GXN23C125ES - Word Related Documents




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547300.8815Emergence of Linezolid Resistance Genes optrA and cfr(D) in an Enterococcus saccharolyticus from Chicken. Background: The emergence of linezolid resistance, mediated by genes such as optrA and cfr(D), poses a growing public health threat. While these genes have been detected in clinical and animal-derived Enterococcus species, their presence in underexplored species like Enterococcus saccharolyticus remains undocumented, leaving a significant gap in our understanding of their dissemination and stability. Method: E. saccharolyticus GXN23C125Es was screened for the presence of known linezolid resistance genes via PCR analysis. Conjugation and stability experiments were used to evaluate the transferability and stability of the resistance genes. The complete genome of GXN23C125Es was obtained using both the Illumina and Nanopore platforms. Results: We report the first identification of optrA and cfr(D) in GXN23C125Es from chicken feces in China. Whole-genome sequencing revealed multiple plasmid-borne resistance genes, including optrA, cfr(D), fexA, and erm(A). Stability testing demonstrated that optrA was highly stable, while cfr(D) was rapidly lost without selective pressure. Conclusions: These findings highlight E. saccharolyticus as a potential reservoir for linezolid resistance genes, underscoring the need for enhanced surveillance of resistance determinants in animal-associated bacteria. Understanding the dissemination dynamics of optrA and cfr(D) is crucial for mitigating their impact on public health and guiding antimicrobial resistance management strategies.202540298468
815710.8813Autologous DNA mobilization and multiplication expedite natural products discovery from bacteria. The transmission of antibiotic-resistance genes, comprising mobilization and relocation events, orchestrates the dissemination of antimicrobial resistance. Inspired by this evolutionarily successful paradigm, we developed ACTIMOT, a CRISPR-Cas9-based approach to unlock the vast chemical diversity concealed within bacterial genomes. ACTIMOT enables the efficient mobilization and relocation of large DNA fragments from the chromosome to replicative plasmids within the same bacterial cell. ACTIMOT circumvents the limitations of traditional molecular cloning methods involving handling and replicating large pieces of genomic DNA. Using ACTIMOT, we mobilized and activated four cryptic biosynthetic gene clusters from Streptomyces, leading to the discovery of 39 compounds across four distinct classes. This work highlights the potential of ACTIMOT for accelerating the exploration of biosynthetic pathways and the discovery of natural products.202439666857
512120.8805Rapid Nanopore Whole-Genome Sequencing for Anthrax Emergency Preparedness. Human anthrax cases necessitate rapid response. We completed Bacillus anthracis nanopore whole-genome sequencing in our high-containment laboratory from a human anthrax isolate hours after receipt. The de novo assembled genome showed no evidence of known antimicrobial resistance genes or introduced plasmid(s). Same-day genomic characterization enhances public health emergency response.202031961318
81130.8798Genomic analysis of five antibiotic-resistant bacteria isolated from the environment. Our study presents the whole-genome sequences and annotation of five bacteria isolates, each demonstrating distinct antibiotic resistance. These isolates include Bacillus paranthracis RIT 841, Atlantibacter hermanii RIT 842, Pantoea leporis RIT 844, Enterococcus casseliflavus RIT 845, and Pseudomonas alkylphenolica RIT 846, underscoring the importance of understanding antimicrobial resistance.202439189722
518840.8789Zoonotic bacterial and parasitic intestinal pathogens in foxes, raccoons and other predators from eastern Germany. In this study, we investigated faecal specimens from legally hunted and road-killed red foxes, raccoons, raccoon dogs, badgers and martens in Germany for parasites and selected zoonotic bacteria. We found that Baylisascaris procyonis, a zoonotic parasite of raccoons, had spread to northeastern Germany, an area previously presumed to be free of this parasite. We detected various pathogenic bacterial species from the genera Listeria, Clostridium (including baratii), Yersinia and Salmonella, which were analysed using whole-genome sequencing. One isolate of Yersinia enterocolitica contained a virulence plasmid. The Salmonella Cholerasuis isolate encoded an aminoglycoside resistance gene and a parC point mutation, conferring resistance to ciprofloxacin. We also found tetracycline resistance genes in Paeniclostridium sordellii and Clostridium baratii. Phylogenetic analyses revealed that the isolates were polyclonal, indicating the absence of specific wildlife-adapted clones. Predators, which scavenge from various sources including human settlements, acquire and spread zoonotic pathogens. Therefore, their role should not be overlooked in the One Health context.202438747071
252150.8781Insights into antimicrobial resistance among long distance migratory East Canadian High Arctic light-bellied Brent geese (Branta bernicla hrota). BACKGROUND: Antimicrobial resistance (AMR) is the most significant threat to global public health and ascertaining the role wild birds play in the epidemiology of resistance is critically important. This study investigated the prevalence of AMR Gram-negative bacteria among long-distance migratory East Canadian High Arctic (ECHA) light-bellied Brent geese found wintering on the east coast of Ireland. FINDINGS: In this study a number of bacterial species were isolated from cloacal swabs taken from ECHA light-bellied Brent geese. Nucleotide sequence analysis identified five species of Gram-negative bacteria; the dominant isolated species were Pantoea spp. (n = 5) followed by Buttiauxella agrestis (n = 2). Antimicrobial susceptibility disk diffusion results identified four of the Pantoea spp. strains, and one of the Buttiauxella agrestis strains resistant to amoxicillin-clavulanic acid. CONCLUSION: To our knowledge this is the first record of AMR bacteria isolated from long distance migratory ECHA light-bellied Brent geese. This indicates that this species may act as reservoirs and potential disseminators of resistance genes into remote natural ecosystems across their migratory range. This population of geese frequently forage (and defecate) on public amenity areas during the winter months presenting a potential human health risk.201527651892
908260.8779GeneMates: an R package for detecting horizontal gene co-transfer between bacteria using gene-gene associations controlled for population structure. BACKGROUND: Horizontal gene transfer contributes to bacterial evolution through mobilising genes across various taxonomical boundaries. It is frequently mediated by mobile genetic elements (MGEs), which may capture, maintain, and rearrange mobile genes and co-mobilise them between bacteria, causing horizontal gene co-transfer (HGcoT). This physical linkage between mobile genes poses a great threat to public health as it facilitates dissemination and co-selection of clinically important genes amongst bacteria. Although rapid accumulation of bacterial whole-genome sequencing data since the 2000s enables study of HGcoT at the population level, results based on genetic co-occurrence counts and simple association tests are usually confounded by bacterial population structure when sampled bacteria belong to the same species, leading to spurious conclusions. RESULTS: We have developed a network approach to explore WGS data for evidence of intraspecies HGcoT and have implemented it in R package GeneMates ( github.com/wanyuac/GeneMates ). The package takes as input an allelic presence-absence matrix of interested genes and a matrix of core-genome single-nucleotide polymorphisms, performs association tests with linear mixed models controlled for population structure, produces a network of significantly associated alleles, and identifies clusters within the network as plausible co-transferred alleles. GeneMates users may choose to score consistency of allelic physical distances measured in genome assemblies using a novel approach we have developed and overlay scores to the network for further evidence of HGcoT. Validation studies of GeneMates on known acquired antimicrobial resistance genes in Escherichia coli and Salmonella Typhimurium show advantages of our network approach over simple association analysis: (1) distinguishing between allelic co-occurrence driven by HGcoT and that driven by clonal reproduction, (2) evaluating effects of population structure on allelic co-occurrence, and (3) direct links between allele clusters in the network and MGEs when physical distances are incorporated. CONCLUSION: GeneMates offers an effective approach to detection of intraspecies HGcoT using WGS data.202032972363
302470.8778Identification of ISVlu1-derived translocatable units containing optrA and/or fexA genes generated by homologous or illegitimate recombination in Lactococcus garvieae of porcine origin. The optrA gene encodes an ABC-F protein which confers cross-resistance to oxazolidinones and phenicols. Insertion sequence ISVlu1, a novel ISL3-family member, was recently reported to be involved in the transmission of optrA in Vagococcus lutrae. However, the role of ISVlu1 in mobilizing resistance genes has not yet fully explored. In this study, two complete and three truncated copies of ISVlu1 were found on plasmid pBN62-optrA from Lactococcus garvieae. Analysis of the genetic context showed that both optrA and the phenicols resistance gene fexA were flanked by the complete or truncated ISVlu1 copies. Moreover, three different-sized ISVlu1-based translocatable units (TUs) carrying optrA and/or fexA, were detected from pBN62-optrA. Sequence analysis revealed that the TU-optrA was generated by homologous recombination while TU-fexA and TU-optrA+fexA were the products of illegitimate recombinations. Importantly, conjugation assays confirmed that pBN62-optrA was able to successfully transfer into the recipient Enterococcus faecalis JH2-2. To our knowledge, this is the first report about an optrA-carrying plasmid in L. garvieae which could horizontally transfer into other species. More importantly, the ISVlu1-flanked genetic structures containing optrA and/or fexA were also observed in bacteria of different species, which underlines that ISVlu1 is highly active and plays a vital role in the transfer of some important resistance genes, such as optrA and fexA.202438479301
815580.8778Gut bacteria enable prostate cancer growth. Testosterone-synthetizing gut bacteria drive resistance to therapy.202134618567
996990.8778Molecular Characterization of pBOq-IncQ and pBOq-95LK Plasmids of Escherichia coli BOq 01, a New Isolated Strain from Poultry Farming, Involved in Antibiotic Resistance. The increase in antimicrobial resistance has raised questions about how to use these drugs safely, especially in veterinary medicine, animal nutrition, and agriculture. Escherichia coli is an important human and animal pathogen that frequently contains plasmids carrying antibiotic resistance genes. Extra chromosomal elements are required for various functions or conditions in microorganisms. Several phage-like plasmids have been identified, which are important in antibiotic resistance. In this work, the molecular characterization of the pBOq-IncQ (4.5 kb) and pBOq-95LK (95 kb) plasmids found in the E. coli strain BOq 01, a multidrug resistant bacteria isolated from a poultry farm, are considered. Plasmid pBOq-IncQ belongs to the incQ incompatibility plasmid family and is involved in sulfonamide resistance. Plasmid pBOq-95LK is a lytic phage-like plasmid that is involved in the lysis of the E. coli BOq 01 strain and carries a bleomycin resistance gene and a strain cured of this plasmid shows bleomycin sensitivity. Induction of the lytic cycle indicates that this phage-like plasmid is an active phage. This type of plasmid has been reported to acquire genes such as mcr-1, which codes for colistin resistance and bacterial persistence and is a significant public health threat. A genome comparison, a pangenomic and phylogenomic analysis with other phage-like plasmids reported in the literature were performed to understand better the evolution of this kind of plasmid in bacteria and its potential importance in antibiotic resistance.202235893567
8156100.8777Innovative Delivery System Combining CRISPR-Cas12f for Combatting Antimicrobial Resistance in Gram-Negative Bacteria. Antimicrobial resistance poses a significant global challenge, demanding innovative approaches, such as the CRISPR-Cas-mediated resistance plasmid or gene-curing system, to effectively combat this urgent crisis. To enable successful curing of antimicrobial genes or plasmids through CRISPR-Cas technology, the development of an efficient broad-host-range delivery system is paramount. In this study, we have successfully designed and constructed a novel functional gene delivery plasmid, pQ-mini, utilizing the backbone of a broad-host-range Inc.Q plasmid. Moreover, we have integrated the CRISPR-Cas12f system into the pQ-mini plasmid to enable gene-curing in broad-host of bacteria. Our findings demonstrate that pQ-mini facilitates the highly efficient transfer of genetic elements to diverse bacteria, particularly in various species in the order of Enterobacterales, exhibiting a broader host range and superior conjugation efficiency compared to the commonly used pMB1-like plasmid. Notably, pQ-mini effectively delivers the CRISPR-Cas12f system to antimicrobial-resistant strains, resulting in remarkable curing efficiencies for plasmid-borne mcr-1 or bla(KPC) genes that are comparable to those achieved by the previously reported pCasCure system. In conclusion, our study successfully establishes and optimizes pQ-mini as a broad-host-range functional gene delivery vector. Furthermore, in combination with the CRISPR-Cas system, pQ-mini demonstrates its potential for broad-host delivery, highlighting its promising role as a novel antimicrobial tool against the growing threat of antimicrobial resistance.202438863339
348110.8776Conjugative DNA transfer in Streptomyces by TraB: is one protein enough? Antibiotic-producing soil bacteria of the genus Streptomyces form a huge natural reservoir of antibiotic resistance genes for the dissemination within the soil community. Streptomyces plasmids encode a unique conjugative DNA transfer system clearly distinguished from classical conjugation involving a single-stranded DNA molecule and a type IV protein secretion system. Only a single plasmid-encoded protein, TraB, is sufficient to translocate a double-stranded DNA molecule into the recipient in Streptomyces matings. TraB is a hexameric pore-forming ATPase that resembles the chromosome segregator protein FtsK and translocates DNA by recognizing specific 8-bp repeats present in the plasmid clt locus. Mobilization of chromosomal genes does not require integration of the plasmid, because TraB also recognizes clt-like sequences distributed all over the chromosome.201223082971
5120120.8775ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads. Antimicrobial resistance (AMR) is one of the major threats to human and animal health worldwide, yet few high-throughput tools exist to analyse and predict the resistance of a bacterial isolate from sequencing data. Here we present a new tool, ARIBA, that identifies AMR-associated genes and single nucleotide polymorphisms directly from short reads, and generates detailed and customizable output. The accuracy and advantages of ARIBA over other tools are demonstrated on three datasets from Gram-positive and Gram-negative bacteria, with ARIBA outperforming existing methods.201729177089
2999130.8775Integrative and conjugative elements in streptococci can act as vectors for plasmids and translocatable units integrated via IS1216E. Mobile genetic elements (MGEs), such as integrative and conjugative elements (ICEs), plasmids and translocatable units (TUs), are important drivers for the spread of antibiotic resistance. Although ICEs have been reported to support the spread of plasmids among different bacteria, their role in mobilizing resistance plasmids and TUs has not yet been fully explored. In this study, a novel TU bearing optrA, a novel non-conjugative plasmid p5303-cfrD carrying cfr(D) and a new member of the ICESa2603 family, ICESg5301 were identified in streptococci. Polymerase chain reaction (PCR) assays revealed that three different types of cointegrates can be formed by IS1216E-mediated cointegration between the three different MGEs, including ICESg5301::p5303-cfrD::TU, ICESg5301::p5303-cfrD, and ICESg5301::TU. Conjugation assays showed that ICEs carrying p5303-cfrD and/or TU successfully transferred into recipient strains, thereby confirming that ICEs can serve as vectors for other non-conjugative MGEs, such as TUs and p5303-cfrD. As neither the TU nor plasmid p5303-cfrD can spread on their own between different bacteria, their integration into an ICE via IS1216E-mediated cointegrate formation not only increases the plasticity of ICEs, but also furthers the dissemination of plasmids and TUs carrying oxazolidinone resistance genes.202336933870
9074140.8770BacAnt: A Combination Annotation Server for Bacterial DNA Sequences to Identify Antibiotic Resistance Genes, Integrons, and Transposable Elements. Whole genome sequencing (WGS) of bacteria has become a routine method in diagnostic laboratories. One of the clinically most useful advantages of WGS is the ability to predict antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) in bacterial sequences. This allows comprehensive investigations of such genetic features but can also be used for epidemiological studies. A plethora of software programs have been developed for the detailed annotation of bacterial DNA sequences, such as rapid annotation using subsystem technology (RAST), Resfinder, ISfinder, INTEGRALL and The Transposon Registry. Unfortunately, to this day, a reliable annotation tool of the combination of ARGs and MGEs is not available, and the generation of genbank files requires much manual input. Here, we present a new webserver which allows the annotation of ARGs, integrons and transposable elements at the same time. The pipeline generates genbank files automatically, which are compatible with Easyfig for comparative genomic analysis. Our BacAnt code and standalone software package are available at https://github.com/xthua/bacant with an accompanying web application at http://bacant.net.202134367079
9075150.8770CamPype: an open-source workflow for automated bacterial whole-genome sequencing analysis focused on Campylobacter. BACKGROUND: The rapid expansion of Whole-Genome Sequencing has revolutionized the fields of clinical and food microbiology. However, its implementation as a routine laboratory technique remains challenging due to the growth of data at a faster rate than can be effectively analyzed and critical gaps in bioinformatics knowledge. RESULTS: To address both issues, CamPype was developed as a new bioinformatics workflow for the genomics analysis of sequencing data of bacteria, especially Campylobacter, which is the main cause of gastroenteritis worldwide making a negative impact on the economy of the public health systems. CamPype allows fully customization of stages to run and tools to use, including read quality control filtering, read contamination, reads extension and assembly, bacterial typing, genome annotation, searching for antibiotic resistance genes, virulence genes and plasmids, pangenome construction and identification of nucleotide variants. All results are processed and resumed in an interactive HTML report for best data visualization and interpretation. CONCLUSIONS: The minimal user intervention of CamPype makes of this workflow an attractive resource for microbiology laboratories with no expertise in bioinformatics as a first line method for bacterial typing and epidemiological analyses, that would help to reduce the costs of disease outbreaks, or for comparative genomic analyses. CamPype is publicly available at https://github.com/JoseBarbero/CamPype .202337474912
1492160.8769Characterization of the tet(M)-bearing transposon Tn7125 of Escherichia coli strain A13 isolated from an intensive pig farm located in Henan province, China. BACKGROUND: Transposons carrying tet(M) in Gram-positive bacteria have been reported extensively, while there is a paucity of data on the transmission characteristics of tet(M) in Gram-negative bacteria. Therefore, the aim of this study was to investigate the genetic characteristics of the tet(M)-bearing transposon Tn7125, and to clarify the transmission mechanism of the plasmids pTA13-1 and pTA13-3 in Escherichia coli strain A13. METHODS: Plasmids from strain A13 and a corresponding transconjugant were determined by whole genome sequencing and analyzed using bioinformatics tools. The plasmids pTA13-1 and pTA13-3 of the transconjugant TA13 were characterized by S1-pulse-field gel electrophoresis, Southern hybridization, stability experiments, and direct competition assays. RESULTS: The conjugated IncF2:A6:B20 plasmid pTA13-1 co-transferred with the 41-kb plasmid pTA13-3, which carried no resistance genes; plasmid pTA13-2, which harbored the replication initiator PO111; and the IncX4 plasmid pTA13-4, which harbored the antibiotic resistance gene mcr-1. The novel IS26-bracked composite transposon Tn7125 was located on plasmid pTA13-1, which mainly consists of three resistance modules: IS26-ctp-lp-tet(M)-hp-IS406tnp, qac-aadA1-cmlA1-aadA2-DUF1010-dfrA12, and ∆ISVSa3-VirD-floR-LysR-ISVSa3. The plasmid pTA13-1 was highly stable in E. coli strain J53 with no fitness cost to the host or disadvantage in growth competition. CONCLUSION: Evolution of co-integrated transposons, such as Tn7125, may convey antibiotic resistance to a wide spectrum of hosts via the plasmids pTA13-1 and pTA13-3, which acts as an adaptable and mobile multidrug resistance reservoir to accelerate dissemination of other genes by co-selection, thereby posing a potentially serious barrier to clinical treatment regimens.202540639501
8672170.8768Pangenomic and functional investigations for dormancy and biodegradation features of an organic pollutant-degrading bacterium Rhodococcus biphenylivorans TG9. Environmental bacteria contain a wealth of untapped potential in the form of biodegradative genes. Leveraging this potential can often be confounded by a lack of understanding of fundamental survival strategies, like dormancy, for environmental stress. Investigating bacterial dormancy-to-degradation relationships enables improvement of bioremediation. Here, we couple genomic and functional assessment to provide context for key attributes of the organic pollutant-degrading strain Rhodococcus biphenylivorans TG9. Whole genome sequencing, pangenome analysis and functional characterization were performed to elucidate important genes and gene products, including antimicrobial resistance, dormancy, and degradation. Rhodococcus as a genus has strong potential for degradation and dormancy, which we demonstrate using R. biphenylivorans TG9 as a model. We identified four Resuscitation-promoting factor (Rpf) encoding genes in TG9 involved in dormancy and resuscitation. We demonstrate that R. biphenylivorans TG9 grows on fourteen typical organic pollutants, and exhibits a robust ability to degrade biphenyl and several congeners of polychlorinated biphenyls. We further induced TG9 into a dormant state and demonstrated pronounced differences in morphology and activity. Together, these results expand our understanding of the genus Rhodococcus and the relationship between dormancy and biodegradation in the presence of environmental stressors.202234688761
9550180.8767Stereoselective Bacterial Metabolism of Antibiotics in Environmental Bacteria - A Novel Biochemical Workflow. Although molecular genetic approaches have greatly increased our understanding of the evolution and spread of antibiotic resistance genes, there are fewer studies on the dynamics of antibiotic - bacterial (A-B) interactions, especially with respect to stereochemistry. Addressing this knowledge gap requires an interdisciplinary synthesis, and the development of sensitive and selective analytical tools. Here we describe SAM (stereoselective antimicrobial metabolism) workflow, a novel interdisciplinary approach for assessing bacterial resistance mechanisms in the context of A-B interactions that utilise a combination of whole genome sequencing and mass spectrometry. Chloramphenicol was used to provide proof-of-concept to demonstrate the importance of stereoselective metabolism by resistant environmental bacteria. Our data shows that chloramphenicol can be stereoselectively transformed via microbial metabolism with R,R-(-)-CAP being subject to extensive metabolic transformation by an environmental bacterial strain. In contrast S,S-(+)-CAP is not metabolised by this bacterial strain, possibly due to the lack of previous exposure to this isomer in the absence of historical selective pressure to evolve metabolic capacity.202133935981
9985190.8766Identification of the First Gene Transfer Agent (GTA) Small Terminase in Rhodobacter capsulatus and Its Role in GTA Production and Packaging of DNA. Genetic exchange mediated by viruses of bacteria (bacteriophages) is the primary driver of rapid bacterial evolution. The priority of viruses is usually to propagate themselves. Most bacteriophages use the small terminase protein to identify their own genome and direct its inclusion into phage capsids. Gene transfer agents (GTAs) are descended from bacteriophages, but they instead package fragments of the entire bacterial genome without preference for their own genes. GTAs do not selectively target specific DNA, and no GTA small terminases are known. Here, we identified the small terminase from the model Rhodobacter capsulatus GTA, which then allowed prediction of analogues in other species. We examined the role of the small terminase in GTA production and propose a structural basis for random DNA packaging.IMPORTANCE Random transfer of any and all genes between bacteria could be influential in the spread of virulence or antimicrobial resistance genes. Discovery of the true prevalence of GTAs in sequenced genomes is hampered by their apparent similarity to bacteriophages. Our data allowed the prediction of small terminases in diverse GTA producer species, and defining the characteristics of a "GTA-type" terminase could be an important step toward novel GTA identification. Importantly, the GTA small terminase shares many features with its phage counterpart. We propose that the GTA terminase complex could become a streamlined model system to answer fundamental questions about double-stranded DNA (dsDNA) packaging by viruses that have not been forthcoming to date.201931534034