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516500.9410Transcription profiling of resistance to Bti toxins in the mosquito Aedes aegypti using next-generation sequencing. The control of mosquitoes transmitting infectious diseases relies mainly on the use of chemical insecticides. However, resistance to most chemical insecticides threatens mosquito control programs. In this context, the spraying of toxins produced by the bacteria Bacillus thuringiensis subsp. israelensis (Bti) in larval habitats represents an alternative to chemical insecticides and is now widely used for mosquito control. Recent studies suggest that resistance of mosquitoes to Bti toxin may occur locally but mechanisms have not been characterized so far. In the present study, we investigated gene transcription level variations associated with Bti toxin resistance in the mosquito Aedes aegypti using a next-generation sequencing approach. More than 6 million short cDNA tags were sequenced from larvae of two strains sharing the same genetic background: a Bti toxins-resistant strain and a susceptible strain. These cDNA tags were mapped with a high coverage (308 reads per position in average) to more than 6000 genes of Ae. aegypti genome and used to quantify and compare the transcription level of these genes between the two mosquito strains. Among them, 86 genes were significantly differentially transcribed more than 4-fold in the Bti toxins resistant strain comparatively to the susceptible strain. These included gene families previously associated with Bti toxins resistance such as serine proteases, alkaline phosphatase and alpha-amylase. These results are discussed in regards of potential Bti toxins resistance mechanisms in mosquitoes.201222115744
519210.9392Genome Sequencing Analysis of a Rare Case of Blood Infection Caused by Flavonifractor plautii. BACKGROUND Flavonifractor plautii belongs to the clostridium family, which can lead to local infections as well as the bloodstream infections. Flavonifractor plautii caused infection is rarely few in the clinic. To understand better Flavonifractor plautii, we investigated the drug sensitivity and perform genome sequencing of Flavonifractor plautii isolated from blood samples in China and explored the drug resistance and pathogenic mechanism of the bacteria. CASE REPORT The Epsilometer test method was used to detect the sensitivity of flavonoid bacteria to antimicrobial agents. PacBio sequencing technology was employed to sequence the whole genome of Flavonifractor plautii, and gene prediction and functional annotation were also analyzed. Flavonifractor plautii displayed sensitivity to most drugs but resistance to fluoroquinolones and tetracycline, potentially mediated by tet (W/N/W). The total genome size of Flavonifractor plautii was 4,573,303 bp, and the GC content was 59.78%. Genome prediction identified 4,506 open reading frames, including 9 ribosomal RNAs and 66 transfer RNAs. It was detected that the main virulence factor-coding genes of the bacteria were the capsule, polar flagella and FbpABC, which may be associated with bacterial movement, adhesion, and biofilm formation. CONCLUSIONS The results of whole-genome sequencing could provide relevant information about the drug resistance mechanism and pathogenic mechanism of bacteria and offer a basis for clinical diagnosis and treatment.202438881048
543520.9392Distribution of fibronectin-binding protein genes (prtF1 and prtF2) and streptococcal pyrogenic exotoxin genes (spe) among Streptococcus pyogenes in Japan. Two hundred and seventy-two strains of Streptococcus pyogenes isolated from patients with invasive and noninvasive infections in Japan were evaluated for the prevalence of fibronectin-binding protein genes (prtF1 and prtF2). The possible associations of the genes with streptococcal pyrogenic exotoxin genes, macrolide resistance genes, and emm types were also evaluated. Overall, about 50% of S. pyogenes isolates carried fibronectin-binding protein genes. The prevalence of the prtF1 gene was significantly higher among isolates from noninvasive infections (71.4%) than among isolates from invasive infections (30.8%; P = 0.0037). Strains possessing both the prtF1 and prtF2 genes were more likely to be isolates from noninvasive infections than isolates from invasive infections (50.6% vs 15.4%; P = 0.019). S. pyogenes isolates with streptococcus pyrogenic exotoxin genes (speA and speZ) were more common among isolates without fibronectin-binding protein genes. The speC gene was more frequently identified among isolates with fibronectin-binding protein genes (P = 0.05). Strains belonging to emm75 or emm12 types more frequently harbored macrolide resistance genes than other emm types (P = 0.0094 and P = 0.043, respectively). Strains carrying more than one repeat at the RD2 region of the prtF1 gene and the FBRD region of the prtF2 gene were more prevalent among strains with macrolide resistance genes than among strains negative for macrolide resistance genes. These genes (i.e., the prtF1, prtF2, and spe genes) may enable host-bacteria interaction, and internalization in the host cell, but may not enable infection complications such as invasive diseases.200920012726
519430.9391Evaluation of the CosmosID Bioinformatics Platform for Prosthetic Joint-Associated Sonicate Fluid Shotgun Metagenomic Data Analysis. We previously demonstrated that shotgun metagenomic sequencing can detect bacteria in sonicate fluid, providing a diagnosis of prosthetic joint infection (PJI). A limitation of the approach that we used is that data analysis was time-consuming and specialized bioinformatics expertise was required, both of which are barriers to routine clinical use. Fortunately, automated commercial analytic platforms that can interpret shotgun metagenomic data are emerging. In this study, we evaluated the CosmosID bioinformatics platform using shotgun metagenomic sequencing data derived from 408 sonicate fluid samples from our prior study with the goal of evaluating the platform vis-à-vis bacterial detection and antibiotic resistance gene detection for predicting staphylococcal antibacterial susceptibility. Samples were divided into a derivation set and a validation set, each consisting of 204 samples; results from the derivation set were used to establish cutoffs, which were then tested in the validation set for identifying pathogens and predicting staphylococcal antibacterial resistance. Metagenomic analysis detected bacteria in 94.8% (109/115) of sonicate fluid culture-positive PJIs and 37.8% (37/98) of sonicate fluid culture-negative PJIs. Metagenomic analysis showed sensitivities ranging from 65.7 to 85.0% for predicting staphylococcal antibacterial resistance. In conclusion, the CosmosID platform has the potential to provide fast, reliable bacterial detection and identification from metagenomic shotgun sequencing data derived from sonicate fluid for the diagnosis of PJI. Strategies for metagenomic detection of antibiotic resistance genes for predicting staphylococcal antibacterial resistance need further development.201930429253
846040.9385Correlation Analysis of the Transcriptome and Gut Microbiota in Salmo trutta Resistance to Aeromonas salmonicida. Aeromonas salmonicida is a major pathogenic bacterium that poses a significant threat to salmonid fish. Yadong County, located in the Xizang Autonomous Region, is renowned for its characteristic industry of Salmo trutta aquaculture. In recent years, the outbreak of Bacterial Gill Disease (BGD) has led to substantial economic losses for S. trutta farmers. Our prior research identified A. salmonicida as one of the primary culprits behind BGD. To mitigate the impact of A. salmonicida on S. trutta, we conducted a comprehensive study aimed at identifying genes associated with resistance to A. salmonicida. This involved transcriptome sequencing and 16S rRNA sequencing of intestinal flora, providing valuable insights for the study of disease resistance in S. trutta. In this study, we identified 324 genera with 5171 ASVs in the susceptible group and 293 genera with 5669 ASVs in the resistant group. Notably, Methylobacterium and Sphingomonas were common bacteria present in the salmon's gut, and their proportions remained relatively stable before and after infection. Shewanella, with its antagonistic relationship with Aeromonas, may play a crucial role in the salmon's defense against A. salmonicida. Several related genes were identified, including angptl4, cipcb, grasp, ccr9a, sulf1, mtmr11, B3GNT3, mt2, PLXDC1, and ank1b.202439458292
516250.9384Genomic identification and characterization of Streptococcus oralis group that causes intraamniotic infection. BACKGROUND: Intraamniotic infection is a cause of spontaneous preterm labor. Streptococcus mitis is a common pathogen identified in intraamniotic infection, with the possible route of hematogenous dissemination from the oral cavity or migration from the vaginal canal. However, there are a few reports on Streptococcus oralis, a member of the S. mitis group, as a cause of pathogen in intraamniotic infection. We reported herein whole genome sequencing and comparative genomic analysis of S. oralis strain RAOG5826 that causes intraamniotic infection. RESULTS: Streptococcus mitis was initially identified from amniotic fluid, vaginal swab, and fetal blood of a patient presenting with preterm prelabor rupture of membranes with intraamniotic infection by the use of conventional microbiological methods (biochemical phenotype, MALDI-ToF, 16 S rRNA). Subsequently, this strain was later identified as S. oralis RAOG5826 by whole-genome hybrid sequencing. Genes involved in macrolide and tetracycline resistance, namely ermB and tet(M), and mutations in penicillin-binding protein were present in the genome. Moreover, potential virulence genes were predicted and compared with other Streptococcal species. CONCLUSION: We reported a comprehensive genomic analysis of S. oralis, which causes intraamniotic infection. S. mitis was initially identified by conventional microbiological identification. However, whole-genome hybrid sequencing demonstrates S. oralis with complete profiles of antimicrobial resistance genes and potential virulence factors. This study highlights the limitations of traditional techniques and underscores the importance of genomic sequencing for accurate diagnosis and tailored antimicrobial treatment. The study also suggests that S. oralis may be an underestimated pathogen in intraamniotic infection.202541023353
538260.9382Characterization of Streptococcus pyogenes from Animal Clinical Specimens, Spain. Streptococcus pyogenes appears to be almost exclusively restricted to humans, with few reports on isolation from animals. We provide a detailed characterization (emm typing, pulsed-field gel electrophoresis [PFGE], and multilocus sequence typing [MLST]) of 15 S. pyogenes isolates from animals associated with different clinical backgrounds. We also investigated erythromycin resistance mechanisms and phenotypes and virulence genes. We observed 2 emm types: emm12 (11 isolates) and emm77 (4 isolates). Similarly, we observed 2 genetic linages, sequence type (ST) 26 and ST63. Most isolates exhibited the M macrolide resistance phenotype and the mefA/ermB genotype. Isolates were grouped into 2 clones on the basis of emm-MLST-PFGE-virulence gene profile combinations: clone 1, characterized by the combined genotype emm12-ST36-pulsotype A-speG; and clone 2, characterized by the genotype emm77-ST63-pulsotype B-speC. Our results do not show conclusively that animals may represent a new reservoir of S. pyogenes but indicate the ability of human-derived S. pyogenes isolates to colonize and infect animals.201729148379
543170.9381A comprehensive analysis of antimicrobial resistance of clinical emm89 Streptococcus pyogenes in Japan. OBJECTIVES: Streptococcus pyogenes is involved in a wide range of diseases, including pharyngitis and life-threatening invasive infections. Increasing prevalence of antimicrobial resistance (AMR) has been reported worldwide in various bacteria, limiting the use of antibiotics in infection cases. The present study investigated the AMR of most prevalent S. pyogenes emm types, including emm89 strains in Japan. METHODS: A total of 368 previously identified S. pyogenes isolates (311 emm89 strains and 57 of other emm types), which were previously isolated from patients with invasive and non-invasive infections throughout Japan, were used in the analyses. The minimum inhibitory concentrations of seven antibiotics, including penicillin-G, azithromycin (AZM) and clindamycin, were determined, and whole-genome sequences of AMR-associated genes were screened. RESULTS: We identified 47 resistant strains, of which 91.49% (43/47) were resistant to AZM and/or clindamycin. A strong correlation was observed between non-invasive phenotypes and AMR. Whole-genome analysis indicated the wide distribution of three AMR-related genes, ermT, folP and lmrP, among the emm89 strains. Additionally, tetO was detected in tetracycline-resistance and soxS and mel was detected in chloramphenicol-resistance only in emm4 strains. CONCLUSIONS: The high prevalence of S. pyogenes resistance to AZM and/or clindamycin poses a threat to public health in Japan; thus, the development of next-generation antimicrobial therapies is imperative.202539973909
219280.9378Distribution and Drug Resistance of Pathogenic Bacteria in Diabetic Patients with Double J-Stent Associated Infections. OBJECTIVE: To analyze the distribution and drug resistance of pathogenic bacteria in diabetic patients with double J-stent associated infections, and to explore the strategies for prevention and treatment of the infections. METHODS: From January 2019 to December 2021, 266 diabetic patients treated with double J-stent placement in our hospital assessed for eligibility were recruited. Urine and double J-stent samples were collected for pathogenicity assay and screened for biofilm bacteria. Pathogenic bacteria distribution and drug resistance were examined. RESULTS: A total of 97 strains (36.5%) of pathogenic bacteria were isolated from urine samples and 129 strains (48.5%) from double J-stent samples (P > 0.05). 3 strains (1.1%) of biofilm bacteria were separated from urine samples and 106 strains (39.8%) from double J-stent samples (P < 0.05). In the double J-stent samples, there were significantly higher ratios of Gram-positive bacteria separated from biofilm bacteria versus the urine-cultured pathogens (44.3%/61.3%, P < 0.05), and higher drug resistance was observed in biofilm bacteria versus urine-cultured pathogens (P < 0.05). Fosfomycin tromethamine showed remarkable susceptibility to both urinary cultured pathogens and double J-stent biofilm bacteria. CONCLUSION: Diabetic patients with double J-stent biofilm-positive bacteria are mainly Gram-positive bacteria, which are prone to biofilm formation and show strong drug resistance.202235652084
236790.9378Vancomycin resistant Streptococcus equi subsp. equi isolated from equines suffering from respiratory manifestation in Egypt. BACKGROUND AND AIM: Upper respiratory tract infections are common in horses and can be caused by a variety of pathogens, mainly Streptococcus equi subsp. equi, which are a significant equine pathogen causing major health issues as well as financial losses to the equine industry. This study aimed to determine the prevalence of Streptococcal bacteria in equines in Egypt, and characterize vancomycin-resistant S. equi subsp. equi phenotypically and genotypically. MATERIALS AND METHODS: S. equi subsp. equi was isolated from internal nares of horses. All strains were confirmed by polymerase chain reaction-based detection of Streptococcus genus-specific 16S rRNA, sodA and seeI genes. Antibiotic susceptibility was determined phenotypically using the disk diffusion method. Genotypic detection of antibiotic resistance genes was performed by analyzing as b-lactamase resistance (blaZ), tetracycline resistance (tetK), vancomycin resistance (vanA), and chloramphenicol resistance (fexA). RESULTS: Eight streptococcal isolates were confirmed as S. equi subsp. equi. The genotypic characterization of antibiotic resistance showed resistance to vanA and tetK, with a frequency of 87.5% and 12.5%, respectively, while the frequency of sensitivity was 100% for blaz gene and fexA gene. CONCLUSION: In this study, we assessed vancomycin-resistant S. equi subsp. equi from equines suffering from respiratory manifestation in Egypt.202134475702
8442100.9378Staphylococcus epidermidis undergoes global changes in gene expression during biofilm maturation in platelet concentrates. BACKGROUND: Staphylococcus epidermidis forms surface-attached aggregates (biofilms) when grown in platelet concentrates (PCs). Comparative transcriptome analyses were undertaken to investigate differential gene expression of S. epidermidis biofilms grown in PCs. STUDY DESIGN AND METHODS: Two S. epidermidis strains isolated from human skin (AZ22 and AZ39) and one strain isolated from contaminated PCs (ST02) were grown in glucose-supplemented Trypticase Soy Broth (TSBg) and PCs. RNA was extracted and sequenced using Illumina HiSeq. Differential expression analysis was done using DESeq, and significantly differentially expressed genes (DEGs) were selected. DEGs were subjected to Kyoto encyclopedia of genes and genomes and Gene Ontology analyses. Differential gene expression was validated with quantitative reverse transcription-PCR. RESULTS: A total of 436, 442, and 384 genes were expressed in AZ22, AZ39, and ST02, respectively. DEG analysis showed that 170, 172, and 117 genes were upregulated in PCs in comparison to TSBg, whereas 120, 135, and 89 genes were downregulated (p < .05) in mature biofilms of AZ22, AZ39, and ST02, respectively. Twenty-seven DEGs were shared by all three strains. While 76 DEGs were shared by AZ22 and AZ39, only 34 and 21 DEGs were common between ST02, and AZ22 and AZ39, respectively. Significant transcriptional expression changes were observed in genes involved in platelet-bacteria interaction, biofilm formation, production of virulence factors, and resistance to antimicrobial peptides and antibiotics. CONCLUSION: Differential gene expression in S. epidermidis is triggered by the stressful PC storage environment. Upregulation of virulence and antimicrobial resistance genes could have clinical implications for transfusion patients.202133904608
8476110.9377Identification of a Major QTL (qRRs-10.1) That Confers Resistance to Ralstonia solanacearum in Pepper (Capsicum annuum) Using SLAF-BSA and QTL Mapping. The soilborne pathogen Ralstonia solanacearum is the causal agent of bacterial wilt (BW), a major disease of pepper (Capsicum annuum). The genetic basis of resistance to this disease in pepper is not well known. This study aimed to identify BW resistance markers in pepper. Analysis of the dynamics of bioluminescent R. solanacearum colonization in reciprocal grafts of a resistant (BVRC 1) line and a susceptible (BVRC 25) line revealed that the resistant rootstock effectively suppressed the spreading of bacteria into the scion. The two clear-cut phenotypic distributions of the disease severity index in 440 F2 plants derived from BVRC 25 × BVRC 1 indicated that a major genetic factor as well as a few minor factors that control BW resistance. By specific-locus amplified fragment sequencing combined with bulked segregant analysis, two adjacent resistance-associated regions on chromosome 10 were identified. Quantitative trait (QTL) mapping revealed that these two regions belong to a single QTL, qRRs-10.1. The marker ID10-194305124, which reached a maximum log-likelihood value at 9.79 and accounted for 19.01% of the phenotypic variation, was located the closest to the QTL peak. A cluster of five predicted R genes and three defense-related genes, which are located in close proximity to the significant markers ID10-194305124 or ID10-196208712, are important candidate genes that may confer BW resistance in pepper.201931771239
5193120.9377Antibiotic resistance genes prediction via whole genome sequence analysis of Stenotrophomonas maltophilia. BACKGROUND: Stenotrophomonas maltophilia (S. maltophilia) is the first dominant ubiquitous bacterial species identified from the genus Stenotrophomonas in 1943 from a human source. S. maltophilia clinical strains are resistance to several therapies, this study is designed to investigate the whole genome sequence and antimicrobial resistance genes prediction in Stenotrophomonas maltophilia (S. maltophilia) SARC-5 and SARC-6 strains, isolated from the nasopharyngeal samples of an immunocompromised patient. METHODS: These bacterial strains were obtained from Pakistan Institute of Medical Sciences (PIMS) Hospital, Pakistan. The bacterial genome was sequenced using a whole-genome shotgun via a commercial service that used an NGS (Next Generation Sequencing) technology called as Illumina Hiseq 2000 system for genomic sequencing. Moreover, detailed in-silico analyses were done to predict the presence of antibiotic resistance genes in S. maltophilia. RESULTS: Results showed that S. maltophilia is a rare gram negative, rod-shaped, non sporulating bacteria. The genome assembly results in 24 contigs (>500 bp) having a size of 4668,850 bp with 65.8% GC contents. Phylogenetic analysis showed that SARC-5 and SARC-6 were closely related to S. maltophilia B111, S. maltophilia BAB-5317, S. maltophilia AHL, S. maltophilia BAB-5307, S. maltophilia RD-AZPVI_04, S. maltophilia JFZ2, S. maltophilia RD_MAAMIB_06 and lastly with S. maltophilia sp ROi7. Moreover, the whole genome sequence analysis of both SARC-5 and SARC-6 revealed the presence of four resistance genes adeF, qacG, adeF, and smeR. CONCLUSION: Our study confirmed that S. maltophilia SARC-5 and SARC-6 are one of the leading causes of nosocomial infection which carry multiple antibiotic resistance genes.202438128408
5774130.9376The correlation between the presence of quorum sensing, toxin-antitoxin system genes and MIC values with ability of biofilm formation in clinical isolates of Pseudomonas aeruginosa. INTRODUCTION: Pseudomonas aeruginosa is a Gram-negative bacterium that considered as important opportunistic human pathogen. One of the mechanisms that help bacteria to tolerate survival in adverse conditions and resistance to antibiotics is biofilm formation through quorum sensing (QS) signals and toxin-antitoxin (TA) systems. QS and TA are two systems that have important roles in biofilm formation. QS is a global regulatory mechanism that enable bacteria to communicate with each other by production of auto inducers (AI) molecules in population. Because of importance biofilm formation in P. aeruginosa infections, here, we studied frequency of QS and TA genes among clinical isolates of P. aeruginosa with ability of biofilm formation. MATERIALS AND METHODS: One hundred and forty clinical isolates of P. aeruginosa were collected from Tehran and Ilam hospitals. The isolates were identified by biochemical tests. Biofilm formation was evaluated by microplate method. After DNA extraction by boiling method, the frequency of QS genes (lasIR, rhlIR), and TA genes (mazEF, relBE, hipBA, ccdAB and mqsR) were analyzed by PCR. RESULTS: Our results showed that maximum resistance is related to aztreonam (72.85%) antibiotic. Most of isolates were able to produce biofilm (87.15%) and the majority of them formed strong biofilm (56.42%). PCR results showed that frequency of mazEF, relBE, hipBA, ccdAB, mqsR, lasIR and rhlIR genes were 85.71, 100, 1.42, 100, 57.14, 93.57 and 83.57 percent, respectively. CONCLUSION: Clinical isolates of P. aeruginosa had high ability to form biofilm, and QS and TA system genes among these isolates were very high (except hipBA genes). There are significaut correlation between biofilm for mation and present of QS and TA system genes.201425870745
2343140.9376Investigation of Virulence Genes of the Predominant Bacteria Associated with Renal Stones and their Correlation with Postoperative Septic Complications. PURPOSE: Nephrolithiasis is a worldwide disease, and 4.7% of the patients may develop postoperative sepsis. Characterization of virulence genes of bacteria associated with renal stones is still lacking in the literature. The study aimed to investigate the virulence genes of the predominant stone bacterial isolate and their association with postoperative septic complications in patients treated with percutaneous nephrolithotomy (PCNL). METHODS: Stone and midstream urine samples were collected from 200 nephrolithiasis patients who underwent PCNL. Microbiological examination and virulence profile were studied for the common bacteria isolated from the stones. RESULTS: Microbiological analysis revealed that Staphylococcus aureus was the predominant organism in stone samples (42.8%), while Escherichia coli (56.6%) was the dominant pathogen in midstream urine. Eight patients (4%) developed septic complications; stone culture was positive for S. aureus in seven and E. coli in one patient, while all but one had negative midstream urine. The patient with positive midstream urine culture had also S. aureus infection. Detection of virulence genes in S. aureus isolated from stones showed a high positivity of the hemolysine gene hla (93.3%) and adhesion gene fnbA (73.3%), whereas enterotoxin genes (sec and sea) were negative in all S. aureus stone cultures. Moreover, the adhesion genes (fnbB and can), hemolysine gene (hlb), panton-valentine leukocidin (pvl) gene and the enterotoxin gene (seb) were significantly higher in septic patients compared to the non-septic ones (p< 0.05). Interestingly, there was a significant relation between the existence of virulence genes and the resistance of antibiotics (p < 0.05). CONCLUSION: There has been a notable shift toward gram-positive organisms (S. aureus) in the stone culture. Moreover, S. aureus virulence genes were significantly attributed to the resistance of some antibiotics and postoperative septic complications, suggesting that the stone culture could be more informative than urine culture, especially in predicting the risk of postoperative sepsis.202235844358
5184150.9376In silico evaluation of genomic characteristics of Streptococcus infantarius subsp. infantarius for application in fermentations. This study aims to evaluate the in silico genomic characteristics of Streptococcus infantarius subsp. infantarius, isolated from Coalho cheese from Paraíba, Brazil, with a view to application in lactic fermentations. rRNA sequences from the 16S ribosomal region were used as input to GenBank, in the search for patterns that could reveal a non-pathogenic behavior of S. infantarius subsp. infantarius, comparing mobile genetic elements, antibiotic resistance genes, pan-genome analysis and multi-genome alignment among related species. S. infantarius subsp. infantarius CJ18 was the only complete genome reported by BLAST/NCBI with high similarity and after comparative genetics with complete genomes of Streptococcus agalactiae (SAG153, NJ1606) and Streptococcus thermophilus (ST106, CS18, IDCC2201, APC151) revealed that CJ18 showed a low number of transposases and integrases, infection by phage bacteria of the Streptococcus genus, absence of antibiotic resistance genes and presence of bacteriocin, folate and riboflavin producing genes. The genome alignment revealed that the collinear blocks of S. thermophilus ST106 and S. agalactiae SAG153 have inverted blocks when compared to the CJ18 genome due to gene positioning, insertions and deletions. Therefore, the strains of S. infantarius subsp. infantarius isolated from Coalho cheese from Paraíba showed genomic similarity with CJ18 and the mobility of genes analyzed in silico showed absence of pathogenicity throughout the genome of CJ18, indicating the potential of these strains for the dairy industry.202236417612
5884160.9375Early genetic diagnosis of clarithromycin resistance in Helicobacter pylori. BACKGROUND: The drug resistance rate of clinical Helicobacter pylori (H. pylori) isolates has increased. However, the mechanism of drug resistance remains unclear. In this study, drug-resistant H. pylori strains were isolated from different areas and different populations of Chinese for genomic analysis. AIM: To investigate drug-resistant genes in H. pylori and find the genes for the early diagnosis of clarithromycin resistance. METHODS: Three drug-resistant H. pylori strains were isolated from patients with gastritis in Bama County, China. Minimal inhibitory concentrations of clarithromycin, metronidazole, and levofloxacin were determined and complete genome sequencing was performed with annotation. Hp1181 and hp1184 genes were found in these strains and then detected by reverse transcription polymerase chain reaction. The relationships between hp1181 or hp1184 and clarithromycin resistance were ascertained with gene mutant and drug-resistant strains. The homology of the strains with hp26695 was assessed through complete genome detection and identification. Differences in genome sequences, gene quantity, and gene characteristics were detected amongst the three strains. Prediction and analysis of the function of drug-resistant genes indicated that the RNA expression of hp1181 and hp1184 increased in the three strains, which was the same in the artificially induced clarithromycin-resistant bacteria. After gene knockout, the drug sensitivity of the strains was assessed. RESULTS: The strains showing a high degree of homology with hp26695, hp1181, and hp1184 genes were found in these strains; the expression of the genes hp1184 and hp1181 was associated with clarithromycin resistance. CONCLUSION: Hp1181 and hp1184 mutations may be the earliest and most persistent response to clarithromycin resistance, and they may be the potential target genes for the diagnosis, prevention, and treatment of clarithromycin resistance.202134239272
1331170.9375Serotypes, antibiotic resistance, and virulence genes of Salmonella in children with diarrhea. BACKGROUND: Salmonella is an important foodborne pathogen that causes acute diarrhea in humans worldwide. This study analyzed the relationships of serotypes and antibiotic resistance with virulence genes of Salmonella isolated from children with salmonellosis. METHODS: Serological typing was performed using the slide-agglutination method. The Kirby-Bauer disk diffusion method was used to test antibiotic susceptibility. Twenty virulence genes were detected by PCR. RESULTS: Salmonella Typhimurium (21 isolates, 34.43%) and S Enteritidis (12 isolates, 19.67%) were the predominant species among the 61 isolates. Ampicillin resistance was most common (63.93%), and among the cephalosporins, resistance was most often found to cefotaxime, a third-generation cephalosporin (19.67%). Among the 20 virulence genes, prgH, ssrB, and pagC were detected in all Salmonella isolates. In S Typhimurium, the detection rates of hilA, sipB, marT, mgtC, sopB, pagN, nlpI, bapA, oafA, and tolC were high. In S Enteritidis, the detection rates of icmF, spvB, spvR, and pefA were high. Nitrofurantoin resistance was negatively correlated with the virulence gene bapA (P = .005) and was positively correlated with icmF, spvB, spvR, and pefA (P = .012, .008, .002, and .005, respectively), The P values between all other virulence genes and antibiotic resistance were >.05. CONCLUSION: Salmonella Typhimurium and S Enteritidis were the main serotypes in children with diarrhea in Hangzhou, China. Salmonella exhibited a high level of resistance to common antibiotics, and a high rate of bacteria carrying virulence genes was observed. However, no significant correlation was found between virulence genes and resistance to common antibiotics.202032797660
2342180.9374Correlation Analysis of Staphylococcus aureus Drug Resistance and Virulence Factors with Blood Cell Counts and Coagulation Indexes. OBJECTIVE: The influence of different Staphylococcus aureus variants on blood cells and coagulation system was evaluated by investigating the carrying status of drug resistance genes and virulence genes of methicillin-resistantStaphylococcus aureus (MRSA) and methicillin-sensitiveStaphylococcus aureus (MSSA). METHODS: A total of 105 blood culture-derivedStaphylococcus aureus strains were collected. The carrying status of drug resistance genes mecA and three virulence genes tst, pvl, and sasX was analyzed by polymerase chain reaction (PCR). The changes in routine blood routine counts and coagulation indexes of patients infected with different strains were analyzed. RESULTS: The results showed that the positive rate of mecA was consistent with that of MRSA. Virulence genes tst and sasX were detected only in MRSA. Compared with MSSA, patients infected with MRSA or MSSA patients infected with virulence factor, leukocyte count and neutrophil count in peripheral blood were significantly increased, and the platelet count decreased to a higher degree. Part thromboplastin time increased, D-dimer increased, but fibrinogen content decreased more. The changes of erythrocyte and hemoglobin had no significant correlation with whether Staphylococcus aureus carried virulence genes. CONCLUSION: The detection rate of MRSA in patients with positive Staphylococcus aureus in blood culture had exceeded 20%. The detected MRSA bacteria carried three virulence genes, tst, pvl, and sasX, which were more likely than MSSA. MRSA, which carries two virulence genes, is more likely to cause clotting disorders.202336846497
5793190.9373Association between Escherichia coli with NotI-restriction resistance and urinary tract infections. BACKGROUND: Escherichia coli is the most common cause of urinary tract infections (UTIs). It is widely accepted that uropathogenic E. coli (UPEC) mainly emerge from the distal gut microbiota. Identification of bacterial characteristics that are able to differentiate UPEC from fecal commensal strains will facilitate the development of novel strategies to detect and monitor the spread of UPEC. METHODS: Fifty fecal commensal, 83 UTI-associated and 40 biliary tract infection (BTI)-associated E. coli isolates were analyzed. The NotI restriction patterns of chromosomal DNA in the isolates were determined by pulse-field gel electrophoresis. The phylogenetic types and the presence of 9 known virulence genes of each isolate were determined by PCR analyses. Additionally, the susceptibilities of the isolates to antibiotics were revealed. Then the associations of NotI resistance with UTI-associated isolates, phylotypes, and antibiotic resistance were assessed. RESULTS: NotI resistance was correlated with UTI-associated isolates, compared to the fecal isolates. Consistently, NotI-resistant isolates harbored a greater number of virulence factors and mainly belonged to phylotype B2. Additionally NotI resistance was correlated with chloramphenicol resistance among the bacteria. Among the fecal, UTI-associated and BTI-associated groups, the distribution of NotI-resistant group B2 isolates was correlated with UTI-associated bacteria. CONCLUSION: NotI resistance alone is a potential marker for distinguishing fecal strains and UPEC, while the combination of NotI resistance and B2 phylogeny is a candidate marker to differentiate UPEC from fecal and other extraintestinal pathogenic E. coli. Additionally, NotI resistance may be valuable for assessing the potential of chloramphenicol resistance of E. coli.202234963576