Multilocus sequence typing analysis and second-generation sequencing analysis of Salmonella Wandsworth. - Related Documents




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248401.0000Multilocus sequence typing analysis and second-generation sequencing analysis of Salmonella Wandsworth. BACKGROUND: Salmonella Wandsworth is a rare serotype of Salmonella. This study analyzed the genotyping, genome structure, and molecular biological functions of Salmonella Wandsworth based on the results of multilocus sequence typing and next-generation sequencing genome assembly analysis. METHODS: Serological typing was performed using the slide-agglutination method. The micro broth dilution method was used to test antibiotic susceptibility. Multilocus sequence typing (MLST) was used to perform the homology analysis, while the second-generation sequencing genome analysis was used to analyze the whole genome of the bacteria. RESULTS: Salmonella Wandsworth is Group Q Salmonella. The MLST of this strain was ST1498. Salmonella Wandsworth was sensitive to antibiotics, such as ceftriaxone, imipenem, chloramphenicol, and colistin, but was resistant to ampicillin, cefalotin, gentamicin, and ciprofloxacin. The second-generation sequencing results showed that the genome sequence length of the bacteria was 5109457bp. Annotated COG library analysis generated 3,746 corresponding genes. After the comparison with the KEGG library, 1,340 genes, which participate in 19 types of metabolic pathways, were obtained. A total of 249 pathogenic factors and 2 disease islands were predicted. 2 CRISPR sites and 8 Cas sites were predicted. It can be seen from the evolutionary tree that Salmonella Wandsworth MLST1498 and Paratyphi B str.SPB7 are gathered together. We identified one resistance gene, namely, aac(6')-Iaa accounting for aminoglycoside resistance. CONCLUSION: Salmonella Wandsworth isolated in this study is Salmonella group Q. Consequently, it is necessary to strengthen the understanding of clinical infections of Salmonella Wandsworth and carry out continuous monitoring and research.202134245607
519810.9994In-depth comparative pathogenome, virulome, and resistome analysis of an extensive drug resistant Ralstonia mannitolilytica strain isolated from blood. INTRODUCTION: Ralstonia mannitolilytica is an global opportunistic pathogen responsible for various diseases. In this study, we reported the genome of a R. mannitolilytica isolate responsible for bacteremia in an acute exacerbation of chronic obstructive pulmonary disease (AECOPD). METHODS: Bacterial identification was performed with a Vitek2™ Automated System and 16S rRNA sequencing with BLASTn against the Non-Redundant Protein Sequence (Nr) database. Genome sequencing and analysis were performed using PacBio RS II sequencer, Hierarchical Genome Assembly Process assembly, as well as multiple annotation databases to better understand the innate features. Antibiotic resistance genes and virulence factors were specifically identified through Antibiotic Resistance Genes database and Virulence Factors of Pathogenic Bacteria databases. RESULTS: The complete genome sequence was assembled into two chromosomes with 3,495,817 bp and 1,342,871 bp in length and GC% of 65.37 % and 66.43 %, respectively. The two chromosomes were fully annotated. In chromosome 1 and 2, 19 and 14 antibiotic resistant genes and 48 and 55 virulence factors were predicted, respectively. Specifically, beta-lactam resistance genes bla(OXA-443), bla(OXA-444) were acquired. CONCLUSIONS: This study aids in the understanding of the innate features of R. mannitolilytica in AECOPD.202439306054
519720.9993Genome analysis of NDM-1 producing Morganella morganii clinical isolate. OBJECTIVE: To analyze the resistome and virulence genes of Morganella morganii F675, a multidrug-resistant clinical isolate using whole genome sequencing (WGS). METHODS: M. morganii F675 was isolated from a patient from Jerusalem, Israel. WGS was performed using both 454 and SOLiD sequencing technologies. Analyses of the bacterial resistome and other virulence genes were performed in addition to comparison with other available M. morganii genomes. RESULTS: The assembled sequence had a genome size of 4,127,528 bp with G+C content of 51%. The resistome consisted of 13 antibiotic resistance genes including blaNDM-1 located in a plasmid likely acquired from Acinetobacter spp. Moreover, we characterized for the first time the whole lipid A biosynthesis pathway in this species along with the O-antigen gene cluster, the urease gene cluster and several other virulence genes. CONCLUSION: The WGS analysis of this pathogen further provides insight into its pathogenicity and resistance to antibiotics.201425081858
546730.9993Whole genome sequencing-based classification of human-related Haemophilus species and detection of antimicrobial resistance genes. BACKGROUND: Bacteria belonging to the genus Haemophilus cause a wide range of diseases in humans. Recently, H. influenzae was classified by the WHO as priority pathogen due to the wide spread of ampicillin resistant strains. However, other Haemophilus spp. are often misclassified as H. influenzae. Therefore, we established an accurate and rapid whole genome sequencing (WGS) based classification and serotyping algorithm and combined it with the detection of resistance genes. METHODS: A gene presence/absence-based classification algorithm was developed, which employs the open-source gene-detection tool SRST2 and a new classification database comprising 36 genes, including capsule loci for serotyping. These genes were identified using a comparative genome analysis of 215 strains belonging to ten human-related Haemophilus (sub)species (training dataset). The algorithm was evaluated on 1329 public short read datasets (evaluation dataset) and used to reclassify 262 clinical Haemophilus spp. isolates from 250 patients (German cohort). In addition, the presence of antibiotic resistance genes within the German dataset was evaluated with SRST2 and correlated with results of traditional phenotyping assays. RESULTS: The newly developed algorithm can differentiate between clinically relevant Haemophilus species including, but not limited to, H. influenzae, H. haemolyticus, and H. parainfluenzae. It can also identify putative haemin-independent H. haemolyticus strains and determine the serotype of typeable Haemophilus strains. The algorithm performed excellently in the evaluation dataset (99.6% concordance with reported species classification and 99.5% with reported serotype) and revealed several misclassifications. Additionally, 83 out of 262 (31.7%) suspected H. influenzae strains from the German cohort were in fact H. haemolyticus strains, some of which associated with mouth abscesses and lower respiratory tract infections. Resistance genes were detected in 16 out of 262 datasets from the German cohort. Prediction of ampicillin resistance, associated with bla(TEM-1D), and tetracycline resistance, associated with tetB, correlated well with available phenotypic data. CONCLUSIONS: Our new classification database and algorithm have the potential to improve diagnosis and surveillance of Haemophilus spp. and can easily be coupled with other public genotyping and antimicrobial resistance databases. Our data also point towards a possible pathogenic role of H. haemolyticus strains, which needs to be further investigated.202235139905
178840.9993Draft 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
468450.9992Genomic 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
520060.9992Whole genome sequencing of the multidrug-resistant Chryseobacterium indologenes isolated from a patient in Brazil. Chryseobacterium indologenes is a non-glucose-fermenting Gram-negative bacillus. This emerging multidrug resistant opportunistic nosocomial pathogen can cause severe infections in neonates and immunocompromised patients. This study aimed to present the first detailed draft genome sequence of a multidrug-resistant C. indologenes strain isolated from the cerebrospinal fluid of an infant hospitalized at the Neonatal Intensive Care Unit of Brazilian Tertiary Hospital. We first analyzed the susceptibility of C. indologenes strain to different antibiotics using the VITEK 2 system. The strain demonstrated an outstanding resistance to all the antibiotic classes tested, including β-lactams, aminoglycosides, glycylcycline, and polymyxin. Next, C. indologenes was whole-genome-sequenced, annotated using Prokka and Rapid Annotation using Subsystems Technology (RAST), and screened for orthologous groups (EggNOG), gene ontology (GO), resistance genes, virulence genes, and mobile genetic elements using different software tools. The draft genome contained one circular chromosome of 4,836,765 bp with 37.32% GC content. The genomic features of the chromosome present numerous genes related to cellular processes that are essential to bacteria. The MDR C. indologenes revealed the presence of genes that corresponded to the resistance phenotypes, including genes to β-lactamases (bla (IND-13), bla (CIA-3), bla (TEM-116), bla (OXA-209), bla (VEB-15)), quinolone (mcbG), tigecycline (tet(X6)), and genes encoding efflux pumps which confer resistance to aminoglycosides (RanA/RanB), and colistin (HlyD/TolC). Amino acid substitutions related to quinolone resistance were observed in GyrA (S83Y) and GyrB (L425I and K473R). A mutation that may play a role in the development of colistin resistance was detected in lpxA (G68D). Chryseobacterium indologenes isolate harbored 19 virulence factors, most of which were involved in infection pathways. We identified 13 Genomic Islands (GIs) and some elements associated with one integrative and conjugative element (ICEs). Other elements linked to mobile genetic elements (MGEs), such as insertion sequence (ISEIsp1), transposon (Tn5393), and integron (In31), were also present in the C. indologenes genome. Although plasmids were not detected, a ColRNAI replicon type and the most resistance genes detected in singletons were identified in unaligned scaffolds. We provided a wide range of information toward the understanding of the genomic diversity of C. indologenes, which can contribute to controlling the evolution and dissemination of this pathogen in healthcare settings.202235966843
246970.9992Whole genome analysis of multidrug-resistant Citrobacter freundii B9-C2 isolated from preterm neonate's stool in the first week. BACKGROUND: Resistance to colistin, the last line therapy for infections caused by multidrug-resistant Gram-negative bacteria, represents a major public health threat. Citrobacter freundii B9-C2 which was isolated from the stool of preterm neonate on the first week of life, displayed resistance to almost all major antibiotics, including colistin. Through whole genome sequencing (WGS), we characterised the genome features that underline the antibiotic-resistance phenotype of this isolate. METHODS: Genome of C. freundii B9-C2 was sequenced on an Illumina MiSeq platform. The assembled genome was annotated and deposited into GenBank under the accession number CP027849. RESULTS: Multiple antimicrobial resistance genes including bla(CMY-66) were identified. Further, the presence of 15 antibiotic efflux pump-encoding resistance genes, including crp, baeR, hns, patA, emrB, msbA, acrA, acrB, emrR, mdtC, mdtB, mdtG, kdpE, mdfA and msrB, were detected and likely to account for the observed cephalosporins, carbapenems, aminoglycosides and monobactams resistance in C. freundii B9-C2. The isolate also presented unique virulence genes related to biofilm formation, motility and iron uptake. The genome was compared to publicly available genomes and it was closely related to strains with environmental origins. CONCLUSION: To the best of our knowledge, this is the first report of intestinal carriage of colistin-resistant C. freundii from the stool of a neonate in Malaysia. Using genomic analysis, we have contributed to the understanding of the potential mechanism of resistance and the phylogenetic relationship of the isolates with draft genomes available in the public domain.202032304769
178980.9992Genomic 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
546690.9992The 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
1642100.9991Characterization of resistance genes and plasmids from sick children caused by Salmonella enterica resistance to azithromycin in Shenzhen, China. INTRODUCTION: Samonella is 1 of 4 key global causes of diarrhoeal diseases, sometimes it can be serious, especially for yong children. Due to the extensive resistance of salmonella serotypes to conventional first-line drugs, macrolides (such as azithromycin) have been designated as the most important antibiotics for the treatment of salmonella. Antimicrobial resistance is a major public health problem in the world, and the mechanism of azithromycin resistance is rarely studied. METHODS: This study determined the azithromycin resistance and plasmids of Salmonella enterica isolates from children attending the Shenzhen Children's Hospital. The susceptibility of ampicillin (AMP), ciprofloxacin (CIP), ceftriaxone (CRO), sulfamethoxazole (SMZ), chloramphenicol (CL), and azithromycin (AZM) were detected and the genes and plasmids from azithromycin-resistant Salmonella were detected by Illumina hi-seq and Nanopore MinIone whole genome sequencing (WGS) using a map-based method, and the genomic background of these factors was evaluated using various bioinformatics tools. RESULTS: In total, 15 strains of nontyphoid Salmonella strains that were isolated (including S. typhimurium, S.London, S. Goldcoast, and S.Stanley) demonstrated resistance to azithromycin (minimum inhibitory concentration,MIC from 32 to >256 µg/mL), and the resistance rate was 3.08% (15/487). The sensitivity test to other antibiotics demonstrated 100% resistance to AMP, and the resistance to SMZ and CL was 86.7% and 80.0%, respectively. Through WGS analysis, all isolates were positive for a plasmid-encoded mphA gene. Plasmid incompatibility typing identified five IncFIB(K), five IncHI2/HI2A/Q1, two IncC, one IncHI2/HI2A/N, one IncR, one IncFII and one IncHI2/HI2A plasmids. Sequence analyses of plasmids revealed extensive homology to various plasmids or transposons in regions involved in plasmid replication/maintenance functions and/or in antibiotic resistance gene clusters. CONCLUSION: mphA is the main gene involved in azithromycin, a macrolide, and resistance to Salmonella. It is usually located on plasmids and easily spreads, hence posing a great threat to the current treatment of Salmonella infection. The plasmid sequence similarities suggest that the plasmids acquired resistance genes from a variety of enterica bacteria and underscore the importance of a further understanding of horizontal gene transfer among enterica bacteria.202337065212
1704110.9991Exploring virulence characteristics of Klebsiella pneumoniae isolates recovered from a Greek hospital. The objective of this study was to characterize the virulence characteristics of a collection of Klebsiella pneumoniae isolates collected from different clinical sources. A collection of 60 non-repetitive K. pneumoniae isolates, was studied. In vitro, virulence was analyzed by testing the survival of bacteria in pooled human serum. Isolates were typed by MLST. The genomes of 23 K. pneumoniae isolates, representatives of different STs and virulence profiles, were completely sequenced using the Illumina platform. Of note, 26/60 of K. pneumoniae isolates were resistant to killing by complement. Serum-resistant isolates belonged to distinct STs. Analysis of WGS data with VFDB showed the presence of several virulence genes related various virulence functions. Specifically, serum-resistant isolates carried a higher number of ORFs, which were associated with serum resistance, compared to serum-sensitive isolates. Additionally, analysis of WGS data showed the presence of multiple plasmid replicons that could be involved with the spread and acquisition of resistance and virulence genes. In conclusion, analysis of virulence characteristics showed that an important percentage (31.6%) of K. pneumoniae isolates were in vitro virulent by exhibiting resistance to serum. Thus, the presence of several virulence factors, in combination with the presence of multidrug resistance, could challenge antimicrobial therapy of infections caused by such bacteria.202540415138
2468120.9991Characterization of Pseudomonas kurunegalensis by Whole-Genome Sequencing from a Clinical Sample: New Challenges in Identification. Backgoround: The genus Pseudomonas encompasses metabolically versatile bacteria widely distributed in diverse environments, including clinical settings. Among these, Pseudomonas kurunegalensis is a recently described environmental species with limited clinical characterization. Objective and Methods: In this study, we report the genomic and phenotypic characterization of a P. kurunegalensis isolate, Pam1317368, recovered from a catheterized urine sample of a post-renal transplant patient without symptoms of urinary tract infection. Initial identification by MALDI-TOF MS misclassified the isolate as Pseudomonas monteilii. Whole-genome sequencing and average nucleotide identity (ANI) analysis (≥95%) confirmed its identity as P. kurunegalensis. The methodology included genomic DNA extraction, Illumina sequencing, genome assembly, ANI calculation, antimicrobial susceptibility testing, resistance gene identification and phylogenetic analysis. Results: Antimicrobial susceptibility testing revealed multidrug resistance, including carbapenem resistance mediated by the metallo-β-lactamase gene VIM-2. Additional resistance determinants included genes conferring resistance to fluoroquinolones and aminoglycosides. Phylogenetic analysis placed the isolate within the P. kurunegalensis clade, closely related to environmental strains. Conclusions: Although the clinical significance of this finding remains unclear, the presence of clinically relevant resistance genes in an environmental Pseudomonas species isolated from a human sample highlights the value of genomic surveillance and accurate species-level identification in clinical microbiology.202540700237
2483130.9991Comparative genomic analysis of Proteus spp. isolated from tree shrews indicated unexpectedly high genetic diversity. Proteus spp. are commensal gastrointestinal bacteria in many hosts, but information regarding the mutual relationships between these bacteria and their hosts is limited. The tree shrew is an alternative laboratory animal widely used for human disease research. However, little is known about the relationship between Proteus spp. and tree shrews. In this study, the complete genome sequencing method was used to analyse the characteristics of Proteus spp. isolated from tree shrews, and comparative genomic analysis was performed to reveal their relationships. The results showed that 36 Proteus spp. bacteria were isolated, including 34 Proteus mirabilis strains and two Proteus vulgaris strains. The effective rate of sequencing was 93.53%±2.73%, with an average GC content of 39.94%±0.25%. Briefly, 3682.89±90.37, 2771.36±36.01 and 2832.06±42.49 genes were annotated in the NCBI non-redundant nucleotide database (NR), SwissProt database and KEGG database, respectively. The high proportions of macrolide-, vancomycin-, bacitracin-, and tetracycline-resistance profiles of the strains were annotated in the Antibiotic Resistance Genes Database (ARDB). Flagella, lipooligosaccharides, type 1 fimbriae and P fimbriae were the most abundantly annotated virulence factors in the Virulence Factor Database (VFDB). SNP variants indicated high proportions of base transitions (Ts), homozygous mutations (Hom) and non-synonymous mutations (Non-Syn) in Proteus spp. (P<0.05). Phylogenetic analysis of Proteus spp. and other references revealed high genetic diversity for strains isolated from tree shrews, and host specificity of Proteus spp. bacteria was not found. Overall, this study provided important information on characteristics of genome for Proteus spp. isolated from tree shrews.202032084183
5949140.9991Genetic Features of Antarctic Acinetobacter radioresistens Strain A154 Harboring Multiple Antibiotic-Resistance Genes. While antibiotic-resistant bacteria have been detected in extreme environments, including Antarctica, to date there are no reports of Acinetobacter species isolated from this region. Here, we characterized by whole-genome sequencing (WGS) the genetic content of a single antibiotic-resistant Acinetobacter spp. isolate (A154) collected in Antarctica. The isolate was recovered in 2013 from soil samples at Fildes Peninsula, Antarctica, and was identified by detection of the intrinsic OXA-23 gene, and confirmed by Tetra Correlation Search (TCS) and WGS. The antibiotic susceptibility profile was determined by disc diffusion, E-test, and broth microdilution methods. From WGS data, the acquired resistome and insertion sequence (IS) content were identified by in silico analyses. Plasmids were studied by the alkaline lysis method followed by pulsed-field gel electrophoresis and conventional PCR. The A154 isolate was identified as A. radioresistens by WGS analysis and displayed >99.9 of similarity by TCS in relation with the databases. Moreover, it was resistant to ampicillin, ceftriaxone, ceftazidime, cefepime, cefotaxime, streptomycin, and kanamycin. Likewise, in addition to the intrinsic bla(OXA-23-like) gene, A154 harbored the plasmid-encoded antibiotic-resistance genes bla(PER-2), tet(B), aph(3')-Vla, strA, and strB, as well as a large diversity of ISs. This is the first report of antibiotic-resistant A. radioresistens in Antarctica. Our findings show the presence of several resistance genes which could be either intrinsic or acquired in the region.201931608244
5199150.9991Whole genome sequencing uncovers a novel IND-16 metallo-β-lactamase from an extensively drug-resistant Chryseobacterium indologenes strain J31. BACKGROUND: Chryseobacterium indologenes is an emerging opportunistic pathogen in hospital-acquired infection, which is intrinsically resistant to most antimicrobial agents against gram-negative bacteria. In the purpose of extending our understanding of the resistance mechanism of C. indologenes, we sequenced and analyzed the genome of an extensively antibiotic resistant C. indologenes strain, isolated from a Chinese prostate cancer patient. We also investigated the presence of antibiotic resistance genes, particularly metallo-β-lactamase (MBL) genes, and performed a comparative genomic analysis with other Chryseobacterium species. RESULTS: 16s rRNA sequencing indicated the isolate belongs to C. indologenes. We assembled a total of 1095M bp clean-filtered reads into 171 contigs by de novo assembly. The draft genome of C. indologenes J31 consisted of 5,830,795 bp with a GC content of 36.9 %. RAST analysis revealed the genome contained 5196 coding sequences (CDSs), 28 rRNAs, 81 tRNAs and 114 pseudogenes. We detected 90 antibiotic resistance genes from different drug classes in the whole genome. Notably, a novel bla(IND) allele bla(IND-16) was identified, which shared 99 % identity with bla(IND-8) and bla(IND-10). By comparing strain J31 genome to the closely four related neighbors in the genus Chryseobacterium, we identified 2634 conserved genes, and 1449 unique genes. CONCLUSIONS: In this study, we described the whole genome sequence of C. indologenes strain J31. Numerous resistance determinants were detected in the genome and might be responsible for the extensively antibiotic resistance of this strain. Comparative genomic analysis revealed the presence of considerable strain-specific genes which would contribute to the distinctive characteristics of strain J31. Our study provides the insight of the multidrug resistance mechanism in genus Chryseobacterium.201627785154
1646160.9991Draft genome analysis of a multidrug-resistant Pseudomonas aeruginosa CMPL223 from hospital wastewater in Dhaka, Bangladesh. OBJECTIVES: Multidrug-resistant (MDR) clones of Pseudomonas aeruginosa can cause complicated infections in human. The emergence of ST664 of MDR P. aeruginosa has been reported in Nepal, Iran and China. Here, we present the draft genome analysis of a MDR P. aeruginosa CMPL223 isolated from hospital wastewater in Bangladesh to understand antimicrobial resistance trends and pathogenicity. METHODS: Cetrimide agar was used for isolation of P. aeruginosa. Polymerase chain reaction (PCR) was carried out for detection of biofilm and integron related genes. Bacterial susceptibility to antibiotics was determined by disc diffusion method. Sequencing of whole genomic DNA was performed using Illumina iSeq 100 platform. Following quality checking of raw reads, assembly and annotation of sequences, a wide array of in silico tools were used for characterization of draft genome. RESULTS: The isolate was a strong biofilm former, carried integron 1 in chromosomal DNA, and was predicted to be pathogenic. It belongs to sequence type ST664 and O7 serogroup. The assembled genome contained 12 acquired antimicrobial resistant (AMR) genes, 2 prophage regions, 240 virulence genes, 71 drug targets, 142 insertion sequences, and 1 CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) array. The isolate was resistant to 21 out of 23 antibiotics, except colistin and imipenem. Comprehensive Antibiotic Resistance Database and ResFinder revealed that bacteria harboured bla(OXA-50), bla(OXA-796), bla(PDC-374,) fosA, tet(G), sul1, catB7, aph(3')-iib and ant(4')-IIb genes, conferring resistance to different classes of antibiotics. The results of in vitro characterization were consistent with the possible expression of detected antibiotic resistant genes through in silico analysis. CONCLUSION: Our data suggested the emergence of MDR P. aeruginosa ST664, which needs control measures for limiting its dissemination.202235793775
2683170.9991High prevalence of virulence genes and multi-drug resistance in Pasteurella multocida from goats in Sichuan, China. Pasteurella multocida is one of the most important pathogens that infect goats, causing serious economic losses in the goat breeding industry. To understand the biological characteristics of P. multocida from goats, a comprehensive characterization of bacteria isolated from 342 nasal swabs and 8 lung tissue samples from goat farms in Sichuan, China, was performed. A total of 34 isolates were assigned to one capsular type, D, and one lipopolysaccharide (LPS) genotype, L3, indicating that the D: L3 was the predominant serotype in goat farms. In the 34 isolates, multiple virulence-related genes were identified, with a detection rate of 100 % (34/34) for the genes ompA, ompH, oma87, exbB, and exbD. It is noteworthy that the prevalence of the toxA gene, which encodes the P. multocida toxin (PMT), was found to be 85.2 % (29/34). Furthermore, antimicrobial susceptibility testing indicated a high prevalence of multidrug resistance, with resistance rates of 41.1 % for ampicillin, 38.2 % for tetracycline, and 32.3 % for kanamycin. Overall, this study provides a foundational understanding of the epidemiology and antimicrobial resistance of P. multocida in goats, offering insights for future prevention and control measures.202540174797
1705180.9991Formation ability and drug resistance mechanism of Klebsiella pneumoniae biofilm and capsule for multidrug-resistant. This study was to explore the formation ability of biofilm and capsule and the drug resistance mechanism for multidrug-resistant Klebsiella pneumoniae. firstly, 55 strains of K. pneumoniae were screened out from the body fluid specimens of the laboratory. The strains were drug-resistant, and the characteristics of clinical infections of these strains were analyzed. Secondly, all strains were tested for the presence of biofilms and capsules, and then the deoxyribonucleic acid (DNA) genomes of the strains extracted were detected using polymerase chain reaction (PCR) technology. Finally, the serotype genes and virulence genes of the strains were screened, and the relationship between these two genes and the formation of capsules and biofilms was analyzed and compared. A new generation of sequencing technology was applied to analyze the genome structure of K. pneumoniae, comparative genomics technology was adopted to analyze the drug resistance plasmids, and molecular cloning and other methods were utilized to clone the drug resistance-related genes. of the 55 strains of K. pneumoniae isolated clinically, 61.8% came from blood with a total number of 34 strains; 8 strains were from secretion specimens (accounting for 14.5% of the total); and 7 strains were from drainage fluid (accounting for 12.7% of the total), including 2 strains from pus, bile, and pleural fluid, respectively. The strains were tested by PCR, of which iroN virulence genes were the most (34 strains), accounting for 61.8%, followed by wabG and fimH (33 strains, accounting for 60% of the total), followed by magA, K2, K20, K1, and K57. The positive rates of the two virulence genes (fimH and wabG) were higher in positive strains of biofilm. The drug susceptibility results showed that ampicillin and amoxicillin were more resistant to capsule-positive strains than the capsule-negative strains. K. pneumoniae had been able to form a complete capsule and biofilm, the formation rate of biofilm was higher than that of the capsule, and there was an increasing trend. The two serotype genes (K20 and K2) accounted for relatively high proportions, and K. pneumoniae carried relatively more virulence genes (wabG and fimH), which may be closely related to the capsule production of K. pneumoniae. In addition, resistance-related genes were also transferred horizontally in different strains of bacteria, forming a wide range of drug resistance, which brought great difficulties to clinical work.202337953580
1701190.9991Type VI secretion system (T6SS) in Klebsiella pneumoniae, relation to antibiotic resistance and biofilm formation. BACKGROUND AND OBJECTIVES: The type VI secretion system (T6SS) was identified as a novel virulence factor in many Gram-negative bacteria. This study aimed to investigate the frequency of the T6SS genes in Klebsiella pneumoniae-causing different nosocomial infections, and to study the association between T6SS, antibiotic resistance, and biofilm formation in the isolated bacteria. MATERIALS AND METHODS: A total of fifty-six non-repetitive K. pneumoniae isolates were collected from different inpatients admitted at Sohag University Hospital from September 2022 to March 2023. Samples were cultured, colonies were identified, and antimicrobial sensitivity was done by VITEK® 2 Compact. Biofilm formation was checked using Congo red agar method. T6SS genes, and capsular serotypes were detected by PCR. RESULTS: Fifty-six K. pneumoniae isolates were obtained in culture. 38 isolates (67.86%) produced biofilm and 44 (78.57%) were positive for T6SS in PCR. There was a significant association between the presence of T6SS and resistance to the following antibiotics: meropenem, ciprofloxacin, and levofloxacin. All biofilm-forming bacteria had T6SS, with significant differences towards T6SS -positive bacteria. There was no significant association between T6SS, and the presence of certain capsular types. CONCLUSION: The T6SS-positive K. pneumoniae has greater antibiotic resistance, and biofilm-forming ability which is considered a potential pathogenicity of this emerging gene cluster.202337941882