Draft genome sequence of Bacillus safensis 2T-2, isolated from drinking water. - Related Documents




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521501.0000Draft genome sequence of Bacillus safensis 2T-2, isolated from drinking water. Bacillus safensis 2T-2 was isolated from potable water at a municipal water treatment facility in the North West province of South Africa, representing the first report of this species in treated drinking water systems. Whole genome sequencing revealed a 3.78 Mb genome with 41.3 % GC content and 4000 coding sequences distributed across 126 contigs. Genome analysis identified six antibiotic resistance genes, including vancomycin resistance genes (vanT, vanY), fosfomycin resistance (fosBx1), chloramphenicol resistance (cat86), and two disinfectant resistance genes (qacG, qacJ). Despite the presence of resistance genes, PathogenFinder analysis confirmed low pathogenic potential (0.168 probability). The strain demonstrated significant biosynthetic capabilities with 12 secondary metabolite gene clusters, including antimicrobial compound production (plantazolicin), biosurfactants (lichenysin), siderophores (bacillibactin, schizokinen), and the lipopeptide fengycin. Five bacteriocin gene clusters were identified, containing three core peptide genes (UviB, plantazolicin, pumilarin) with associated modification and transport genes. Phylogenetic analysis positioned strain 2T-2 closest to B. safensis F0-36b, confirming species identification. These findings highlight the dual nature of environmental bacteria in water systems, possessing both concerning antibiotic resistance traits and beneficial biotechnological potential, emphasizing the need for enhanced water treatment strategies while revealing opportunities for bioactive compound discovery.202540727027
178910.9989Genomic and phylogenetic analysis of a multidrug-resistant Burkholderia contaminans strain isolated from a patient with ocular infection. OBJECTIVES: The genus Burkholderia comprises rod-shaped, non-spore-forming, obligately aerobic Gram-negative bacteria that is found across diverse ecological niches. Burkholderia contaminans, an emerging pathogen associated with cystic fibrosis, is frequently isolated from contaminated medical devices in hospital settings. The aim of this study was to understand the genomic characteristics, antimicrobial resistance profile and virulence determinants of B. contaminans strain SBC01 isolated from the eye of a patient hit by a cow's tail. METHODS: A hybrid sequence of isolate SBC01 was generated using Illumina HiSeq and Oxford Nanopore Technology platforms. Unicycler was used to assemble the hybrid genomic sequence. The draft genome was annotated using the NCBI Prokaryotic Genome Annotation Pipeline. Antimicrobial susceptibility testing was performed by VITEK®2. Antimicrobial resistance and virulence genes were identified using validated bioinformatics tools. RESULTS: The assembled genome size is 8 841 722 bp with a G+C content of 66.33% distributed in 19 contigs. Strain SBC01 was found to possess several antimicrobial resistance and efflux pump genes. The isolate was susceptible to tetracyclines, meropenem and ceftazidime. Many genes encoding potential virulence factors were identified. CONCLUSION: Burkholderia contaminans SBC01 belonging to sequence type 482 (ST482) is a multidrug-resistant strain containing diverse antimicrobial resistance genes, revealing the risks associated with infections by new Burkholderia spp. The large G+C-rich genome has a myriad of virulence factors, highlighting its pathogenic potential. Thus, while providing insights into the antimicrobial resistance and virulence potential of this uncommon species, the present analysis will aid in understanding the evolution and speciation in the Burkholderia genus.202133965629
178820.9988Draft genome sequence of a multidrug-resistant Stenotrophomonas sp. B1-1 strain isolated from radiation-polluted soil and its pathogenic potential. OBJECTIVES: Stenotrophomonas is a genus of Gram-negative bacteria with several potential industrial uses as well as an increasingly relevant pathogen that may cause dangerous nosocomial infections. Here we present the draft genome sequence of a multidrug-resistant Stenotrophomonas sp. B1-1 isolated from radiation-polluted soil in Xinjiang Uyghur Autonomous Region, China. METHODS: The genome of Stenotrophomonas sp. B1-1 was sequenced using a BGISEQ-500 platform. The generated sequencing reads were de novo assembled using SOAPdenovo and the resulting sequences were predicted and annotated to identify antimicrobial resistance genes and virulence factors using the ARDB and VFDB databases, respectively. RESULTS: The Stenotrophomonas sp. B1-1 genome assembly resulted in a total genome size of 4,723,769 bp with a GC content of 67.47%. There were 4280 predicted genes with 68 tRNAs, 2 rRNAs and 163 sRNAs. A number of antimicrobial resistance genes were identified conferring resistance to various antibiotics as well as numerous virulence genes. CONCLUSION: The genome sequence of Stenotrophomonas sp. B1-1 will provide timely information for comparison of the Stenotrophomonas genus and to help further understand the pathogenesis and antimicrobial resistance of this genus.202133373734
613830.9987Draft genome of five Cupriavidus plantarum strains: agave, maize and sorghum plant-associated bacteria with resistance to metals. Five strains of Cupriavidus plantarum, a metal-resistant, plant-associated bacterium, were selected for genome sequencing through the Genomic Encyclopedia of Bacteria and Archaea (GEBA) Phase IV project at the Joint Genome Institute (JGI) of the U.S. Department of Energy (DOE). The genome of the strains was in the size range of 6.2-6.4 Mbp and encoded 5605-5834 proteins; 16.9-23.7% of these genes could not be assigned to a COG-associated functional category. The G + C content was 65.83-65.99%, and the genomes encoded 59-67 stable RNAs. The strains were resistant in vitro to arsenite, arsenate, cobalt, chromium, copper, nickel and zinc, and their genomes possessed the resistance genes for these metals. The genomes also encoded the biosynthesis of potential antimicrobial compounds, such as terpenes, phosphonates, bacteriocins, betalactones, nonribosomal peptides, phenazine and siderophores, as well as the biosynthesis of cellulose and enzymes such as chitinase and trehalase. The average nucleotide identity (ANI) and DNA-DNA in silico hybridization of the genomes confirmed that C. plantarum is a single species. Moreover, the strains cluster within a single group upon multilocus sequence analyses with eight genes and a phylogenomic analyses. Noteworthy, the ability of the species to tolerate high concentrations of different metals might prove useful for bioremediation of naturally contaminated environments.202032405446
515040.9987Cultivation and Genomic Characterization of the Bile Bacterial Species From Cholecystitis Patients. The microbes in human bile are closely related to gallbladder health and other potential disorders. Although the bile microbial community has been investigated by recent studies using amplicon or metagenomic sequencing technologies, the genomic information of the microbial species resident in bile is rarely reported. Herein, we isolated 138 bacterial colonies from the fresh bile specimens of four cholecystitis patients using a culturome approach and genomically characterized 35 non-redundant strains using whole-genome shotgun sequencing. The bile bacterial isolates spanned 3 classes, 6 orders, 10 families, and 14 genera, of which the members of Enterococcus, Escherichia-Shigella, Lysinibacillus, and Enterobacter frequently appeared. Genomic analysis identified three species, including Providencia sp. D135, Psychrobacter sp. D093, and Vibrio sp. D074, which are not represented in existing reference genome databases. Based on the genome data, the functional capacity between bile and gut isolates was compared. The bile strains encoded 5,488 KEGG orthologs, of which 4.9% were specific to the gut strains, including the enzymes involved in biofilm formation, two-component systems, and quorum-sensing pathways. A total of 472 antibiotic resistance genes (ARGs) were identified from the bile genomes including multidrug resistance proteins (42.6%), fluoroquinolone resistance proteins (12.3%), aminoglycoside resistance proteins (9.1%), and β-lactamase (7.2%). Moreover, in vitro experiments showed that some bile bacteria have the capabilities for bile salt deconjugation or biotransformation (of primary bile acids into secondary bile acids). Although the physiological or pathological significance of these bacteria needs further exploration, our works expanded knowledge about the genome, diversity, and function of human bile bacteria.202134790179
178450.9987Draft genome sequence of a multidrug-resistant emerging pathogenic isolate of Vibrio alginolyticus from the Red Sea. The marine ecosystem is a growing reservoir of antimicrobial-resistant bacteria, and thus an emerging risk to human health. In this study, we report the first draft genome sequence of multidrug-resistant Vibrio alginolyticus strain OS1T-47, isolated from an offshore site in the Red Sea. The draft genome of V. alginolyticus OS1T-47 is 5 157 150 bp in length and has DNA G + C content of 44.83%. Strain OS1T-47 possesses 22 antimicrobial resistance genes, including those associated with multidrug-resistant efflux pumps.202033294196
178660.9987Correlation analysis of whole genome sequencing of a pathogenic Escherichia coli strain of Inner Mongolian origin. Anal swabs of 1-month-old Holstein calves with diarrhea were collected from an intensive cattle farm, and a highly pathogenic Escherichia coli strain was obtained by isolation and purification. To study the virulence and resistance genes of pathogenic E. coli that cause diarrhea in calves, a strain of E. coli E12 isolated from calf diarrhea samples was used as experimental material in this experiment, and the virulence of the E12 strain were identified by the mouse infection test, and the whole genome map of the E12 strain were obtained by whole-genome sequencing and analyzed for genome characterization. The results showed that the lethality of strain E12 was 100%, the total length of E12-encoded genes was 4,294,530 bp, Cluster of Orthologous Groups of proteins (COG) annotated to 4,194 functional genes, and the virulence genes of sequenced strain E12 were compared with the virulence genes of sequenced strain E12 from the Virulence Factors of Pathogenic Bacteria (VFDB), which contained a total of 366 virulence genes in sequenced strain E12. The analysis of virulence genes of E12 revealed a total of 52 virulence genes in the iron transferrin system, 56 virulence genes in the secretory system, 41 virulence genes in bacterial toxins, and a total of 217 virulence genes in the Adhesin and Invasins group. The antibiotic resistance genes of sequenced strain E12 were identified through the Antibiotic Resistance Genes Database (ARDB) and Comprehensive Antibiotic Research Database, and it was found that its chromosome and plasmid included a total of 127 antibiotic resistance genes in four classes, and that E12 carried 71 genes related to the antibiotic efflux pumps, 36 genes related to antibiotic inactivation, and 14 antibiotic target alteration and reduced penetration into antibiotics, and 6 antibiotic resistance genes, and the resistance phenotypes were consistent with the genotypes. The pathogenic E. coli that causes diarrhea in calves on this ranch contains a large number of virulence and resistance genes. The results provide a theoretical basis for the prevention and treatment of diarrhea and other diseases caused by E. coli disease.202438969720
546870.9986Whole-genome sequence of a putative pathogenic Bacillus sp. strain SD-4 isolated from cattle feed. OBJECTIVES: The present study describes the draft genome sequence of a novel Bacillus sp. strain SD-4 isolated from animal feed. The study aims to get a deeper insight into antimicrobial resistance and secondary metabolite biosynthetic gene clusters (BGCs) and the association between them. METHODS: The strain SD-4 was preliminarily evaluated for antibacterial activities, motility, biofilm formation, and enterotoxin production using in vitro assays. The genome of strain SD-4 was sequenced using the Illumina HiSeq 2500 platform with paired-end reads. The reads were assembled and annotated using SPAdes and PGAP, respectively. The genome was further analysed using several bioinformatics tools, including TYGS, AntiSMASH, RAST, PlasmidFinder, VFDB, VirulenceFinder, CARD, PathogenFinder, MobileElement finder, IslandViewer, and CRISPRFinder. RESULTS: In vitro assays showed that the strain is motile, synthesises biofilm, and produces an enterotoxin and antibacterial metabolites. The genome analysis revealed that the strain SD-4 carries antimicrobial resistance genes (ARGs), virulence factors, and beneficial secondary metabolite BGCs. Further genome analysis showed interesting genome architectures containing several mobile genetic elements, including two plasmid replicons (repUS22 and rep20), five prophages, and at least four genomic islands (GIs), including one Listeria pathogenicity island LIPI-1. Moreover, the strain SD-4 is identified as a putative human pathogen. CONCLUSION: The genome of strain SD-4 harbours several BGCs coding for biologically active metabolites. It also contains antimicrobial resistance genes and is identified as a potential human pathogen. These results can be used to better comprehend antibiotic resistance in environmental bacteria that are not influenced by human intervention.202235413450
546680.9986The Trade-Off Between Sanitizer Resistance and Virulence Genes: Genomic Insights into E. coli Adaptation. BACKGROUND: Escherichia coli is one of the most studied bacteria worldwide due to its genetic plasticity. Recently, in addition to characterizing its pathogenic potential, research has focused on understanding its resistance profile to inhibitory agents, whether these be antibiotics or sanitizers. OBJECTIVES: The present study aimed to investigate six of the main serogroups of foodborne infection (O26, O45, O103, O111, O121, and O157) and to understand the dynamics of heterogeneity in resistance to sanitizers derived from quaternary ammonium compounds (QACs) and peracetic acid (PAA) using whole-genome sequencing (WGS). METHODS: Twenty-four E. coli strains with varied resistance profiles to QACs and PAA were analyzed by WGS using NovaSeq6000 (150 bp Paired End reads). Bioinformatic analyses included genome assembly (Shovill), annotation via Prokka, antimicrobial resistance gene identification using Abricate, and core-genome analysis using Roary. A multifactorial multiple correspondence analysis (MCA) was conducted to explore gene-sanitizer relationships. In addition, a large-scale analysis utilizing the NCBI Pathogen Detection database involved a 2 × 2 chi-square test to examine associations between the presence of qac and stx genes. RESULTS: The isolates exhibited varying antimicrobial resistance profiles, with O45 and O157 being the most resistant serogroups. In addition, the qac gene was identified in only one strain (S22), while four other strains carried the stx gene. Through multifactorial multiple correspondence analysis, the results obtained indicated that strains harboring genes encoding Shiga toxin (stx) presented profiles that were more likely to be sensitive to QACs. To further confirm these results, we analyzed 393,216 E. coli genomes from the NCBI Pathogen Detection database. Our results revealed a significant association (p < 0.001) between the presence of qac genes and the absence of stx1, stx2, or both toxin genes. CONCLUSION: Our findings highlight the complexity of bacterial resistance mechanisms and suggest that non-pathogenic strains may exhibit greater tolerance to QAC sanitizer than those carrying pathogenicity genes, particularly Shiga toxin genes.202540149102
496190.9986Draft genome of Serratia sp. R1 gives an insight into the antibiotic resistant genes against multiple antibiotics. BACKGROUND: Serratia is a pathogenic bacterium, commonly associated with neonatal intensive care units, and harbors antibiotic-resistant genes against multiple antibiotics e.g., resistance against penams, aminoglycosides, tetracyclines, cephalosporins, and macrolides. In the long-term contaminated habitat, the bacterial communities carry both antibiotic and metal resistance genes. This draft genome sequencing aimed to explore the alarming level of ARGs in the environment, additionally heavy metal-resistant genes were also explored in the draft genome. METHODS: Whole-genome sequencing was used to investigate ARGs in Serratia sp. R1. The bacteria were sequenced using Illumina Nova seq sequencer and subjected to genome annotation. The bacterial genome was explored for antibiotic- and metal-resistant genes. RESULTS: Sequencing resulted in 8.4 Mb genome and a total of 4411 functional genes were characterized in the draft genome. Genes resistant to Beta-lactams, cephalosporins, macrolides, fluoroquinolones, and tetracycline are present in the draft genome. Multiple metal-resistant genes are also present in the sequenced genome. CONCLUSION: The genes and proteins providing heavy metal and antibiotic resistance may be used in the bioremediation of environmental antibiotic residues to prevent the spread of antibiotic resistance. The current study can help us to adopt suitable mitigation measures against the multidrug-resistant Serratia.202235237932
5469100.9986Whole genome sequencing of nine Vibrio parahaemolyticus strains encoding (Pir) toxin-like genes from shrimp cultures in northern Peru using Oxford Nanopore technology. Nine Peruvian isolates of Vibrio parahaemolyticus were characterized through sequencing, revealing the presence of simple sequence repeat, Pir toxin-like genes, and genes associated with antibiotic resistance, toxic components, and transposable elements. These findings expand our understanding of the genetic diversity, disease resistance, and virulence in cultivated shrimp populations in Peru.202438345394
5148110.9986Unveiling the whole genomic features and potential probiotic characteristics of novel Lactiplantibacillus plantarum HMX2. This study investigates the genomic features and probiotic potential of Lactiplantibacillus plantarum HMX2, isolated from Chinese Sauerkraut, using whole-genome sequencing (WGS) and bioinformatics for the first time. This study also aims to find genetic diversity, antibiotic resistance genes, and functional capabilities to help us better understand its food safety applications and potential as a probiotic. L. plantarum HMX2 was cultured, and DNA was extracted for WGS. Genomic analysis comprised average nucleotide identity (ANI) prediction, genome annotation, pangenome, and synteny analysis. Bioinformatics techniques were used to identify CoDing Sequences (CDSs), transfer RNA (tRNA) and ribosomal RNA (rRNA) genes, and antibiotic resistance genes, as well as to conduct phylogenetic analysis to establish genetic diversity and evolution. The study found a significant genetic similarity (99.17% ANI) between L. plantarum HMX2 and the reference strain. Genome annotation revealed 3,242 coding sequences, 65 tRNA genes, and 16 rRNA genes. Significant genetic variety was found, including 25 antibiotic resistance genes. A phylogenetic study placed L. plantarum HMX2 among closely related bacteria, emphasizing its potential for probiotic and food safety applications. The genomic investigation of L. plantarum showed essential genes, including plnJK and plnEF, which contribute to antibacterial action against foodborne pathogens. Furthermore, genes such as MurA, Alr, and MprF improve food safety and probiotic potential by promoting bacterial survival under stress conditions in food and the gastrointestinal tract. This study introduces the new genomic features of L. plantarum HMX2 about specific genetics and its possibility of relevant uses in food security and technologies. These findings of specific genes involved in antimicrobial activity provide fresh possibilities for exploiting this strain in forming probiotic preparations and food preservation methods. The future research should focus on the experimental validation of antibiotic resistance genes, comparative genomics to investigate functional diversity, and the development of novel antimicrobial therapies that take advantage of L. plantarum's capabilities.202439611087
4684120.9986Genomic characterization and assessment of the virulence and antibiotic resistance of the novel species Paenibacillus sp. strain VT-400, a potentially pathogenic bacterium in the oral cavity of patients with hematological malignancies. BACKGROUND: Paenibacillus sp. strain VT-400, a novel spore-forming bacterium, was isolated from patients with hematological malignancies. METHODS: Paenibacillus sp. strain VT-400 was isolated from the saliva of four children with acute lymphoblastic leukemia. The genome was annotated using RAST and the NCBI Prokaryotic Genome Annotation Pipeline to characterize features of antibiotic resistance and virulence factors. Susceptibility to antibiotics was determined by the Kirby-Bauer disc diffusion method. We used a mouse model of pneumonia to study virulence in vivo. Mice were challenged with 7.5 log10-9.5 log10 CFU, and survival was monitored over 7 days. Bacterial load was measured in the lungs and spleen of surviving mice 48 h post-infection to reveal bacterial invasion and dissemination. RESULTS: Whole-genome sequencing revealed a large number of virulence factors such as hemolysin D and CD4+ T cell-stimulating antigen. Furthermore, the strain harbors numerous antibiotic resistance genes, including small multidrug resistance proteins, which have never been previously found in the Paenibacillus genus. We then compared the presence of antibiotic resistance genes against results from antibiotic susceptibility testing. Paenibacillus sp. strain VT-400 was found to be resistant to macrolides such as erythromycin and azithromycin, as well as to chloramphenicol and trimethoprim-sulphamethoxazole. Finally, the isolate caused mortality in mice infected with ≥8.5 log10 CFU. CONCLUSIONS: Based on our results and on the available literature, there is yet no strong evidence that shows Paenibacillus species as an opportunistic pathogen in immunocompromised patients. However, the presence of spore-forming bacteria with virulence and antibiotic resistance genes in such patients warrants special attention because infections caused by spore-forming bacteria are poorly treatable.201626900405
3614130.9986Structure and diversity of arsenic resistant bacteria in an old tin mine area of Thailand. The microbial community structure in Thailand soils contaminated with low and high levels of arsenic was determined by denaturing gradient gel electrophoresis (DGGE). Band pattern analysis indicated that the bacterial community was not significantly different in the two soils. Phylogenetic analysis obtained by excising and sequencing six bands indicated that the soils were dominated by Arthobacter koreensis and proteobacteria. Two hundred and sixty-two bacterial isolates were obtained from arsenic contaminated soils. The majority of the As resistant isolates were gram-negative bacteria. MIC studies indicated that all of the tested bacteria had greater resistance to arsenate than arsenite. Some strains were capable of growing in medium containing up to 1,500 mg/l arsenite and arsenate. Correlations analysis of resistance patterns of arsenite resistance indicated that the isolated bacteria could be categorized into 13 groups, with a maximum similarity value of 100%. All strains were also evaluated for resistance to eight antibiotics. The antibiotic resistance patterns divided the strains into 100 unique groups, indicating that the strains were very diverse. Isolates from each antibiotic resistance group were characterized in more detail by using the repetitive extragenic palindromic-PCR (rep-PCR) DNA fingerprinting technique with ERIC primers. PCR products were analyzed by agarose gel electrophoresis. The genetic relatedness of 100 bacterial fingerprints, determined by using Pearson product moment similarity coefficient, showed that the isolates could be divided into four clusters, with similarity values ranging from 5-99%. While many isolates were genetically diverse, others were clonal in nature Additionally, the arsenic-resistant isolates were examined for the presence of arsenic resistance (ars) genes by using PCR, and 30% of the isolates were found to carry an arsenate reductase encoded by the arsC gene.201020134249
1761140.9986Whole Genome Sequence Analysis of Burkholderia contaminans FFH2055 Strain Reveals the Presence of Putative β-Lactamases. Burkholderia contaminans is a member of the Burkholderia cepacia complex (Bcc), a pathogen with increasing prevalence among cystic fibrosis (CF) patients and the cause of numerous outbreaks due to the use of contaminated commercial products. The antibiotic resistance determinants, particularly β-lactamases, have been poorly studied in this species. In this work, we explored the whole genome sequence (WGS) of a B. contaminans isolate (FFH 2055) and detected four putative β-lactamase-encoding genes. In general, these genes have more than 93% identity with β-lactamase genes found in other Bcc species. Two β-lactamases, a class A (Pen-like, suggested name PenO) and a class D (OXA-like), were further analyzed and characterized. Amino acid sequence comparison showed that Pen-like has 82% and 67% identity with B. multivorans PenA and B. pseudomallei PenI, respectively, while OXA-like displayed strong homology with class D enzymes within the Bcc, but only 22-44% identity with available structures from the OXA family. PCR reactions designed to study the presence of these two genes revealed a heterogeneous distribution among clinical and industrial B. contaminans isolates. Lastly, bla(PenO) gene was cloned and expressed into E. coli to investigate the antibiotic resistance profile and confers an extended-spectrum β-lactamase (ESBL) phenotype. These results provide insight into the presence of β-lactamases in B. contaminans, suggesting they play a role in antibiotic resistance of these bacteria.201930783798
5936150.9986Antibiotic Resistance Characterization and Molecular Characteristics of Enterococcus Species Isolated from Combination Probiotic Preparations in China. Enterococci can act as reservoirs for antibiotic-resistant genes that are potentially at risk of being transferred to other bacteria that inhabit in the gastrointestinal tract. The aim of this study was to determine the phenotypic and molecular characteristics of antibiotic-resistant enterococci isolated from probiotic preparations. In total, we isolated 15 suspected Enterococcus species from 5 compound probiotics, which were identified by 16S rDNA as 12 Enterococcus faecium and 3 Enterococcus faecalis. Determination of antimicrobial susceptibility by the microdilution broth method showed widespread resistance to sulfamethoxazole (100%), norfloxacin (99.3%), azithromycin (99.3%), gentamicin (86.7%), and chloramphenicol (20%). Whole genome sequencing of five resistant strains revealed that all had circular DNA chromosomes and that E. faecium J-1-A to J-4-A contained a plasmid, while E. faecalis J-5-A did not. The results of the resistance gene analysis revealed that each strain contained approximately 30 resistance genes, with the antibiotic resistance genes and the multidrug resistance efflux pump genes mdtG, lmrC, and lmrD detected in all strains. The chloramphenicol resistance genes ykkC and ykkD were first identified in E. faecalis. And there were 21, 19, 21, 21, and 29 virulence factors involved in strains, respectively. Further analysis of the gene islands (GIs) revealed that each strain contained more than 10 GIs. The above results confirm the existence of hidden dangers in the safety of probiotics and remind us to carefully select probiotic preparations containing enterococcal strains to avoid the potential spread of resistance and pathogenicity.202437824752
5621160.9986Comparative Genomics of DH5α-Inhibiting Escherichia coli Isolates from Feces of Healthy Individuals Reveals Common Co-Occurrence of Bacteriocin Genes with Virulence Factors and Antibiotic Resistance Genes. Background/Objectives: The presence of multi-drug-resistant (MDR) bacteria in healthy individuals poses a significant public health concern, as these strains may contribute to or even facilitate the dissemination of antibiotic resistance genes (ARGs) and virulence factors. In this study, we investigated the genomic features of antimicrobial-producing Escherichia coli strains from the gut microbiota of healthy individuals in Singapore. Methods: Using a large-scale screening approach, we analyzed 3107 E. coli isolates from 109 fecal samples for inhibitory activity against E. coli DH5α and performed whole-genome sequencing on 37 representative isolates. Results: Our findings reveal genetically diverse strains, with isolates belonging to five phylogroups (A, B1, B2, D, and F) and 23 unique sequence types (STs). Bacteriocin gene clusters were widespread (92% of isolates carried one or more bacteriocin gene clusters), with colicins and microcins dominating the profiles. Notably, we identified an hcp-et3-4 gene cluster encoding an effector linked to a Type VI secretion system. Approximately 40% of the sequenced isolates were MDR, with resistance for up to eight antibiotic classes in one strain (strain D96). Plasmids were the primary vehicles for ARG dissemination, but chromosomal resistance determinants were also detected. Additionally, over 55% of isolates were classified as potential extraintestinal pathogenic E. coli (ExPEC), raising concerns about their potential pathogenicity outside the intestinal tract. Conclusions: Our study highlights the co-occurrence of bacteriocin genes, ARGs, and virulence genes in gut-residing E. coli, underscoring their potential role in shaping microbial dynamics and antibiotic resistance. While bacteriocin-producing strains show potential as probiotic alternatives, careful assessment of their safety and genetic stability is necessary for therapeutic applications.202541009839
3122170.9986Hybrid sequence-based analysis reveals the distribution of bacterial species and genes in the oral microbiome at a high resolution. Bacteria in the oral microbiome are poorly identified owing to the lack of established culture methods for them. Thus, this study aimed to use culture-free analysis techniques, including bacterial single-cell genome sequencing, to identify bacterial species and investigate gene distribution in saliva. Saliva samples from the same individual were classified as inactivated or viable and then analyzed using 16S rRNA sequencing, metagenomic shotgun sequencing, and bacterial single-cell sequencing. The results of 16S rRNA sequencing revealed similar microbiota structures in both samples, with Streptococcus being the predominant genus. Metagenomic shotgun sequencing showed that approximately 80 % of the DNA in the samples was of non-bacterial origin, whereas single-cell sequencing showed an average contamination rate of 10.4 % per genome. Single-cell sequencing also yielded genome sequences for 43 out of 48 wells for the inactivated samples and 45 out of 48 wells for the viable samples. With respect to resistance genes, four out of 88 isolates carried cfxA, which encodes a β-lactamase, and four isolates carried erythromycin resistance genes. Tetracycline resistance genes were found in nine bacteria. Metagenomic shotgun sequencing provided complete sequences of cfxA, ermF, and ermX, whereas other resistance genes, such as tetQ and tetM, were detected as fragments. In addition, virulence factors from Streptococcus pneumoniae were the most common, with 13 genes detected. Our average nucleotide identity analysis also suggested five single-cell-isolated bacteria as potential novel species. These data would contribute to expanding the oral microbiome data resource.202438708423
5151180.9985Comparative Genome Analysis of Bacillus amyloliquefaciens Focusing on Phylogenomics, Functional Traits, and Prevalence of Antimicrobial and Virulence Genes. Bacillus amyloliquefaciens is a gram-positive, nonpathogenic, endospore-forming, member of a group of free-living soil bacteria with a variety of traits including plant growth promotion, production of antifungal and antibacterial metabolites, and production of industrially important enzymes. We have attempted to reconstruct the biogeographical structure according to functional traits and the evolutionary lineage of B. amyloliquefaciens using comparative genomics analysis. All the available 96 genomes of B. amyloliquefaciens strains were curated from the NCBI genome database, having a variety of important functionalities in all sectors keeping a high focus on agricultural aspects. In-depth analysis was carried out to deduce the orthologous gene groups and whole-genome similarity. Pan genome analysis revealed that shell genes, soft core genes, core genes, and cloud genes comprise 17.09, 5.48, 8.96, and 68.47%, respectively, which demonstrates that genomes are very different in the gene content. It also indicates that the strains may have flexible environmental adaptability or versatile functions. Phylogenetic analysis showed that B. amyloliquefaciens is divided into two clades, and clade 2 is further dived into two different clusters. This reflects the difference in the sequence similarity and diversification that happened in the B. amyloliquefaciens genome. The majority of plant-associated strains of B. amyloliquefaciens were grouped in clade 2 (73 strains), while food-associated strains were in clade 1 (23 strains). Genome mining has been adopted to deduce antimicrobial resistance and virulence genes and their prevalence among all strains. The genes tmrB and yuaB codes for tunicamycin resistance protein and hydrophobic coat forming protein only exist in clade 2, while clpP, which codes for serine proteases, is only in clade 1. Genome plasticity of all strains of B. amyloliquefaciens reflects their adaption to different niches.202134659348
5708190.9985Successful expansion of hospital-associated clone of vanA-positive vancomycin-resistant Enterococcus faecalis ST9 to an anthropogenically polluted mangrove in Brazil. Mangrove ecosystems are hotspots of biodiversity, but have been threatened by anthropogenic activities. Vancomycin-resistant enterococci (VRE) are nosocomial bacteria classified as high priority by the World Health Organization (WHO). Herein, we describe the identification and genomic characteristics of a vancomycin-resistant Enterococcus faecalis strain isolated from a highly impacted mangrove ecosystem of the northeastern Brazilian, in 2021. Genomic analysis confirmed the existence of the transposon Tn1546-vanA and clinically relevant antimicrobial resistance genes, such as streptogramins, tetracycline, phenicols, and fluoroquinolones. Virulome analysis identified several genes associated to adherence, immune modulation, biofilm, and exoenzymes production. The UFSEfl strain was assigned to sequence type (ST9), whereas phylogenomic analysis with publicly available genomes from a worldwide confirmed clonal relatedness with a hospital-associated Brazilian clone. Our findings highlight the successful expansion of hospital-associated VRE in a mangrove area and shed light on the need for strengthening genomic surveillance of WHO priority pathogens in these vital ecosystems.202438056291