Genomic analysis of five antibiotic-resistant bacteria isolated from the environment. - Related Documents




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81101.0000Genomic 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
844110.9903Genomic and phenotypic attributes of novel salinivibrios from stromatolites, sediment and water from a high altitude lake. BACKGROUND: Salinivibrios are moderately halophilic bacteria found in salted meats, brines and hypersaline environments. We obtained three novel conspecific Salinivibrio strains closely related to S. costicola, from Socompa Lake, a high altitude hypersaline Andean lake (approx. 3,570 meters above the sea level). RESULTS: The three novel Salinivibrio spp. were extremely resistant to arsenic (up to 200 mM HAsO42-), NaCl (up to 15%), and UV-B radiation (19 KJ/m2, corresponding to 240 minutes of exposure) by means of phenotypic tests. Our subsequent draft genome ionsequencing and RAST-based genome annotation revealed the presence of genes related to arsenic, NaCl, and UV radiation resistance. The three novel Salinivibrio genomes also had the xanthorhodopsin gene cluster phylogenetically related to Marinobacter and Spiribacter. The genomic taxonomy analysis, including multilocus sequence analysis, average amino acid identity, and genome-to-genome distance revealed that the three novel strains belong to a new Salinivibrio species. CONCLUSIONS: Arsenic resistance genes, genes involved in DNA repair, resistance to extreme environmental conditions and the possible light-based energy production, may represent important attributes of the novel salinivibrios, allowing these microbes to thrive in the Socompa Lake.201424927949
252120.9902Insights 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
548730.9902Rapid Transmission and Divergence of Vancomycin-Resistant Enterococcus faecium Sequence Type 80, China. We investigated genomic evolution of vancomycin-resistant Enterococcus faecium (VREF) during an outbreak in Shenzhen, China. Whole-genome sequencing revealed 2 sequence type 80 VREF subpopulations diverging through insertion sequence-mediated recombination. One subpopulation acquired more antimicrobial resistance and carbohydrate metabolism genes. Persistent VREF transmission underscores the need for genomic surveillance to curb spread.202540305388
521540.9901Draft 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
178450.9900Draft 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
518760.9900Recovery of 52 bacterial genomes from the fecal microbiome of the domestic cat (Felis catus) using Hi-C proximity ligation and shotgun metagenomics. We used Hi-C proximity ligation with shotgun sequencing to retrieve metagenome-assembled genomes (MAGs) from the fecal microbiomes of two domestic cats (Felis catus). The genomes were assessed for completeness and contamination, classified taxonomically, and annotated for putative antimicrobial resistance (AMR) genes.202337695121
513370.9899Draft genome sequence of Marinobacter sp. DUT-3, a manganese-oxidizing and potential antibiotic-resistant bacterium from Bohai coastal sediments. A manganese-oxidizing bacterium, Marinobacter sp. DUT-3, was isolated from Bohai coastal sediments. A total of 24 contigs with GC content of 57.91% and 3,817 protein-coding genes were obtained by genome sequencing. Isolation of this strain suggests potential for synergistic antibiotics removal via biogenic manganese oxides and intrinsic resistance.202541081498
36280.9899Complete Genome Sequences of Highly Arsenite-Resistant Bacteria Brevibacterium sp. Strain CS2 and Micrococcus luteus AS2. The complete genome sequences of two highly arsenite-resistant Actinomycetales isolates are presented. Both genomes are G+C rich and consist of a single chromosome containing homologs of known arsenite resistance genes.201931371538
519190.9898Draft genome sequences data of Mammaliicoccus lentus isolated from horse farm soil. Mammallicoccus lentus is a member of the commensal microflora of the Staphylococcaceae family, which colonizes the skin of several species of farm animals, including poultry and dairy animals (Huber et al., 2011; Zhang et al., 2009). The study of the members of the Staphylococcaceae family, such as the Mammaliicoccus genus, isolated from various sources is of great importance for agriculture and public health as contributes to the accumulation of knowledge and understanding of the mechanisms of antibiotic resistance gene transmission among bacterial pathogens. This thesis is supported by recent studies showing that some members of the Mammallicoccus genus serve as a reservoir of virulence and antibiotic resistance genes and may also be a source of horizontal gene transfer (Saraiva et al., 2021). Here, we present a draft genome sequence of Mammallicoccus lentus strain PVZ.22 from a horse farm soil sample. The sequencing was performed on the Illumina MiSeq platform. The genome was assembled using the Geneious software package. The genome contains 2,802,282 bp with a total of 2805 genes, 8 perfect and 12 strict AMR genes and 58 tRNAs genes.202338075610
479100.9897Genome sequences of Methylobacterium and Methylorubrum isolates from Cd-contaminated soils in the Tar Creek Superfund site. Soil bacteria were isolated from the Tar Creek Superfund site in the presence of cadmium. Eight of these strains belong to the genus Methylobacterium, whereas one strain belongs to the genus Methylorubrum. Here, we report drafts of their genome sequences and highlight cadmium-resistance genes required in an exceptionally contaminated environment.202539835800
3671110.9896Antibiotic resistance genes detected in the marine sponge Petromica citrina from Brazilian coast. Although antibiotic-resistant pathogens pose a significant threat to human health, the environmental reservoirs of the resistance determinants are still poorly understood. This study reports the detection of resistance genes (ermB, mecA, mupA, qnrA, qnrB and tetL) to antibiotics among certain culturable and unculturable bacteria associated with the marine sponge Petromica citrina. The antimicrobial activities elicited by P. citrina and its associated bacteria are also described. The results indicate that the marine environment could play an important role in the development of antibiotic resistance and the dissemination of resistance genes among bacteria.201627287338
480120.9896Permanent draft genome sequences of cadmium-resistant isolates of Cupriavidus from soils within the Tar Creek Superfund site. Soil samples taken near the abandoned town of Picher, OK, USA, were used to enrich and isolate bacteria in the presence of cadmium. Isolates reported belong to the genus Cupriavidus. Here, we report their permanent draft sequences with an emphasis on genes conferring resistance to cadmium.202539589146
5121130.9895Rapid 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
483140.9895Present-day mercury resistance transposons are common in bacteria preserved in permafrost grounds since the Upper Pleistocene. Transposons closely related to mercury resistance transposons Tn5041, Tn5053, and Tn5056, which have been previously described in present-day bacteria, were detected in a survey of 12 mercury-resistant Pseudomonas strains isolated from permafrost samples aged 15-40 thousand years. In addition, Tn5042, a novel type of mercury resistance transposon, was revealed in the permafrost strain collection and its variants found to be common among present-day bacteria. The results reveal that no drastic changes in the distribution mode of the different types of mercury resistance transposons among environmental bacteria have taken place in the last 15-40 thousand years.200516084067
6139150.9895Complete genome and two plasmids sequences of Lactiplantibacillus plantarum L55 for probiotic potentials. In this study, we report the complete genome sequence of Lactiplantibacillus plantarum L55, a probiotic strain of lactic acid bacteria isolated from kimchi. The genome consists of one circular chromosome (2,077,416 base pair [bp]) with a guanine cytosine (GC) content of 44.5%, and two circular plasmid sequences (54,267 and 19,592 bp, respectively). We also conducted a comprehensive analysis of the genome, which identified the presence of functional genes, genomic islands, and antibiotic-resistance genes. The genome sequence data presented in this study provide insights into the genetic basis of L. plantarum L55, which could be beneficial for the future development of probiotic applications.202338616876
5139160.9894Adaptation of metal and antibiotic resistant traits in novel β-Proteobacterium Achromobacter xylosoxidans BHW-15. Chromosomal co-existence of metal and antibiotic resistance genes in bacteria offers a new perspective to the bacterial resistance proliferation in contaminated environment. In this study, an arsenotrophic bacterium Achromobacter xylosoxidans BHW-15, isolated from Arsenic (As) contaminated tubewell water in the Bogra district of Bangladesh, was analyzed using high throughput Ion Torrent Personal Genome Machine (PGM) complete genome sequencing scheme to reveal its adaptive potentiality. The assembled draft genome of A. xylosoxidans BHW-15 was 6.3 Mbp containing 5,782 functional genes, 1,845 pseudo genes, and three incomplete phage signature regions. Comparative genome study suggested the bacterium to be a novel strain of A. xylosoxidans showing significant dissimilarity with other relevant strains in metal resistance gene islands. A total of 35 metal resistance genes along with arsenite-oxidizing aioSXBA, arsenate reducing arsRCDAB, and mercury resistance merRTPADE operonic gene cluster and 20 broad range antibiotic resistance genes including β-lactams, aminoglycosides, and multiple multidrug resistance (MDR) efflux gene complex with a tripartite system OM-IM-MFP were found co-existed within the genome. Genomic synteny analysis with reported arsenotrophic bacteria revealed the characteristic genetic organization of ars and mer operonic genes, rarely described in β-Proteobacteria. A transposon Tn21 and mobile element protein genes were also detected to the end of mer (mercury) operonic genes, possibly a carrier for the gene transposition. In vitro antibiotic susceptibility assay showed a broad range of resistance against antibiotics belonging to β-lactams, aminoglycosides, cephalosporins (1st, 2nd, and 3rd generations), monobactams and even macrolides, some of the resistome determinants were predicted during in silico analysis. KEGG functional orthology analysis revealed the potential of the bacterium to utilize multiple carbon sources including one carbon pool by folate, innate defense mechanism against multiple stress conditions, motility, a proper developed cell signaling and processing unit and secondary metabolism-combination of all exhibiting a robust feature of the cell in multiple stressed conditions. The complete genome of the strain BHW-15 stands as a genetic basis for the evolutionary adaptation of metal and the antibiotic coexistence phenomenon in an aquatic environment.201930886770
5476170.9894Bile Carriage of optrA-Positive Enterococcus faecium in a Patient with Choledocholith. We isolated one Enterococcus faecium isolate SZ21B15 from a bile sample of a patient with choledocholith in Shenzhen, China in 2021. It was positive for oxazolidinone resistance gene optrA and was intermediate to linezolid. The whole genome of E. faecium SZ21B15 was sequenced by Illumina Hiseq. It belonged to ST533 within the clonal complex 17. The optrA gene and additional two resistance genes fexA and erm(A) were located within a 25,777-bp multiresistance region, which was inserted into the chromosomal radC gene, being chromosomal intrinsic resistance genes. The chromosomal optrA gene cluster found in E. faecium SZ21B15 was closely related to the corresponding regions of multiple optrA-carrying plasmids or chromosomes from Enterococcus, Listeria, Staphylococcus, and Lactococcus strains. It further highlights the ability of the optrA cluster that transfers between plasmids and chromosomes and evolves by a series of molecular recombination events. IMPORTANCE Oxazolidinone are effective antimicrobial agents for the treatment of infections caused by multidrug-resistant Gram-positive bacteria, including vancomycin-resistant enterococci. The emergence and global spread of transferable oxazolidinone resistance genes such as optrA is worrisome. Enterococcus spp. can become causes of hospital-associated infections and are also widely distributed in the gastrointestinal tracts of animals and the natural environment. In this study, one E. faecium isolate from bile sample carried chromosomal optrA, being intrinsic resistance gene. optrA-positive E. faecium in bile not only makes the treatment of gallstones difficult, but also may become a reservoir of resistance genes in the body.202336976027
5869180.9894Detection of the sul2-strA-strB gene cluster in an ice core from Dome Fuji Station, East Antarctica. OBJECTIVES: Bacteria harbouring antimicrobial resistance genes (ARGs) have been isolated from various locations, including ancient microbiomes, indicating that these genes pre-date the discovery of antibiotics. To gain further information regarding ARGs in the pre-antibiotic era, ice samples derived from Dome Fuji Station, Eastern Antarctica, were examined. METHODS: DNA was extracted from firn or ice core samples (n=3; 1200-1400ybp, 1700-2100ybp and 2200-2800ybp, respectively) under sterile conditions. Whole-genome amplification and PCR analyses were utilised to detect ARGs. RESULTS: A 2764-bp gene cluster containing the type II dihydropteroate synthase gene sul2 and the aminoglycoside phosphotransferase genes strA and strB was detected in the 1200-1400-year-old Antarctic ice core (DF-63.5). The sul2-strA-strB gene cluster is frequently associated with plasmid RSF1010 and transposon Tn5393; however, these elements were not detected in sample DF-63.5. The gene cluster exhibited a high level of sequence identity to sequences harboured in present-day bacteria, although there were sequence polymorphisms in the strA gene. Furthermore, expression of this gene cluster in Escherichia coli resulted in reduced susceptibility to dihydrostreptomycin and sulfamethoxazole. CONCLUSION: The results of this study provide further evidence that certain ARGs existed in the pre-antibiotic era. Because the sul2 gene confers resistance to the synthetic compound sulfamethoxazole, these findings suggest that ARGs against synthetic antimicrobials emerged in bacteria during the pre-antibiotic era.201930468914
5178190.9894Thermophilic Pseudomonas aeruginosa strain Ch39 isolated from Chignahuapan hot springs in Puebla, Mexico. Thermophilic bacteria have specific metabolic specializations to survive at high temperatures. This study focuses on Pseudomonas aeruginosa strain Ch39, a new isolate from mineral-rich thermal water from Chignahuapan, Puebla, Mexico. Biochemical testing, whole genome sequencing, and antimicrobial resistance profiling of strain Ch39 yielded significant detailed results. Genome sequencing yielded a high-quality 6.68 Mb assembly with a GC content of 66.13%, and annotation identified 4 356 protein-coding genes, including heat shock and antibiotic resistance genes. Comparative analysis of growth kinetics with the reference strains ATCC 27853 and PAO1 showed that Ch39 exhibited good growth and thermotolerance, with viability at 45°C, due to putative genetic adaptations such as heat shock proteins. Antibiotic resistance profiling showed variability in resistance profiles and the presence of resistance genes. In particular, strain Ch39 showed increased minimum inhibitory concentrations for some of the antibiotics tested, such as tetracycline (>1000 µg/mL), compared to the control strains. The observations made here emphasize the thermoadaptation of the strain and its suitability as a reservoir for antibiotic-resistance genes. This study expands our understanding of the thermophilic adaptation of P. aeruginosa and its ecological and clinical significance.202540240292