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To sequence the whole genome of strains isolated from Fuzhou between 2018 and 2023, predict virulence genes, antimicrobial resistance genes, and sequence loci information, analyze the genetic relationships among different strains, and provide evidence for cholera prevention and control. Methods Whole genome sequencing was performed on 60 strains of Vibrio cholerae, and bioinformatics software was used for quality control, gene assembly, and prediction of the sequencing data. PubMLST, ResFinder, and VFDB databases were used to predict the multilocus sequence typing, antimicrobial resistance genes, and virulence genes of different strains. Combined with the NCBI database, the phylogenetic tree was constructed by the maximum likelihood method through the core cgSNP phylogenetic analysis and derecombination analysis. Results Based on the typing of 7 housekeeping genes, 60 Vibrio cholerae strains can be categorized into 16 known STs and 38 newly assigned STs. The clinical isolate H339 of serogroup O1 was identified as ST75. Serogroup O1 food isolates H13, H363, and H381 were all ST175. H263 and H357, the NOVC isolates, were both ST1218. H293 and H306 were ST1700. H311, H314, and H316 were all ST1699, with the remaining isolates displaying diversity. A total of 29 antimicrobial resistance genes were predicted, including aminoglycosides, β -lactams, quinolones, and folate pathway antagonists, with the majority of the strains carrying quinolones antimicrobial resistance genes. According to the VFDB prediction, all isolates had the virulence factors rtx and hlyA, 96.7% (58/60) of the strains carried the tlh genes, all serogroup O1 isolates carried tcp, zot, and ace genes, and all serogroup O1 clinical isolates carried ctxA genes. Phylogenetic tree analysis of the whole genome divided all strains into 20 branches, indicating high genomic divergence. Conclusions Thirty-eight new STs were identified. Genetic correlations were found among serogroup O1 food isolates, whereas serogroup O1 clinical isolates and serogroup O1 food isolates, as well as between serogroup O1 and NOVC strains, show distant phylogenetic relationships. There was diversity among the isolates. This study provides data support for the traceability of foodborne diseases. [ABSTRACT FROM AUTHOR]

Objective To perform the pathogenic and genomics analyses on isolates of Streptococcus suis (Ss) from three human infections in Shenzhen, aiming to provide a basis for the prevention and control of Ss outbreaks. Methods The suspected bacterial strains from three blood plate cultures of three critically ill patients in three hospitals were subjected to biochemical identification, matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS), and real-time fluorescent PCR identification, resulting in the identification of three strains positive for Streptococcus suis serotype 2 (SS2). Pure positive cultures were taken for an antimicrobial susceptibility test and extracted nucleic acids for whole-genome sequencing and analysis. The whole-genome sequencing and analysis included species identification, antibiotic resistance genes alignment, multilocus sequence typing (MLST), virulence genes alignment, and coregene-based phylogenetic tree analysis. Results The blood agar isolates from three patients were all identified as Ss, the VITEK 2 identified them as SS2, and MALDI-TOF-MS identified them as Ss. Real-time PCR results for the universal gene gdh and serotype 2 cps2 gene of Ss were both positive. The antimicrobial susceptibility test results showed that all three strains were resistant to erythromycin and clindamycin, with variable sensitivity to tetracycline. Whole-genome sequencing results showed that all three strains were identified as Ss, including one ST7 strain and two ST1 strains. The virulence gene prediction results based on the VFDB database showed that all three strains were positive for mrp, sly, and cps, indicating high virulence gene characteristics. The analysis of the phylogenetic tree based on coregene showed that the three strains were in different evolutionary branches, with two ST1 strains having a closer evolutionary distance. Conclusions The pathogens responsible for these three critically ill patients were SS2, and all three strains were resistant to erythromycin and clindamycin. Genetically, they all carried virulence genes that are found in highly virulent strains, while showed differences in MLST typing and phylogenetic tree analysis, indicating the presence of different genotypes of high pathogenicity SS2 in Shenzhen area and had caused sporadic cases, which requires high attention. [ABSTRACT FROM AUTHOR]

Objective To understand the distribution, serotype, and drug resistance of Salmonella in domestic sewage in Jining city, and to analyze the whole genome sequencing so as to provide scientific basis for the prevention and control of Salmonella. Methods From February to March in 2023, two samples of sewage from the intake of 3 urban sewage plants with 500 ml each were collected continuously for 7 weeks. A total of 42 sewage samples were collected for culture, isolation, and identification of Salmonella. The isolated Salmonella was tested for serum agglutination test and fluorescent quantitative PCR serotyping. In total 41 strains of Salmonella were tested for minimum inhibitory concentration (MIC) of 17 drugs in 9 classes by microbroth dilution method, followed by genome sequencing and phylogenetic analysis. Results The isolation rate of Salmonella from domestic sewage in Jining city was high. Among 24 positive samples, 41 strains of Salmonella were isolated, belonging to 9 serotypes, mainly S.Agona and S.Kentucky. Liying and Jidong sewage treatment plants had their own unique serotypes. Only one strain of S.Give was not resistant, and the other 40 strains of Salmonella were multi-drug resistant. The resistance rates to sulfamethoxazole, tetracycline, ampicillin, and streptomycin were more than 90%, and the resistance rate to ampicillin/sulbactam was more than 80%. There were 19 kinds of drug resistance spectra, of which SXT-TET-STR-AMP-AMS ranked the first place. The resistance spectra of different serotypes of Salmonella were different. S.Kentucky, S.Gold Coast, and S.Infant were multi-drug resistant seriously. The resistance spectrum of the same serotype was also inconsistent in different sewage plants, and the resistance was the most serious in Liying sewage plant. The CARD database was used to prediet drug resistance genes, mainly predicting 18 drug resistance genes in 8 types of drug resistance families, and the drug resistance phenotypes and drug resistance genes were almost all consistent. The ST types of different serotypes of Salmonella were different, and ST13 S.Agona was dominant. The phylogenetic tree was divided into 6 clusters, and strains in different sewage plants were in different branches, indicating that their genomes were different and had different sources. Conclusion There are various serotypes of salmonella in domestic sewage in Jining city, suggesting that they might have exist and spread in the population. Almost all strains are multi-drug resistant bacteria, carrying resistance genes extensively. Some types of strains live persistently and distribute across regions, leading to the potential risk to population. It is necessary to carry out continuous monitor, and scientific prevention and control measures need to be formulated to control the epidemic of salmonella and the aggravation of drug resistance. [ABSTRACT FROM AUTHOR]