Antibiotic resistance in the environment: a link to the clinic?

Interactions within higher-order antibiotic combinations do not influence the rate of adaptation in bacteria

The prevalence and strength of antibiotic resistance has led to an ongoing battle between the development of new treatments and the evolution of resistance. Combining multiple drugs simultaneously is a potential solution for combating antibiotic resistance. However, this approach introduces new factors that must be considered, including the influence of drug interactions on the rate of resistance evolution. When antibiotics are used in combination, their effects can be additive, synergistic, or antagonistic. In this study, we investigated the effect of higher-order interactions involving 3 drugs on resistance evolution in Staphylococcus epidermidis. Previous studies have shown that synergistic interactions can increase the adaptation rate. However, the effects of higher-order interactions on rates of adaptation are unclear. We investigated the adaptation of Staphylococcus epidermidis to single-, 2-, and 3-drug environments to assess how interactions within drug combinations influence the rate of adaptation. We analyzed both the overall interaction and emergent interaction, the latter being a unique interaction that occurs in 3-drug combinations due to the presence of all three drugs, rather than simply strong pairwise interactions. Our results show that neither the overall interactions nor the emergent interactions affect adaptation rates.

A novel sensor array combined with machine learning for the effective differentiation of multiple classes of antibiotics based on copper-based nanozymes with laccase-like activity

A nanozyme sensor array was developed combining with machine learning algorithms for the effective identification and differentiation of multiple antibiotic classes and antibiotic individuals. The four channel sensor array was composed by four copper-based nanozymes with laccase-like activity. The significant structural differences between different classes of antibiotics (such as Aminoglycosides, Tetracyclines, β-lactams, Nitroimidazole, Sulfonamides, Quinolones) resulted in the different effect on the nanozymatic reactions through interact with copper、substrate and so on. In addition, the differences between antibiotics in the same class also made certain effect on the nanozymatic reactions. Based on the above affect and differences, we combined the machine learning algorithms to successfully realize the identification of six major classes and sixteen individuals of antibiotics simultaneously for the first time. The proposed sensing strategy realized the facile identification of major categories of antibiotics, which has good application prospects in the rapid antibiotic identification in environmental water bodies.

Prevalence of Salmonella enterica Serotypes Isolated From Broiler Liver and Their Antibiotic Resistance Profiles

Salmonella is an important foodborne pathogen of worldwide significance. The objective of this research was to determine the prevalence of Salmonella in chicken livers in Türkiye. This study obtained 104 packaged chicken liver samples, 13 from each of the 8 brands, from the province of Kırklareli, northwest of Türkiye. The overall prevalence of Salmonella spp. in liver samples was 36.5%. The 38 Salmonella isolates obtained were serotyped by slide agglutination using antisera by the Kauffmann White Le Minor Scheme. Based on standard serotyping results, the dominant serovar was S. Infantis (81.6%), followed by S. Enteritidis (13.1%) and S. Agona (5.3%). Antimicrobial susceptibility testing of 38 Salmonella isolates was performed using disk diffusion method. The Salmonella isolates (n = 38) were resistant to cefepime (60.5%), chloramphenicol (57.9%), trimethoprim-sulfamethoxazole (50.0%), amoxicillin-clavulanic acid (39.5%), azithromycin (28.9%), ofloxacin (26.3%), and cefoxitin (13.2%). Multidrug-resistance (MDR) accounted for 47.4% of Salmonella isolates. MDR was observed in S. Infantis (17/31, 54.8%) and S. Agona (1/2, 50.0%), nevertheless not in S. Enteritidis.

Comparative analysis of diarrheagenic and uropathogenic Escherichia coli isolates: antimicrobial resistance, virulence, and genomic profiling

AIMS

Escherichia coli is a key pathogen causing gastrointestinal and urinary tract infections. Diarrheagenic E. coli (DEC) and uropathogenic E. coli (UPEC) are distinct major pathotypes linked to specific clinical outcomes. Therefore, this study aimed to compare DEC and UPEC isolates regarding distribution, antimicrobial resistance, serotypes, resistance, and virulence gene profiles.

MATERIALS AND METHODS

A total of 400 clinical samples (200 stools and 200 urine) were analyzed using phenotypic and genotypic methods. Antimicrobial resistance, serotyping, and detection of resistance and virulence genes were performed. Phylogenetic and correlation analyses were conducted to explore genetic relationships and interactions.

RESULTS

Of 97 E. coli isolates (24.25% prevalence), 56 DEC and 41 UPEC were detected. DEC isolates primarily included serotypes O26, O45, and O55, while UPEC predominantly featured O1 and O25. UPEC showed higher multidrug resistance, while DEC was more virulent. UPEC carried unique markers (ureC, papC), and DEC harbored stx and aggR genes associated with gastrointestinal infections. Phylogenetic analysis showed separate clustering for DEC and UPEC, with limited genetic overlap. Correlation analysis identified strong associations within resistance and virulence genes but a negative correlation between these traits.

CONCLUSION

This study compared the phenotypic and genetic features of DEC and UPEC, highlighting their distinct pathogenic traits. Limited genetic overlap suggests potential gene transfer, influencing adaptability, and evolution.

Agriculturally Sourced Multidrug-Resistant Escherichia coli for Use as Control Strains

Bacteriological control strains with known characteristics ensure consistency and reproducibility of assay performance across different laboratories and are an important cornerstone of quality control in the microbiology laboratory. Ideally, control strains should be representative of the assay target and be widely available from reputable sources. However, for work involving antibiotic resistance most controls come from human and veterinary clinical sources and are not optimized for work in agriculturally impacted environments or not widely available. The objective of this work was to identify and make widely available two E. coli isolates sourced from agricultural production settings that could be used as external controls supporting method development, research and environmental monitoring for extended spectrum β-lactamase producing (ESBL) and tetracycline resistant Escherichia coli. Previously collected E. coli suspects were screened based on antimicrobial susceptibility testing data, then confirmed as E. coli and characterized both phenotypically and genotypically. The positive control strain, ARS-C301 was ESBL positive and contained the CTX-M-55 and tet(A) genes, and the negative control strain, ARS-C101 was negative for both targets. Here we introduce two agriculturally sourced, fully characterized, and genetically sequenced control strains for use as laboratory controls in research involving extended-spectrum β-lactamase producing (ESBL) and tetracycline-resistant Escherichia coli isolated from the environment, available via publicly accessible culture collections, and commercially as a quantitative pellet.

Environmental drivers of the resistome across the Baltic Sea

BACKGROUND

Antimicrobial resistance is a major global health concern, with the environment playing a key role in its emergence and spread. Understanding the relationships between environmental factors, microbial communities, and resistance mechanisms is vital for elucidating environmental resistome dynamics. In this study, we characterized the environmental resistome of the Baltic Sea and evaluated how environmental gradients and spatial variability, alongside its microbial communities and associated functional genes, influence resistome diversity and composition across geographic regions.

RESULTS

We analyzed the metagenomes of benthic sediments from 59 monitoring stations across a 1,150 km distance of the Baltic Sea, revealing an environmental resistome comprised of predicted antimicrobial resistance genes (ARGs) associated with resistance against 26 antibiotic classes. We observed spatial variation in its resistance profile, with higher resistome diversity in the northern regions and a decline in the dead zones and the southern areas. The combined effects of salinity and temperature gradients, alongside nutrient availability, created a complex environmental landscape that shaped the diversity and distribution of the predicted ARGs. Salinity predominantly influenced microbial communities and predicted ARG composition, leading to clear distinctions between high-saline regions and those with lower to mid-level salinity. Furthermore, our analysis suggests that microbial community composition and mobile genetic elements might be crucial in shaping ARG diversity and composition.

CONCLUSIONS

We presented that salinity and temperature were identified as the primary environmental factors influencing resistome diversity and distribution across geographic regions, with nutrient availability further shaping these patterns in the Baltic Sea. Our study also highlighted the interplay between microbial communities, resistance, and associated functional genes in the benthic ecosystem, underscoring the potential role of microbial and mobile genetic element composition in ARG distribution. Understanding how environmental factors and microbial communities modulate environmental resistomes will help predict the impact of future environmental changes on resistance mechanisms in complex aquatic ecosystems. Video Abstract.

Microbiome and Resistome in Poultry Litter-Fertilized and Unfertilized Agricultural Soils

Background: Poultry litter is the main waste of poultry farming and is widely used as an agricultural fertilizer. However, owing to the use of antimicrobials in animal production, it can accumulate antimicrobial residues, antimicrobial-resistant bacteria (ARB), and antimicrobial resistance genes (ARGs). This study aimed to evaluate the impact of poultry litter use on the microbiome and resistome of agricultural soils. Methods: Soil samples from fertilized and unfertilized plots were collected from two horticultural farms that intensively use poultry litter. Microbiome composition was assessed using 16S rRNA sequencing. A culture-dependent method was used to isolate resistant strains on CHROMagar plates supplemented with sulfamethoxazole or ciprofloxacin. ARGs and integrase-encoding genes were identified by PCR. Results: Microbiome analysis revealed significant differences in structure and composition between poultry litter-fertilized and unfertilized soils. Fertilized soils exhibited greater alpha diversity and richness. Bacillota, commonly found in the avian gastrointestinal tract, were more abundant in fertilized soils. A total of 62 resistant strains were isolated, and 23 clinically relevant strains harbored ARGs, including fluoroquinolone (qnrA and qnrB) and β-lactam (blaGES, blaTEM, and blaSHV) resistance genes. Class 1 and 2 integron-associated genes (intI1 and intI2) were also detected. Notably, the rare blaGES gene was detected in Bacillus sp. from unfertilized soil. Similarly, qnrA co-occurred with blaSHV in a Bosea sp. strain from unfertilized soil. Conclusions: These findings highlight the potential for ARB dissemination in agricultural environments, where ARB and ARGs, once introduced into soils, may spread by weathering and other environmental factors, complicating negative control selection in in situ studies.

Exploring the Ecological Impacts of Herbicides on Antibiotic Resistance Genes and Microbial Communities

The widespread application of herbicides has profound ecological consequences, particularly regarding the distribution of antibiotic resistance genes (ARGs) and microbial communities. In this study, we analyzed herbicide-related metagenomic data to assess the impact of herbicide exposure on ARGs and microbial populations. Our results demonstrate that herbicide application significantly increased the abundance of ARGs, particularly those associated with multidrug resistance, sulfonamides, and bacitracin, with notable increases in subtypes such as bacA and sul1. Microbial community analyses revealed a dominance of Pseudomonadota and Actinomycetota, along with a significant down-regulation of genera like Fibrisoma, Gilsonvirus, Limnobacter, and Wilnyevirus in the experimental group. Additionally, herbicide exposure led to a marked reduction in biodiversity. When threshold values were relaxed, correlation analyses revealed a co-occurrence pattern between multiple genes and sul1, suggesting that horizontal gene transfer plays a pivotal role in the spread of antibiotic resistance in herbicide-contaminated soils. Moreover, environmental factors were found to significantly influence both microbial community composition and ARG distribution. These findings highlight the complex ecological effects of herbicides on microbial diversity and the dissemination of resistance genes, emphasizing the need for further research into the long-term environmental and public health implications of herbicide use.

Explore the Contamination of Antibiotic Resistance Genes (ARGs) and Antibiotic-Resistant Bacteria (ARB) of the Processing Lines at Typical Broiler Slaughterhouse in China

Farms are a major source of antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB), and previous research mainly focuses on polluted soils and breeding environments. However, slaughtering is an important link in the transmission of ARGs and ARB from farmland to dining table. In this study, we aim to reveal the pollution of ARGs and ARB in the slaughter process of broilers. First, by qualitative and quantitative analysis of ARGs in samples collected from the broiler slaughtering and processing production chain, the contamination level of ARGs was reflected; secondly, potential hosts for ARGs and microbial community were analyzed to reflect the possible transmission rules; thirdly, through the antibiotic susceptibility spectrum analysis of four typical food-borne pathogens, the distribution of ARB was revealed. The results showed that 24 types of ARGs were detected positive on the broiler slaughter production line, and tetracycline-resistance genes (20.45%) were the most frequently detected. The types of ARGs vary with sampling process, and all sampling links contain high levels of sul2 and intI1. The most abundant ARGs were detected in chicken surface in the scalding stage and entrails surface in the evisceration stage. There was a significant correlation between intI1 and tetM, suggesting that tetM might be able to enter the human food chain through class-1 integrons. The host range of the oqxB gene is the most extensive, including Sphingobacterium, Bacteroidia unclassified, Rothia, Microbacterium, Algoriella, etc. In the relevant links of the slaughter production line, the microbial community structure is similar. Removing viscera may cause diffusion of ARGs carried by intestinal microorganisms and contaminate chicken and following processing production. The four food-borne pathogens we tested are widely present in all aspects of the slaughter process, and most of them have multi-drug resistance and even have a high degree of resistance to some veterinary drugs banned by the Ministry of Agriculture. Our study preliminarily revealed the pollution of ARGs and ARB in the slaughter process of broilers, and these results are helpful to carry out food safety risk assessment and formulate corresponding control measures.

Rethinking the words hostspot reservoir and pristine in the environmental dimensions of antimicrobial resistance

We assess three words commonly used to represent the environmental dimensions of antimicrobial resistance (AMR) - 'hotspot', 'reservoir' and 'pristine' - through two questions: how are these terms used in published research; and how do these terms shape research being conducted? We advocate for the community to reflect on and improve its use of language, and suggest four potentially more productive and precise terms for AMR hazard: presence; transmission; evolution and connectivity.

Effects of UVC doses on the removal of antimicrobial resistance elements from secondary treated sewage

Wastewater treatment plants (WWTPs) currently face major challenges toward the removal of microcontaminants and/or microbial matrices and consequently play an important role in the potential dissemination of biological resistance in freshwater. The ultraviolet (UV) system is a tertiary treatment strategy increasingly applied worldwide, although many studies have shown that disinfected effluent can still contain antibiotic-resistant bacteria and resistance genes. Therefore, to better understand the effects of UV radiation doses on the removal of all resistance elements (antibiotics, antibiotic-resistant bacteria, and antibiotic resistance genes), the present study was designed using a pilot-scale photoreactor. The UV doses could be varied to investigate whether there is an optimal UV dose capable of removing all resistance elements and also if the UV dose frequently applied in full-scale systems is able to reduce the resistance elements. The effect of different UV doses (A, 0-10 mJ/cm2; B, 10-15 mJ/cm2; and C, > 15 mJ/cm2) in a pilot-scale photoreactor on the removal of antibiotics, antibiotic-resistant bacteria, and genes from the effluent of a UASB reactor followed by a biological trickling filter system (UASB-TF) fed with real sanitary sewage was investigated. Samples of influent and effluent from the UVC photoreactor were collected, and the concentration levels of norfloxacin (NOR), ciprofloxacin (CIP), and levofloxacin (LEV) were assessed. The qnrB, sul1, ermB, integron-integrase (intI1), and 16S rRNA genes, total heterotrophic bacteria (THB), and bacterial resistance to azithromycin and sulfamethoxazole were also investigated. Results indicated that LEV and intI1 were found in the highest median concentrations in the photoreactor influent. Although most antibiotics (NOR and CIP) and ARGs (intI1, 16S rRNA, and qnrB) were apparently better removed with the highest UV dose (> 15 mJ/cm2) applied, except for LEV, sul1, and ermB genes, the Kruskal-Wallis test reported no significant difference between low and high doses. ARB removal (from 80 to 100%) was observed at all UV doses. Principal component analysis (PCA) suggested a clear pattern of pollutant groups, i.e., antibiotics, ARG, and ARB, which exhibited low (median of 8-16%), medium (37-96%), and high (> 97%) removal percentages, respectively. These results demonstrated that UVC photoreactors can be an alternative to complement biological treatment in sewage treatment plants at the dose normally applied in full-scale WWTPs (> 15 mJ/cm2). However, there was no optimal single dose capable of removing all the resistance elements investigated.

Surveillance of public health pathogens in Lagos wastewater canals: a cross-sectional study

BACKGROUND

Wastewater-based epidemiology (WBE) is already being adopted for the surveillance of health conditions of communities and shows great potential for the monitoring of infectious pathogens of public health importance. There is however paucity of robust data to support extensive WBE in Nigeria. This study evaluated the prevalence of clinically relevant infectious pathogens and provided antimicrobial resistance profiles of bacteria pathogens in wastewater canals in Lagos State at a single point in time.

METHODS

This is a cross-sectional survey of wastewater canals in 20 Local Government Areas (LGAs) in Lagos State for detection of bacteria pathogens of public health importance including non-tuberculous mycobacteria and SARS-Cov-2 virus using cultural analysis and conventional Polymerase Chain Reaction (PCR) techniques. Descriptive epidemiological survey of communities around the canals was done using questionnaires to assess exposure pathways. Statistical analysis was done using SPSS version 27 while P value of < 0.05 was considered as significant.

RESULTS

Three thousand and fifty-four (3054) questionnaires were administered to 1215 (39.8%) females and 1658 (54.3%) males in communities situated around 40 canals in 20 LGAs. Although majority (81.8%) reported using water closet toilet system and pit latrine (12.5%), a few of them admitted to open defaecation [101 (3.3%)] while 299 (9.8%) engaged in open field waste disposal. SARS-CoV-2 was not detected from wastewater in this study. Two mycobacterial species that included Mycobacterium fortitium group (13, 32.5%) and Mycobacterium kansasii (11, 27.5%) were identified in 15 out of 20 LGAs sampled. A total of 123 bacteria pathogens were isolated across the 40 canals. Prominent enteropathogens isolated included Escheriachia coli (28.5%), Salmonella spp (16.3%), Vibro cholerae (10.6%) and Shigella spp (5.7%). Extended spectrum beta-lactamase genes were prominent (87.5%) in the wastewater samples with almost a half (42.5%) of the canals containing both SHV and CTX-M.

CONCLUSION

This study highlights the presence of pathogens with potential to cause epidemic in wastewater canals in Lagos State and provides evidence to inform policy and strategies for wastewater monitoring and treatment. Further studies involving longitudinal monitoring of time-based variations is needed to identify trends in pathogen loads and AMR patterns over time.

Prevalence of Antibiotic Resistance Genes in Differently Processed Smoothies and Fresh Produce from Austria

Plant-derived foods are potential vehicles for microbial antibiotic resistance genes (ARGs), which can be transferred to the human microbiome if consumed raw or minimally processed. The aim of this study was to determine the prevalence and the amount of clinically relevant ARGs and mobile genetic elements (MGEs) in differently processed smoothies (freshly prepared, cold-pressed, pasteurized and high-pressure processed) and fresh produce samples (organically and conventionally cultivated) to assess potential health hazards associated with their consumption. The MGE ISPps and the class 1 integron-integrase gene intI1 were detected by probe-based qPCR in concentrations up to 104 copies/mL in all smoothies, lettuce, carrots and a single tomato sample. The highest total (2.2 × 105 copies/mL) and the most diverse ARG and MGE loads (16/26 targets) were observed in freshly prepared and the lowest prevalences (5/26) and concentrations (4.1 × 103 copies/mL) in high-pressure-processed (HPP) smoothies. BlaCTX-M-1-15 (1.2 × 105 c/mL) and strB (6.3 × 104 c/mL) were the most abundant, and qacEΔ1 (95%), blaTEM1 (85%), ermB and sul1 (75%, each) were the most prevalent ARGs. QnrS, vanA, sat-4, blaKPC, blaNDM-1 and blaOXA-10 were never detected. HPP treatment reduced the microbial loads by ca. 5 logs, also destroying extracellular DNA potentially encoding ARGs that could otherwise be transferred by bacterial transformation. The bacterial microbiome, potential pathogens, bacterial ARG carriers and competent bacteria able to take up ARGs were identified by Illumina 16S rRNA gene sequencing. To reduce the risk of AMR spread from smoothies, our data endorse the application of DNA-disintegrating processing techniques such as HPP.

Novel antibiotic resistance profiles in bacteria isolated from oil fly larvae Helaeomyia petrolei living in the La Brea Tar Pits

Larvae from the petroleum oil fly, Helaeomyia petrolei, live in the asphaltene and polyaromatic hydrocarbon rich asphalt seeps of Rancho La Brea, Los Angeles, California. These larvae pass high amounts of viscous asphalt through their digestive system, and their gut microbiota is exposed to these extreme conditions. Environmental stress response mechanisms can co-select for antibiotic resistance, and in the current study we used 16S rRNA and genomic sequencing along with the Comprehensive Antibiotic Resistance Database (CARD) tools to characterize antibiotic resistance profiles from six bacteria previously isolated from the oil fly larval intestinal tract, linking phenotypic and genotypic resistance profiles. The isolates contain a core set of antibiotic resistance determinants along with determinants that are rarely found in these species. Comparing these oil fly isolates to the phenotypic prevalence data generated by the CARD Resistance Gene Identifier revealed sixteen instances where the oil fly bacteria appeared to carry a resistance not seen in related taxa in the database, suggesting a novel suite of resistance families in the oil fly isolates compared to other members of the same taxa. Results highlight the functional duality of genes that simultaneously code for antibiotic resistance and survival under extreme conditions, and expand our understanding of the ecological and evolutionary role of antibiotic resistance genes in environmental habitats.

An in silico approach for identification of lead compound as FtsZ inhibitor

The remarkable conservation of the FtsZ among Gram-positive and Gram-negative bacteria, a crucial GTPase in bacterial cell division, has emerged as a promising antibacterial drug target to combat antibacterial resistance. There have been several coordinated efforts to develop inhibitors against FtsZ which can also serve as potential candidates for future antibiotics. In the present study, a natural product-like library (≈50,000 compounds) was employed to conduct HTVS against Staphylococcus aureus FtsZ protein (PDB Id: 6KVP). Additionally, molecular docking was carried out in two modes, SP and XP docking, using the Schrödinger suite. The glide scores of ligands obtained by XP docking were further summarized and compared with the control ligands (ZI1- co-crystal and PC190723-a compound undergoing clinical trial). Using the Prime-MM-GBSA approach, BFE calculations were performed on the top XP-scored ligands (≈598 compounds). These hits were also evaluated for ADMET parameters using the Qikprop algorithm, SwissADME, and in silico carcinogenicity testing using Carcinopred-El. Based on the results, ligand 4-FtsZ complex was considered for the 300 ns MDS analysis to get insights into its binding modes within the catalytic pocket of FtsZ protein. The analysis revealed that the amide linkage sandwiched between the triazole and 1-oxa-8-azaspirodecan-8-ium moiety (Val203) as well as the aminoethyl group present at 1st position on the triazole moiety (Leu209, Leu200, Asp210, and Ala202) were responsible for the FtsZ inhibitory activity, owing to their crucial interactions with key amino acid residues. Further, the complex also displayed good protein-ligand stability, ultimately predicting ligand 4 as a potent lead compound for the inhibition of FtsZ. Thus, our in silico findings will serve as a framework for in-depth in-vitro and in-vivo investigations encouraging the development of FtsZ inhibitors as a new generation of antibacterial agents.

Metagenomics insights into bacterial diversity and antibiotic resistome of the sewage in the city of Belém, Pará, Brazil

Introduction

The advancement of antimicrobial resistance is a significant public health issue today. With the spread of resistant bacterial strains in water resources, especially in urban sewage, metagenomic studies enable the investigation of the microbial composition and resistance genes present in these locations. This study characterized the bacterial community and antibiotic resistance genes in a sewage system that receives effluents from various sources through metagenomics.

Methods

One liter of surface water was collected at four points of a sewage channel, and after filtration, the total DNA was extracted and then sequenced on an NGS platform (Illumina® NextSeq). The sequenced data were trimmed, and the microbiome was predicted using the Kraken software, while the resistome was analyzed on the CARD webserver. All ecological and statistical analyses were performed using the. RStudio tool.

Results and discussion

The complete metagenome results showed a community with high diversity at the beginning and more restricted diversity at the end of the sampling, with a predominance of the phyla Bacteroidetes, Actinobacteria, Firmicutes, and Proteobacteria. Most species were considered pathogenic, with an emphasis on those belonging to the Enterobacteriaceae family. It was possible to identify bacterial groups of different threat levels to human health according to a report by the U.S. Centers for Disease Control and Prevention. The resistome analysis predominantly revealed genes that confer resistance to multiple drugs, followed by aminoglycosides and macrolides, with efflux pumps and drug inactivation being the most prevalent resistance mechanisms. This work was pioneering in characterizing resistance in a sanitary environment in the Amazon region and reinforces that sanitation measures for urban sewage are necessary to prevent the advancement of antibiotic resistance and the contamination of water resources, as evidenced by the process of eutrophication.

Whole-Genome Sequencing And Characterization Of Two Bacillus velezensis Strains from Termitarium and A Comprehensive Comparative Genomic Analysis of Biosynthetic Gene Clusters

The species Bacillus velezensis is known for its biosynthetic potential and metabolic versatility in producing several secondary metabolites and promoting plant growth. In this study, we isolated two B. velezensis strains, WGTg-8 and WGTm-299, from the termite gut and termitarium, which exhibited antimicrobial activity against multiple clinical and phytopathogens. The whole genomes of these strains were sequenced using the Illumina platform and annotated. The genome mining of the draft genome sequences revealed 48 biological gene clusters (BGCs) responsible for synthesizing various secondary metabolites. The construction of the similarity network of the BGCs and the comparative analysis with the genetically related organisms are aided in the identification of metabolites produced by these strains. We identified biosynthetic gene clusters (BGCs) coding for macrolactin H, bacilysin, bacillibactin, amylocyclin, comX4, and LCI, found in both strains with 100% similarity. The difficidin, bacillaene, thusin_alpha, and cericidin BGCs are exclusively found in strain WGTg-8, while the colicin BGC is exclusively present in the WGTm-299 strain. The fengycin and surfactin gene clusters are present in both strains with 80% similarity. Furthermore, 28 putative NRPS BGCs, NRPS-T1PKS hybrid clusters, a T1PKS, and a bacteriocin BGC were identified with very low similarity (≤ 25%) or no similarity with known antibiotics. In addition, we found several genes coding for plant growth-promoting properties, including nitrogen metabolism, hormone synthesis, sulfur metabolism, phosphate metabolism, and a few other properties.

Metagenomic profiling of cecal microbiota and antibiotic resistome in rodents

The rodent gut microbiota is a known reservoir of antimicrobial resistance, yet the distribution of antibiotic resistance genes (ARGs) within rodent cecal microbial communities and the specific bacterial species harboring these ARGs remain largely underexplored. This study employed high-throughput sequencing of 122 samples from five distinct rodent species to comprehensively profile the diversity and distribution of ARGs and to identify the bacterial hosts of these genes. A gene catalog of the rodent cecal microbiome was constructed, comprising 22,757,369 non-redundant genes. Analysis of the microbial composition and diversity revealed that Bacillota and Bacteroidota were the dominant bacterial phyla across different rodent species, with significant variations in species composition among the rodents. In total, 3703 putative antimicrobial resistance protein-coding genes were identified, corresponding to 392 unique ARG types classified into 32 resistance classes. The most enriched ARGs in the rodent cecal microbiome were associated with multidrug resistance, followed by glycopeptide and elfamycin antibiotics. Procrustes analysis demonstrated a correlation between the structure of the microbial community and the resistome. Metagenomic assembly-based host tracking indicated that most ARG-carrying contigs originated from the bacterial family Oscillospiraceae. Additionally, 130 ARGs showed significant correlations with mobile genetic elements. These findings provide new insights into the cecal microbiota and the prevalence of ARGs across five rodent species. Future research on a wider range of wild rodent species carrying ARGs will further elucidate the mechanisms underlying the transmission of antimicrobial resistance.

Klebsiella in Wildlife: Clonal Dynamics and Antibiotic Resistance Profiles, a Systematic Review

Klebsiella spp. are a genus of Gram-negative, opportunistic bacteria frequently found in the flora of the mucosal membranes of healthy animals and humans, and in the environment. Species of this group can cause serious infections (meningitis, sepsis, bacteraemia, urinary tract infections, liver damage) and possible death in immunocompromised organisms (and even in immunocompetent ones in the case of hypervirulent K. pneumoniae) that are exposed to them. K. pneumoniae is part of the ESKAPE organisms, and so it is important to understand this genus in terms of multidrug-resistant bacteria and as a carrier of antibiotic resistance mechanisms. As it is a durable bacterium, it survives well even in hostile environments, making it possible to colonize all kinds of habitats, even the mucosal flora of wildlife. This systematic review explores the prevalence of Klebsiella spp. bacteria in wild animals, and the possibility of transmission to humans according to the One Health perspective. The isolates found in this review proved to be resistant to betalactams (blaTEM, blaOXA-48…), aminoglycosides (strAB, aadA2…), fosfomycin, tetracyclines, sulphonamides, trimethoprim, phenicols (catB4), and polymyxins (mcr4).

Investigating the resistome of haemolytic bacteria in Arctic soils

Microorganisms inhabiting hostile Arctic environments express a variety of functional phenotypes, some of clinical interest, such as haemolytic ability and antimicrobial resistance. We studied haemolytic bacterial isolates from Arctic habitats, assessing their minimum inhibitory concentration (MIC) against antimicrobials. We then performed whole genome sequencing and analysed them for features conferring antimicrobial resistance. MIC data showed that Micromonospora spp. belong to 33% non-wild type (NWT) for erythromycin and penicillin and 22% NWT for tetracycline. Both Pseudomonas spp. belong to 43% NWT for nalidixic acid and streptomycin and 29% NWT for colistin. Finally, the Pedobacter isolate was in 80% NWT for antimicrobials tested. Whole-genome sequencing analyses revealed that fluoroquinolones, tetracyclines, macrolides and penams were the most frequent drug classes against which genotypic resistance was found. Additionally, resistance genes to heavy metals and disinfectants were identified. Our research demonstrates the presence of antimicrobial resistance in bacteria from Arctic habitats and highlights the importance of conservation efforts in these environments, where anthropogenic influence is becoming more evident. Furthermore, our data suggest the possible presence of novel resistance mechanisms, which could pose a threat if the responsible genes are transferable between species or become widespread due to environmental stress and alterations brought about by climate change.

Challenges and effective tracking down strategies of antibiotic contamination in aquatic ecosystem

A growing environmental concern revolves around the widespread use of medicines, particularly antibiotics, which adversely impact water quality and various life forms. The unregulated production and utilization of antibiotics not only affect non-targeted organisms but also exert significant evolutionary pressures, leading to the rapid development of antimicrobial resistance (AMR) in bacterial communities. To address this issue, global studies have been conducted to assess the prevalence and quantities of antibiotics in various environmental components including freshwater, ocean, local sewage, and fish. These studies aim to establish effective analytical methods for identifying and measuring antibiotic residues in environmental matrices that might enable authorities to establish norms for the containment and disposal of antibiotics. This article offers a comprehensive overview of methods used to extract antibiotics from environmental matrices exploring purification techniques such as liquid-liquid extraction, solid-phase extraction, green extraction techniques, and concentration methods like lyophilization and rotary evaporation. It further highlights qualitative and quantitative analysis methods, high-performance liquid chromatography, ultra-high-performance liquid chromatography, and liquid chromatography-tandem along with analytical methods such as UV-Vis and tandem mass spectrometry for detecting and measuring antibiotics. Urgency is underscored for proactive strategies to curb antibiotic contamination, safeguarding the integrity of aquatic ecosystems and public health on a global scale.

Health risk ranking of antibiotic resistance genes in the Yangtze River

Antibiotic resistance is an escalating global health concern, exacerbated by the pervasive presence of antibiotic resistance genes (ARGs) in natural environments. The Yangtze River, the world's third-longest river, traversing areas with intense human activities, presents a unique ecosystem for studying the impact of these genes on human health. Here, we explored ARGs in the Yangtze River, examining 204 samples from six distinct habitats of approximately 6000 km of the river, including free-living and particle-associated settings, surface and bottom sediments, and surface and bottom bank soils. Employing shotgun sequencing, we generated an average of 13.69 Gb reads per sample. Our findings revealed a significantly higher abundance and diversity of ARGs in water-borne bacteria compared to other habitats. A notable pattern of resistome coalescence was observed within similar habitat types. In addition, we developed a framework for ranking the risk of ARG and a corresponding method for calculating the risk index. Applying them, we identified water-borne bacteria as the highest contributors to health risks, and noted an increase in ARG risks in particle-associated bacteria correlating with heightened anthropogenic activities. Further analysis using a weighted ARG risk index pinpointed the Chengdu-Chongqing and Yangtze River Delta urban agglomerations as regions of elevated health risk. These insights provide a critical new perspective on ARG health risk assessment, highlighting the urgent need for strategies to mitigate the impact of ARGs on human health and to preserve the ecological and economic sustainability of the Yangtze River for future human use.

The distribution and key influential factors of antibiotic resistance genes in agricultural soils polluted by multiple heavy metals

Due to anthropogenic activities such as mining, several agricultural soils are polluted by multiple heavy metals. However, it is still unclear whether multiple heavy metals could affect the distribution of antibiotic resistance genes (ARGs), and how metals affect ARGs. To understand ARGs' distribution in heavy metal-polluted soils, we chose soils contaminated by different types and contents of heavy metals to determine the ARGs' number and abundance through high-throughput quantitative real-time PCR (HT-qPCR) in this study. Additionally, the factors affecting ARGs' distribution, such as soil properties, mobile genetic genes (MGEs), and bacterial communities, were explored. The results demonstrated that the sampled soils were primarily contaminated by Cd, As, Pb, and Zn, and the pollution load index (PLI) values of these metals ranged from 1.3 to 2.7, indicating a low to moderate degree of heavy metal contamination. The number and abundance of ARGs ranged from 44 to 113 and from 2.74 × 107 copies/g to 1.07 × 108 copies/g, respectively. Besides, abundant MGEs in soils, ranging from 1.84 × 106 copies/g to 5.82 × 106 copies/g, were observed. The pathway analysis suggested that MGEs were the most important factor directly affecting ARG abundance (0.89). Notably, heavy metals also affected the ARG abundance. Proteobacteria and Actinobacteria, the main heavy metal tolerant bacteria, were found to be the main hosts of ARGs through network analysis. ARG-carrying pathogens (ACPs) in agricultural soils were found to carry MGEs, indicating a high risk of dissemination. This study provided important information for understanding the ARGs' fate and also the key factors affecting ARGs' spread in multiple heavy metal-contaminated soils.

Research progress of fluorescent composites based on cyclodextrins: Preparation strategies, fluorescence properties and applications in sensing and bioimaging

Fluorescence analysis has been regarded as one of the commonly used analytical methods because of its advantages of simple operation, fast response, low cost and high sensitivity. So far, various fluorescent probes, with noble metal nanoclusters, quantum dots, organic dyes and metal organic frameworks as representatives, have been widely reported. However, single fluorescent probe often suffers from some deficiencies, such as low quantum yield, poor chemical stability, low water solubility and toxicity. To overcome these disadvantages, the introduction of cyclodextrins into fluorescent probes has become a fascinating approach. This review (with 218 references) systematically covers the research progress of fluorescent composites based on cyclodextrins in recent years. Preparation strategies, fluorescence properties, response mechanisms and applications in sensing (ions, organic pollutants, bio-related molecules, temperature, pH) and bioimaging of fluorescent composites based on cyclodextrins are summarized in detail. Finally, the current challenges and future perspectives of these composites in relative research fields are discussed.

Viral Communities Suppress the Earthworm Gut Antibiotic Resistome by Lysing Bacteria on a National Scale

Earthworms are critical in regulating soil processes and act as filters for antibiotic resistance genes (ARGs). Yet, the geographic patterns and main drivers of earthworm gut ARGs remain largely unknown. We collected 52 earthworm and soil samples from arable and forest ecosystems along a 3000 km transect across China, analyzing the diversity and abundance of ARGs using shotgun metagenomics. Earthworm guts harbored a lower diversity and abundance of ARGs compared to soil, resulting in a stronger distance-decay rate of ARGs in the gut. Greater deterministic assembly processes of ARGs were found in the gut than in soil. The earthworm gut had a lower frequency of co-occurrence patterns between ARGs and mobile genetic elements (MGEs) in forest than in arable systems. Viral diversity was higher in the gut compared to soil and was negatively correlated with bacterial diversity. Bacteria such as Streptomyces and Pseudomonas were potential hosts of both viruses and ARGs. Viruses had negative effects on the diversity and abundance of ARGs, likely due to the lysis on ARG-bearing bacteria. These findings provide new insights into the variations of ARGs in the earthworm gut and highlight the vital role of viruses in the regulation of ARGs in the soil ecosystem.

Isolation and characterization of enterococci from poultry reveals high incidence of Enterococcus thailandicus in Victoria, Australia

AIMS

Antibiotic resistance is a global health crisis. Roughly two-thirds of all antibiotics used are in production animals, which have the potential to impact the development of antibiotic resistance in bacterial pathogens of humans. There is little visibility on the extent of antibiotic resistance in the Australian food chain. This study sought to establish the incidence of antibiotic resistance among enterococci from poultry in Victoria.

METHODS AND RESULTS

In 2016, poultry from a Victorian processing facility were swabbed immediately post-slaughter and cultured for Enterococcus species. All isolates recovered were speciated and tested for antibiotic susceptibility to 12 antibiotics following the Clinical Laboratory Standards Institute guidelines. A total of 6 farms and 207 birds were sampled and from these 285 isolates of Enterococcus were recovered. Eight different enterococcal species were identified as follows: E. faecalis (n = 122; 43%), E. faecium (n = 92; 32%), E. durans (n = 35; 12%), E. thailandicus (n = 23; 8%), E. hirae (n = 10; 3%), and a single each of E. avium, E. gallinarum, and E. mundtii. Reduced susceptibility to older classes of antibiotics was common, in particular: erythromycin (73%), rifampin (49%), nitrofurantoin (40%), and ciprofloxacin (39%). Two vancomycin-intermediate isolates were recovered, but no resistance was detected to either linezolid or gentamicin.

CONCLUSIONS

The relatively high numbers of a recently described species, E. thailandicus, suggest this species might be well adapted to colonize poultry. The incidence of antibiotic resistance is lower in isolates from poultry than in human medicine in Australia. These results suggest that poultry may serve as a reservoir for older antibiotic resistance genes but is not driving the emergence of antimicrobial resistance in human bacterial pathogens. This is supported by the absence of resistance to linezolid and gentamicin.

Filamentous bacteria-induced sludge bulking can alter antibiotic resistance gene profiles and increase potential risks in wastewater treatment systems

Sludge bulking caused by filamentous bacteria is a prevalent issue in wastewater treatment systems. While previous studies have primarily concentrated on controlling sludge bulking, the biological risks associated with it have been overlooked. This study demonstrates that excessive growth of filamentous bacteria during sludge bulking can significantly increase the abundance of antibiotic resistance genes (ARGs) in activated sludge. Through metagenomic analysis, we identified specific ARGs carried by filamentous bacteria, such as Sphaerotilus and Thiothrix, which are responsible for bulking. Additionally, by examining over 1,000 filamentous bacterial genomes, we discovered a diverse array of ARGs across different filamentous bacteria derived from wastewater treatment systems. Our findings indicate that 74.84% of the filamentous bacteria harbor at least one ARG, with the occurrence frequency of ARGs in these bacteria being approximately 1.5 times higher than that in the overall bacterial population in activated sludge. Furthermore, genomic and metagenomic analyses have shown that the ARGs in filamentous bacteria are closely linked to mobile genetic elements and are frequently found in potentially pathogenic bacteria, highlighting potential risks posed by these filamentous bacteria. These insights enhance our understanding of ARGs in activated sludge and underscore the importance of risk management in wastewater treatment systems.

Antimicrobial Resistance in Equines: A Growing Threat to Horse Health and Beyond-A Comprehensive Review

The equine industry holds substantial economic importance not only in the USA but worldwide. The occurrence of various infectious bacterial diseases in horses can lead to severe health issues, economic losses, and restrictions on horse movement and trade. Effective management and control of these diseases are therefore crucial for the growth and sustainability of the equine industry. While antibiotics constitute the primary treatment strategy for any bacterial infections in horses, developing resistance to clinically important antibiotics poses significant challenges to equine health and welfare. The adverse effects of antimicrobial overuse and the escalating threat of resistance underscore the critical importance of antimicrobial stewardship within the equine industry. There is limited information on the epidemiology of antimicrobial-resistant bacterial infections in horses. In this comprehensive review, we focus on the history and types of antimicrobials used in horses and provide recommendations for combating drug-resistant bacterial infections in horses. This review also highlights the epidemiology of antimicrobial resistance (AMR) in horses, emphasizing the public health significance and transmission dynamics between horses and other animals within a One Health framework. By fostering responsible practices and innovative control measures, we can better help the equine industry combat the pressing threat of AMR and thus safeguard equine as well as public health.

Antimicrobial Resistance Elements in Coastal Water of Llanquihue Lake, Chile

Antimicrobial resistance has been stated to be a global health problem. In Chile, the use of antibiotics should be declared by medical prescription, but it is unknown what happens to the drugs once the treatment ends. Among the possibilities for their disposal are the trash or the drain; regardless of which scenario arises, antibiotics could accumulate in the environment, stimulating the emergence of antimicrobial resistance mechanisms and their transfer between microorganisms. Unfortunately, sometimes wastewater ends up in bodies of water, due to the dragging of elements by rain, or by the presence of illegal water discharges. In this work, shotgun metagenomics was used to elucidate the functional and microbial composition of biohazard elements in the bay of Puerto Varas City, Chile. As expected, a high diversity of microorganisms was found, including bacterial elements described as human or animal pathogens. Also, a diverse repertory of antimicrobial resistant genes (ARGs) was detected, which confers mainly resistance to macrolides, beta-lactams, and tetracyclines, consistent with the families of antibiotics most used in Chile. Similar ARGs were identified in DNA mobile elements. In addition, we tested the antimicrobial susceptibility in 14 bacterial strains isolated from Llanquihue Lake. This is the first report of the presence of genomic elements that could constitute a health problem, considering the importance of the interconnection between environmental, animal, and human health, a concept known as One Health.

The influence of the phylum Planctomycetota in the environmental resistome

Antimicrobial resistance is one of the leading causes of death worldwide and research on this topic has been on the spotlight for a long time. More recently and in agreement with the One Health Approach, the focus has moved towards the environmental resistome. Members of the phylum Planctomycetota are ubiquitously present in the environment including in hotspots for antimicrobial resistance selection and dissemination. Furthermore, phenotypic broad-range resistance has been observed in diverse members of this phylum. Here we review the evidence available on antimicrobial resistance in the underexploited Planctomycetota and highlight key aspects for future studies.

From remote to urbanized: Dispersal of antibiotic-resistant bacteria under the aspect of anthropogenic influence

Antibiotic resistance is a growing global concern, but our understanding of the spread of resistant bacteria in remote regions remains limited. While some level of intrinsic resistance likely contributes to reduced susceptibility to antimicrobials in the environment, it is evident that human actions, particularly the (mis)use of antibiotics, play a significant role in shaping the environmental resistome, even in seemingly distant habitats like glacier ice sheets. Our research aims to bridge this knowledge gap by investigating the direct influence of human activities on the presence of antibiotic-resistant bacteria in various habitats. To achieve a comprehensive assessment of anthropogenic impact across diverse and seemingly isolated sampling sites, we developed an innovative approach utilizing Corine Land Cover data and heatmaps generated from sports activity trackers. This method allowed us to make meaningful comparisons across relatively pristine environments. Our findings indicate a noteworthy increase in culturable antibiotic-resistant bacteria with heightened human influence, as evidenced by our analysis of glacier, snow, and lake water samples. Notably, the most significant concentrations of antibiotic-resistant and multidrug-resistant microorganisms were discovered in two highly impacted sampling locations, namely the Tux Glacier and Gas Station Ellmau.

Bacteria populating freshly appeared supraglacial lake possess metals and antibiotic-resistant genes

Antibiotic resistance (AR) has been extensively studied in natural habitats and clinical applications. AR is mainly reported with the use and misuse of antibiotics; however, little is known about its presence in antibiotic-free remote supraglacial lake environments. This study evaluated bacterial strains isolated from supraglacial lake debris and meltwater in Dook Pal Glacier, northern Pakistan, for antibiotic-resistant genes (ARGs) and metal-tolerant genes (MTGs) using conventional PCR. Several distinct ARGs were reported in the bacterial strains isolated from lake debris (92.5%) and meltwater (100%). In lake debris, 57.5% of isolates harbored the blaTEM gene, whereas 58.3% of isolates in meltwater possessed blaTEM and qnrA each. Among the ARGs, qnrA was dominant in debris isolates (19%), whereas in meltwater isolates, qnrA (15.2%) and blaTEM (15.2%) were dominant. ARGs were widely distributed among the bacterial isolates and different bacteria shared similar types of ARGs. Relatively greater number of ARGs were reported in Gram-negative bacterial strains. In addition, 92.5% of bacterial isolates from lake debris and 83.3% of isolates from meltwater harbored MTGs. Gene copA was dominant in meltwater isolates (50%), whereas czcA was greater in debris bacterial isolates (45%). Among the MTGs, czcA (18.75%) was dominant in debris strains, whereas copA (26.0%) was greater in meltwater isolates. This presents the co-occurrence and co-selection of MTGs and ARGs in a freshly appeared supraglacial lake. The same ARGs and MTGs were present in different bacteria, exhibiting horizontal gene transfer (HGT). Both positive and negative correlations were determined between ARGs and MTGs. The research provides insights into the existence of MTGs and ARGs in bacterial strains isolated from remote supraglacial lake environments, signifying the need for a more detailed study of bacteria harboring ARGs and MTGs in supraglacial lakes.

Anthropogenic contamination sources drive differences in antimicrobial-resistant Escherichia coli in three urban lakes

Antimicrobial resistance (AMR) is an ever-present threat to the treatment of infectious diseases. However, the potential relevance of this phenomenon in environmental reservoirs still raises many questions. Detection of antimicrobial-resistant bacteria in the environment is a critical aspect for understanding the prevalence of resistance outside of clinical settings, as detection in the environment indicates that resistance is likely already widespread. We isolated antimicrobial-resistant Escherichia coli from three urban waterbodies over a 15-month time series, determined their antimicrobial susceptibilities, investigated their population structure, and identified genetic determinants of resistance. We found that E. coli populations at each site were composed of different dominant phylotypes and showed distinct patterns of antimicrobial and multidrug resistance, despite close geographic proximity. Many strains that were genome-sequenced belonged to sequence types of international concern, particularly the ST131 clonal complex. We found widespread resistance to clinically important antimicrobials such as amoxicillin, cefotaxime, and ciprofloxacin, but found that all strains were susceptible to amikacin and the last-line antimicrobials meropenem and fosfomycin. Resistance was most often due to acquirable antimicrobial resistance genes, while chromosomal mutations in gyrA, parC, and parE conferred resistance to quinolones. Whole-genome analysis of a subset of strains further revealed the diversity of the population of E. coli present, with a wide array of AMR and virulence genes identified, many of which were present on the chromosome, including blaCTX-M. Finally, we determined that environmental persistence, transmission between sites, most likely mediated by wild birds, and transfer of mobile genetic elements likely contributed significantly to the patterns observed.IMPORTANCEA One Health perspective is crucial to understand the extent of antimicrobial resistance (AMR) globally, and investigation of AMR in the environment has been increasing in recent years. However, most studies have focused on waterways that are directly polluted by sewage, industrial manufacturing, or agricultural activities. Therefore, there remains a lack of knowledge about more natural, less overtly impacted environments. Through phenotypic and genotypic investigation of AMR in Escherichia coli, this study adds to our understanding of the extent and patterns of resistance in these types of environments, including over a time series, and showed that complex biotic and abiotic factors contribute to the patterns observed. Our study further emphasizes the importance of incorporating the surveillance of microbes in freshwater environments in order to better comprehend potential risks for both human and animal health and how the environment may serve as a sentinel for potential future clinical infections.

Study of an Enterococcus faecium strain isolated from an artisanal Mexican cheese, whole-genome sequencing, comparative genomics, and bacteriocin expression

Enterococci are ubiquitous microorganisms in almost all environments, from the soil we step on to the food we eat. They are frequently found in naturally fermented foods, contributing to ripening through protein, lipid, and sugar metabolism. On the other hand, these organisms are also leading the current antibiotic resistance crisis. In this study, we performed whole-genome sequencing and comparative genomics of an Enterococcus faecium strain isolated from an artisanal Mexican Cotija cheese, namely QD-2. We found clear genomic differences between commensal and pathogenic strains, particularly in their carbohydrate metabolic pathways, resistance to vancomycin and other antibiotics, bacteriocin production, and bacteriophage and CRISPR content. Furthermore, a bacteriocin transcription analysis performed by RT-qPCR revealed that, at the end of the log phase, besides enterocins A and X, two putative bacteriocins not reported previously are also transcribed as a bicistronic operon in E. faecium QD-2, and are expressed 1.5 times higher than enterocin A when cultured in MRS broth.

The occurrence of heavy metals and antimicrobials in sewage sludge and their predicted risk to soil - Is there anything to fear?

The study assessed the occurrence of legally-monitored heavy metals and unmonitored antimicrobials in sludge from small, medium, large and very large municipal wastewater treatment plants (WWTPs), and the predicted environmental risk and risk of resistance selection associated with sludge administration to soil. The temporal variations of the studied compounds in sludge and associated risks to soil were determined by sampling over a year. Although the highest concentrations of heavy metals were noted in sludge from the largest WWTP, i.e. from 1.50 mg/kg (mean 1.61 mg/kg) for Cd to 2188 mg/kg (mean 1332 mg/kg) for Zn, the obtained values only reached a few percent of the legal limits. The same WWTP also demonstrated lower concentrations of antimicrobials compared to the smaller ones. The highest concentrations of antimicrobials, ranging from 24.04 μg/kg for trimethoprim to 900.24 μg/kg for tetracycline, were found in the small and medium WWTPs. However, due to lack of regulations at the national and EU levels, the results cannot be compared with legal limits. Principal Component Analysis (PCA), cluster and heatmap analysis separated samples according to WWTP size. Small WWTP demonstrated correlation with antimicrobials (tetracycline, trimethoprim, clindamycin, ciprofloxacin and ofloxacin), while the large and very large WWTP revealed correlations with heavy metals (Cu and Cr). The obtained environmental risk quotients confirmed that the heavy metals did not present a threat, measured either as individual risk quotients (RQenv), cumulative risk (RQcumulative) or risk of mixture of heavy metals (RQmix-metals). In the case of antimicrobials, only tetracycline demonstrated moderate RQenv, RQcumulative and RQmix-antimicrobials in the small WWTP sludge, with values of 0.1 to 1. Our findings highlight the importance of monitoring sewage sludge before soil application, especially from small WWTPs, to reduce the potential environmental impact of antimicrobials. They also confirm our previous data regarding the environmental risk associated with various toxic compounds, including emerging contaminants, in the sludge from small WWTPs.

Bacillus amyloliquefaciens Probiotics Mix Supplementation in a Broiler Leaky Gut Model

The supplementation of antimicrobial growth promoters (AGPs) has been banned in many countries because of the emergence of antimicrobial-resistant pathogens in poultry products and the environment. Probiotics have been broadly studied and demonstrated as a promising AGP substitute. Our study is centred on the effects of a multi-strain Bacillus-based probiotic product on broiler production performance and gut microbial profile in a dexamethasone-induced leaky gut challenge. Two hundred and fifty-six broiler chicks were hatched and randomly assigned into four groups (wheat-soybean meal basal diet (BD) = non-supplemented control (C), BD supplemented with dexamethasone in week 4 (CD), BD containing a probiotic from day one (P), and BD containing a probiotic from day one and supplemented with dexamethasone during challenge week 4 (PD)). The production performance and caecal, gizzard, jejunal lumen and jejunal mucosa swab microbiota were studied by 16S rRNA gene sequencing. The Bacillus probiotic product significantly improved production performance and altered caecal gut microbiota (p ≤ 0.05), but no significant impact on microbiota was observed in other gut sections.

Activated mesenchymal stem cells increase drug susceptibility of methicillin-resistant Staphylococcus aureus and Pseudomonas aeruginosa

Methicillin-resistant Staphylococcus aureus (MRSA) and Pseudomonas aeruginosa are major causes of hospital-acquired infections and sepsis. Due to increasing antibiotic resistance, new treatments are needed. Mesenchymal stem cells (MSCs) have antimicrobial effects, which can be enhanced by preconditioning with antibiotics. This study investigated using antibiotics to strengthen MSCs against MRSA and P. aeruginosa. MSCs were preconditioned with linezolid, vancomycin, meropenem, or cephalosporin. Optimal antibiotic concentrations were determined by assessing MSC survival. Antimicrobial effects were measured by minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC), and antimicrobial peptide (AMP) gene expression. Optimal antibiotic concentrations for preconditioning MSCs without reducing viability were 1 μg/mL for linezolid, meropenem, and cephalosporin and 2 μg/mL for vancomycin. In MIC assays, MSCs preconditioned with linezolid, vancomycin, meropenem, or cephalosporin inhibited MRSA or P. aeruginosa growth at lower concentrations than non-preconditioned MSCs (p ≤ 0.001). In MBC assays, preconditioned MSCs showed enhanced bacterial clearance compared to non-preconditioned MSCs, especially when linezolid and vancomycin were used against MRSA (p ≤ 0.05). Preconditioned MSCs showed increased expression of genes encoding the antimicrobial peptide genes hepcidin and LL-37 compared to non-preconditioned MSCs. The highest hepcidin expression was seen with linezolid and vancomycin preconditioning (p ≤ 0.001). The highest LL-37 expression was with linezolid preconditioning (p ≤ 0.001). MSCs' preconditioning with linezolid, vancomycin, meropenem, or cephalosporin at optimal concentrations enhances their antimicrobial effects against MRSA and P. aeruginosa without compromising viability. This suggests preconditioned MSCs could be an effective adjuvant treatment for antibiotic-resistant infections. The mechanism may involve upregulation of AMP genes.

Rare resistome rather than core resistome exhibited higher diversity and risk along the Yangtze River

As important freshwater ecosystems, the occurrence and distribution of antibiotic resistance genes (ARGs) in rivers are relevant to public health. However, studies investigating ARGs of different environmental media in river ecosystems are limited. In this study, we analyzed the ARGs of microbes in free-living setting, particle-associated setting, sediment and bank soil of the Yangtze River using metagenomics. Twenty-six ARGs were found in all samples regardless of media (core resistome) with a diversity of 8.6 %-34.7 %, accounting for 22.7 %-89.2 % of the relative abundance of the overall ARGs. The core resistome of the Yangtze River was dominated by multidrug resistance genes consisting mainly of efflux pumps and bacitracin resistance genes. The rare resistome was dominated by multidrug, sulfonamide, and aminoglycoside resistance genes. The core resistome was more prevalent in chromosomes, implying that these ARGs with low diversity and high relative abundance may be intrinsic to microbes in the Yangtze River. The rare resistome was more prevalent in plasmids, suggesting these ARGs with high diversity and low relative abundance were acquired under environmental stresses and had transfer potential. Additionally, we found that core and rare resistome were mainly carried by specific bacteria. Noteworthily, twenty-two ARGs of high clinical concern were identified in rare resistome, especially aac(6')-I, sul1, and tetM, which were plasmid-borne and hosted by clinically relevant pathogens. Both core and rare resistome hosts showed the highest niche breadths in particle-associated setting compared to other media, and particle-associated setting could provide more stable and ideal conditions for resistome hosts to survive. This study elucidated the genetic locations of ARGs and the community assembly mechanisms of ARG hosts in freshwater environments.

Antibiotic resistance genes in integrated surface ice, cryoconite, and glacier-fed stream in a mountain glacier in Central Asia

Glacier ice, cryoconite, and glacier-fed streams are interconnected features that have important implications for the dynamics and distribution of abiotic and biotic materials. However, the presence and behavior of antibiotic resistance genes (ARGs) within these glacial environments remained largely unexplored. Addressing this gap, we hypothesized that ARGs are widely distributed and exhibit distinct yet interconnected patterns of diversity and dynamics in these glacial environments. Here, we investigated ARGs in a mountain glacier in Central Asia. A total of 944 ARGs, spanning 22 antibiotic classes, were identified, with 633 ARGs shared across all three environments. Cryoconite exhibited the highest ARG richness, followed by ice, while stream biofilm displayed the lowest value. Exploring ARG profiles, we observed a consistent pattern in terms of antibiotic class and resistance mechanism across all three environments. Beta-lactam resistance genes exhibited the highest diversity, followed by multidrug, glycopeptide, and MLS. The predominant mechanisms were antibiotic inactivation, antibiotic efflux, and target alteration. The most prevalent ARG is cls, followed by mdfA, ropB, fabI, and macB. The similarity in ARG profiles between surface ice and cryoconite samples was more pronounced than their resemblance to stream biofilm samples. The variations of ARG profiles between any pair of environments were largely contributed by turnover component. Further insights into microbial interactions revealed 2328 significant associations between 80 OTUs and 356 ARGs, indicating complex relationships. Certain OTUs, including those from the genera Polaromonas, Ferruginibacter, Hymenobacter, Phormidesmis, Novosphingobium, and Polymorphobacter, were speculated as potential hosts for a variety of ARGs. Our findings underscore the intricate dynamics of antibiotic resistance in glacial ecosystems, emphasizing the need for a holistic understanding of ARG distribution, diversity, and associations across diverse environmental compartments. This research contributes valuable insights into the potential ecological implications of antibiotic resistance dissemination in cold environments, particularly as influenced by increasing climate change.

The soil-microbe-plant resistome: A focus on the source-pathway-receptor continuum

The One World, One Health concept implies that antibiotic resistance (AR) in the soil-microbe-plant resistome is intricately linked to the human resistome. However, the literature is mainly confined to sources and types of AR in soils or microbes, but comprehensive reviews tracking AR in the soil-microbe-plant resistome are limited. The present review applies the source-pathway-receptor concept to understand the sources, behaviour, and health hazards of the soil-microbe-plant resistome. The results showed that the soil-microbe-plant system harbours various antibiotic-resistance genes (ARGs), antibiotic-resistant bacteria (ARB), and mobile genetic elements (MGEs). Anthropogenic sources and drivers include soil application of solid waste, wastewater, biosolids, and industrial waste. Water-, wind-, and human-driven processes and horizontal gene transfer circulate AR in the soil-microbe-plant resistome. The AR in bulk soil, soil components that include soil microorganisms, soil meso- and macro-organisms, and possible mechanisms of AR transfer to soil components and ultimately to plants are discussed. The health risks of the soil-microbe-plant resistome are less studied, but potential impacts include (1) the transfer of AR to previously susceptible organisms and other resistomes, including the human resistome. Overall, the study tracks the behaviour and health risks of AR in the soil-plant system. Future research should focus on (1) ecological risks of AR at different levels of biological organization, (2) partitioning of AR among various phases of the soil-plant system, (3) physico-chemical parameters controlling the fate of AR, and (4) increasing research from low-income regions particularly Africa as most of the available literature is from developed countries.

Salmonellosis: An Overview of Epidemiology, Pathogenesis, and Innovative Approaches to Mitigate the Antimicrobial Resistant Infections

Salmonella is a major foodborne pathogen and a leading cause of gastroenteritis in humans and animals. Salmonella is highly pathogenic and encompasses more than 2600 characterized serovars. The transmission of Salmonella to humans occurs through the farm-to-fork continuum and is commonly linked to the consumption of animal-derived food products. Among these sources, poultry and poultry products are primary contributors, followed by beef, pork, fish, and non-animal-derived food such as fruits and vegetables. While antibiotics constitute the primary treatment for salmonellosis, the emergence of antibiotic resistance and the rise of multidrug-resistant (MDR) Salmonella strains have highlighted the urgency of developing antibiotic alternatives. Effective infection management necessitates a comprehensive understanding of the pathogen's epidemiology and transmission dynamics. Therefore, this comprehensive review focuses on the epidemiology, sources of infection, risk factors, transmission dynamics, and the host range of Salmonella serotypes. This review also investigates the disease characteristics observed in both humans and animals, antibiotic resistance, pathogenesis, and potential strategies for treatment and control of salmonellosis, emphasizing the most recent antibiotic-alternative approaches for infection control.

Review of emerging contaminants in green stormwater infrastructure: Antibiotic resistance genes, microplastics, tire wear particles, PFAS, and temperature

Green stormwater infrastructure is a growing management approach to capturing, infiltrating, and treating runoff at the source. However, there are several emerging contaminants for which green stormwater infrastructure has not been explicitly designed to mitigate and for which removal mechanisms are not yet well defined. This is an issue, as there is a growing understanding of the impact of emerging contaminants on human and environmental health. This paper presents a review of five emerging contaminants - antibiotic resistance genes, microplastics, tire wear particles, PFAS, and temperature - and seeks to improve our understanding of how green stormwater infrastructure is impacted by and can be designed to mitigate these emerging contaminants. To do so, we present a review of the source and transport of these contaminants to green stormwater infrastructure, specific treatment mechanisms within green infrastructure, and design considerations of green stormwater infrastructure that could lead to their removal. In addition, common removal mechanisms across these contaminants and limitations of green infrastructure for contaminant mitigation are discussed. Finally, we present future research directions that can help to advance the use of green infrastructure as a first line of defense for downstream water bodies against emerging contaminants of concern.

Simultaneous stream assessment of antibiotics, bacteria, antibiotic resistant bacteria, and antibiotic resistance genes in an agricultural region of the United States

Antimicrobial resistance (AMR) is now recognized as a leading global threat to human health. Nevertheless, there currently is a limited understanding of the environment's role in the spread of AMR and antibiotic resistance genes (ARGs). In 2019, the U.S. Geological Survey conducted the first statewide assessment of antibiotic resistant bacteria (ARB) and ARGs in surface water and bed sediment collected from 34 stream locations across Iowa. Environmental samples were analyzed for a suite of 29 antibiotics and plated on selective media for 15 types of bacteria growth; DNA was extracted from culture growth and used in downstream polymerase chain reaction (PCR) assays for the detection of 24 ARGs. ARGs encoding resistance to antibiotics of clinical importance to human health and disease prevention were prioritized as their presence in stream systems has the potential for environmental significance. Total coliforms, Escherichia coli (E. coli), and staphylococci were nearly ubiquitous in both stream water and stream bed sediment samples, with enterococci present in 97 % of water samples, and Salmonella spp. growth present in 94 % and 67 % of water and bed sediment samples. Bacteria enumerations indicate that high bacteria loads are common in Iowa's streams, with 23 (68 %) streams exceeding state guidelines for primary contact for E. coli in recreational waters and 6 (18 %) streams exceeding the secondary contact advisory level. Although antibiotic-resistant E. coli growth was detected from 40 % of water samples, vancomycin-resistant enterococci (VRE) and penicillinase-resistant Staphylococcus aureus (MRSA) colony growth was detected from nearly all water samples. A total of 14 different ARGs were detected from viable bacteria cells from 30 Iowa streams (88 %, n = 34). Study results provide the first baseline understanding of the prevalence of ARB and ARGs throughout Iowa's waterways and health risk potential for humans, wildlife, and livestock using these waterways for drinking, irrigating, or recreating.

High prevalence of antibiotic-resistant and metal-tolerant cultivable bacteria in remote glacier environment

Studies of antibiotic-resistant bacteria (ARB) have mainly originated from anthropic-influenced environments, with limited information from pristine environments. Remote cold environments are major reservoirs of ARB and have been determined in polar regions; however, their abundance in non-polar cold habitats is underexplored. This study evaluated antibiotics and metals resistance profiles, prevalence of antibiotic resistance genes (ARGs) and metals tolerance genes (MTGs) in 38 ARB isolated from the glacier debris and meltwater from Baishui Glacier No 1, China. Molecular identification displayed Proteobacteria (39.3%) predominant in debris, while meltwater was dominated by Actinobacteria (30%) and Proteobacteria (30%). Bacterial isolates exhibited multiple antibiotic resistance index values > 0.2. Gram-negative bacteria displayed higher resistance to antibiotics and metals than Gram-positive. PCR amplification exhibited distinct ARGs in bacteria dominated by β-lactam genes blaCTX-M (21.1-71.1%), blaACC (21.1-60.5%), tetracycline-resistant gene tetA (21.1-60.5%), and sulfonamide-resistant gene sulI (18.4-52.6%). Moreover, different MTGs were reported in bacterial isolates, including mercury-resistant merA (21.1-63.2%), copper-resistant copB (18.4-57.9%), chromium-resistant chrA (15.8-44.7%) and arsenic-resistant arsB (10.5-44.7%). This highlights the co-selection and co-occurrence of MTGs and ARGs in remote glacier environments. Different bacteria shared same ARGs, signifying horizontal gene transfer between species. Strong positive correlation among ARGs and MTGs was reported. Metals tolerance range exhibited that Gram-negative and Gram-positive bacteria clustered distinctly. Gram-negative bacteria were significantly tolerant to metals. Amino acid sequences of blaACC,blaCTX-M,blaSHV,blaampC,qnrA, sulI, tetA and blaTEM revealed variations. This study presents promising ARB, harboring ARGs with variations in amino acid sequences, highlighting the need to assess the transcriptome study of glacier bacteria conferring ARGs and MTGs.

Investigating the Role of Metabolism for Antibiotic Combination Therapies in Pseudomonas aeruginosa

Antibacterial resistance poses a severe threat to public health; an anticipated 14-fold increase in multidrug-resistant (MDR) bacterial infections is expected to occur by 2050. Contrary to antibiotics, combination therapies are the standard of care for antiviral and anticancer treatments, as synergistic drug-drug interactions can decrease dosage and resistance development. In this study, we investigated combination treatments of a novel succinate dehydrogenase inhibitor (promysalin) with specific inhibitors of metabolism and efflux alongside a panel of clinically approved antibiotics in synergy studies. Through these investigations, we determined that promysalin can work synergistically with vancomycin and antagonistically with aminoglycosides and a glyoxylate shunt pathway inhibitor at subinhibitory concentrations; however, these cooperative effects do not reduce minimum inhibitory concentrations. The variability of these results underscores the complexity of targeting metabolism for combination therapies in antibiotic development.

Antibiotic resistance genes prevalence prediction and interpretation in beaches affected by urban wastewater discharge

Background

The annual death toll of over 1.2 million worldwide is attributed to infections caused by resistant bacteria, driven by the significant impact of antibiotic misuse and overuse in spreading these bacteria and their associated antibiotic resistance genes (ARGs). While limited data suggest the presence of ARGs in beach environments, efficient prediction tools are needed for monitoring and detecting ARGs to ensure public health safety. This study aims to develop interpretable machine learning methods for predicting ARGs in beach waters, addressing the challenge of black-box models and enhancing our understanding of their internal mechanisms.

Methods

In this study, we systematically collected beach water samples and subsequently isolated bacteria from these samples using various differential and selective media supplemented with different antibiotics. Resistance profiles of bacteria were determined by using Kirby-Bauer disk diffusion method. Further, ARGs were enumerated by using the quantitative polymerase chain reaction (qPCR) to detect and quantify ARGs. The obtained qPCR data and hydro-meteorological were used to create an ML model with high prediction performance and we further used two explainable artificial intelligence (xAI) model-agnostic interpretation methods to describe the internal behavior of ML model.

Results

Using qPCR, we detected blaCTX-M, blaNDM, blaCMY, blaOXA, blatetX, blasul1, and blaaac(6'-Ib-cr) in the beach waters. Further, we developed ML prediction models for blaaac(6'-Ib-cr), blasul1, and blatetX using the hydro-metrological and qPCR-derived data and the models demonstrated strong performance, with R2 values of 0.957, 0.997, and 0.976, respectively.

Conclusions

Our findings show that environmental factors, such as water temperature, precipitation, and tide, are among the important predictors of the abundance of resistance genes at beaches.

Risk assessment of Enterococcus faecium, Klebsiella pneumoniae, and Pseudomonas aeruginosa in environmental water sources: Development of surrogate models for antibiotic resistance genes

The presence of Enterococcus faecium (E. faecium), Klebsiella pneumoniae (K. pneumoniae), Pseudomonas aeruginosa (P. aeruginosa), and the aminoglycoside resistance genes, aac(6')-Ib and aac(6')-aph(2″), was investigated in environmental water sources obtained from informal settlements in the Western Cape (South Africa). Using ethidium monoazide bromide quantitative polymerase chain reaction (EMA-qPCR) analysis, E. faecium, K. pneumoniae, and P. aeruginosa were detected in 88.9 %, 100 %, and 93.3 % of the samples (n = 45), respectively, with a significantly higher mean concentration recorded for K. pneumoniae (7.83 × 104 cells/100 mL) over the sampling period. The aac(6')-Ib gene was detected in 95.6 % (43/45) of the environmental water samples [mean concentration of 7.07 × 106 gene copies (GC)/100 mL], while the aac(6')-aph(2″) gene was detected in 100 % (n = 45) of the samples [mean concentration of 6.68 × 105 GC/100 mL]. Quantitative microbial risk assessment (QMRA) subsequently indicated that the risks posed by K. pneumoniae and P. aeruginosa were linked to intentional drinking, washing/bathing, cleaning of the home, and swimming, in the samples collected from the various sampling sites. Surrogate risk assessment models were then designed and applied for Gram-positive [aac(6')-aph(2″) gene] and Gram-negative [aac(6')-Ib gene] pathogens that may exhibit aminoglycoside resistance. The results indicated that only the Gram-negative pathogens posed a risk (>10-4) in all the samples for cleaning of the home and intentional drinking, as well as for washing laundry by hand, garden hosing, garden work, washing/bathing, accidental consumption, and swimming at the stream and marsh sites. Thus, while environmental waters may pose a health risk of exposure to pathogenic bacteria, the results obtained indicate that screening for antibiotic resistant genes, associated with multiple genera/species, could serve as a surrogate model for estimating risks with the target group under investigation.

Metagenome meta-analysis reveals an increase in the abundance of some multidrug efflux pumps and mobile genetic elements in chemically polluted environments

Many human activities contaminate terrestrial and aquatic environments with numerous chemical pollutants that not only directly alter the environment but also affect microbial communities in ways that are potentially concerning to human health, such as selecting for the spread of antibiotic-resistance genes (ARGs) through horizontal gene transfer. In the present study, metagenomes available in the public domain from polluted (with antibiotics, with petroleum, with metal mining, or with coal-mining effluents) and unpolluted terrestrial and aquatic environments were compared to examine whether pollution has influenced the abundance and composition of ARGs and mobile elements, with specific focus on IS26 and class 1 integrons (intI1). When aggregated together, polluted environments had a greater relative abundance of ARGs than unpolluted environments and a greater relative abundance of IS26 and intI1. In general, chemical pollution, notably with petroleum, was associated with an increase in the prevalence of ARGs linked to multidrug efflux pumps. Included in the suite of efflux pumps were mexK, mexB, mexF, and mexW that are polyspecific and whose substrate ranges include multiple classes of critically important antibiotics. Also, in some instances, β-lactam resistance (TEM181 and OXA-541) genes increased, and genes associated with rifampicin resistance (RNA polymerases subunits rpoB and rpoB2) decreased in relative abundance. This meta-analysis suggests that different types of chemical pollution can enrich populations that carry efflux pump systems associated with resistance to multiple classes of medically critical antibiotics.IMPORTANCEThe United Nations has identified chemical pollution as being one of the three greatest threats to environmental health, through which the evolution of antimicrobial resistance, a seminally important public health challenge, may be favored. While this is a very plausible outcome of continued chemical pollution, there is little evidence or research evaluating this risk. The objective of the present study was to examine existing metagenomes from chemically polluted environments and evaluate whether there is evidence that pollution increases the relative abundance of genes and mobile genetic elements that are associated with antibiotic resistance. The key finding is that for some types of pollution, particularly in environments exposed to petroleum, efflux pumps are enriched, and these efflux pumps can confer resistance to multiple classes of medically important antibiotics that are typically associated with Pseudomonas spp. or other Gram-negative bacteria. This finding makes clear the need for more investigation on the impact of chemical pollution on the environmental reservoir of ARGs and their association with mobile genetic elements that can contribute to horizontal gene transfer events.

Factors Associated with Extended-Spectrum β-Lactamases and Carbapenem-Resistant Klebsiella pneumoniae Bloodstream Infections: A Five-Year Retrospective Study

Klebsiella pneumoniae is one of the leading causes of nosocomial infections. It has been estimated that nosocomial infection by Klebsiella pneumoniae comprises 3-8% of all nosocomial infections. Klebsiella pneumoniae bloodstream infections (BSIs) occur worldwide with varying mortality. Resistant strains, like those producing extended-spectrum beta-lactamases (ESBL) and carbapenemases, are becoming increasingly common, especially in hospital settings, posing therapeutic challenges. In this article, we aimed to study the epidemiology and risk factors of BSIs due to resistant Klebsiella pneumoniae strains in the period 1 January 2014-31 December 2018 at the Nicosia General Hospital, the largest tertiary hospital in Cyprus. Data on demographics, co-morbidities, prior hospitalization, prior intensive care unit (ICU) admission, previous antimicrobial use, nosocomial acquisition of the infection, the presence of a prosthetic device or surgery, and the primary site of infection were retrospectively recorded. Associations between the detection of ESBL Klebsiella pneumoniae BSIs and factors/covariates were examined using logistic regression. This study involved 175 patients with BSI caused by Klebsiella pneumoniae. Of these, 61 BSIs were caused by ESBL strains, 101 by non-ESBL, and 13 by carbapenem-resistant (CR) strains. In univariable analyses, age, sex, heart disease, antimicrobial use during current admission, previous hospitalization (ward or ICU), and primary BSI were associated with the presence of an ESBL strain. Antibiotic use during current admission and heart disease remained statistically significantly associated with ESBL Klebsiella pneumoniae BSI in multivariable models. Antibiotic use during current admission, respiratory infection, and a recent history of surgery were more prevalent among CR Klebsiella pneumoniae BSI patients than among non-CR Klebsiella pneumoniae BSI patients. Our study showed that recent antimicrobial use and heart disease were associated with BSI due to ESBL-producing Klebsiella pneumoniae. This finding could inform clinical practice in hospital settings.