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

Effects of nitrogen-driven eutrophication on the horizontal transfer of extracellular antibiotic resistance genes in water-sediment environments

Excessive nitrogen and other nutrients can trigger the eutrophication of freshwater bodies. Antibiotic resistance genes (ARGs) are now recognized as environmental pollutants, with extracellular ARGs (eARGs) being the dominant form in sediments. However, research on the propagation characteristics of eARGs remains limited. This study investigated the transfer characteristics of kanamycin resistance (KR) genes in the pEASY-T1 plasmid to intracellular DNA (iDNA) and extracellular DNA (eDNA) in water and sediment microenvironments under increasing nitrogen concentrations, as well as the community structure of free-living (FL) and particle-attached (PA) bacteria. The results revealed KR genes relative abundance in free extracellular DNA (f-eDNA) and adsorbed extracellular DNA (a-eDNA) of the water initially decreased and then increased with rising nitrogen concentrations. Its abundance in iDNA of the sediments decreased significantly with increasing nitrogen content, with relative abundance ranging from 5.09 × 10-4 to 1.14 × 10-3 copies/16SrRNA. The transfer from eDNA to iDNA in the water showed a rising and then falling trend as nitrogen concentration rose. The transfer of iDNA from the water to iDNA in sediments exhibited the opposite pattern. Additionally, copper (Cu) and zinc (Zn) were identified as key factors influencing the abundance of KR genes in the water, but total phosphorus (TP) was the primary determinant of KR gene distribution in sediments according to random forest analysis. These findings reveal novel mechanisms of eARG propagation in eutrophic environments, providing a theoretical foundation for managing antibiotic resistance in aquatic ecosystems.

Exploring molecular mechanisms of drug resistance in bacteria and progressions in CRISPR/Cas9-based genome expurgation solutions

Antibiotic resistance in bacteria is a critical global health challenge, driven by molecular mechanisms such as genetic mutations, efflux pumps, enzymatic degradation of antibiotics, target site modifications, and biofilm formation. Horizontal gene transfer (HGT) further accelerates the spread of resistance genes across bacterial populations. These mechanisms contribute to the emergence of multidrug-resistant (MDR) strains, rendering conventional antibiotics ineffective. Recent advancements in CRISPR/Cas9-based genome editing offer innovative solutions to combat drug resistance. CRISPR/Cas9 enables precise targeting of resistance genes, facilitating their deletion or inactivation, and provides a potential method to eliminate resistance-carrying plasmids. Furthermore, phage-delivered CRISPR systems show promise in selectively killing resistant bacteria while leaving susceptible strains unaffected. Despite challenges such as efficient delivery, off-target effects, and potential bacterial resistance to CRISPR itself, ongoing research and technological innovations hold promise for using CRISPR-based antimicrobials to reverse bacterial drug resistance and develop more effective therapies. These abstract highlights the molecular mechanisms underlying bacterial drug resistance and explores how CRISPR/Cas9 technology could revolutionize treatment strategies against resistant pathogens.

Urban afforestation converges soil resistome and mitigates the abundance of human pathogenic bacteria

Afforestation has emerged as a nature-based strategy for climate mitigation and urban sustainability, yet its effects on antibiotic resistance genes (ARGs) in soils remain underexplored. This study investigates how the conversion of croplands into plantation forests affects the soil resistome, bacterial communities, and physicochemical properties in an urban environment. Using high-throughput metagenomic and 16S rRNA amplicon sequencing, we analyzed soil samples from croplands and afforested plots with Chinese pine (Pinus tabulaeformis) and Chinese scholar (Sophora japonica) trees, across two-time points post-afforestation. Our results show that afforestation promotes the convergence of both bacterial and ARG communities over time, accompanied by a significant reduction in the relative abundance of human pathogenic bacteria. Afforested soils exhibited a lower prevalence of high-risk ARGs (e.g., qnrA, qnrB from the quinolone class) and reduced co-occurrence between ARGs and mobile genetic elements (MGEs), particularly transposases and recombinases, suggesting diminished horizontal gene transfer. Additionally, afforestation-induced changes in soil pH and nutrient dynamics emerged as key ecological factors shaping ARG profiles. Differences between afforestation types were also observed, with Pinus plantations presenting lower ARG-derived risks than Sophora forests. This study supports afforestation as a nature-based solution for enhancing urban sustainability, reducing public health risks, and achieving resilient ecosystems under anthropogenic influence.

Phenotypic antibiotic resistance prediction using antibiotic resistance genes and machine learning models in Mannheimia haemolytica

Mannheimia haemolytica is one of the most common causative agents of bovine respiratory disease (BRD); however, antibiotic resistance in this species is increasing, making treatment more difficult. Integrative-conjugative elements (ICE), a subset of mobile genetic elements (MGE), encoding up to 100 genes have been reported in Mannheimia haemolytica genomes to confer multidrug resistance, including resistance to antibiotics commonly used in the treatment of BRD. However, the presence of antibiotic resistance genes (ARGs) does not always agree with phenotypic resistance. Prior investigations have reported an overall phenotype-genotype concordance less than 75 % in BRD pathogens. The objective of the current study was to compare genotype-phenotype concordance either by annotating known resistance genes in genomes or predicting antibiotic resistance determinants de novo with machine learning (ML). The genotype-phenotype concordance rates of ARGs were generally > 90 %, while that of ML models were > 80 %. For all seven antibiotics (danofloxacin, enrofloxacin, florfenicol, tetracycline, tildipirosin, tilmicosin, and tulathromycin), the genotype-phenotype concordance rates were more accurate with ARGs. The annotations of ML models for all antibiotics included various types of sequences, including coding sequences such as DNA topoisomerase IV (danofloxacin) and non-coding sequences near tetracycline genes (multiple antibiotics), MGE (tetracycline and tildipirosin), or virulence genes (danofloxacin and enrofloxacin). When tested on an external set of isolates for validation, the best predictor of antibiotic resistance performed similarly to the training/testing datasets for each antibiotic. Incorporating single nucleotide polymorphisms and ARGs unknown during previous studies resulted in higher concordance rates (>90 %) for fluoroquinolones and tilmicosin, respectively. By finding increased concordance rates for known ARGs, this study was able to show that ARGs should continue to be utilized to predict phenotypic resistance.

Monitoring Antibiotic Resistance in Wastewater: Findings from Three Treatment Plants in Sicily, Italy

Antimicrobial resistance (AMR) poses a global public health threat. Wastewater analysis provides valuable insights into antimicrobial resistance genes (ARGs), identifying sources and trends and evaluating AMR control measures. Between February 2022 and March 2023, pre-treatment urban wastewater samples were collected weekly from treatment plants in Pantano D'Arci, Siracusa, and Giarre (Sicily, Italy). Monthly composite DNA extracts were prepared by combining weekly subsamples from each site, yielding 42 composite samples-14 from each treatment plant. Real-time PCR analysis targeted specific ARGs, including blaSHV, erm(A), erm(B), blaOXA, blaNDM, blaVIM, blaTEM, and blaCTX-M. The preliminary findings revealed that blaERM-B, blaOXA, blaTEM, and blaCTX-M were present in all samples, with erm(B) (median value: 8.51; range: 1.67-30.93), blaSHV (0.78; 0.00-6.36), and blaTEM (0.72; 0.34-4.30) showing the highest relative abundance. These results underscore the importance of integrating ARG data with broader research to understand the persistence and proliferation mechanisms of ARGs in wastewater environments. Future studies should employ metagenomic analyses to profile resistomes in urban, hospital, agricultural, and farm wastewater. Comparing these profiles will help identify contamination pathways and inform the development of targeted ARG surveillance programs. Monitoring shifts in ARG abundance could signal cross-sectoral contamination, enabling more effective AMR control strategies.

Evaluation of Xpert® Carba-R Assay Performance from FecalSwab™ Samples

Background/Objectives: The emergence and spread of carbapenemase-producing Enterobacterales (CPE) represents a significant challenge prompting the need to optimize diagnostic tools to detect CPE carriers. The Xpert® Carba-R assay (Cepheid, Sunnyvale, CA, USA), a Real-Time PCR-based test, can detect the blaKPC, blaVIM, blaOXA-48, blaNDM and blaIMP carbapenemase genes directly from rectal swabs. This study assessed the performance of the Xpert® Carba-R assay using FecalSwab™ (Copan, Brescia, Italy), a liquid-based collection device. Methods: The first part of the study aimed to establish the FecalSwabTM volume which gave the most similar Ct values to those obtained by the Transystem™ double swab (Copan). The best volume was then used to assess the limit of detection (LoD) for each target and compare the accuracy of different FecalSwabTM storage conditions (room temperature or 4 °C after 16 h compared to T0). Results: The results indicated that using 200 µL of the FecalSwab™ medium provided reliable Ct values, with the lowest number of invalid samples compared to traditional methods. The average LoDs for different carbapenemases ranged from 4.7 × 103 to 6.8 × 103 CFU/mL. FecalSwab™ showed a better performance after 16 h at room temperature compared to storage at 4 °C. Conclusions: This study supports single sampling with the FecalSwab™ medium for both molecular and cultural methods, for the potential optimization of CPE screening.

Different combinations of operating temperature and solids retention time during two-phase anaerobic digestion impacts removal of antibiotic resistance genes

Two-phase anaerobic digestion (AD) performance is significantly influenced by operating parameters such as temperature and solids retention time (SRT), while their impact on antibiotic resistance genes (ARGs) during the acidogenic (AP) and methanogenic (MP) phases remains unclear. This study assessed the abundance of eight ARGs in full-scale two-phase AD, then operated lab-scale two-phase AD systems to evaluate temperature combinations (thermophilic-thermophilic, thermophilic-mesophilic, mesophilic-thermophilic, and mesophilic-mesophilic) at a constant SRT (AP = 2/MP = 13d) and to further assess different SRTs (AP = 2/MP = 13d and AP = 4/MP = 11d). qPCR results revealed that full-scale two-phase AD reduced total ARGs abundance by 87.70 ± 0.50 %. In lab-scale tests, the thermophilic-thermophilic configuration achieved nearly complete ARGs removal (97.61 ± 0.21 %), while the combination of AP = 4/MP = 11d had the highest removal efficiency (83.39 ± 1.17 %). Network analysis indicated that Firmicutes, Bacteroidota, and Proteobacteria were the primary ARG hosts, with Firmicutes dominant. These findings highlight the optimal operating parameters in two-phase AD for maximizing ARGs removal.

Profiling lateral gene transfer events in the human microbiome using WAAFLE

Lateral gene transfer (LGT), also known as horizontal gene transfer, facilitates genomic diversification in microbial populations. While previous work has surveyed LGT in human-associated microbial isolate genomes, the landscape of LGT arising in personal microbiomes is not well understood, as there are no widely adopted methods to characterize LGT from complex communities. Here we developed, benchmarked and validated a computational algorithm (WAAFLE or Workflow to Annotate Assemblies and Find LGT Events) to profile LGT from assembled metagenomes. WAAFLE prioritizes specificity while maintaining high sensitivity for intergenus LGT. Applying WAAFLE to >2,000 human metagenomes from diverse body sites, we identified >100,000 high-confidence previously uncharacterized LGT (~2 per microbial genome-equivalent). These were enriched for mobile elements, as well as restriction-modification functions associated with the destruction of foreign DNA. LGT frequency was influenced by biogeography, phylogenetic similarity of involved pairs (for example, Fusobacterium periodonticum and F. nucleatum) and donor abundance. These forces manifest as networks in which hub taxa donate unequally with phylogenetic neighbours. Our findings suggest that human microbiome LGT may be more ubiquitous than previously described.

Prevalence and antibiotic resistance patterns of Pseudomonas aeruginosa and Acinetobacter baumannii strains isolated from chicken droppings on poultry farms in Gondar city, Northwest Ethiopia

Background

Pseudomonas aeruginosa and Acinetobacter baumannii are common nosocomial pathogens in hospital settings. Recently, they have also been found in non-hospital environments, such as poultry farms. While most studies in Ethiopia have focused on these bacteria's antibiotic resistance patterns in hospitals, information regarding their prevalence and resistance in veterinary settings, particularly poultry farms, is limited. This study aimed to assess the prevalence and antibiotic resistance patterns of P. aeruginosa and A. baumannii isolated from chicken droppings on poultry farms.

Methods

A cross-sectional study was conducted from March 2022 to June 2022. A total of 87 poultry farms were included in this study, and pooled chicken dropping samples were collected. The samples were subsequently transferred to buffered peptone water and cultured on MacConkey agar. Species of the isolates were identified via routine biochemical tests, including oxidase, catalase, urease, Simon's citrate, sulfide indole motility medium, triple sugar iron agar and growth at temperatures of 37 °C and 42 °C. The Kirby-Bauer disk diffusion technique was used for antibiotic susceptibility testing. The data were entered into EpiData version 4.6 and then exported to SPSS version 26 for analysis. Fisher's exact test was used to observe an appropriate association between independent variables and the occurrence of isolates. The results are presented in the text, figures and tables.

Results

Among the 87 poultry farms, 41 (47.1 %) were positive for Pseudomonas and Acinetobacter. Among these strains, 24 (27.6 %) P. aeruginosa strains and 13 (14.9 %) A. baumannii strains were recovered. P. aeruginosa showed complete resistance to tetracycline (24, 100.0 %) and trimethoprim-sulfamethoxazole (24, 100.0 %). Additionally, there was a high rate of resistance to ciprofloxacin (13, 54.2 %) and amikacin (12, 50.0 %). Similarly, 13 (100.0 %) A. baumannii isolates were resistant to tetracycline, and 12 (92.3 %) were resistant to trimethoprim-sulfamethoxazole. However, both isolates presented lower resistance rates to piperacillin-tazobactam (4, 9.8 %) and cefepime (7, 17.1 %). Both A. baumannii and P. aeruginosa exhibited multidrug resistance in 10/13 (76.9 %) and 16/24 (66.7 %) of the strains, respectively. The overall prevalence of multidrug resistance in this study was 28/41 (68.3 %).

Conclusion

This study demonstrated that poultry farms may be potential reservoirs for P. aeruginosa and A. baumannii, including antibiotic-resistant strains. This is a significant concern to public health because poultry farmers may be contaminated, increasing their dissemination to the community. Therefore, poultry farmers should improve sanitation and reduce the misuse and overuse of antibiotics at poultry farms.

A nationwide survey of antimicrobial resistance of Escherichia coli isolated from broiler chickens in Malawi

Background

Antimicrobial resistance is a global health challenge with profound implications across sectors. Livestock, a significant field at the One Health interface, lacks sufficient information, particularly in low-resource settings such as Malawi.

Objectives

We determined the antimicrobial resistance rates of Escherichia coli isolated from broiler chickens in Malawi and explored the relationship between resistance genes across sectors using genomic analysis.

Methods

In 2023, we isolated 115 E. coli strains from 116 faecal and caecal samples from broiler chickens across Malawi. Antimicrobial susceptibility tests were performed using agar dilution method according to the Clinical Laboratory Standard Institute guidelines. Whole-genome sequencing was performed using Illumina sequencing.

Results

Notably, 50 isolates (44%) were resistant to cefotaxime. We detected ESBL bla CTX-M genes (bla CTX-M-55, bla CTX-M-14, bla CTX-M-65, bla CTX-M-27, bla CTX-M-15, bla CTX-M-1, and bla CTX-M-3) in 48 cefotaxime-resistant isolates, which exhibited higher resistance rates to levofloxacin than non-ESBL-encoding isolates (29/48; 60% versus 20/67; 30%). All isolates were susceptible to colistin and carbapenems. High resistance rates were observed for tetracycline and co-trimoxazole commonly used in broiler chickens (90% and 70%, respectively). Sequence type 206 and phylogroup A were predominant (14% and 65%, respectively). In the genetic context of bla CTX-M genes, whole-genome alignment of the ESBL-producing isolates with reference plasmids from E. coli of various origins indicated significant similarity.

Conclusions

Antimicrobial resistance is highly prevalent among E. coli from broiler chickens in Malawi. Genomic analysis suggests potential transmission pathways for ESBL genes across sectors, necessitating further studies from One Health perspective.

Prevalence and molecular characteristics of intestinal pathogenic Escherichia coli isolated from diarrheal pigs in Southern China

Intestinal pathogenic Escherichia coli (InPEC) is one of the most common causes of bacterial diarrhea in farm animals, including profuse neonatal diarrhea and post weaning diarrhea (PWD) in piglets. In this study, we investigated the prevalence of InPEC and associated primary virulence factors among 543 non-duplicate E. coli isolates from diarrheal pigs from 15 swine farms in southern China. Six major virulence genes associated with InPEC were identified among 69 (12.71 %) E. coli isolates and included est (6.62 %), K88 (4.79 %), elt (3.68 %), eae (1.47 %), stx2 (0.92 %) and F18 (0.55 %). Three pathotypes of InPEC were identified including ETEC (8.10 %), EPEC (1.29 %) and STEC/ETEC (0.92 %). In particular, K88 was only found in ETEC from breeding farms, whereas F18 was only present in STEC/ETEC hybrid from finishing farms. Whole genome sequence analysis of 37 E. coli isolates revealed that InPEC strains frequently co-carried multiple antibiotic resistance gene (ARG). est, elt and F18 were also found to co-locate with ARGs on a single IncFIB/IncFII plasmid. InPEC isolates from different pathotypes also possessed different profiles of virulence genes and antimicrobial resistance genes. Population structure analysis demonstrated that InPEC isolates from different pathotypes were highly heterogeneous whereas those of the same pathotype were extremely similar. Plasmid analysis revealed that K88 and/or est/elt were found on pGX18-2-like/pGX203-2-like and pGX203-1-like IncFII plasmids, while F18 and elt/est, as well as diverse ARGs were found to co-locate on IncFII/IncFIB plasmids with a non-typical backbone. Moreover, these key virulence genes were flanked by or adjacent to IS elements. Our findings indicated that both clonal expansion and horizontal spread of epidemic IncFII plasmids contributed to the prevalence of InPEC and the specific virulence genes (F4, F18, elt and est) in the tested swine farms.

Guidelines in Designing a Universal Primer Mixture to Probe and Quantify Antibiotic-Resistant Genes Using the Polymerase Chain Reaction (PCR)

Multidrug resistance efflux pumps (MDREPs) in biofilm communities have become an increasingly expensive problem in clinical settings. Polymerase chain reaction (PCR)-based detection can be used to diagnose and characterize these genes, but this requires effective primer design to minimize false positives and negatives in test conclusions. A universal primer approach has previously been used to detect conserved core genes but not for accessory genes such as MDREPs. This study describes a guideline for the design of primers used in the detection of MDREP genes and an optimization approach for creating primers by using multiple sequence alignments to target conserved regions in silico, progressing from in silico to in vitro to generate working primers. Using this approach, this paper was able to generate primers to target sugE, a small multidrug resistance (SMR) protein found in microbial species. Primers were tested positively against synthetic DNA sequences but were inconsistent with DNA extracted from the organism of interest. Primer design informs the shortfalls of this detection technique and the difficulty in characterizing such genomic elements.

Phylogenetics and Mobilization of Genomic Traits of Cephalosporin-Resistant Escherichia coli Originated from Retail Meat

Contaminations with cephalosporin-resistant Escherichia coli across the food chain may pose a significant threat to public health because those antimicrobials are critically important in human medicine. The impact of the presented data is especially significant concerning Poland's role as one of the leading food producers in the EU. This work aimed to characterize the genomic contents of cephalosporin-resistant Escherichia coli (n = 36) isolated from retail meat to expand the official AMR monitoring reported by EFSA. The ESBL mechanism was predominant (via blaCTX-M-1 and blaSHV-12), with the AmpC-type represented by the blaCMY-2 variant. The strains harbored multiple resistance genes, mainly conferring resistance to aminoglycosides, sulfonamides, trimethoprim, tetracyclines. In some isolates, virulence factors-including intimin (eae) and its receptor (tir) were detected, indicating significant pathogenic potential. Resistance genes showed a link with IncI1 and IncB/O/K/Z plasmids. Cephalosporinases were particularly linked to ISEc9/ISEc1 (blaCTX-M-1 and blaCMY-2). The association of virulence with mobile elements was less common-mostly with IncF plasmids. The analysis of E. coli isolated from retail meat indicates accumulation of ARGs and their association with various mobile genetic elements, thus increasing the potential for the transmission of resistance across the food chain.

Distribution and community structure of antibiotic resistance genes in the Three Gorges Reservoir Area

Antibiotic resistance genes (ARG) are widespread across various regions. While several studies have investigated the distribution of antibiotic resistance in natural environments, the occurrence and diversity of ARGs in the Three Gorges Reservoir have not been fully elucidated. In this study, we employed metagenomic sequencing techniques to investigate the abundance, diversity, and influencing factors of ARGs in the ecosystem of the Three Gorges Reservoir. A total of 874 ARGs, 20 antibiotic classes, and 6 resistance mechanisms were detected. The dominant ARG is the macB, the dominant antibiotic class is multidrug resistance (MDR), and the dominant resistance mechanism is antibiotic efflux. The microorganisms with the highest contribution to ARGs are Betaproteobacteria and Gammaproteobacteria. In this region, pH and NH4+ concentration were significantly negatively correlated with the relative abundance of most ARGs, while NO3- concentration and TN were significantly positively correlated with the relative abundance of most ARGs. The results indicate that the Three Gorges Reservoir constitutes a significant reservoir of ARGs. By studying the distribution of ARGs in the sediments of the Three Gorges Reservoir Area and the relationship between environmental factors and ARGs, we can more comprehensively understand the pollution status of ARGs in this area, and provide theoretical support for subsequent treatment.

High-throughput profiling the effects of zinc on antibiotic resistance genes in the anaerobic digestion of swine manure

The problem of antibiotic resistance genes (ARGs) caused by heavy metals has attracted extensive attention of human beings. Zn, a widely used feed additive, has a very high residue in swine manure, but the distribution characteristics of ARGs imposed by Zn in anaerobic digestion (AD) products are not clear. In this study, the behaviour of mobile genetic elements (MGEs), bacterial community, and their association with ARGs were determined in the presence of 125 and 1250 mg L-1 Zn in AD system of swine manure. Zn-treated enriched the abundance of ARGs, and produced some new genotypes that were not detected in CK treatment. In addition, low concentration of Zn significantly increased the relative abundance of ARGs, as compared to higher Zn and CK group. Correspondingly, the abundances of most top30 genus were highest in ZnL (125 mg L-1 Zn), followed by CK and ZnH (1250 mg L-1 Zn). Notably, network analysis showed that the relationship between ARGs and MGEs is closer than that ARGs and bacteria, suggesting that ARGs increased in Zn-treated, especially low level Zn, may be due to the amplification transfer of ARGs among varied microorganisms by horizontal transfer with MGEs. Therefore, strengthen the management of in livestock manure is crucial to control the spread of ARGs in organic fertilizers.

Genomics-based analysis of four porcine-derived lactic acid bacteria strains and their evaluation as potential probiotics

The search for probiotics and exploration of their functions are crucial for livestock farming. Recently, porcine-derived lactic acid bacteria (LAB) have shown great potential as probiotics. However, research on the evaluation of porcine-derived LAB as potential probiotics through genomics-based analysis is relatively limited. The present study analyzed four porcine-derived LAB strains (Lactobacillus johnsonii L16, Latilactobacillus curvatus ZHA1, Ligilactobacillus salivarius ZSA5 and Ligilactobacillus animalis ZSB1) using genomic techniques and combined with in vitro tests to evaluate their potential as probiotics. The genome sizes of the four strains ranged from 1,897,301 bp to 2,318,470 bp with the GC contents from 33.03 to 41.97%. Pan-genomic analysis and collinearity analysis indicated differences among the genomes of four strains. Carbohydrate active enzymes analysis revealed that L. johnsonii L16 encoded more carbohydrate active enzymes than other strains. KEGG pathway analysis and in vitro tests confirmed that L. johnsonii L16 could utilize a wide range of carbohydrates and had good utilization capacity for each carbohydrate. The four strains had genes related to acid tolerance and were tolerant to low pH, with L. johnsonii L16 showing the greatest tolerance. The four strains contained genes related to bile salt tolerance and were able to tolerate 0.1% bile salt. Four strains had antioxidant related genes and exhibited antioxidant activity in in vitro tests. They contained the genes linked with organic acid biosynthesis and exhibited antibacterial activity against enterotoxigenic Escherichia coli K88 (ETEC K88) and Salmonella 6,7:c:1,5, wherein, L. johnsonii L16 and L. salivarius ZSA5 had gene clusters encoding bacteriocin. Results suggest that genome analysis combined with in vitro tests is an effective approach for evaluating different strains as probiotics. The findings of this study indicate that L. johnsonii L16 has the potential as a probiotic strain among the four strains and provide theoretical basis for the development of probiotics in swine production.

Dynamics of Antimicrobial Resistance Carriage in Koalas (Phascolarctos Cinereus) and Pteropid Bats (Pteropus Poliocephalus) Before, During and After Wildfires

In the 2019-2020 summer, wildfires decimated the Australian bush environment and impacted wildlife species, including koalas (Phascolarctos cinereus) and grey headed flying fox pups (Pteropid bats, Pteropus poliocephalus). Consequently, hundreds of koalas and thousands of bat pups entered wildlife hospitals with fire-related injuries/illness, where some individuals received antimicrobial therapy. This study investigated the dynamics of antimicrobial resistance (AMR) in pre-fire, fire-affected and post-fire koalas and Pteropid bat pups. PCR and DNA sequencing were used to screen DNA samples extracted from faeces (koalas and bats) and cloacal swabs (koalas) for class 1 integrons, a genetic determinant of AMR, and to identify integron-associated antibiotic resistance genes. Class 1 integrons were detected in 25.5% of koalas (68 of 267) and 59.4% of bats (92 of 155). Integrons contained genes conferring resistance to aminoglycosides, trimethoprim and beta-lactams. Samples were also screened for blaTEM (beta-lactam) resistance genes, which were detected in 2.6% of koalas (7 of 267) and 25.2% of bats (39 of 155). Integron occurrence was significantly higher in fire-affected koalas in-care compared to wild pre-fire koalas (P < 0.0001). Integron and blaTEM occurrence were not significantly different in fire-affected bats compared to pre-fire bats (P > 0.05), however, their occurrence was significantly higher in fire-affected bats in-care compared to wild fire-affected bats (P < 0.0001 and P = 0.0488 respectively). The observed shifts of AMR dynamics in wildfire-impacted species flags the need for judicious antibiotic use when treating fire-affected wildlife to minimise unwanted selective pressure and negative treatment outcomes associated with carriage of resistance genes and antibiotic resistant bacteria.

Heat stress enhances the occurrence of erythromycin resistance of Enterococcus isolates in mice feces

Heat stress is a common environmental factor in livestock breeding that has been shown to impact the development of antibiotic resistance within the gut microbiota of both human and animals. However, studies investigating the effect of temperature on antibiotic resistance in Enterococcus isolates remain limited. In this study, specific pathogen free (SPF) mice were divided into a control group maintained at normal temperature and an experimental group subjected to daily 1-h heat stress at 38 °C, respectively. Gene expression analysis was conducted to evaluate the activation of heat shock responsive genes in the liver of mice. Additionally, the antibiotic-resistant profile and antibiotic resistant genes (ARGs) in fecal samples from mice were analyzed. The results showed an upregulation of heat-inducible proteins HSP27, HSP70 and HSP90 following heat stress exposure, indicating successful induction of cellular stress within the mice. Furthermore, heat stress resulted in an increase in the proportion of erythromycin-resistant Enterococcus isolates, escalating from 0 % to 0.23 % over a 30-day duration of heat stress. The resistance of Enterococcus isolates to erythromycin also had a 128-fold increase in minimum inhibitory concentration (MIC) within the heated-stressed group compared to the control group. Additionally, a 2∼8-fold rise in chloramphenicol MIC was observed among these erythromycin-resistant Enterococcus isolates. The acquisition of ermB genes was predominantly responsible for mediating the erythromycin resistance in these Enterococcus isolates. Moreover, the abundance of macrolide, lincosamide and streptogramin (MLS) resistant-related genes in the fecal samples from the heat-stressed group exhibited a significant elevation compared to the control group, primarily driven by changes in bacterial community composition, especially Enterococcaceae and Planococcaceae, and the transfer of mobile genetic elements (MGEs), particularly insertion elements. Collectively, these results highlight the role of environmental heat stress in promoting antibiotic resistance in Enterococcus isolates and partly explain the increasing prevalence of erythromycin-resistant Enterococcus isolates observed among animals in recent years.

Convergence of resistance and evolutionary responses in Escherichia coli and Salmonella enterica co-inhabiting chicken farms in China

Sharing of genetic elements among different pathogens and commensals inhabiting same hosts and environments has significant implications for antimicrobial resistance (AMR), especially in settings with high antimicrobial exposure. We analysed 661 Escherichia coli and Salmonella enterica isolates collected within and across hosts and environments, in 10 Chinese chicken farms over 2.5 years using data-mining methods. Most isolates within same hosts possessed the same clinically relevant AMR-carrying mobile genetic elements (plasmids: 70.6%, transposons: 78%), which also showed recent common evolution. Supervised machine learning classifiers revealed known and novel AMR-associated mutations and genes underlying resistance to 28 antimicrobials, primarily associated with resistance in E. coli and susceptibility in S. enterica. Many were essential and affected same metabolic processes in both species, albeit with varying degrees of phylogenetic penetration. Multi-modal strategies are crucial to investigate the interplay of mobilome, resistance and metabolism in cohabiting bacteria, especially in ecological settings where community-driven resistance selection occurs.

Fungus reduces tetracycline-resistant genes in manure treatment by predation of bacteria

New strategies to remove antibiotic resistance genes (ARGs), one of the most pressing threats to public health, are urgently needed. This study showed that the fungus Phanerochaete chrysosporium seeded to a composting reactor (CR) could remarkably reduce tetracycline-resistant genes (TRGs). The reduction efficiencies for the five main TRGs (i.e., tetW, tetO, tetM, tetPA, and tet(32)) increased by 8 to 100 folds compared with the control without P. chrysosporium, and this could be attributed to the decrease in the quantity of bacteria. Enumeration based on green fluorescence protein labeling further showed that P. chrysosporium became dominant in the CR. Meanwhile, the bacteria in the CR invaded the fungal cells via the cell wall defect of chlamydospore or active invasion. Most of the invasive bacteria trapped inside the fungus could not survive, resulting in bacterial death and the degradation of their TRGs by the fungal nucleases. As such, the predation of tetracycline-resistant bacteria by P. chrysosporium was mainly responsible for the enhanced removal of TRGs in the swine manure treatment. This study offers new insights into the microbial control of ARGs.

Insights into the circular: The cryptic plasmidome and its derived antibiotic resistome in the urban water systems

Plasmids have been a concern in the dissemination and evolution of antibiotic resistance in the environment. In this study, we investigated the total pool of plasmids (plasmidome) and its derived antibiotic resistance genes (ARGs) in different compartments of urban water systems (UWSs) in three European countries representing different antibiotic usage regimes. We applied a direct plasmidome approach using wet-lab methods to enrich circular DNA in the samples, followed by shotgun sequencing and in silico contig circularisation. We identified 9538 novel sequences in a total of 10,942 recovered circular plasmids. Of these, 66 were identified as conjugative, 1896 mobilisable and 8970 non-mobilisable plasmids. The UWSs' plasmidome was dominated by small plasmids (≤10 Kbp) representing a broad diversity of mobility (MOB) types and incompatibility (Inc) groups. A shared collection of plasmids from different countries was detected in all treatment compartments, and plasmids could be source-tracked in the UWSs. More than half of the ARGs-encoding plasmids carried mobility genes for mobilisation/conjugation. The richness and abundance of ARGs-encoding plasmids generally decreased with the flow, while we observed that non-mobilisable ARGs-harbouring plasmids maintained their abundance in the Spanish wastewater treatment plant. Overall, our work unravels that the UWS plasmidome is dominated by cryptic (i.e., non-mobilisable, non-typeable and previously unknown) plasmids. Considering that some of these plasmids carried ARGs, were prevalent across three countries and could persist throughout the UWSs compartments, these results should alarm and call for attention.

Concentrations, distribution, and key influencing factors of antibiotic resistance genes and bacterial community in water and reared fish tissues in a typical tilapia farm in South China

Although previous studies have investigated the occurrence of antibiotic resistance genes (ARGs) in aquaculture, few have monitored the concentrations and propagation of ARGs in biological tissues or investigated the key factors influencing their spread in aquaculture. This study investigated the concentration, propagation, and distribution of ARGs and bacterial communities in water sources, pond water, and tilapia tissues, and their key influencing factors, in a typical tilapia farm. ErmF, sul1, and sul2 were the dominant ARGs with high concentrations. The total concentrations of ARGs (TCAs) in tilapia tissues decreased in the following order: stomach > scales > intestine > gills (P < 0.05). Redundancy analysis and multiple linear regression revealed that suspended solids (SS) and chemical oxygen demand (COD) were positively correlated with the dominant ARGs ermF sul2, and the TCAs (P < 0.05); additionally, Chloroflexi and Bacteroidetes in tilapia aquaculture water were positively correlated with the dominant ARGs ermF and sul2, as well as the TCAs (P < 0.05). This study suggests that SS and COD were the key factors driving the distribution and spread of ARGs in tilapia aquaculture water. Additionally, Chloroflexi and Bacteroidetes were the key bacterial flora affecting the propagation of ARGs in tilapia aquaculture systems.

A metagenomic analysis for combination therapy of multiple classes of antibiotics on the prevention of the spread of antibiotic-resistant genes

Antibiotics used systemically to treat infections may have off-target effects on the gut microbiome, potentially resulting in the emergence of drug-resistant bacteria or selection of pathogenic species. These organisms may present a risk to the host and spread to the environment with a risk of transmission in the community. To investigate the risk of emergent antibiotic resistance in the gut microbiome following systemic treatment with antibiotics, this metagenomic analysis project used next-generation sequencing, a custom-built metagenomics pipeline, and differential abundance analysis to study the effect of antibiotics (ampicillin, ciprofloxacin, and fosfomycin) in monotherapy and different combinations at high and low doses, to determine the effect on resistome and taxonomic composition in the gut of Balb/c mice. The results showed that low-dose monotherapy treatments showed little change in microbiome composition but did show an increase in expression of many antibiotic-resistant genes (ARGs) posttreatment. Dual combination treatments allowed the emergence of some conditionally pathogenic bacteria and some increase in the abundance of ARGs despite a general decrease in microbiota diversity. Triple combination treatment was the most successful in inhibiting emergence of relevant opportunistic pathogens and completely suppressed all ARGs after 72 h of treatment. The relative abundances of mobile genetic elements that can enhance transmission of antibiotic resistance either decreased or remained the same for combination therapy while increasing for low-dose monotherapy. Combination therapy prevented the emergence of ARGs and decreased bacterial diversity, while low-dose monotherapy treatment increased ARGs and did not greatly change bacterial diversity.

A review on the effects of discharging conventionally treated livestock waste to the environmental resistome

Globally, animal production has developed rapidly as a consequence of the ongoing population growth, to support food security. This has consequently led to an extensive use of antibiotics to promote growth and prevent diseases in animals. However, most antibiotics are not fully metabolized by these animals, leading to their excretion within urine and faeces, thus making these wastes a major reservoir of antibiotics residues, antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB) in the environment. Farmers normally depend on conventional treatment methods to mitigate the environmental impact of animal waste; however, these methods are not fully efficient to remove the environmental resistome. The present study reviewed the variability of residual antibiotics, ARB, as well as ARGs in the conventionally treated waste and assessed how discharging it could increase resistome in the receiving environments. Wherein, considering the efficiency and environmental safety, an addition of pre-treatments steps with these conventional treatment methods could enhance the removal of antibiotic resistance agents from livestock waste.

Analysis of Resistance Gene Diversity in the Intestinal Microbiome of Broilers from Two Types of Broiler Farms in Hebei Province, China

The crucial reservoir of antibiotic resistance genes (ARGs) within the chicken intestinal microbiome poses a serious threat to both animal and human health. In China, the overuse of antibiotics has significantly contributed to the proliferation of ARGs in the chicken intestinal microbiome, which is a serious concern. However, there has been relatively little research on the diversity of resistance genes in the chicken intestinal microbiome since the implementation of the National Pilot Work Program for Action to Reduce the Use of Veterinary Antimicrobial Drugs in China. The objective of this study was to analyze the diversity of antibiotic resistance genes carried by the chicken intestinal microbiome in both standard farms (SFs), which implement antibiotic reduction and passed national acceptance, and nonstandard farms (NSFs), which do not implement antibiotic reductions, in Hebei Province. Fresh fecal samples of broiler chickens were collected from SFs (n = 4) and NSF (n = 1) and analyzed using high-throughput qPCR technology. Our findings revealed that all five farms exhibited a wide range of highly abundant ARGs, with a total of 201 ARGs and 7 MGEs detected in all fecal samples. The dominant ARGs identified conferred resistance to aminoglycosides, macrolide-lincosamide-streptomycin B (MLSB), and tetracycline antibiotics. Cellular protection mechanisms were found to be the primary resistance mechanism for these ARGs. The analysis of the co-occurrence network demonstrated a significant positive correlation between the abundance of MGEs and ARGs. The SF samples showed a significantly lower relative abundance of certain ARGs than the NSF samples (p < 0.05). The results of this study show that the abundance of ARGs demonstrated a downward trend after the implementation of the National Pilot Work Program for Action to Reduce the Usage of Veterinary Antimicrobial Drugs in Hebei Province, China.

High rate of multidrug resistance and integrons in Escherichia coli isolates from diseased ducks in select regions of China

With the increasing number of ducks being raised and consumed, it is crucial to monitor the presence of multidrug resistant (MDR) bacteria in duck farming. Waterfowl, such as ducks, can contribute to the rapid dissemination of antibiotic resistance genes (ARGs). The objective of this study was to investigate the antimicrobial resistance (AMR), ARGs, and mobile genetic elements (MGEs), such as IS26, tbrC, ISEcp1 in Escherichia coli(E. coli) isolated from the intestinal contents of diseased ducks between 2021 and 2022 in Sichuan, Chongqing and Anhui, China. The AMR phenotypes of 201 isolated E. coli strains were determined using the minimum inhibitory concentrations (MICs) method. Subsequently, polymerase chain reaction and sequencing techniques were employed to screen for integron-integrase genes (intI1, intI2, intI3 genes), gene cassettes (GCs), MGEs, and ARGs. The results demonstrated that 96.5% of the E. coli isolates were resistant to at least 1 antibiotic, with 88.1% of the strains displaying MDR phenotype. The highest AMR phenotype observed was for trimethoprim-sulfamethoxazole (88.1%). Furthermore, class 1 and class 2 integrons were detected in 68.2% and 3.0% of all the isolates, respectively, whereas no class 3 integrons were found. Ten types of GCs were identified in the variable regions of class 1 and class 2 integrons. Moreover, 10 MGEs were observed in 46 combinations, with IS26 exhibiting the highest detection rate (89.6%). Among the 22 types of ARGs, tetA (77.1%) was the most frequently detected. In the conjugational transfer experiment, transconjugants were found to carry specific ARGs and MGEs, with their MIC values were significantly higher than those of recipient E. coli J53, indicating their status as MDR bacteria. This study emphasizes the necessity of monitoring MGEs, ARGs, and integrons in duck farms. It provides valuable insights into the complex formation mechanisms of AMR and may aid in preventing and controlling the spread of MDR bacteria in waterfowl breeding farm.

Impact of soil supplemented with pig manure on the abundance of antibiotic resistant bacteria and their associated genes

This study was conducted to evaluate the abundance of antibiotic resistant bacteria and their resistance genes from agriculture soil supplemented with pig manure. Uncultivable soil sample was supplemented with pig manure samples under microcosm experimental conditions and plated on Luria-Bertani (LB) agar incorporated with commercial antibiotics. The supplementation of soil with 15% pig manure resulted in the highest increase in the population of antibiotic resistant bacteria (ARB)/multiple antibiotic resistant bacteria (MARB). Seven genera that included Pseudomonas, Escherichia, Providencia, Salmonella, Bacillus, Alcaligenes and Paenalcaligenes were the cultivable ARB identified. A total of ten antibiotic resistant bacteria genes (ARGs) frequently used in clinical or veterinary settings and two mobile genetic elements (MGEs) (Class 1 and Class 2 integrons) were detected. Eight heavy metal, copper, cadmium, chromium, manganese, lead, zinc, iron, and cobalt were found in all of the manure samples at different concentrations. Tetracycline resistance genes were widely distributed with prevalence of 50%, while aminoglycoside and quinolone-resistance gene had 16% and 13%, respectively. Eighteen ARB isolates carried more than two ARGs in their genome. Class 1 integron was detected among all the 18 ARB with prevalence of 90-100%, while Class 2 integron was detected among 11 ARB. The two classes of integron were found among 10 ARB. Undoubtedly, pig manure collected from farms in Akure metropolis are rich in ARB and their abundance might play a vital role in the dissemination of resistance genes among clinically-relevant pathogens.

Tackling Soil ARG-Carrying Pathogens with Global-Scale Metagenomics

Antibiotic overuse and the subsequent environmental contamination of residual antibiotics poses a public health crisis via an acceleration in the spread of antibiotic resistance genes (ARGs) through horizontal gene transfer. Although the occurrence, distribution, and driving factors of ARGs in soils have been widely investigated, little is known about the antibiotic resistance of soilborne pathogens at a global scale. To explore this gap, contigs from 1643 globally sourced metagnomes are assembled, yielding 407 ARG-carrying pathogens (APs) with at least one ARG; APs are detected in 1443 samples (sample detection rate of 87.8%). The richness of APs is greater in agricultural soils (with a median of 20) than in non-agricultural ecosystems. Agricultural soils possess a high prevalence of clinical APs affiliated with Escherichia, Enterobacter, Streptococcus, and Enterococcus. The APs detected in agricultural soils tend to coexist with multidrug resistance genes and bacA. A global map of soil AP richness is generated, where anthropogenic and climatic factors explained AP hot spots in East Asia, South Asia, and the eastern United States. The results herein advance this understanding of the global distribution of soil APs and determine regions prioritized to control soilborne APs worldwide.

Integrons in the development of antimicrobial resistance: critical review and perspectives

Antibiotic resistance development and pathogen cross-dissemination are both considered essential risks to human health on a worldwide scale. Antimicrobial resistance genes (AMRs) are acquired, expressed, disseminated, and traded mainly through integrons, the key players capable of transferring genes from bacterial chromosomes to plasmids and their integration by integrase to the target pathogenic host. Moreover, integrons play a central role in disseminating and assembling genes connected with antibiotic resistance in pathogenic and commensal bacterial species. They exhibit a large and concealed diversity in the natural environment, raising concerns about their potential for comprehensive application in bacterial adaptation. They should be viewed as a dangerous pool of resistance determinants from the "One Health approach." Among the three documented classes of integrons reported viz., class-1, 2, and 3, class 1 has been found frequently associated with AMRs in humans and is a critical genetic element to serve as a target for therapeutics to AMRs through gene silencing or combinatorial therapies. The direct method of screening gene cassettes linked to pathogenesis and resistance harbored by integrons is a novel way to assess human health. In the last decade, they have witnessed surveying the integron-associated gene cassettes associated with increased drug tolerance and rising pathogenicity of human pathogenic microbes. Consequently, we aimed to unravel the structure and functions of integrons and their integration mechanism by understanding horizontal gene transfer from one trophic group to another. Many updates for the gene cassettes harbored by integrons related to resistance and pathogenicity are extensively explored. Additionally, an updated account of the assessment of AMRs and prevailing antibiotic resistance by integrons in humans is grossly detailed-lastly, the estimation of AMR dissemination by employing integrons as potential biomarkers are also highlighted. The current review on integrons will pave the way to clinical understanding for devising a roadmap solution to AMR and pathogenicity. Graphical AbstractThe graphical abstract displays how integron-aided AMRs to humans: Transposons capture integron gene cassettes to yield high mobility integrons that target res sites of plasmids. These plasmids, in turn, promote the mobility of acquired integrons into diverse bacterial species. The acquisitions of resistant genes are transferred to humans through horizontal gene transfer.

Profiling novel lateral gene transfer events in the human microbiome

Lateral gene transfer (LGT) is an important mechanism for genome diversification in microbial populations, including the human microbiome. While prior work has surveyed LGT events in human-associated microbial isolate genomes, the scope and dynamics of novel LGT events arising in personal microbiomes are not well understood, as there are no widely adopted computational methods to detect, quantify, and characterize LGT from complex microbial communities. We addressed this by developing, benchmarking, and experimentally validating a computational method (WAAFLE) to profile novel LGT events from assembled metagenomes. Applying WAAFLE to >2K human metagenomes from diverse body sites, we identified >100K putative high-confidence but previously uncharacterized LGT events (~2 per assembled microbial genome-equivalent). These events were enriched for mobile elements (as expected), as well as restriction-modification and transport functions typically associated with the destruction of foreign DNA. LGT frequency was quantifiably influenced by biogeography, the phylogenetic similarity of the involved taxa, and the ecological abundance of the donor taxon. These forces manifest as LGT networks in which hub species abundant in a community type donate unequally with their close phylogenetic neighbors. Our findings suggest that LGT may be a more ubiquitous process in the human microbiome than previously described. The open-source WAAFLE implementation, documentation, and data from this work are available at http://huttenhower.sph.harvard.edu/waafle.

Extensive screening reveals previously undiscovered aminoglycoside resistance genes in human pathogens

Antibiotic resistance is a growing threat to human health, caused in part by pathogens accumulating antibiotic resistance genes (ARGs) through horizontal gene transfer. New ARGs are typically not recognized until they have become widely disseminated, which limits our ability to reduce their spread. In this study, we use large-scale computational screening of bacterial genomes to identify previously undiscovered mobile ARGs in pathogens. From ~1 million genomes, we predict 1,071,815 genes encoding 34,053 unique aminoglycoside-modifying enzymes (AMEs). These cluster into 7,612 families (<70% amino acid identity) of which 88 are previously described. Fifty new AME families are associated with mobile genetic elements and pathogenic hosts. From these, 24 of 28 experimentally tested AMEs confer resistance to aminoglycoside(s) in Escherichia coli, with 17 providing resistance above clinical breakpoints. This study greatly expands the range of clinically relevant aminoglycoside resistance determinants and demonstrates that computational methods enable early discovery of potentially emerging ARGs.

Metagenomic Profiles of Yak and Cattle Manure Resistomes in Different Feeding Patterns before and after Composting

Antibiotic resistance is a global threat to public health, with antibiotic resistance genes (ARGs) being one of the emerging contaminants; furthermore, animal manure is an important reservoir of biocide resistance genes (BRGs) and metal resistance genes (MRGs). However, few studies have reported differences in the abundance and diversity of BRGs and MRGs between different types of animal manure and the changes in BRGs and MRGs before and after composting. This study employed a metagenomics-based approach to investigate ARGs, BRGs, MRGs, and mobile genetic elements (MGEs) of yak and cattle manure before and after composting under grazing and intensive feeding patterns. The total abundances of ARGs, clinical ARGs, BRGs, MRGs, and MGEs were lower in the manure of grazing livestock than in the manure of the intensively fed group. After composting, the total abundances of ARGs, clinical ARGs, and MGEs in intensively fed livestock manure decreased, whereas those of ARGs, clinical ARGs, MRGs, and MGEs increased in grazing livestock manure. The synergy between MGEs mediated horizontal gene transfer and vertical gene transmission via host bacteria proliferation, which was the main driver that altered the abundance and diversity of ARGs, BRGs, and MRGs in livestock manure and compost. Additionally, tetQ, IS91, mdtF, and fabK were potential indicators for estimating the total abundance of clinical ARGs, BRGs, MRGs, and MGEs in livestock manure and compost. These findings suggest that grazing livestock manure can be directly discharged into the fields, whereas intensively fed livestock manure should be composted before returning to the field. IMPORTANCE The recent increase in the prevalence of antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), and metal resistance genes (MRGs) in livestock manure poses risks to human health. Composting is known to be a promising technology for reducing the abundance of resistance genes. This study investigated the differences and changes in the abundances of ARGs, BRGs, and MRGs between yak and cattle manure under grazing and intensive feeding patterns before and after composting. The results indicate that the feeding pattern significantly affected the abundances of resistance genes in livestock manure. Manure in intensive farming should be composted before being discharged into the field, while grazing livestock manure is not suitable for composting due to an increased number of resistance genes.

Tracing the Sources and Prevalence of Class 1 Integrons, Antimicrobial Resistance, and Trace Elements Using European Honey Bees

Surveillance of antimicrobial resistance is essential for an effective One Health response. This study explores the efficacy of European honey bees (Apis mellifera) for biomonitoring antimicrobial resistance (AMR) in urban areas. Class 1 integrons (intI1) are investigated as a universal AMR indicator, as well as associated cassette arrays and trace element contaminants at a city-wide scale. Class 1 integrons were found to be pervasive across the urban environment, occurring in 52% (75/144) of the honey bees assessed. The area of waterbodies within the honey bee's foraging radius was associated with intI1 prevalence, indicating an exposure pathway for future investigation to address. Trace element concentrations in honey bees reflected urban sources, supporting the application of this biomonitoring approach. As the first study of intI1 in honey bees, we provide insights into the environmental transfer of bacterial DNA to a keystone species and demonstrate how intI1 biomonitoring can support the surveillance of AMR.

Sub-inhibitory gentamicin pollution induces gentamicin resistance gene integration in class 1 integrons in the environment

Antibiotics at sub-inhibitory concentrations are often found in the environment. Here they could impose selective pressure on bacteria, leading to the selection and dissemination of antibiotic resistance, despite being under the inhibitory threshold. The goal of this study was to evaluate the effects of sub-inhibitory concentrations of gentamicin on environmental class 1 integron cassettes in natural river microbial communities. Gentamicin at sub-inhibitory concentrations promoted the integration and selection of gentamicin resistance genes (GmRG) in class 1 integrons after only a one-day exposure. Therefore, sub-inhibitory concentrations of gentamicin induced integron rearrangements, increasing the mobilization potential of gentamicin resistance genes and potentially increasing their dissemination in the environment. This study demonstrates the effects of antibiotics at sub-inhibitory concentrations in the environment and supports concerns about antibiotics as emerging pollutants.

Antibiotic resistance gene sequencing is necessary to reveal the complex dynamics of immigration from sewers to activated sludge

Microbial community composition has increasingly emerged as a key determinant of antibiotic resistance gene (ARG) content. However, in activated sludge wastewater treatment plants (AS-WWTPs), a comprehensive understanding of the microbial community assembly process and its impact on the persistence of antimicrobial resistance (AMR) remains elusive. An important part of this process is the immigration dynamics (or community coalescence) between the influent and activated sludge. While the influent wastewater contains a plethora of ARGs, the persistence of a given ARG depends initially on the immigration success of the carrying population, and the possible horizontal transfer to indigenously resident populations of the WWTP. The current study utilized controlled manipulative experiments that decoupled the influent wastewater composition from the influent microbial populations to reveal the fundamental mechanisms involved in ARG immigration between sewers and AS-WWTP. A novel multiplexed amplicon sequencing approach was used to track different ARG sequence variants across the immigration interface, and droplet digital PCR was used to quantify the impact of immigration on the abundance of the targeted ARGs. Immigration caused an increase in the abundance of over 70 % of the quantified ARGs. However, monitoring of ARG amplicon sequence variants (ARG-ASVs) at the immigration interface revealed various immigration patterns such as (i) suppression of the indigenous mixed liquor ARG-ASV by the immigrant, or conversely (ii) complete immigration failure of the influent ARG-ASV. These immigration profiles are reported for the first time here and highlight the crucial information that can be gained using our novel multiplex amplicon sequencing techniques. Future studies aiming to reduce AMR in WWTPs should consider the impact of influent immigration in process optimisation and design.

Evidence for wastewaters as environments where mobile antibiotic resistance genes emerge

The emergence and spread of mobile antibiotic resistance genes (ARGs) in pathogens have become a serious threat to global health. Still little is known about where ARGs gain mobility in the first place. Here, we aimed to collect evidence indicating where such initial mobilization events of clinically relevant ARGs may have occurred. We found that the majority of previously identified origin species did not carry the mobilizing elements that likely enabled intracellular mobility of the ARGs, suggesting a necessary interplay between different bacteria. Analyses of a broad range of metagenomes revealed that wastewaters and wastewater-impacted environments had by far the highest abundance of both origin species and corresponding mobilizing elements. Most origin species were only occasionally detected in other environments. Co-occurrence of origin species and corresponding mobilizing elements were rare in human microbiota. Our results identify wastewaters and wastewater-impacted environments as plausible arenas for the initial mobilization of resistance genes.

Whole genome analysis of Gram-negative bacteria using the EPISEQ CS application and other bioinformatic platforms

OBJECTIVES

To determine genomic characteristics and molecular epidemiology of carbapenem non-susceptible Klebsiella pneumoniae, Escherichia coli, Acinetobacter baumannii, and Pseudomonas aeruginosa from medical centres of Mexico using whole genome sequencing data analysed with the EPISEQ^Ⓡ CS application and other bioinformatic platforms.

METHODS

Clinical isolates collected from 28 centres in Mexico included carbapenem-non-susceptible K. pneumoniae (n = 22), E. coli (n = 24), A. baumannii (n = 16), and P. aeruginosa (n = 13). Isolates were subjected to whole genome sequencing using the Illumina (MiSeq) platform. FASTQ files were uploaded to the EPISEQ^Ⓡ CS application for analysis. Additionally, the tools Kleborate v2.0.4 and Pathogenwatch were used as comparators for Klebsiella genomes, and the bacterial whole genome sequence typing database was used for E. coli and A. baumannii.

RESULTS

For K. pneumoniae, both bioinformatic approaches detected multiple genes encoding aminoglycoside, quinolone, and phenicol resistance, and the presence of bla_NDM-1 explained carbapenem non-susceptibility in 18 strains and bla_KPC-3 in four strains. Regarding E. coli, both EPISEQ^Ⓡ CS and bacterial whole genome sequence typing database analyses detected multiple virulence and resistance genes: 20 of 24 (83.3%) strains carried bla_NDM, 3 of 24 (12.4%) carried bla_OXA-232, and 1 carried bla_OXA-181. Genes that confer resistance to aminoglycosides, tetracyclines, sulfonamides, phenicols, trimethoprim, and macrolides were also detected by both platforms. Regarding A. baumannii, the most frequent carbapenemase-encoding gene detected by both platforms was bla_OXA-72, followed by bla_OXA-66. Both approaches detected similar genes for aminoglycosides, carbapenems, tetracyclines, phenicols, and sulfonamides. Regarding P. aeruginosa, bla_VIM, bla_IMP, and bla_GES were the more frequently detected. Multiple virulence genes were detected in all strains.

CONCLUSION

Compared to the other available platforms, EPISEQ^Ⓡ CS enabled a comprehensive resistance and virulence analysis, providing a reliable method for bacterial strain typing and characterization of the virulome and resistome.

Genomic Characteristics and Molecular Epidemiology of Multidrug-Resistant Klebsiella pneumoniae Strains Carried by Wild Birds

This study aimed to explore the relationship between wild birds and the transmission of multidrug-resistant strains. Klebsiella pneumoniae was isolated from fresh feces of captured wild birds and assessed by the broth microdilution method and comparative genomics. Four Klebsiella pneumoniae isolates showed different resistance phenotypes; S90-2 and S141 were both resistant to ampicillin, cefuroxime, and cefazolin, while M911-1 and S130-1 were sensitive to most of the 14 antibiotics tested. S90-2 belongs to sequence type 629 (ST629), and its genome includes 30 resistance genes, including blaCTX-M-14 and blaSHV-11, while its plasmid pS90-2.3 (IncR) carries qacEdelta1, sul1, and aph(3')-Ib. S141 belongs to ST1662, and its genome includes a total of 27 resistance genes, including blaSHV-217. M911-1 is a new ST, carrying blaSHV-1 and fosA6, and its plasmid pM911-1.1 (novel) carries qnrS1, blaLAP-2, and tet(A). S130-1 belongs to ST3753, carrying blaSHV-11 and fosA6, and its plasmid pS130-1 [IncFIB(K)] carries only one resistance gene, tet(A). pM911-1.1 and pS90-2.3 do not have conjugative transfer ability, but their resistance gene fragments are derived from multiple homologous Enterobacteriaceae strain chromosomes or plasmids, and the formation of resistance gene fragments (multidrug resistance region) involves interactions between multiple mobile element genes, resulting in a complex and diverse resistance plasmid structure. The homologous plasmids related to pM911-1.1 and pS90-2.3 were mainly from isolated human-infecting bacteria in China, namely, K. pneumoniae and Escherichia coli. The multidrug-resistant K. pneumoniae isolates carried by wild birds in this study had drug resistance phenotypes conferred primarily by multidrug resistance plasmids that were closely related to human-infecting bacteria. IMPORTANCE Little is known about the pathogenic microorganisms carried by wild animals. This study found that the multidrug resistance phenotype of Klebsiella pneumoniae isolates carried by wild birds was mainly attributed to multidrug resistance plasmids, and these multidrug resistance plasmids from wild birds were closely related to human-infecting bacteria. Wild bird habitats overlap to a great extent with human and livestock habitats, which further increases the potential for horizontal transfer of multidrug-resistant bacteria among humans, animals, and the environment. Therefore, wild birds, as potential transmission hosts of multidrug-resistant bacteria, should be given attention and monitored.

Effect of graphene and graphene oxide on antibiotic resistance genes during copper-contained swine manure anaerobic digestion

Copper is an important selectors for antibiotic resistance genes (ARGs) transfer because of metal-antibiotic cross-resistance and/or coresistance. Due to carbon-based materials' good adsorption capacity for heavy metals, graphene and graphene oxide have great potential to reduce ARGs abundance in the environment with copper pollution. To figure out the mechanics, this study investigated the effects of graphene and graphene oxide on the succession of ARGs, mobile genetic elements (MGEs), heavy metal resistance genes (HMRGs), and bacterial communities during copper-contained swine manure anaerobic digestion. Results showed that graphene and graphene oxide could reduce ARGs abundance in varying degrees with the anaerobic reactors that contained a higher concentration of copper. Nevertheless, graphene decreased the abundance of ARGs more effectively than graphene oxide. Phylum-level bacteria such as Firmicutes, Bacteroidetes, Spirochaetes, and Verrucomicrobiaat were significantly positively correlated with most ARGs. Network and redundancy analyses demonstrated that alterations in the bacterial community are one of the main factors leading to the changes in ARGs. Firmicutes, Bacteroidetes, and Spirochaetes were enriched lower in graphene reactor than graphene oxide in anaerobic digestion products, which may be the main reason that graphene is superior to graphene oxide in reduced ARGs abundance. Additionally, ARGs were close to HMRGs than MGEs in the treatments with graphene, the opposite in graphene oxide reactors. Therefore, we speculate that the reduction of HMRGs in graphene may contribute to the result that graphene is superior to graphene oxide in reduced ARGs abundance in anaerobic digestion.

Genomic Characteristics and Phylogenetic Analyses of a Multiple Drug-Resistant Klebsiella pneumoniae Harboring Plasmid-Mediated MCR-1 Isolated from Tai'an City, China

Klebsiella pneumoniae is a clinically common opportunistic pathogen that causes pneumonia and upper respiratory tract infection in humans as well as community-and hospital-acquired infections, posing significant threats to public health. Moreover, the insertion of a plasmid carrying the mobile colistin resistance (MCR) genes brings obstacles to the clinical treatment of K. pneumoniae infection. In this study, a strain of colistin-resistant K. pneumoniae (CRKP) was isolated from sputum samples of a patient who was admitted to a tertiary hospital in Tai'an city, China, and tested for drug sensitivity. The results showed that KPTA-2108 was multidrug-resistant (MDR), being resistant to 21 of 26 selected antibiotics, such as cefazolin, amikacin, tigecycline and colistin but sensitive to carbapenems via antibiotic resistance assays. The chromosome and plasmid sequences of the isolated strain KPTA-2108 were obtained using whole-genome sequencing technology and then were analyzed deeply using bioinformatics methods. The whole-genome sequencing analysis showed that the length of KPTA-2108 was 5,306,347 bp and carried four plasmids, pMJ4-1, pMJ4-2, pMJ4-3, and pMJ4-4-MCR. The plasmid pMJ4-4-MCR contained 30,124 bp and was found to be an IncX4 type. It was the smallest plasmid in the KPTA-2108 strain and carried only one resistance gene MCR-1. Successful conjugation tests demonstrated that pMJ4-4-MCR carrying MCR-1 could be horizontally transmitted through conjugation between bacteria. In conclusion, the acquisition and genome-wide characterization of a clinical MDR strain of CRKP may provide a scientific basis for the treatment of K. pneumoniae infection and epidemiological data for the surveillance of CRKP.

Characterization and comparative genomics analysis of RepA_N multi-resistance plasmids carrying optrA from Enterococcus faecalis

Introduction

This research aimed to investigate the antibiotic resistance of Enterococcus faecalis from swine farms in Zhejiang Province and the prevalence and transmission mechanism of oxazolidone resistance gene optrA.

Method

A total of 226 Enterococcus faecalis were isolated and their resistance to 14 antibiotics was detected by broth microdilution. The resistance genes were detected by PCR.

Results

The antibiotic resistance rate of 226 isolates to nearly 57% (8/14) of commonly used antibiotics was higher than 50%. The resistance rate of tiamulin was highest (98.23%), that of tilmicosin, erythromycin, tetracycline and florfenicol was higher than 80%, and that of oxazolidone antibiotic linezolid was 38.49%. The overall antibiotics resistance in Hangzhou, Quzhou and Jinhua was more serious than that in the coastal cities of Ningbo and Wenzhou. The result of PCR showed that optrA was the main oxazolidinone and phenicols resistance gene, with a detection rate of 71.68%, and optrA often coexisted with fexA in the isolates. Through multi-locus sequence typing, conjugation transfer, and replicon typing experiments, it was found that the horizontal transmission mediated by RepA_N plasmid was the main mechanism of optrA resistance gene transmission in E. faecalis from Zhejiang Province. Two conjugative multi-resistance plasmids carrying optrA, RepA_N plasmid pHZ318-optrA from Hangzhou and Rep3 plasmid from Ningbo, were sequenced and analyzed. pHZ318-optrA contain two multidrug resistance regions (MDR), which contributed to the MDR profile of the strains. optrA and fexA resistance genes coexisted in IS1216E-fexA-optrA-ferr-erm(A)-IS1216E complex transposon, and there was a partial sequence of Tn554 transposon downstream. However, pNB304-optrA only contain optrA, fexA and an insertion sequence ISVlu1. The presence of mobile genetic elements at the boundaries can possibly facilitate transfer among Enterococcus through inter-replicon gene transfer.

Discussion

This study can provide theoretical basis for ensuring the quality and safety of food of animal origin, and provide scientific guidance for slowing down the development of multi-antibiotic resistant Enterococcus.

Distribution and influencing factors of antibiotic resistance genes of crayfish (Procambarus clarkii) intestine in main crayfish breeding provinces in China

The propagation of antibiotic resistance genes (ARGs) has become a global public health concern. However, the distribution and influencing factors of ARGs, especially high-risk ARGs, in the gut of aquaculture animals remain unclear. Here, we employed 16S rRNA gene sequencing and high-throughput quantitative PCR techniques to determine crayfish gut microbiota and ARGs collected from 40 culture ponds in major crayfish farming provinces of China. We detected 74 ARGs in crayfish gut. Among them, the beta-lactamase and tetracycline resistance genes were dominant. The total ARG abundance was the highest in Hubei Province. High-risk ARGs were also found in crayfish gut, and ermB had the highest abundance and distributed in Anhui, Hubei, Henan and Jiangxi Province. In addition, opportunistic pathogens (Streptococcus, Aeromonas and Acinetobacter) might be potential hosts for ARGs, including high-risk ARGs. Finally, habitat, environmental factors (NO₃-N, pH and temperature), microbial alpha diversity and mobile genetic elements (MGEs) showed significant influence on ARGs profiles. Generally, our results illustrate that ARGs are prevalent in crayfish gut and may pose potential risk to human health, which will help develop targeted strategies for the risk management and assessment of ARGs in the aquaculture.

Pdif-mediated antibiotic resistance genes transfer in bacteria identified by pdifFinder

Modules consisting of antibiotic resistance genes (ARGs) flanked by inverted repeat Xer-specific recombination sites were thought to be mobile genetic elements that promote horizontal transmission. Less frequently, the presence of mobile modules in plasmids, which facilitate a pdif-mediated ARGs transfer, has been reported. Here, numerous ARGs and toxin-antitoxin genes have been found in pdif site pairs. However, the mechanisms underlying this apparent genetic mobility is currently not understood, and the studies relating to pdif-mediated ARGs transfer onto most bacterial genera are lacking. We developed the web server pdifFinder based on an algorithm called PdifSM that allows the prediction of diverse pdif-ARGs modules in bacterial genomes. Using test set consisting of almost 32 thousand plasmids from 717 species, PdifSM identified 481 plasmids from various bacteria containing pdif sites with ARGs. We found 28-bp-long elements from different genera with clear base preferences. The data we obtained indicate that XerCD-dif site-specific recombination mechanism may have evolutionary adapted to facilitate the pdif-mediated ARGs transfer. Through multiple sequence alignment and evolutionary analyses of duplicated pdif-ARGs modules, we discovered that pdif sites allow an interspecies transfer of ARGs but also across different genera. Mutations in pdif sites generate diverse arrays of modules which mediate multidrug-resistance, as these contain variable numbers of diverse ARGs, insertion sequences and other functional genes. The identification of pdif-ARGs modules and studies focused on the mechanism of ARGs co-transfer will help us to understand and possibly allow controlling the spread of MDR bacteria in clinical settings. The pdifFinder code, standalone software package and description with tutorials are available at https://github.com/mjshao06/pdifFinder.

The global distribution and environmental drivers of the soil antibiotic resistome

BACKGROUND

Little is known about the global distribution and environmental drivers of key microbial functional traits such as antibiotic resistance genes (ARGs). Soils are one of Earth's largest reservoirs of ARGs, which are integral for soil microbial competition, and have potential implications for plant and human health. Yet, their diversity and global patterns remain poorly described. Here, we analyzed 285 ARGs in soils from 1012 sites across all continents and created the first global atlas with the distributions of topsoil ARGs.

RESULTS

We show that ARGs peaked in high latitude cold and boreal forests. Climatic seasonality and mobile genetic elements, associated with the transmission of antibiotic resistance, were also key drivers of their global distribution. Dominant ARGs were mainly related to multidrug resistance genes and efflux pump machineries. We further pinpointed the global hotspots of the diversity and proportions of soil ARGs.

CONCLUSIONS

Together, our work provides the foundation for a better understanding of the ecology and global distribution of the environmental soil antibiotic resistome. Video Abstract.

Antibiotic resistance bacteria and antibiotic resistance genes survived from the extremely acidity posing a risk on intestinal bacteria in an in vitro digestion model by horizontal gene transfer

Antibiotic resistance bacteria (ARB) and antibiotic resistance genes (ARGs) are emerging contaminants posing risk to human health. To investigate the pathogenic ARBs and the horizontal gene transfer (HGT) via both extracellular ARGs (eARGs) and intracellular ARGs (iARGs), an in vitro digestion simulation system was established to monitoring the ARB and ARGs passing through the artificial digestive tract. The results showed that ARB was mostly affected by the acidity of the gastric fluid with about 99% ARB (total population of 2.45 × 10⁹-2.54 × 10⁹) killed at pH 2.0 and severe damage of bacterial cell membrane. However, more than 80% ARB (total population of 2.71 × 10⁹-3.90 × 10⁹) survived the challenge when the pH of the gastric fluid was 3.0 and above. Most ARB died from the high acidity, but its ARGs, intI1 and 16 S rRNA could be detected. The eARGs (accounting for 0.03-24.56% of total genes) were less than iARGs obviously. The eARGs showed greater HGT potential than that of iARGs, suggesting that transformation occurred more easily than conjugation. The transferring potential followed: tet (100%) > sul (75%) > bla (58%), related to the high correlation of intI1 with tetA and sul2 (p < 0.01). Moreover, gastric juice of pH 1.0 could decrease the transfer frequency of ARGs by 2-3 order of magnitude compared to the control, but still posing potential risks to human health. Under the treatment of digestive fluid, ARGs showed high gene horizontal transfer potential, suggesting that food-borne ARBs pose a great risk of horizontal transfer of ARGs to intestinal bacteria.

Bioavailability of potentially toxic elements influences antibiotic resistance gene and mobile genetic element abundances in urban and rural soils

Antibiotic resistance genes (ARGs) that can encode resistance traits in bacteria are found across the environment. While it is often difficult to discern their origin, their prevalence and diversity depends on many factors, one of which is their exposure to potentially toxic elements (PTE, i.e., metals and metalloids) in soils. Here, we investigated how ambient ARGs and mobile genetic elements (MGEs) relate to the relative bioavailability of different PTEs (total versus exchangeable and carbonate-bound PTE) in rural and urban soils in northeast England. The average relative abundances of ARGs in rural sites varied over a 3-log range (7.24 × 10^-7 to 1.0 × 10^-4 genes/16S rRNA), and relative ARG abundances in urban sites varied by four orders of magnitude (1.75 × 10^-6 to 2.85 × 10^-2 genes/16S rRNA). While beta-lactam and aminoglycoside resistance genes dominated rural and urban sites, respectively, non-specific ARGs, also called multidrug-resistance genes, were significantly more abundant in urban sites (p < 0.05). Urban sites also had higher concentrations of total and exchangeable forms of PTE than rural sites, whereas rural sites were higher in carbonate-bound forms. Significant positive Spearman correlations between PTEs, ARGs and MGEs were apparent, especially with bioavailable PTE fractions and at urban sites. This study found significant positive correlations between ARGs and beryllium (Be), which has not previously been reported. Overall, our results show that PTE bioavailability is important in explaining the relative selection of ARGs in soil settings and must be considered in future co-selection and ARG exposure studies.

Antimicrobial resistance and genomic characterization of Salmonella enterica serovar Senftenberg isolates in production animals from the United States

In the USA, Salmonella enterica subspecies enterica serovar Senftenberg is among the top five serovars isolated from food and the top 11 serovars isolated from clinically ill animals. Human infections are associated with exposure to farm environments or contaminated food. The objective of this study was to characterize S. Senftenberg isolates from production animals by analyzing phenotypic antimicrobial resistance profiles, genomic features and phylogeny. Salmonella Senftenberg isolates (n = 94) from 20 US states were selected from NVSL submissions (2014-2017), tested against 14 antimicrobial drugs, and resistance phenotypes determined. Resistance genotypes were determined using whole genome sequencing analysis with AMRFinder and the NCBI and ResFinder databases with ABRicate. Plasmids were detected using PlasmidFinder. Integrons were detected using IntFinder and manual alignment with reference genes. Multilocus-sequence-typing (MLST) was determined using ABRicate with PubMLST database, and phylogeny was determined using vSNP. Among 94 isolates, 60.6% were resistant to at least one antimicrobial and 39.4% showed multidrug resistance. The most prevalent resistance findings were for streptomycin (44.7%), tetracycline (42.6%), ampicillin (36.2%) and sulfisoxazole (32.9%). The most commonly found antimicrobial resistance genes were aac(6')-Iaa (100%), aph(3″)-Ib and aph(6)-Id (29.8%) for aminoglycosides, followed by bla _TEM-1 (26.6%) for penicillins, sul1 (25.5%) and sul2 (23.4%) for sulfonamides and tetA (23.4%) for tetracyclines. Quinolone-resistant isolates presented mutations in gyrA and/or parC genes. Class 1 integrons were found in 37 isolates. Thirty-six plasmid types were identified among 77.7% of the isolates. Phylogenetic analysis identified two distinct lineages of S. Senftenberg that correlated with the MLST results. Isolates were classified into two distinct sequence types (ST): ST14 (97.9%) and ST 185 (2.1%). The diversity of this serotype suggests multiple introductions into animal populations from outside sources. This study provided antimicrobial susceptibility and genomic characteristics of S. Senftenberg clinical isolates from production animals in the USA during 2014 to 2017. This study will serve as a base for future studies focused on the phenotypic and molecular antimicrobial characterization of S. Senftenberg isolates in animals. Monitoring of antimicrobial resistance to detect emergence of multidrug-resistant strains is critical.

Antibiotic Resistomes and Microbiomes in the Surface Water along the Code River in Indonesia Reflect Drainage Basin Anthropogenic Activities

Water and sanitation are important factors in the emergence of antimicrobial resistance in low- and middle-income countries. Drug residues, metals, and various wastes foster the spread of antibiotic resistance genes (ARGs) with the help of mobile genetic elements (MGEs), and therefore, rivers receiving contaminants and effluents from multiple sources are of special interest. We followed both the microbiome and resistome of the Code River in Indonesia from its pristine origin at the Merapi volcano through rural and then city areas to the coast of the Indian Ocean. We used a SmartChip quantitative PCR with 382 primer pairs for profiling the resistome and MGEs and 16S rRNA gene amplicon sequencing to analyze the bacterial communities. The community structure explained the resistome composition in rural areas, while the city sampling sites had lower bacterial diversity and more ARGs, which correlated with MGEs, suggesting increased mobility potential in response to pressures from human activities. Importantly, the vast majority of ARGs and MGEs were no longer detectable in marine waters at the ocean entrance. Our work provides information on the impact of different influents on river health as well as sheds light on how land use contributes to the river resistome and microbiome.

Emergence of a NDM-1-producing ST25 Klebsiella pneumoniae strain causing neonatal sepsis in China

Carbapenem-resistant Klebsiella pneumoniae (CRKP) seriously threaten the efficacy of modern medicine with a high associated mortality rate and unprecedented transmission rate. In this study, we isolated a clinical K. pneumoniae strain DY1928 harboring bla_NDM-1 from a neonate with blood infection. Antimicrobial susceptibility testing indicated that DY1928 was resistant to various antimicrobial agents, including meropenem, imipenem, ceftriaxone, cefotaxime, ceftazidime, cefepime, piperacillin-tazobactam, and amoxicillin-clavulanate. S1 nuclease-pulsed field gel electrophoresis (S1-PFGE), southern blot and conjugation experiment revealed that the bla_NDM-1 gene was located on a conjugative plasmid of IncA/C2 type with a 147.9 kb length. Whole-genome sequencing showed that there was a conservative structure sequence (bla_NDM-1-ble-trpF-dsbD) located downstream of the bla_NDM-1 gene. Multilocus sequence typing (MLST) classified DY1928 as ST25, which was a hypervirulent K. pneumoniae type. Phylogenetic analysis of genomic data from all ST25 K. pneumoniae strains available in the NCBI database suggested that all bla_NDM-1 positive strains were isolated in China and had clinical origins. A mouse bloodstream infection model was constructed to test the virulence of DY1928, and 11 K. pneumoniae strains homologous to DY1928 were isolated from the feces of infected mice. Moreover, we found that DY1928 had a tendency to flow from the blood into the intestine in mice and caused multiple organ damage. To our knowledge, this is the first study to report an infection caused by bla_NDM-1-positive ST25 K. pneumoniae in the neonatal unit. Our findings indicated that stricter surveillance and more effective actions were needed to reduce the risk of disseminating such K. pneumoniae strains in clinical settings, especially in neonatal wards.

Structural insight into Tn3 family transposition mechanism

Transposons are diverse mobile genetic elements that play the critical role as genome architects in all domains of life. Tn3 is a widespread family and among the first identified bacterial transposons famed for their contribution to the dissemination of antibiotic resistance. Transposition within this family is mediated by a large TnpA transposase, which facilitates both transposition and target immunity. Howtever, a structural framework required for understanding the mechanism of TnpA transposition is lacking. Here, we describe the cryo-EM structures of TnpA from Tn4430 in the apo form and paired with transposon ends before and after DNA cleavage and strand transfer. We show that TnpA has an unusual architecture and exhibits a family specific regulatory mechanism involving metamorphic refolding of the RNase H-like catalytic domain. The TnpA structure, constrained by a double dimerization interface, creates a peculiar topology that suggests a specific role for the target DNA in transpososome assembly and activation.