Resistance Genes Research Articles

Polyvinyl chloride microplastics disseminate antibiotic resistance genes in Chinese soil: A metagenomic analysis

The widespread prevalence of microplastics (MPs) in the environment poses concerns as they are vectors of antibiotic resistance genes (ARGs). The relationships between antibiotic resistomes and MPs remain unexplored in soil which was considered as the reservoirs of MPs and ARGs. This study investigated the effects of polyvinyl chloride (PVC) MPs on soil bacterial communities and ARG abundance which soil samples sourced from 20 provinces across China. We found that PVC significantly influences soil bacterial community structure and ARG abundance. Structural equation modeling revealed that PVC alters soil characteristics, ultimately affecting soil bacterial communities, including ARG-containing bacterial hosts, and the relative abundance of ARGs. This study enhances our understanding of how MPs influence the proliferation and hosts of ARGs within diverse soil environments, offering crucial insights for future strategies in plastic management and disposal.

Risk level and removal performance of antibiotic resistance genes and bacterial pathogens in static composting with different temperatures

The effect of different levels of temperature on resistance genes is not clear in mesophilic static composting (<50 °C). This study conducted livestock manure composting with different temperature gradients from 20 to 50 °C, it was found that the reduction rates of risk rank-I antibiotic resistance genes (from 3 % to 66 %), metal resistance genes (from −50 % to 76 %) and bacterial pathogens (from 72 % to 91 %) all increased significantly with increasing temperature from 20 to 50°C. The vulnerability of bacterial communities increased significantly, and the assembly process of bacterial communities changed from deterministic to stochastic with the increase of composting temperature. Higher temperature could accelerate the removal of thermolabile resistance genes hosts or pathogenic hosts carrying mobile genetic elements by directly or indirectly affecting organic acids content. Therefore, for soil safety, the temperature of the manure recycling process should be increased as much as possible.

In treacherous waters: detection of colistin-resistant bacteria in water and plastic litter from a recreational estuary.

Colistin resistance poses a major therapeutic challenge and resistant strains have now been reported worldwide. However, the occurrence of such bacteria in aquatic environments is considerably less understood. This study aimed to isolate and characterize colistin-resistant strains from water and plastic litter collected in an urban recreational estuary. Altogether, 64 strains with acquired colistin resistance were identified, mainly Acinetobacter spp. and Enterobacter spp. From these, 40.6% were positive for at least one mcr variant (1-9), 26.5% harbored, extended-spectrum beta-lactamases, 23.4% harbored, sulfonamide resistance genes, and 9.3% harbored, quinolone resistance genes. merA, encoding mercury resistance, was detected in 10.5% of these strains, most of which were also strong biofilm producers. The minimum inhibitory concentration toward colistin was determined for the mcr-positive strains and ranged from 2 to≥512µg ml-1. Our findings suggest that Gram-negative bacteria highly resistant to a last-resort antimicrobial can be found in recreational waters and plastic litter, thereby evidencing the urgency of the One Health approach to mitigate the antimicrobial resistance crisis.

Whole-Genome Sequencing Reveals Temporal Trends in Antibiotic Resistance Genes in Escherichia coli Causing Pediatric Urinary Tract Infections in Central Vietnam

(1) Background: Pediatric urinary tract infections (UTIs) pose significant challenges due to drug-resistant Escherichia coli (E. coli) strains. This study utilizes whole-genome sequencing to analyze temporal trends in antibiotic resistance genes (ARGs) in clinical E. coli isolates from pediatric UTI cases in central Vietnam. (2) Methods: We conducted whole-genome sequencing on 71 E. coli isolates collected from pediatric UTI patients between 2018 and 2020. ARGs were identified, and their prevalence over time was analyzed. Statistical tests were used to correlate ARG presence with antibiotic resistance. (3) Results: Of the 47 E. coli isolates with complete data, 40 distinct ARGs were identified, with a median of 10 resistance genes per isolate. A significant increase in the total number of ARGs per isolate was observed over time, from an average of 8.88 before June 2019 to 11.63 after. Notably, the prevalence of the aadA2 gene (aminoglycoside resistance) rose from 0% to 26.7%, and that of the blaNDM-5 gene (beta-lactam and carbapenem resistance) increased from 0% to 23.3%. Key correlations include blaEC with cephalosporin resistance, blaNDM-5 with carbapenem resistance, and sul2 with sulfamethoxazole/trimethoprim resistance. (4) Conclusions: Whole-genome sequencing reveals complex and evolving antibiotic resistance patterns in pediatric E. coli UTIs in central Vietnam, with a marked increase in ARG prevalence over time. Continuous surveillance and targeted treatments are essential to address these trends. Understanding genetic foundations is crucial for effective intervention strategies.

A study of the influence of the T2DL.2DS-2SS translocation and the 5S(5D) substitution from Aegilops speltoides on breeding-valuable traits of common wheat.

The use of the gene pool of wild relatives for expanding the genetic diversity of common wheat is an important task of breeding programs. However, the practical application of common wheat lines with alien genetic material is constrained by the lack of information on chromosomal rearrangements and the negative impact of the transferred material on agronomically important traits. This research is aimed at studying 14 introgression lines with the T2DL.2DS-2SS translocation and the 5S(5D) substitution from Aegilops speltoides obtained from crossing common wheat varieties (Aurora, Krasnodarskaya 99, Nika Kubani) with the genome-substituted form Avrodes (BBAASS). Hybrid lines with different combinations of T2DL.2DS-2SS and T1BL.1RS translocations and 5S(5D) substitution were characterized by resistance to leaf and yellow rusts, productivity components and technological qualities of grain. The assessment of the varieties' resistance to rust diseases showed that Krasnodarskaya 99, Nika Kubani and the Aurora variety, which is a carrier of the T1BL.1RS translocation, are highly susceptible to diseases, while the presence of the T2DL.2DS-2SS translocation and the 5S(5D) substitution, both together and separately, provides resistance to fungal pathogens. The analysis of the lines using markers designed for known resistance genes of Ae. speltoides did not reveal the presence of the Lr28, Lr35 and Lr51 genes in the lines. The results suggest that the genetic material of Ae. speltoides transferred to chromosomes 2D and 5D contains new resistance genes. To determine the effect of the T2DL.2DS-2SS translocation and the 5S(5D) substitution on the productivity and technological qualities of grain, the lines were assessed by weight of 1000 grains, grain weight and number of ears per 1 m2, by protein and gluten content, gluten quality and general baking evaluation. A positive effect was determined upon the weight of 1000 grains, protein and gluten content. There were no significant differences in other characteristics. The T2DL.2DS-2SS translocation and the 5S(5D) substitution did not have a negative effect on the productivity and technological quality of grain, and are of interest for breeding practice.

Case study on the relationship between transmission of antibiotic resistance genes and microbial community under freeze-thaw cycle on cold-region dairy farm

Freeze-thaw cycle (FTC) is a naturally occurring phenomenon in high-latitude terrestrial ecosystems, which may exert influence on distribution and evolution of microbial community in the soil. The relationship between transmission of antibiotic resistance genes (ARGs) and microbial community was investigated upon the case study on the soil of cold-region dairy farm under seasonal FTC. The results demonstrated that 37 ARGs underwent decrease in the abundance of blaTEM from 80.4 % for frozen soil to 71.7 % for thawed soil, and that sul2 from 8.8 % for frozen soil to 6.5 % for thawed soil, respectively. Antibiotic deactivation was identified to be closely related to the highest relative abundance of blaTEM, and the spread of sulfonamide resistance genes (SRGs) occurred mainly via target modification. Firmicutes in frozen soil were responsible for dominating the abundance of ARGs by suppressing the native bacteria under starvation effect in cold regions, and then underwent horizontal gene transfer (HGT) among native bacteria through mobile genetic elements (MGEs). The TRB-C (32.6–49.1 %) and tnpA-06 (0.27–7.5 %) were significantly increased in frozen soil, while Int3 (0.67–10.6 %) and tnpA-04 (11.1–19.4 %) were up-regulated in thawed soil. Moreover, the ARGs in frozen soil primarily underwent HGT through MGEs, i.e. TRB-C and tnpA-06, with increased number of Firmicutes serving as carrier. The case study not only demonstrated relationship between transmission of ARGs and microbial community in the soil under practically relevant FTC condition, but also emphasized the importance for formulating better strategies for preventing FTC-induced ARGs in dairy farm in cold regions.

Unnoticed antimicrobial resistance risk in Tibetan cities unveiled by sewage metagenomic surveillance: Compared to the eastern Chinese cities

Sewage surveillance is a cost-effective tool for assessing antimicrobial resistance (AMR) in urban populations. However, research on sewage AMR in remote areas is still limited. Here, we used shotgun metagenomic sequencing to profile antibiotic resistance genes (ARGs) and ARG-carrying pathogens (APs) across 15 cities in Tibetan Plateau (TP) and the major cities in eastern China. Notable regional disparities in sewage ARG composition were found, with a significantly higher ARG abundance in TP (2.97 copies/cell). A total of 542 and 545 APs were identified in sewage from TP and the East, respectively, while more than 40 % carried mobile genetic elements (MGEs). Moreover, 65 MGEs-carrying APs were identified as World Health Organization (WHO) priority-like bacterial and fungal pathogens. Notably, a fungal zoonotic pathogen, Enterocytozoon bieneusi, was found for the first time to carry a nitroimidazole resistance gene (nimJ). Although distinct in AP compositions, the relative abundances of APs were comparable in these two regions. Furthermore, sewage in TP was found to be comparable to the cities in eastern China in terms of ARG mobility and AMR risks. These findings provide insights into ARGs and APs distribution in Chinese sewage and stress the importance of AMR surveillance and management strategies in remote regions.

Presence of extended-spectrum beta-lactamase-producing Escherichia coli and carbapenem resistance in ready-to-eat stuffed mussels in Istanbul

AbstractFoodborne pathogens' transmission is essential in the spread of antibiotic resistance, and extended-spectrum beta-lactamase-producing Escherichia coli especially threatens public health. E. coli plays an essential role in the resistance to commonly used beta-lactam group antibiotics. Ready-to-eat (RTE) stuffed mussels are among many restaurants and street vendors, presenting potential health risks of food hygiene origin. 200 RTE stuffed mussels were collected from the Asian and European sides of Istanbul and analysed for the presence of E. coli. As a result of PCR analysis, E. coli was detected in 7 (3.5%) samples. An antibiotic susceptibility test was performed using the disc diffusion method to determine ESBL and carbapenem resistance. All isolates were resistant to ampicillin. The double-disk synergy test was performed as an ESBL phenotypic confirmation test, and no phenotypically ESBL-producing E. coli were detected. The blaTEM gene was detected in one isolate (14.2%) by mPCR, but blaCTX-M, blaSHV, and blaOXA genes were not observed. Meropenem and imipenem were used with the disk diffusion method for carbapenem resistance study, and no resistant isolate was found. Carbapenem resistance genes were investigated by monoplex PCR, and blaNDM-1, blaOXA-48, blaVIM, and blaIMP resistance genes were not detected. This is the first report on ESBL-producing E. coli in RTE stuffed mussels in Türkiye, which draws attention to a public health risk.

Unveiling the pathogenic and multidrug-resistant profiles of Vibrio alfacsensis: A potential identified threat in turbot (Scophthalmus maximus) aquaculture

Vibrio alfacsensis is traditionally seen as an environmental symbiont within its genus, with no detailedly documented pathogenicity in marine aquaculture to date. This study delves into the largely unexplored pathogenic potential and emerging antibiotic resistance of V. alfacsensis. The VA-1 strain, isolated from recirculating aquaculture system (RAS) effluent of cultured turbot (Scophthalmus maximus), underwent comprehensive analysis including biochemical identification, antibiotic susceptibility testing and reinfection trials. The results confirmed VA-1's pathogenicity and significant multiple antibiotic resistance. VA-1 could induce systemic infection in turbot, with symptoms like kidney enlargement, exhibiting virulence comparable to known Vibrio pathogens, with an LD50 around 2.36 × 106 CFU/fish. VA-1's remarkable resistance phenotype (14/22) suggested potential for genetic exchange and resistance factor acquisition in aquaculture environments. Phylogenetic analysis based on 16S rDNA sequences and whole-genome sequencing has firmly placed VA-1 within the V. alfacsensis clade, while genome-wide analysis highlights its similarity and diversity in relation to strains from across the globe. VA-1 contained numerous replicons, indicating the possibility for the spread of resistance and virulence genes. This study suggests V. alfacsensis may acquire and transfer pathogenic and resistant traits through horizontal gene transfer, a likelihood intensified by changing environmental and aquaculture conditions, highlighting the need for vigilant pathogen monitoring and new non-antibiotic treatments.

Genetic traits and transmission of antimicrobial resistance characteristics of cephalosporin resistant Escherichia coli in tropical aquatic environments

This study investigates the genetic traits and transmission mechanisms of cephalosporin-resistant Escherichia coli in tropical aquatic environments in Singapore. From 2016 to 2020, monthly samples were collected from wastewater treatment plants, marine niches, community sewage, beaches, reservoirs, aquaculture farms, and hospitals, yielding 557 isolates that were analyzed for antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) using genomic methods. Findings reveal significant genotypic similarities between environmental and hospital-derived strains, particularly the pandemic E. coli ST131. Environmental strains exhibited high levels of intrinsic resistance mechanisms, including mutations in porins and efflux pumps, with key ARGs such as CMY-2 and NDM-9 predominantly carried by MGEs, which facilitate horizontal gene transfer. Notably, pathogenic EPEC and EHEC strains were detected in community sewage and aquaculture farms, posing substantial public health risks. This underscores the critical role of these environments as reservoirs for multidrug-resistant pathogens and emphasizes the interconnectedness of human activities and environmental health.

A system to analyze the initiation of random X-chromosome inactivation using time-lapse imaging of single cells

In female eutherian mammal development, X-chromosome inactivation (XCI) of one of the two X chromosomes is initiated early. Understanding the relationship between the initiation of XCI and cell fate is critical for understanding early female development and requires a system that can monitor XCI in single living cells. Traditional embryonic stem cells (ESCs) used for XCI studies often lose X chromosomes spontaneously during culture and differentiation, making accurate monitoring difficult. Additionally, most XCI assessment methods necessitate cell disruption, hindering cell fate tracking. We developed the Momiji (version 2) ESC line to address these difficulties, enabling real-time monitoring of X-chromosome activity via fluorescence. We inserted green and red fluorescent reporter genes and neomycin and puromycin resistance genes into the two X chromosomes of PGK12.1 ESCs, creating a female ESC line that retains two X chromosomes more faithfully during differentiation. Momiji (version 2) ESCs exhibit a more stable XX karyotype than other ESC lines, including the parental PGK12.1 line. This new tool offers valuable insights into the relationship between XCI and cell fate, improving our understanding of early female development.

Exosomes: Key Factors in Ovarian Cancer Peritoneal Metastasis and Drug Resistance

Ovarian cancer remains a leading cause of death among gynecological cancers, largely due to its propensity for peritoneal metastasis and the development of drug resistance. This review concentrates on the molecular underpinnings of these two critical challenges. We delve into the role of exosomes, the nano-sized vesicles integral to cellular communication, in orchestrating the complex interactions within the tumor microenvironment that facilitate metastatic spread and thwart therapeutic efforts. Specifically, we explore how exosomes drive peritoneal metastasis by promoting epithelial–mesenchymal transition in peritoneal mesothelial cells, altering the extracellular matrix, and supporting angiogenesis, which collectively enable the dissemination of cancer cells across the peritoneal cavity. Furthermore, we dissect the mechanisms by which exosomes contribute to the emergence of drug resistance, including the sequestration and expulsion of chemotherapeutic agents, the horizontal transfer of drug resistance genes, and the modulation of critical DNA repair and apoptotic pathways. By shedding light on these exosome-mediated processes, we underscore the potential of exosomal pathways as novel therapeutic targets, offering hope for more effective interventions against ovarian cancer’s relentless progression.

Antimicrobial potential of Streptomyces sp. NP73 isolated from the forest soil of Northeast India against multi-drug resistant Escherichia coli.

This study reports the isolation and characterization of a Streptomyces sp. from soil, capable of producing bioactive secondary metabolites active against a variety of bacterial human pathogens. We targeted the antimicrobial activity against Escherichia coli ATCC-BAA 2469, a clinically relevant strain of bacteria harbouring resistance genes for carbapenems, extended spectrum beta-lactams, tetracyclines, fluoroquinones, etc. Preliminary screening using the spot inoculation technique identified Streptomyces sp. NP73 as the potent strain among the 74 isolated Actinomycetia strain. 16S rRNA gene and whole genome sequencing (WGS) confirmed its taxonomical identity and helped in the construction of the phylogenetic tree. WGS revealed the predicted pathways and biosynthetic gene clusters responsible for producing various types of antibiotics including the isolated compound. Bioactivity guided fractionation and chemical characterization of the active fraction, carried out using liquid chromatography, gas chromatography-mass spectrometry, infra-red spectroscopy, and nuclear magnetic resonance spectroscopy, led to the tentative identification of the active compound as Pyrrolo[1,2-a] pyrazine-1,4-dione, hexahydro-, a diketopiperazine molecule. This compound exhibited excellent antimicrobial and anti-biofilm properties against E. coli ATCC-BAA 2469 with an MIC value of 15.64µg ml-1, and the low cytotoxicity of the compound identified in this study provides hope for future drug development.

Antimicrobial resistance profiling of bacteria isolated from wastewater and environmental samples of pharmaceutical industries in South India

The study was aimed to determine the phenotypic and genotypic antimicrobial resistance in the isolated bacteria from the influent (25), effluent (15), surface and ground water samples (15) surrounding the pharmaceutical industries located in south India. From 55 samples, 48 isolates of 10 different bacteria were obtained. The identified bacterial isolates were viz. Klebsiella pneumoniae, Pseudomonas aeruginosa, Enterobacter aerogenes, Corynebacterium sp., Acinetobacter sp., Aeromonas punctata, Ralstonia picketti, Staphylococcus aureus, Stenotrophomonas maltophillia, and Citrobacter freundii. The phenotypic profile of resistance through antibiotic susceptibility test was carried out against sixteen different antibiotics. Standard PCR technique was used for the detection of 12 resistance genes encoding carbapenems, quinoline, aminoglycoside, β-lactam belonging blaOXA-58,blaOXA-22,qnrA, qnrB, aac(6)-Ib-cr, aac (3)-XI, mec A, qepA, aadB, blaVIM, blaOXA-48 and blaNDM. Pseudomonas aeruginosa (1: TN/I/2020) showed presence of 3 resistance genes. qnrB (489 bp) gene was present in maximum of 7 isolates while blaVIM (196 bp) gene was present in 6 isolates. The resistance genes blaNDM (621 bp) was present in three different isolates; aac (X):6)-lb-cr (482 bp), qepA (495 bp), aadB (500 bp), blaOXA-58 (843 bp) resistant genes were present in two different isolates each among the bacterial isolates obtained in this study. In phenotypic resistance profiling by AST method, out of 16 antibiotics tested, 14 showed resistance. Similarly, in genotypic resistance profiling, among 12 resistance genes tested, a maximum of three resistance genes were noticed in Pseudomonas aeruginosa. There were positive and negative correlations observed between phenotypic and genotypic resistance among different antibiotics and their resistance genes indicating the variations in the resistance gene expression.

Molecular Evolution of Rice Blast Resistance Gene bsr-d1

Rice blast, caused by the fungus Magnaporthe oryzae, reduces rice yields by 10% to 35%. Incorporating plant blast resistance genes into breeding programs is an effective strategy to combat this disease. Understanding the genetic variants that confer resistance is crucial to this strategy. The gene Bsr-d1 encodes a C2H2-like transcription factor, and its recessive allele confers broad-spectrum resistance against infections by various strains of M. oryzae. In this study, we investigated the molecular evolution of the rice blast resistance gene bsr-d1 in a representative population consisting of 827 cultivated and wild rice varieties. Our results revealed that wild rice exhibited significantly higher nucleotide diversity, with polymorphic regions primarily concentrated in the promoter region, in contrast to indica and japonica rice varieties. The Bsr-d1 gene displayed significant differentiation between indica and japonica, with the bsr-d1 resistance allele being unique to indica. Haplotype network and phylogenetic analyses suggested that the bsr-d1 resistance allele most likely originated from Oryza nivara in the region adjacent to the Indian Peninsula and the Indochina Peninsula. Moreover, we explored the utilization of bsr-d1 resistance alleles in China and designed a pair of DNA primers based on the polymorphic sites for the detection of the bsr-d1 resistance gene. In summary, our study uncovering the origin and evolution of bsr-d1 will enhance our comprehension of resistance gene variation and expedite the resistance breeding process.

Comparative Analysis of Genetic Landscape of Carbapenem-Resistant Acinetobacter baumannii in India: A Computational Whole-Genome Study

Acinetobacter baumannii is a Gram-negative, aerobic bacterium responsible for multidrug-resistant nosocomial infections, especially in Intensive Care Units. This study investigated the genetic diversity, antimicrobial genes, virulence factors, and mobile genetic elements, resistance genes in clinically relevant strains of A. baumannii circulating in the Indian population, consistent with reports from other Asian countries, including China, Southeast Asia, and Thailand. A comprehensive analysis of carbapenem-resistant A. baumannii strains was conducted using publicly available genomic data. Pan-genome fanalysis revealed an open genome structure, indicating the pathogen's potential for ongoing genetic evolution. The study identified significant resistance genes, including blaOXA-23, AdeIJK and AdeFGH type efflux pumps, and carbapenemases. Virulence factors such as OmpA, phospholipase, and Csu pili were prevalent, contributing to the bacterium's pathogenicity. Mobile genetic elements, including Tn2006 and ISAba1/blaOXA-23 gene combinations, were also identified, highlighting the mechanisms behind the rapid spread of resistance genes. Subtractive proteomics was employed to identify core proteins essential to the bacterium but non-homologous to humans, highlighting them as potential drug targets. This analysis identified 2,165 core proteins, with 550 non-homologous essential proteins located in the cytoplasm. Further evaluation of these proteins based on stability and involvement in essential pathways, we identified 15 druggable proteins as potential targets for antimicrobial agents. The findings underscore the critical need for continuous surveillance, innovative drug development, and targeted therapeutic strategies to mitigate the impact of multidrug-resistant A. baumannii in healthcare settings. Addressing antimicrobial resistance in A. baumannii remains a global health priority, especially in high-burden regions like India, where the prevalence of resistant strains is notably high. This study provides a foundation for future research and development in combating this formidable pathogen.

The emergence of transposon-driven multidrug resistance in invasive nontypeable Haemophilus influenzae over the last decade

Nontypeable Haemophilus influenzae (NTHi), once considered a harmless commensal, has emerged as a significant concern due to the increased prevalence of multidrug-resistant (MDR) strains and their association with invasive infections. This study aimed to explore the epidemiology and molecular resistance mechanisms of 51 NTHi isolates collected from patients with invasive infections in northern Taiwan between 2011 and 2020. This investigation revealed substantial genetic diversity, encompassing 29 distinct sequence types and 18 clonal complexes. Notably, 68.6% of the isolates exhibited ampicillin resistance, with 28 categorised as MDR and four isolates were even resistant to up to six antibiotic classes. Among the MDR isolates, 18 pulsotypes were identified, indicating diverse genetic lineages. Elucidation of their resistance mechanisms revealed 18 β-lactamase-producing amoxicillin–clavulanate-resistant (BLPACR) isolates, 12 β-lactamase-producing ampicillin-resistant (BLPAR) isolates, and 5 β-lactamase-nonproducing ampicillin-resistant (BLNAR) isolates. PBP3 analysis revealed 22 unique substitutions in BLPACR and BLNAR, potentially contributing to cephem resistance. Notably, novel transposons, Tn7736-Tn7739, which contain critical resistance genes, were discovered. Three strains harboured Tn7739, containing seven resistance genes [aph(3′)-Ia, blaTEM-1, catA, sul2, strA, strB, and tet(B)], while four other strains carried Tn7736, Tn7737, and Tn7738, each containing three resistance genes [blaTEM-1, catA, and tet(B)]. The emergence of these novel transposons underscores the alarming threat posed by highly resistant NTHi strains. Our findings indicated that robust surveillance and comprehensive genomic studies are needed to address this growing public health challenge.

PQEB1: a hospital outbreak plasmid lineage carrying bla KPC-2.

While conducting genomic surveillance of carbapenemase-producing Enterobacteriaceae (CPE) from patient colonisation and clinical infections at Birmingham's Queen Elizabeth Hospital (QE), we identified an N-type plasmid lineage, pQEB1, carrying several antibiotic resistance genes, including the carbapenemase gene bla KPC-2. The pQEB1 lineage is concerning due to its conferral of multidrug resistance, its host range and apparent transmissibility, and its potential for acquiring further resistance genes. Representatives of pQEB1 were found in three sequence types (STs) of Citrobacter freundii, two STs of Enterobacter cloacae, and three species of Klebsiella. Hosts of pQEB1 were isolated from 11 different patients who stayed in various wards throughout the hospital complex over a 13 month period from January 2023 to February 2024. At present, the only representatives of the pQEB1 lineage in GenBank were carried by an Enterobacter hormaechei isolated from a blood sample at the QE in 2016 and a Klebsiella pneumoniae isolated from a urine sample at University Hospitals Coventry and Warwickshire (UHCW) in May 2023. The UHCW patient had been treated at the QE. Long-read whole-genome sequencing was performed on Oxford Nanopore R10.4.1 flow cells, facilitating comparison of complete plasmid sequences. We identified structural variants of pQEB1 and defined the molecular events responsible for them. These have included IS26-mediated inversions and acquisitions of multiple insertion sequences and transposons, including carriers of mercury or arsenic resistance genes. We found that a particular inversion variant of pQEB1 was strongly associated with the QE Liver speciality after appearing in November 2023, but was found in different specialities and wards in January/February 2024. That variant has so far been seen in five different bacterial hosts from six patients, consistent with recent and ongoing inter-host and inter-patient transmission of pQEB1 in this hospital setting.

Genomic and transcriptomic analyses of the elite rice variety Huizhan provide insight into disease resistance and heat tolerance

The indica rice variety Huizhan shows elite traits of disease resistance and heat tolerance. However, the underlying genetic basis of these traits is not fully understood due to limited genomic resources. Here, we used Nanopore long-read and next-generation sequencing technologies to generate a chromosome-scale genome assembly of Huizhan. Comparative genomics analysis uncovered a large chromosomal inversion and expanded gene families that are associated with plant growth, development and stress responses. Functional rice blast resistance genes, including Pi2, Pib and Ptr, and bacterial blight resistance gene Xa27, contribute to disease resistance of Huizhan. Furthermore, integrated genomics and transcriptomics analyses showed that OsHIRP1, OsbZIP60, the SOD gene family, and various transcription factors are involved in heat tolerance of Huizhan. The high-quality genome assembly and comparative genomics results presented in this study facilitate the use of Huizhan as an elite parental line in developing rice varieties adapted to disease pressure and climate challenges.

Distribution of tetracycline resistance genes within an organic fertilizer-amended soil–rice continuum

The transmission of antibiotic resistance genes (ARGs) to humans through the consumption of plants grown in manure-amended soils is a critical concern. However, the effect of manure application on the profiles of tetracycline resistance genes (TRGs) within the soil–rice continuum remains unclear. In this study, tetracycline (TC) content, bacterial communities, abundance of 8 TRGs, and class 1 integron (intI1) were characterized using high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS), Illumina sequencing, and quantitative PCR (qPCR) in rhizosphere soils, roots, and grains of rice exposed to pig manure (PM), rapeseed cake (RC), and chemical fertilizer (CF), respectively. Our findings indicate that the type of sample was the primary determinant of TRGs abundance variation within the soil-rice continuum, with a consistent decline from rhizosphere soils to roots to grains. Furthermore, fertilization type significantly influenced TRGs abundance, with the highest levels observed in PM treatment. TetZ and tetX were predominant, constituting over 90% of total TRGs abundance across all samples. In addition, the mechanism of TRGs profile formation varies with sample types. Bacterial communities-TC content-intI1 interactions determined the change in TRGs abundance in rhizosphere soils, and bacterial communities constituted the most important factor affecting TRGs abundance within the roots. However, bacterial communities and/or intI1 poorly explained the change in TRGs abundance within the grains. Our study attempts to explore the underlying mechanism for the profiles of TRGs in soil–rice continuums exposed to manure, as well as provides a theoretical basis for controlling the spread of endogenous antibiotic resistance within rice grown in soil receiving pig manure.