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613300.9642Comparative genomic study of three species within the genus Ornithinibacillus, reflecting the adaption to different habitats. In the present study, we report the whole genome sequences of two species, Ornithinibacillus contaminans DSM22953(T) isolated from human blood and Ornithinibacillus californiensis DSM 16628(T) isolated from marine sediment, in genus Ornithinibacillus. Comparative genomic study of the two species was conducted together with their close relative Ornithinibacillus scapharcae TW25(T), a putative pathogenic bacteria isolated from dead ark clam. The comparisons showed O. contaminans DSM22953(T) had the smallest genome size of the three species indicating that it has a relatively more stable habitat. More stress response and heavy metal resistance genes were found in the genome of O. californiensis DSM 16628(T) reflecting its adaption to the complex marine environment. O. scapharcae TW25(T) contained more antibiotic resistance genes and virus factors in the genome than the other two species, which revealed its pathogen potential.201626706221
82210.9591Exoglucanase-encoding genes from three Wickerhamomyces anomalus killer strains isolated from olive brine. Wickerhamomyces anomalus killer strains are important for fighting pathogenic yeasts and for controlling harmful yeasts and bacteria in the food industry. Targeted disruption of key genes in β-glucan synthesis of a sensitive Saccharomyces cerevisiae strain conferred resistance to the toxins of W. anomalus strains BS91, BCA15 and BCU24 isolated from olive brine. Competitive inhibition of the killing activities by laminarin and pustulan refer to β-1,3- and β-1,6-glucans as the main primary toxin targets. The extracellular exoglucanase-encoding genes WaEXG1 and WaEXG2 from the three strains were sequenced and were found to display noticeable similarities to those from known potent W. anomalus killer strains.201323148020
521320.9591Draft genome sequences of Limosilactobacillus fermentum IJAL 01 335, isolated from a traditional cereal fermented dough. Limosilactobacillus fermentum IJAL 01 335 was isolated from mawè, a spontaneously fermented cereal dough from Benin. The 1.83 Mb draft genome sequence (52.37% GC) comprises 154 contigs, 1,836 coding sequences, and 23 predicted antibiotic resistance genes, providing insights into its genetic features and potential application in food fermentation.202541170963
538130.9586Draft genome sequence of Staphylococcus urealyticus strain MUWRP0921, isolated from the urine of an adult female Ugandan. Staphylococcus urealyticus bacteria are pathogenic among immune-compromised individuals. A strain (MUWRP0921) of Staphylococcus urealyticus with a genome of 2,708,354 bp was isolated from Uganda and carries genes that are associated with antibiotic resistance, including resistance to macrolides (erm(C) and mph(C')), aminoglycosides (aac(6")-aph(2")), tetracyclines (tet(K)), and trimethoprim (dfrG).202438078696
614040.9585Complete genome sequence of bacteriocin-producing Lactobacillus plantarum KLDS1.0391, a probiotic strain with gastrointestinal tract resistance and adhesion to the intestinal epithelial cells. Lactobacillus plantarum KLDS1.0391 is a probiotic strain isolated from the traditional fermented dairy products and identified to produce bacteriocin against Gram-positive and Gram-negative bacteria. Previous studies showed that the strain has a high resistance to gastrointestinal stress and has a high adhesion ability to the intestinal epithelial cells (Caco-2). We reported the entire genome sequence of this strain, which contains a circular 2,886,607-bp chromosome and three circular plasmids. Genes, which are related to the biosynthesis of bacteriocins, the stress resistance to gastrointestinal tract environment and adhesive performance, were identified. Whole genome sequence of Lactobacillus plantarum KLDS1.0391 will be helpful for its applications in food industry.201728676278
521550.9584Draft 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
518560.9583Genomic characterisation of nasal isolates of coagulase-negative Staphylococci from healthy medical students reveals novel Staphylococcal cassette chromosome mec elements. Coagulase-negative staphylococci (CoNS) are a diverse group of Gram-positive bacteria that are part of the normal human microbiota. Once thought to be non-pathogenic, CoNS has emerged in recent years as opportunistic pathogens of concern particularly in healthcare settings. In this study, the genomes of four methicillin-resistant CoNS isolates obtained from the nasal swabs of healthy university medical students in Malaysia were sequenced using the Illumina short-read platform. Genome sequencing enabled the identification of the four isolates as Staphylococcus warneri UTAR-CoNS1, Staphylococcus cohnii subsp. cohnii UTAR-CoNS6, Staphylococcus capitis subsp. urealyticus UTAR-CoNS20, and Staphylococcus haemolyticus UTAR-CoNS26. The genome of S. cohnnii UTAR-CoNS6 harboured the mecA methicillin-resistance gene on a Staphylococcal cassette chromosome mec (SCCmec) element similar to SCCmec type XIV (5 A) but the SCCmec cassettes identified in the other three CoNS genomes were novel and untypeable. Some of these SCCmec elements also encoded heavy metal resistance genes while the SCCmec type XIV (5 A) variant in S. cohnii UTAR-CoNS6 harboured the complete ica operon, a known virulence factor that functions in biofilm formation. In S. cohnii UTAR-CoNS6, the macrolide resistance genes msrA and mphC along with copper and cadmium resistance genes were located on a 26,630 bp plasmid, pUCNS6. This study showcased the diversity of CoNS in the nasal microbiota of medical students but the discovery of novel SCCmec elements, various antimicrobial and heavy metal resistance along with virulence genes in these isolates is of concern and warrants vigilance due to the likelihood of spread, especially to hospitalised patients.202540595841
520270.9580Complete genome sequence data of multidrug-resistant Stenotrophomonas sp. strain SXG-1. Objectives A multidrug-resistant bacterium, Stenotrophomonas sp. SXG-1, was isolated from the liver of diseased hybrid sturgeon from Guizhou province, China. Methods Whole-genome sequencing was performed on the Illumina HiSeq 2500-PE125 platform with MPS (massively parallel sequencing) Illumina technology. All good quality paired reads were assembled using the SOAPdenovo into a number of scaffolds. PHI (Pathogen Host Interactions), VFDB (Virulence Factors of Pathogenic Bacteria) and ARDB (Antibiotic Resistance Genes Database) were used to analyses pathogenicity and drug resistance. Results Here we reported the complete genome sequence of Stenotrophomonas sp. SXG-1, which comprised 4534,602bp in 4077 coding sequences (CDS) with a G+C content of 66.42%. The genome contained 4 gene islands, 72 tRNAs and 13 rRNAs. According to the annotation analysis, strain SXG-1 encoded 22 genes related to the multidrug resistance. In addition to 10 genes conferring resistance to antimicrobial drugs of different classes via alternative mechanisms, 12 genes of efflux pumps were presented, 9 of which were reported for the first time in Stenotrophomonas maltophilia. Conclusion This was the first complete genome sequence of Stenotrophomonas sp. isolated from the sturgeon. The complete genome sequence of Stenotrophomonas sp. strain SXG-1 may provide insights into the mechanism of antimicrobial resistance and prevent disease.202032311503
612380.9580Genomic analysis of a hop-resistance Lactobacillus brevis strain responsible for food spoilage and capable of entering into the VBNC state. BACKGROUND: Lactobacillus brevis is a major contaminant of spoiled beer. And it was able to enter VBNC state and cause false negative detection, which poses a major challenge to the brewing industry. METHODS: The genomic DNA of L. brevis BM-LB13908 was extracted and purified to form a sequencing library that meets the quality requirements and was sequenced. The sequencing results were then screened and assembled to obtain the entire genome sequence of L. brevis. Predicted genes were annotated by GO database, KEGG pathway database and COG functional classification system. RESULTS: The final assembly yielded 275 scaffolds of a total length of 2 840 080 bp with a G + C content of 53.35%. There were 2357, 701, 1519 predicted genes with corresponding GO functional, COG functional, and KEGG biological pathway annotations, respectively. The genome of L. brevis BM-LB13908 contains hop resistance gene horA and multiple genes related to the formation of VBNC state. CONCLUSIONS: This report describes the draft genome sequence of L. brevis BM-LB13908, a spoilage strain isolated from finished beer sample. This study may support further study on L. brevis and other beer spoilage bacteria, and prevent and control beer spoilage caused by microorganisms.202032272213
613590.9578Complete genome sequence of Bifidobacterium animalis subsp. lactis KLDS 2.0603, a probiotic strain with digestive tract resistance and adhesion to the intestinal epithelial cells. Bifidobacterium animalis subsp. lactis KLDS 2.0603 (abbreviated as KLDS 2.0603) is a probiotic strain isolated from the feces of an adult human. Previous studies showed that KLDS 2.0603 has a high resistance to simulated digestive tract conditions and a high ability to adhere to intestinal epithelial cells (Caco-2). These two characteristics are essential requirements for the selection of probiotic bacteria. To explore the stress resistance mechanism to the digestive tract environment and the adhesive proteins of this strain, in this paper, we reported the complete genome sequence of KLDS 2.0603, which contains 19,469bp and encodes 1614 coding sequences(CDSs), 15 rRNA genes, 52 tRNA genes with 1678 open reading frames.201626795356
6139100.9576Complete 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
827110.9576Characterization of a ST137 multidrug-resistant Campylobacter jejuni strain with a tet(O)-positive genomic island from a bloodstream infection patient. Campylobacter jejuni (C. jejuni) is a major cause of gastroenteritis and rarely cause bloodstream infection. Herein, we characterized a multidrug-resistant C. jejuni strain LZCJ isolated from a tumor patient with bloodstream infection. LZCJ was resistant to norfloxacin, ampicillin, ceftriaxone, ciprofloxacin and tetracycline. It showed high survival rate in serum and acidic environment. Whole genome sequencing (WGS) analysis revealed that strain LZCJ had a single chromosome of 1,629,078 bp (30.6 % G + C content) and belonged to the ST137 lineage. LZCJ shared the highest identity of 99.66 % with the chicken-derived C. jejuni MTVDSCj20. Four antimicrobial resistance genes (ARGs) were detected, bla(OXA-61), tet(O), gyrA (T86I), and cmeR (G144D and S207G). In addition, a 12,746 bp genomic island GI_LZCJ carrying 15 open reading frames (ORFs) including the resistance gene tet(O) was identified. Sequence analysis found that the GI_LZCJ was highly similar to the duck-derived C. jejuni ZS004, but with an additional ISChh1-like sequence. 137 non-synonymous mutations in motility related genes (flgF, fapR, flgS), capsular polysaccharide (CPS) coding genes (kpsE, kpsF, kpsM, kpsT), metabolism associated genes (nuoF, nuoG, epsJ, holB), and transporter related genes (comEA, gene0911) were confirmed in LZCJ compared with the best closed chicken-derived strain MTVDSCj20. Our study showed that C. jejuni strain LZCJ was highly similar to the chicken-derived strain MTVDSCj20 but with a lot of SNPs involved in motility, CPS and metabolism coding genes. This strain possessed a tet(O)-positive genomic island GI_LZCJ, which was closed to duck-derived C. jejuni ZS004, but with an additional ISChh1-like sequence. The above data indicated that the LZCJ strain may originate from foodborne bacteria on animals and the importance of continuous surveillance for the spread of foodborne bacteria.202439208964
1789120.9576Genomic 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
5210130.9576Whole genome sequence data of Lactiplantibacillus plantarum IMI 507027. Here we report the draft genome sequence of the Lactiplantibacillus plantarum IMI 507027 strain. The genome consists of 37 contigs with a total size of 3,235,614 bp and a GC% of 44.51. After sequence trimming, 31 contigs were annotated, revealing 3,126 genes, of which 3,030 were coding sequences. The Average Nucleotide Identity (ANI) gave a value of 99.9926% between IMI 507027 and L. plantarum JDM1, identifying the strain as L. plantarum. No genes of concern for safety-related traits such as antimicrobial resistance or virulence factors were found. The annotated genome and raw sequence reads were deposited at NCBI under Bioproject with the accession number PRJNA791753.202235310818
5883140.9574Genome-wide analysis reveals the emergence of multidrug resistant Stenotrophomonas acidaminiphila strain SINDOREI isolated from a patient with sepsis. Stenotrophomonas acidaminiphila, the most recent reported species in genus Stenotrophomonas, is a relatively rare bacteria and is an aerobic, glucose non-fermentative, Gram-negative bacterium. However, little information of S. acidaminiphila is known to cause human infections. In this research, we firstly reported a multidrug-resistant strain S. acidaminiphila SINDOREI isolated from the blood of a patient with sepsis, who was dead of infection eventually. The whole genome of strain SINDOREI was sequenced, and genome comparisons were performed among six closely related S. acidaminiphila strains. The core genes (2,506 genes) and strain-specific genes were identified, respectively, to know about the strain-level diversity in six S. acidaminiphila stains. The presence of a unique gene (narG) and essential genes involved in biofilm formation in strain SINDOREI are important for the pathogenesis of infections. Strain SINDOREI was resistant to trimethoprim/sulfamethoxazole, ciprofloxacin, ofloxacin, cefepime, ceftazidime, and aztreonam. Several common and specific antibiotic resistance genes were identified in strain SINDOREI. The presence of two sul genes and exclusive determinants GES-1, aadA3, qacL, and cmlA5 is responsible for the resistance to multidrug. The virulence factors and resistance determinants can show the relationship between the phenotype and genotype and afford potential therapeutic strategies for infections.202236212813
5203150.9573Draft genome sequence analysis of a novel MLST (ST5028) and multidrug-resistant Klebsiella quasipneumoniae subsp. similipneumoniae (Kp4) strain 456S1 isolated from a pig farm in China. OBJECTIVES: The avian breeding industry is an important element in exposing bacteria to antibiotics. As one of the major animal welfare and economic problems for the poultry industry, multidrug-resistant Klebsiella spp. have become a substantial source of antibiotic resistance genes. In the present work, we reported the draft genome sequence of a novel multilocus sequence type (MLST) (ST5028) Klebsiella quasipneumoniae subsp. similipneumoniae (Kp4) strain 456S1, which was isolated from a pig farm in China with broad-spectrum antimicrobial activities. METHODS: Classical microbiological methods were applied to isolate and identify the strain, genomic DNA was sequenced using an Illumina HiSeq platform, and the reads were de novo assembled into contigs using CLC Genomics Workbench. The assembled contigs were annotated, and whole-genome sequencing (WGS) analysis was performed. RESULTS: WGS analysis revealed that the genome of strain 456S1 comprised a circular chromosome of 5,419,059 bp (GC content, 57.8%), harbouring 12 important antibiotic resistance genes: aac(6')-ib-cr, aadA16, floR, dfrA27, fosA, tet(D), blaOKP-B-3, oqxA, oqxB, qnrB6, sul1 and arr-3. The Klebsiella quasipneumoniae subsp. similipneumoniae (Kp4) 456S1 was also found to belong to a novel sequence type (ST5028) determined by MLST. CONCLUSION: The genome sequence reported herein will provide useful information for antibiotic resistance and pathogenic mechanisms in Klebsiella quasipneumoniae and will be a reference for comparative analysis with genomic features among different sources of clinically important multidrug-resistant strains, especially among bacteria of animal and human origin.202133516893
1342160.9573Prevalence, Toxin Genes, and Antibiotic Resistance Profiles of Bacillus cereus Isolates from Spices in Antalya and Isparta Provinces in Türkiye. Bacillus cereus is a pathogenic bacterium commonly found in nature and can produce toxins that cause food poisoning. This study aimed to detect the prevalence of B. cereus group bacteria in 50 unpackaged and 20 packaged spice samples frequently used as flavoring in Turkish cuisine, as well as investigate the presence of toxin genes and antibiotic resistance in the isolates. A total of 48 B. cereus group bacteria were isolated from 27 of 70 (38.57%) spice samples. The prevalence of B. cereus group bacteria in packaged (25%, 5/20) and unpackaged (44%, 22/50) spice samples did not differ significantly (P ˃ 0.05). All B. cereus group isolates were identified as B. cereus sensu stricto (B. cereus) using molecular methods. The hemolytic activity tests revealed that the most strains (44/48, 91.67%) are β-hemolytic. The distributions of toxin genes in isolates were investigated by PCR. It was determined that all isolates were identified to have 2-8 toxin genes, except B. cereus SBC3. The three most common toxin genes were found to be nheA (47/48, 97.92%), nheB (46/48, 95.83%), and entFM (46/48, 95.83%). All B. cereus isolates were susceptible to linezolid and vancomycin, while 35.42% (17/48) showed resistance to erythromycin. Multi-drug resistance (MDR) was detected in 8.3% (4/48) of B. cereus isolates, while 33.33% of the isolates showed multiple antibiotic resistance (MAR) index values higher than 0.2. The findings indicate that B. cereus may pose a health risk in packaged and unpackaged spices if present in high quantities. Therefore, the presence of B. cereus strains in both packaged and unpackaged spices should be monitored regarding consumer health and product safety.202338031610
6134170.9573Complete genome and gene expression analyses of Asaia bogorensis reveal unique responses to culture with mammalian cells as a potential opportunistic human pathogen. Asaia bogorensis, a member of acetic acid bacteria (AAB), is an aerobic bacterium isolated from flowers and fruits, as well as an opportunistic pathogen that causes human peritonitis and bacteraemia. Here, we determined the complete genomic sequence of the As. bogorensis type strain NBRC 16594, and conducted comparative analyses of gene expression under different conditions of co-culture with mammalian cells and standard AAB culture. The genome of As. bogorensis contained 2,758 protein-coding genes within a circular chromosome of 3,198,265 bp. There were two complete operons encoding cytochrome bo3-type ubiquinol terminal oxidases: cyoABCD-1 and cyoABCD-2. The cyoABCD-1 operon was phylogenetically common to AAB genomes, whereas the cyoABCD-2 operon belonged to a lineage distinctive from the cyoABCD-1 operon. Interestingly, cyoABCD-1 was less expressed under co-culture conditions than under the AAB culture conditions, whereas the converse was true for cyoABCD-2. Asaia bogorensis shared pathogenesis-related genes with another pathogenic AAB, Granulibacter bethesdensis, including a gene coding pathogen-specific large bacterial adhesin and additional genes for the inhibition of oxidation and antibiotic resistance. Expression alteration of the respiratory chain and unique hypothetical genes may be key traits that enable the bacterium to survive under the co-culture conditions.201526358298
5882180.9572PCR Analysis Methods for Detection and Identification of Beer-Spoilage Lactic Acid Bacteria. Polymerase chain reaction (PCR) analysis enables rapid and accurate detection of beer-spoilage lactic acid bacteria (LAB). Hop resistance genes, horA and horC, are utilized as genetic markers to determine the spoilage ability of LAB strains. PCR analysis of horA and horC, combined with multiplex PCR methods of 12 beer-spoilage species, enables simultaneous and comprehensive detection easily and inexpensively.201930506252
6137190.9570Genomic and phenotypic analyses of Carnobacterium jeotgali strain MS3(T), a lactate-producing candidate biopreservative bacterium isolated from salt-fermented shrimp. Carnobacterium jeotgali strain MS3(T) was isolated from traditionally fermented Korean shrimp produced with bay salt. The bacterium belongs to the family Carnobacteriaceae, produces lactic acid and contains gene clusters involved in the production of lactate, butyrate, aromatic compounds and exopolysaccharides. Carnobacterium jeotgali strain MS3(T) was characterized through extensive comparison of the virulence potential, genomic relatedness and sequence similarities of its genome with the genomes of other Carnobacteria and lactic acid bacteria. In addition, links between predicted functions of genes and phenotypic characteristics, such as antibiotic resistance and lactate and butyrate production, were extensively evaluated. Genomic and phenotypic analyses of strain MS3(T) revealed promising features, including minimal virulence genes and lactate production, which make this bacterium a desirable candidate for exploitation by the fermented food industry.201525868912