridging angle being 180.00°. Whereas 1 can be viewed as an example of a copper(II)-based compound displaying a rare μ3:η1:η1:η1 bridging mode of the SO42- group, 2 is the first example of any copper(II)-based compound showing an unsupported linear Cu-O-Cu oxido-bridge. Employing variable-temperature SQUID magnetometry, the magnetic susceptibility data were measured and analyzed exemplarily for 1 in the temperature range of 2-300 K, revealing the occurrence of antiferromagnetic interactions among the paramagnetic copper centers. Both 1 and 2 exhibited potent antibacterial and antibiofilm activities against methicillin-resistant Staphylococcus aureus (MRSA BAA1717) and the clinically isolated culture of methicillin-resistant S. aureus (MRSA CI1). The mechanism of antibacterial and antibiofilm activities of these multicopper clusters was investigated by analyzing and determining the intracellular reactive oxygen species (ROS) generation, lipid peroxidation, microscopic observation of cell membrane disruption, membrane potential, and leakage of cellular components. Additionally, 1 and 2 showed a synergistic effect with commercially available antibiotics such as vancomycin with enhanced antibacterial activity. However, 1 possesses higher antibacterial, antibiofilm, and antivirulence actions, making it a potent therapeutic agent against both MRSA BAA1717 and MRSA CI1 strains.

Towards an actionable One Health approach

BACKGROUND

Despite the increasing focus on strengthening One Health capacity building on global level, challenges remain in devising and implementing real-world interventions particularly in the Asia-Pacific region. Recognizing these gaps, the One Health Action Commission (OHAC) was established as an academic community for One Health action with an emphasis on research agenda setting to identify actions for highest impact.

MAIN TEXT

This viewpoint describes the agenda of, and motivation for, the recently formed OHAC. Recognizing the urgent need for evidence to support the formulation of necessary action plans, OHAC advocates the adoption of both bottom-up and top-down approaches to identify the current gaps in combating zoonoses, antimicrobial resistance, addressing food safety, and to enhance capacity building for context-sensitive One Health implementation.

CONCLUSIONS

By promoting broader engagement and connection of multidisciplinary stakeholders, OHAC envisions a collaborative global platform for the generation of innovative One Health knowledge, distilled practical experience and actionable policy advice, guided by strong ethical principles of One Health.

Global diversity, coexistence and consequences of resistome in inland waters

Human activities have long impacted the health of Earth's rivers and lakes. These inland waters, crucial for our survival and productivity, have suffered from contamination which allows the formation and spread of antibiotic-resistant genes (ARGs) and consequently, ARG-carrying pathogens (APs). Yet, our global understanding of waterborne pathogen antibiotic resistance remains in its infancy. To shed light on this, our study examined 1240 metagenomic samples from both open and closed inland waters. We identified 22 types of ARGs, 19 types of mobile genetic elements (MGEs), and 14 types of virulence factors (VFs). Our findings showed that open waters have a higher average abundance and richness of ARGs, MGEs, and VFs, with more robust co-occurrence network compared to closed waters. Out of the samples studied, 321 APs were detected, representing a 43 % detection rate. Of these, the resistance gene 'bacA' was the most predominant. Notably, AP hotspots were identified in regions including East Asia, India, Western Europe, the eastern United States, and Brazil. Our research underscores how human activities profoundly influence the diversity and spread of resistome. It also emphasizes that both abiotic and biotic factors play pivotal roles in the emergence of ARG-carrying pathogens.

Evaluating human exposure to antibiotic resistance genes

Antibiotic resistance is an escalating global concern, leading to millions of annual fatalities. Antibiotic resistance genes (ARGs) present in bacteria equip them to withstand the effects of antibiotics. Intra- and interspecific ARGs transmission through horizontal gene transfer further exacerbates resistance dissemination. The presence of ARGs in the environment heightens the probability of human exposure via direct inhalation, ingestion, or contact with polluted air, food, or water, posing substantial biosafety and health hazards. Consequently, ARGs represent a critical focal point in public health and environmental safety and are classified as emerging contaminants. This perspective underscores the necessity to assess ARG exposure within the One Health framework and to accord greater attention to the mitigation strategies and tactics associated with ARGs.

A Metagenomic Investigation of Potential Health Risks and Element Cycling Functions of Bacteria and Viruses in Wastewater Treatment Plants

The concentration of viruses in sewage sludge is significantly higher (10-1000-fold) than that found in natural environments, posing a potential risk for human and animal health. However, the composition of these viruses and their role in the transfer of pathogenic factors, as well as their role in the carbon, nitrogen, and phosphorus cycles remain poorly understood. In this study, we employed a shotgun metagenomic approach to investigate the pathogenic bacteria and viral composition and function in two wastewater treatment plants located on a campus. Our analysis revealed the presence of 1334 amplicon sequence variants (ASVs) across six sludge samples, with 242 ASVs (41.22% of total reads) identified as pathogenic bacteria. Arcobacter was found to be the most dominant pathogen accounting for 6.79% of total reads. The virome analysis identified 613 viral genera with Aorunvirus being the most abundant genus at 41.85%. Approximately 0.66% of these viruses were associated with human and animal diseases. More than 60% of the virome consisted of lytic phages. Host prediction analysis revealed that the phages primarily infected Lactobacillus (37.11%), Streptococcus (21.11%), and Staphylococcus (7.11%). Furthermore, our investigation revealed an abundance of auxiliary metabolic genes (AMGs) involved in carbon, nitrogen, and phosphorus cycling within the virome. We also detected a total of 113 antibiotic resistance genes (ARGs), covering major classes of antibiotics across all samples analyzed. Additionally, our findings indicated the presence of virulence factors including the clpP gene accounting for approximately 4.78%, along with toxin genes such as the RecT gene representing approximately 73.48% of all detected virulence factors and toxin genes among all samples analyzed. This study expands our understanding regarding both pathogenic bacteria and viruses present within sewage sludge while providing valuable insights into their ecological functions.

Antibiotic resistance genes alterations in murine guts microbiome are associated with different types of drinking water

Antibiotic resistance genes (ARGs) are emerging contaminants threatening public health and commonly found in drinking water. However, the effect of different types of drinking water on ARG alterations in the gut microbiome is unclear. This study examines this issue in murine models in three phases (phase I: acclimation using ddH2O; phase II: treatment using different types of water, i.e. river water (RW), tap water (TW) and commercial bottled water (CBW); and phase III: recovery using ddH2O) using high-throughput qPCR and 16S rRNA amplicon sequencing. Results reveal that exposure to different types of drinking water could lead to significant changes in the gut microbiome, mobile genetic elements (MGEs), and ARGs. In phase II, treatment of RW and TW significantly increased the abundance of aminoglycoside and tetracycline resistance genes in mice guts (P < 0.01). In the recovery phase, consuming distilled water was found to restore ARG profiles to a certain extent in mice guts. Procrustes, network, redundancy and variation partitioning analysis indicated that ARG alterations in mice guts might relate to MGEs and bacterial communities. Our work suggests that the type of drinking water consumed may play a crucial role in shaping ARGs in gut microbiomes, emphasizing the urgent need for access to clean drinking water to mitigate the growing threat of antimicrobial resistance.

Characterising proximal and distal drivers of antimicrobial resistance: An umbrella review

INTRODUCTION

Antimicrobial resistance (AMR) is a multifactorial challenge driven by a complex interplay of proximal drivers, such as the overuse and misuse of antimicrobials and the high burden of infectious diseases, and distal factors, encompassing broader societal conditions such as poverty, inadequate sanitation, and healthcare system deficiencies. However, distinguishing between proximal and distal drivers remains a conceptual challenge.

OBJECTIVES

We conducted an umbrella review, aiming to systematically map current evidence about proximal and distal drivers of AMR and to investigate their relationships.

METHODS

Forty-seven reviews were analysed, and unique causal links were retained to construct a causality network of AMR. To distinguish between proximal and distal drivers, we calculated a 'driver distalness index (Di)', defined as an average relative position of a driver in its causal pathways to AMR.

RESULTS

The primary emphasis of the literature remained on proximal drivers, with fragmented existing evidence about distal drivers. The network analysis showed that proximal drivers of AMR are associated with risks of resistance transmission (Di = 0.49, SD = 0.14) and antibiotic use (Di = 0.58, SD = 0.2), which are worsened by intermediate drivers linked with challenges of antibiotic discovery (Di = 0.62, SD = 0.07), infection prevention (Di = 0.67, SD = 0.14) and surveillance (Di = 0.69, SD = 0.16). Distal drivers, such as living conditions, access to sanitation infrastructure, population growth and urbanisation, and gaps in policy implementation were development and governance challenges, acting as deep leverage points in the system in addressing AMR.

CONCLUSIONS

Comprehensive AMR strategies aiming to address multiple chronic AMR challenges must take advantage of opportunities for upstream interventions that specifically address distal drivers.

Why prescribe antibiotics? A systematic review of knowledge, tension, and motivation among clinicians in low-, middle- and high-income countries

Medical professionals such as physicians and veterinarians are responsible for appropriate antimicrobial prescription (AMP) and use. Although seemingly straightforward, the factors influencing antibiotic prescription, a category of antimicrobials, are complex. Many studies have been conducted in the past two decades on this subject. As a result, there is a plethora of empirical evidence regarding the factors influencing clinicians' AMP practices.

AIM

A systematic review of AMR studies on AMP was conducted, condensing findings according to a combination of the Knowledge, Attitude, and Practice (KAP) and Capacity, Opportunity, Motivation-Behavior (COM-B) models. Review findings were then synthesized and analyzed for policy implementation according to the Consolidated Framework for Implementation Research (CFIR).

DESIGN AND METHODOLOGY

A systematic literature review was conducted according to PRISMA guidelines to identify peer-reviewed papers indexed in pre-determined medical science, social sciences, and humanities databases that apply the KAP model in their investigations. Antimicrobial prescription factors were compared and contrasted among low- and middle-income countries (LMICs) and high-income countries (HICs).

FINDINGS

The KAP model is a heuristic and structured framework for identifying and classifying respondents' knowledge. However, other than medical knowledge, factors that influence prescription decision-making can be expanded to include attitudes, perception, personal affinities, professional circumstances, relational pressure, and social norms.

Antibiotic resistance through the lens of One Health: A study from an urban and a rural area in Sri Lanka

This study aimed to investigate and compare the proportion of AMR Escherichia coli (E. coli) between urban (Dompe in the Western province) and rural (Dambana in the Sabaragamuwa province) areas in Sri Lanka. The overall hypothesis of the study is that there is a difference in the proportion of AMR E. coli between the urban and the rural areas. Faecal samples were collected from healthy humans (n = 109), dairy animals (n = 103), poultry (n = 35), wild mammals (n = 81), wild birds (n = 76), soil (n = 80) and water (n = 80) from both areas. A total of 908 E. coli isolates were tested for susceptibility to 12 antimicrobials. Overall, E. coli isolated from urban area was significantly more likely to be resistant than those isolated from rural area. The human domain of the area had a significantly higher prevalence of AMR E. coli, but it was not significantly different in urban (98%) and rural (97%) areas. AMR E. coli isolated from dairy animals, wild animals and water was significantly higher in the urban area compared with the rural area. There was no significant difference in the proportion of multidrug resistance (MDR) E. coli isolated from humans, wild animals and water between the two study sites. Resistant isolates found from water and wild animals suggest contamination of the environment. A multi-sectorial One Health approach is urgently needed to control the spread of AMR and prevent the occurrences of AMR in Sri Lanka.

Treatment seeking and antibiotic use for urinary tract infection symptoms in the time of COVID-19 in Tanzania and Uganda

Background

There is still little empirical evidence on how the outbreak of coronavirus disease 2019 (COVID-19) and associated regulations may have disrupted care-seeking for non-COVID-19 conditions or affected antibiotic behaviours in low- and middle-income countries (LMICs). We aimed to investigate the differences in treatment-seeking behaviours and antibiotic use for urinary tract infection (UTI)-like symptoms before and during the pandemic at recruitment sites in two East African countries with different COVID-19 control policies: Mbarara, Uganda and Mwanza, Tanzania.

Methods

In this repeated cross-sectional study, we used data from outpatients (pregnant adolescents aged >14 and adults aged >18) with UTI-like symptoms who visited health facilities in Mwanza, Tanzania and Mbarara, Uganda. We assessed the prevalence of self-reported behaviours (delays in care-seeking, providers visited, antibiotics taken) at three different time points, labelled as 'pre-COVID-19 phase' (February 2019 to February 2020), 'COVID-19 phase 1' (March 2020 to April 2020), and 'COVID-19 phase 2' (July 2021 to February 2022).

Results

In both study sites, delays in care-seeking were less common during the pandemic than they were in the pre-COVID phase. Patients in Mwanza, Tanzania had shorter care-seeking pathways during the pandemic compared to before it, but this difference was not observed in Mbarara, Uganda. Health centres were the dominant sources of antibiotics in both settings. Over time, reported antibiotic use for UTI-like symptoms became more common in both settings. During the COVID-19 phases, there was a significant increase in self-reported use of antibiotics like metronidazole (<30% in the pre-COVID-19 phase to 40% in COVID phase 2) and doxycycline (30% in the pre-COVID-19 phase to 55% in COVID phase 2) that were not recommended for treating UTI-like symptoms in the National Treatment Guidelines in Mbarara, Uganda.

Conclusions

There was no clear evidence that patients with UTI-like symptoms attending health care facilities had longer or more complex treatment pathways despite strict government-led interventions related to COVID-19. However, antibiotic use increased over time, including some antibiotics not recommended for treating UTI, which has implications for future antimicrobial resistance.

Mussel-inspired antibacterial sponge for highly efficient water purification and sterilization

With the current expansion of urban areas and industrial development, the increasing discharge of wastewater containing bacteria poses a threat to human health. Although substantial advancements have been made in antibacterial materials, there is still a need for an efficient method that can thoroughly remove bacteria through sterilization and adsorption during wastewater treatment. Here, we report a mussel-inspired antibacterial sponge with outstanding antibacterial efficiency exceeding 95% and a high removal ratio of the bacterial corpses for water purification after contacting for 30 min. The high-efficient antibacterial performance is attributed to the stable releasing property of Ag+ and the charge interaction with quaternary amine salts. Combining the key features, including high-efficient, synergistic mechanism, and corpse capture, the antibacterial sponge shows excellent disinfection effects. This study provides a new method for water purification without bacterial residue.

Effects of breastfeeding on children's gut colonization with multidrug-resistant Enterobacterales in peri-urban Lima, Peru

Children living in low-resource settings are frequently gut-colonized with multidrug-resistant bacteria. We explored whether breastfeeding may protect against children's incident gut colonization with extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-Ec) and Klebsiella, Enterobacter, or Citrobacter spp. (ESBL-KEC). We screened 937 monthly stool samples collected from 112 children aged 1-16 months during a 2016-19 prospective cohort study of enteric infections in peri-urban Lima. We used 52,816 daily surveys to examine how exposures to breastfeeding in the 30 days prior to a stool sample were associated with children's risks of incident gut-colonization, controlling for antibiotic use and other covariates. We sequenced 78 ESBL-Ec from 47 children to explore their diversity. Gut-colonization with ESBL-Ec was increasingly prevalent as children aged, approaching 75% by 16 months, while ESBL-KEC prevalence fluctuated between 18% and 36%. Through 6 months of age, exclusively providing human milk in the 30 days prior to a stool sample did not reduce children's risk of incident gut-colonization with ESBL-Ec or ESBL-KEC. From 6 to 16 months of age, every 3 additional days of breastfeeding in the prior 30 days was associated with 6% lower risk of incident ESBL-Ec gut-colonization (95% CI: 0.90, 0.98, p = .003). No effects were observed on incident ESBL-KEC colonization. We detected highly diverse ESBL-Ec among children and few differences between children who were predominantly breastfed (mean age: 4.1 months) versus older children (10.8 months). Continued breastfeeding after 6 months conferred protection against children's incident gut colonization with ESBL-Ec in this setting. Policies supporting continued breastfeeding should be considered in efforts to combat antibiotic resistance.

pts promoter influences antibiotic resistance via proton motive force and ROS in Escherichia coli

Introduction

Glucose level is related to antibiotic resistance. However, underlying mechanisms are largely unknown.

Methods

Since glucose transport is performed by phosphotransferase system (PTS) in bacteria, pts promoter-deleted K12 (Δpts-P) was used as a model to investigate effect of glucose metabolism on antibiotic resistance. Gas chromatography-mass spectrometry based metabolomics was employed to identify a differential metabolome in Δpts-P compared with K12, and with glucose as controls.

Results

Δpts-P exhibits the resistance to β-lactams and aminoglycosides but not to quinolones, tetracyclines, and macrolide antibiotics. Inactivated pyruvate cycle was determined as the most characteristic feature in Δpts-P, which may influence proton motive force (PMF), reactive oxygen species (ROS), and nitric oxide (NO) that are related to antibiotic resistance. Thus, they were regarded as three ways for the following study. Glucose promoted PMF and β-lactams-, aminoglycosides-, quinolones-mediated killing in K12, which was inhibited by carbonyl cyanide 3-chlorophenylhydrazone. Exogenous glucose did not elevated ROS in K12 and Δpts-P, but the loss of pts promoter reduced ROS by approximately 1/5, which was related to antibiotic resistance. However, NO was neither changed nor related to antibiotic resistance.

Discussion

These results reveal that pts promoter regulation confers antibiotic resistance via PMF and ROS in Escherichia coli.