Genomic analysis of a hop-resistance Lactobacillus brevis strain responsible for food spoilage and capable of entering into the VBNC state. - Related Documents




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612301.0000Genomic 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
514810.9990Unveiling 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
588220.9990PCR 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
603730.9988The Complete Genome of Probiotic Lactobacillus sakei Derived from Plateau Yak Feces. Probiotic bacteria are receiving increased attention due to the potential benefits to their hosts. Plateau yaks have resistance against diseases and stress, which is potentially related to their inner probiotics. To uncover the potential functional genes of yak probiotics, we sequenced the whole genome of Lactobacillus sakei (L. sakei). The results showed that the genome length of L. sakei was 1.99 Mbp, with 1943 protein coding genes (21 rRNA, 65 tRNA, and 1 tmRNA). There were three plasmids found in this bacteria, with 88 protein coding genes. EggNOG annotation uncovered that the L. sakei genes were found to belong to J (translation, ribosomal structure, and biogenesis), L (replication, recombination, and repair), G (carbohydrate transport and metabolism), and K (transcription). GO annotation showed that most of the L. sakei genes were related to cellular processes, metabolic processes, biological regulation, localization, response to stimulus, and organization or biogenesis of cellular components. CAZy annotation found that there were 123 CAZys in the L. sakei genome, with glycosyl transferases and glycoside hydrolases. Our results revealed the genome characteristics of L. sakei, which may give insight into the future employment of this probiotic bacterium for its functional benefits.202033371298
514540.9988Genome sequence and comparative analysis of a putative entomopathogenic Serratia isolated from Caenorhabditis briggsae. BACKGROUND: Entomopathogenic associations between nematodes in the genera Steinernema and Heterorhabdus with their cognate bacteria from the bacterial genera Xenorhabdus and Photorhabdus, respectively, are extensively studied for their potential as biological control agents against invasive insect species. These two highly coevolved associations were results of convergent evolution. Given the natural abundance of bacteria, nematodes and insects, it is surprising that only these two associations with no intermediate forms are widely studied in the entomopathogenic context. Discovering analogous systems involving novel bacterial and nematode species would shed light on the evolutionary processes involved in the transition from free living organisms to obligatory partners in entomopathogenicity. RESULTS: We report the complete genome sequence of a new member of the enterobacterial genus Serratia that forms a putative entomopathogenic complex with Caenorhabditis briggsae. Analysis of the 5.04 MB chromosomal genome predicts 4599 protein coding genes, seven sets of ribosomal RNA genes, 84 tRNA genes and a 64.8 KB plasmid encoding 74 genes. Comparative genomic analysis with three of the previously sequenced Serratia species, S. marcescens DB11 and S. proteamaculans 568, and Serratia sp. AS12, revealed that these four representatives of the genus share a core set of ~3100 genes and extensive structural conservation. The newly identified species shares a more recent common ancestor with S. marcescens with 99% sequence identity in rDNA sequence and orthology across 85.6% of predicted genes. Of the 39 genes/operons implicated in the virulence, symbiosis, recolonization, immune evasion and bioconversion, 21 (53.8%) were present in Serratia while 33 (84.6%) and 35 (89%) were present in Xenorhabdus and Photorhabdus EPN bacteria respectively. CONCLUSION: The majority of unique sequences in Serratia sp. SCBI (South African Caenorhabditis briggsae Isolate) are found in ~29 genomic islands of 5 to 65 genes and are enriched in putative functions that are biologically relevant to an entomopathogenic lifestyle, including non-ribosomal peptide synthetases, bacteriocins, fimbrial biogenesis, ushering proteins, toxins, secondary metabolite secretion and multiple drug resistance/efflux systems. By revealing the early stages of adaptation to this lifestyle, the Serratia sp. SCBI genome underscores the fact that in EPN formation the composite end result - killing, bioconversion, cadaver protection and recolonization- can be achieved by dissimilar mechanisms. This genome sequence will enable further study of the evolution of entomopathogenic nematode-bacteria complexes.201526187596
47050.9988Sporulation genes in members of the low G+C Gram-type-positive phylogenetic branch ( Firmicutes). Endospore formation is a specific property found within bacteria belonging to the Gram-type-positive low G+C mol% branch ( Firmicutes) of a phylogenetic tree based on 16S rRNA genes. Within the Gram-type-positive bacteria, endospore-formers and species without observed spore formation are widely intermingled. In the present study, a previously reported experimental method (PCR and Southern hybridization assays) and analysis of genome sequences from 52 bacteria and archaea representing sporulating, non-spore-forming, and asporogenic species were used to distinguish non-spore-forming (void of the majority of sporulation-specific genes) from asporogenic (contain the majority of sporulation-specific genes) bacteria. Several sporulating species lacked sequences similar to those of Bacillus subtilis sporulation genes. For some of the genes thought to be sporulation specific, sequences with weak similarity were identified in non-spore-forming bacteria outside of the Gram-type-positive phylogenetic branch and in archaea, rendering these genes unsuitable for the intended classification into sporulating, asporogenic, and non-spore-forming species. The obtained results raise questions regarding the evolution of sporulation among the Firmicutes.200415340788
461560.9988Effect of conditioned media from Aeromonas caviae on the transcriptomic changes of the porcine isolates of Pasteurella multocida. BACKGROUND: Pasteurella multocida is an opportunistic pathogen causing porcine respiratory diseases by co-infections with other bacterial and viral pathogens. Various bacterial genera isolated from porcine respiratory tracts were shown to inhibit the growth of the porcine isolates of P. multocida. However, molecular mechanisms during the interaction between P. multocida and these commensal bacteria had not been examined.  METHODS: This study aimed to investigate the interaction between two porcine isolates of P. multocida (PM2 for type D and PM7 for type A) with Aeromonas caviae selected from the previously published work by co-culturing P. multocida in the conditioned media prepared from A. caviae growth and examining transcriptomic changes using RNA sequencing and bioinformatics analysis.  RESULTS: In total, 629 differentially expressed genes were observed in the isolate with capsular type D, while 110 genes were significantly shown in type A. High expression of genes required for energy metabolisms, nutrient uptakes, and quorum sensing were keys to the growth and adaptation to the conditioned media, together with the decreased expression of those in the unurgent pathways, including translation and antibacterial resistance. CONCLUSION: This transcriptomic analysis also displayed the distinct capability of the two isolates of P. multocida and the preference of the capsular type A isolate in response to the tough environment of the A. caviae conditioned media. Therefore, controlling the environmental sensing and nutrient acquisition mechanisms of P. multocida would possibly prevent the overpopulation of these bacteria and reduce the chance of becoming opportunistic pathogens.202236368971
515170.9988Comparative 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
603680.9988Comprehensive Phenotypic Characterization and Genomic Analysis Unveil the Probiotic Potential of Bacillus velezensis K12. Bacillus spp. have emerged as pivotal sources of probiotic preparations, garnering considerable attention in recent years owing to their vigorous bacteriostatic activity and antimicrobial resistance. This study aimed to investigate these probiotic characteristics in depth and verify the safety of Bacillus velezensis K12, a strain isolated from broiler intestine. The K12 strain was identified as Bacillus velezensis based on its morphology and 16S rDNA sequence homology analysis. Subsequently, B. velezensis K12 was evaluated for acid resistance, bile salt resistance, gastrointestinal tolerance, drug sensitivity, and antimicrobial activity. Additionally, whole-genome sequencing technology was employed to dissect its genomic components further, aiming to explore its potential applications as a probiotic strain. B. velezensis K12 was sensitive to six antibiotics and had acid tolerance. Furthermore, it showed potent antimicrobial activity against a wide range of pathogenic bacteria, including Escherichia coli (E. coli), Staphylococcus aureus, Salmonella, Clostridium perfringens, Bacillus cereus, and Vibrio parahaemolyticus. The complete genome sequencing of B. velezensis K12 revealed a genomic length of 3,973,105 base pairs containing 4123 coding genes, among which 3973 genes were functionally annotated. The genomic analysis identified genes associated with acid and bile tolerance, adhesion, antioxidants, and secondary metabolite production, whereas no functional genes related to enterotoxins or transferable antibiotic resistance were detected, thereby confirming the probiotic properties of B. velezensis K12. B. velezensis K12 exhibits broad-spectrum bacteriostatic activity and in vitro safety, positioning it as a potential candidate strain for developing probiotic Bacillus preparations.202540150327
546890.9988Whole-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
6122100.9988Metatranscriptome and Resistome of the Endodontic Microbiome. INTRODUCTION: In this study, we used metatranscriptomics for the first time to investigate microbial composition, functional signatures, and antimicrobial resistance gene expression in endodontic infections. METHODS: Root canal samples were collected from ten teeth, including five primary and five persistent/secondary endodontic infections. RNA from endodontic samples was extracted, and RNA sequencing was performed on a NovaSeq6000 system (Illumina). Taxonomic analysis was performed using the Kraken2 bacterial database. Then, sequences with a taxonomic classification were annotated against the Universal Protein Knowledgebase for functional annotation and the Comprehensive Antibiotic Resistance Database for AR-like gene identification. RESULTS: Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria represented the dominant phyla, whereas Fusobacteria, Spirochetes, and Synergistetes were among the nondominant phyla. The top ten species were mainly represented by obligate (or quasiobligate) anaerobes, including Gram-negative (eg, Capnocytophaga sp. oral taxon 323, Fusobacterium nucleatum, Prevotella intermedia, Prevotella oris, Tannerella forsythia, and Tannerella sp. oral taxon HOT-286) and Gram-positive species (eg, Olsenella uli and Parvimonas micra). Transcripts encoding moonlighting proteins (eg, glycolytic proteins, translational elongation factors, chaperonin, and heat shock proteins) were highly expressed, potentially affecting bacterial adhesion, biofilm formation, host defense evasion, and inflammation induction. Endodontic bacteria expressed genes conferring resistance to antibiotic classes commonly used in dentistry, with a high prevalence and expression of tetracycline and lincosamide resistance genes. Antibiotic efflux and antibiotic target alteration/protection were the main resistance mechanisms. CONCLUSIONS: Metatranscriptomics revealed the activity of potential endodontic pathogens, which expressed putative virulence factors and a wide diversity of genes potentially involved in AR.202438719087
4683110.9988Characterization of Bacteroides fragilis from the vagina of a giant panda (Ailuropoda melanoleuca) with vaginitis. BACKGROUND: Bacteroides fragilis is a prevalent anaerobic bacterium typically resides in the human vagina. It is known to potentially induce infections under specific conditions. Interestingly, there have been no previous reports of B. fragilis being isolated from the vagina of giant pandas. CASE PRESENTATION: A novel strain of anaerobic bacteria was isolated from the vaginal tract of a giant panda exhibiting symptoms of vaginitis. This strain, designated as GPBF01, was identified as Bacteroides fragilis, a species commonly found in the vaginal microbiome of humans and other animals. After purifying of the single colony, a series of evaluations were conducted including morphological examination, physiological and biochemical identification, antibiotic resistance analysis, resistance genes detection, 16S rRNA sequence, and phylogenetic tree sequence analysis to investigate its biological characteristics. The findings indicated the presence of a predominant anaerobic bacterium, which was identified as B. fragilis and temporarily named GPBF01 with unique biological traits not previously. CONCLUSIONS: This study is the first to report B. fragilis in the vaginal tract of giant pandas. The analysis of antibiotic resistance patterns among anaerobic bacteria, as conducted in this research, is critical for informing the selection of appropriate antimicrobial agents in the clinical treatment of vaginitis in this species. The findings of this report substantially enhance the scientific basis needed to understand the etiology and refine therapeutic approaches for vaginitis in giant pandas.202439605068
4617120.9987A maximum likelihood QTL analysis reveals common genome regions controlling resistance to Salmonella colonization and carrier-state. BACKGROUND: The serovars Enteritidis and Typhimurium of the Gram-negative bacterium Salmonella enterica are significant causes of human food poisoning. Fowl carrying these bacteria often show no clinical disease, with detection only established post-mortem. Increased resistance to the carrier state in commercial poultry could be a way to improve food safety by reducing the spread of these bacteria in poultry flocks. Previous studies identified QTLs for both resistance to carrier state and resistance to Salmonella colonization in the same White Leghorn inbred lines. Until now, none of the QTLs identified was common to the two types of resistance. All these analyses were performed using the F2 inbred or backcross option of the QTLExpress software based on linear regression. In the present study, QTL analysis was achieved using Maximum Likelihood with QTLMap software, in order to test the effect of the QTL analysis method on QTL detection. We analyzed the same phenotypic and genotypic data as those used in previous studies, which were collected on 378 animals genotyped with 480 genome-wide SNP markers. To enrich these data, we added eleven SNP markers located within QTLs controlling resistance to colonization and we looked for potential candidate genes co-localizing with QTLs. RESULTS: In our case the QTL analysis method had an important impact on QTL detection. We were able to identify new genomic regions controlling resistance to carrier-state, in particular by testing the existence of two segregating QTLs. But some of the previously identified QTLs were not confirmed. Interestingly, two QTLs were detected on chromosomes 2 and 3, close to the locations of the major QTLs controlling resistance to colonization and to candidate genes involved in the immune response identified in other, independent studies. CONCLUSIONS: Due to the lack of stability of the QTLs detected, we suggest that interesting regions for further studies are those that were identified in several independent studies, which is the case of the QTL regions on chromosomes 2 and 3, involved in resistance to both Salmonella colonization and carrier state. These observations provide evidence of common genes controlling S. Typhimurium colonization and S. Enteritidis carrier-state in chickens.201222613937
6136130.9987Complete genome sequences of Lacticaseibacillus paracasei INIA P272 (CECT 8315) and Lacticaseibacillus rhamnosus INIA P344 (CECT 8316) isolated from breast-fed infants reveal probiotic determinants. Lacticaseibacillus paracasei INIA P272 and Lacticaseibacillus rhamnosus INIA P344, isolated from breast-fed infants, are two promising bacterial strains for their use in functional foods according to their demonstrated probiotic and technological characteristics. To better understand their probiotic characteristics and evaluate their safety, here we report the draft genome sequences of both strains as well as the analysis of their genetical content. The draft genomes of L. paracasei INIA P272 and L. rhamnosus INIA P344 comprise 3.01 and 3.26 Mb, a total of 2994 and 3166 genes and a GC content of 46.27 % and 46.56 %, respectively. Genomic safety was assessed following the EFSA guidelines: the identification of both strains was confirmed through Average Nucleotide Identity, and the absence of virulence, pathogenic and antibiotic resistance genes was demonstrated. The genome stability analysis revealed the presence of plasmids and phage regions in both genomes, however, CRISPR sequences and other mechanisms to fight against phage infections were encoded. The probiotic abilities of both strains were supported by the presence of genes for the synthesis of SCFA, genes involved in resistance to acid and bile salts or a thiamine production cluster. Moreover, the encoded exopolysaccharide biosynthesis genes could provide additional protection against the deleterious gastrointestinal conditions, besides which, playing a key role in adherence and coaggregation of pathogenic bacteria together with the high number of adhesion proteins and domains encoded by both genomes. Additionally, the bacteriocin cluster genes found in both strains, could provide an advantageous ability to compete against pathogenic bacteria. This genomic study supports the probiotic characteristics described previously for these two strains and satisfies the safety requirements to be used in food products.202235868412
8372140.9987A Plasmid-Encoded Putative Glycosyltransferase Is Involved in Hop Tolerance and Beer Spoilage in Lactobacillus brevis. Lactobacillus brevis beer-spoiling strains harbor plasmids that contain genes such as horA, horC, and hitA which are known to confer hop tolerance. The L. brevis beer-spoiling strain UCCLBBS124, which possesses four plasmids, was treated with novobiocin, resulting in the isolation of UCCLBBS124 derivatives exhibiting hop sensitivity and an inability to grow in beer. One selected derivative was shown to have lost a single plasmid, here designated UCCLBBS124_D, which harbors the UCCLBBS124_pD0015 gene, predicted to encode a glycosyltransferase. Hop tolerance and growth in beer were restored when UCCLBBS124_pD0015 was introduced in one of these hop-sensitive derivatives on a plasmid. We hypothesize that this gene modifies the surface composition of the polysaccharide cell wall, conferring protection against hop compounds. Furthermore, the introduction of this gene in trans in L. brevis UCCLB521, a strain that cannot grow in and spoil beer, was shown to furnish the resulting strain with the ability to grow in beer, while its expression also conferred phage resistance. This study underscores how the acquisition of certain mobile genetic elements plays a role in hop tolerance and beer spoilage for strains of this bacterial species.IMPORTANCELactobacillus brevis is a member of the lactic acid bacteria and is often reported as the causative agent of food or beverage spoilage, in particular, that of beer. Bacterial spoilage of beer may result in product withdrawal or recall, with concomitant economic losses for the brewing industry. A very limited number of genes involved in beer spoilage have been identified and primarily include those involved in hop resistance, such as horA, hitA, and horC However, since none of these genes are universal, it is clear that there are likely (many) other molecular players involved in beer spoilage. Here, we report on the importance of a plasmid-encoded glycosyltransferase associated with beer spoilage by L. brevis that is involved in hop tolerance. The study highlights the complexity of the genetic requirements to facilitate beer spoilage and the role of multiple key players in this process.202031757821
1788150.9987Draft 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
1789160.9987Genomic 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
4684170.9987Genomic 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
251180.9987Deep sequencing analysis of the Kineococcus radiotolerans transcriptome in response to ionizing radiation. Kineococcus radiotolerans is a gram-positive, radiation-resistant bacterium that was isolated from a radioactive environment. The synergy of several groups of genes is thought to contribute to the radio-resistance of this species of bacteria. Sequencing of the transcriptome, RNA sequencing (RNA-seq), using deep sequencing technology can reveal the genes that are differentially expressed in response to radiation in this bacterial strain. In this study, the transcriptomes of two samples (with and without irradiation treatment) were sequencing by deep sequencing technology. After the bioinformatics process, 143 genes were screened out by the differential expression (DE) analysis. In all 143 differentially expressed genes, 20 genes were annotated to be related to the radio-resistance based on the cluster analysis by the cluster of orthologous groups of proteins (COG) annotation which were validated by the quantitative RT-PCR. The pathway analysis revealed that these 20 validated genes were related to DNA damage repair, including recA, ruvA and ruvB, which were considered to be the key genes in DNA damage repair. This study provides the foundation to investigate the regulatory mechanism of these genes.201525467197
5166190.9987Illegitimate recombination: an efficient method for random mutagenesis in Mycobacterium avium subsp. hominissuis. BACKGROUND: The genus Mycobacterium (M.) comprises highly pathogenic bacteria such as M. tuberculosis as well as environmental opportunistic bacteria called non-tuberculous mycobacteria (NTM). While the incidence of tuberculosis is declining in the developed world, infection rates by NTM are increasing. NTM are ubiquitous and have been isolated from soil, natural water sources, tap water, biofilms, aerosols, dust and sawdust. Lung infections as well as lymphadenitis are most often caused by M. avium subsp. hominissuis (MAH), which is considered to be among the clinically most important NTM. Only few virulence genes from M. avium have been defined among other things due to difficulties in generating M. avium mutants. More efforts in developing new methods for mutagenesis of M. avium and identification of virulence-associated genes are therefore needed. RESULTS: We developed a random mutagenesis method based on illegitimate recombination and integration of a Hygromycin-resistance marker. Screening for mutations possibly affecting virulence was performed by monitoring of pH resistance, colony morphology, cytokine induction in infected macrophages and intracellular persistence. Out of 50 randomly chosen Hygromycin-resistant colonies, four revealed to be affected in virulence-related traits. The mutated genes were MAV_4334 (nitroreductase family protein), MAV_5106 (phosphoenolpyruvate carboxykinase), MAV_1778 (GTP-binding protein LepA) and MAV_3128 (lysyl-tRNA synthetase LysS). CONCLUSIONS: We established a random mutagenesis method for MAH that can be easily carried out and combined it with a set of phenotypic screening methods for the identification of virulence-associated mutants. By this method, four new MAH genes were identified that may be involved in virulence.201222966811