To characterize the genomes of different emm-type group A Streptococcus (GAS), their virulence genes and drug resistance profiles in Tianjin City from 2011 to 2024. After PCR, a total of 42 strains with different years and emm types were selected for whole genome sequencing and multi-locus sequence typing (MLST), and the core genomes were used to generate a phylogenetic tree, after which the virulence genes and resistance genes were identified and analyzed, followed by the drug susceptibility test. In this study, the GAS strains were dominated by emm1 (50.0%) and emm12 (40.4%), and the MLST phenotypes were categorized into six types: ST36 (40.4%), ST1274 (26.1%), ST28 (23.8%), ST921 (4.7%), ST46 (2.3%), and ST403 (2.3%). There was a high consistency between their emm-types and ST types. A total of 68 virulence genes were detected in the genomes of 42 GAS strains, involving functional genes encoding exotoxin, bacterial adhesion, extracellular enzymes, etc. The virulence genes they carried were significantly different between emm1-type and emm12-type strains, such as speA. At the same time, the carrying rates of some virulence genes in the same emm-type strains changed with time, such as hyl. The resistance genes were basically the same among different emm-type strains except for the vanSE gene detected in all emm12 strains. The results of drug sensitivity showed that the GAS strains isolated in Tianjin City from 2011 to 2024 were sensitive to penicillin, cefazolin, chloramphenicol, vancomycin, and levofloxacin, while the resistance rates to erythromycin, azithromycin, clarithromycin, and clindamycin ranged from 88.5% to 100.0%, and there was a certain degree of consistency between the resistance phenotypes and the detected resistance genes. Overall, the main emm types and evolutionary features of GAS in Tianjin City from 2011 to 2024 were consistent with the dominant types in China, and the carrying rate of virulence genes and drug resistance genes differed significantly among different emm-type strains, and there were continuous evolution and variation in the prevalence of virulence genes in GAS.

To characterize the genomes of different emm-type group A Streptococcus (GAS), their virulence genes and drug resistance profiles in Tianjin City from 2011 to 2024. After PCR, a total of 42 strains with different years and emm types were selected for whole genome sequencing and multi-locus sequence typing (MLST), and the core genomes were used to generate a phylogenetic tree, after which the virulence genes and resistance genes were identified and analyzed, followed by the drug susceptibility test. In this study, the GAS strains were dominated by emm1 (50.0%) and emm12 (40.4%), and the MLST phenotypes were categorized into six types: ST36 (40.4%), ST1274 (26.1%), ST28 (23.8%), ST921 (4.7%), ST46 (2.3%), and ST403 (2.3%). There was a high consistency between their emm-types and ST types. A total of 68 virulence genes were detected in the genomes of 42 GAS strains, involving functional genes encoding exotoxin, bacterial adhesion, extracellular enzymes, etc. The virulence genes they carried were significantly different between emm1-type and emm12-type strains, such as speA. At the same time, the carrying rates of some virulence genes in the same emm-type strains changed with time, such as hyl. The resistance genes were basically the same among different emm-type strains except for the vanSE gene detected in all emm12 strains. The results of drug sensitivity showed that the GAS strains isolated in Tianjin City from 2011 to 2024 were sensitive to penicillin, cefazolin, chloramphenicol, vancomycin, and levofloxacin, while the resistance rates to erythromycin, azithromycin, clarithromycin, and clindamycin ranged from 88.5% to 100.0%, and there was a certain degree of consistency between the resistance phenotypes and the detected resistance genes. Overall, the main emm types and evolutionary features of GAS in Tianjin City from 2011 to 2024 were consistent with the dominant types in China, and the carrying rate of virulence genes and drug resistance genes differed significantly among different emm-type strains, and there were continuous evolution and variation in the prevalence of virulence genes in GAS.

Objective:To understand the contamination risk, drug resistance and virulence characteristics of cooked food pathogens in Tianjin.Methods:Pathogenic bacteria were isolated and identified in cooked food sold in Tianjin from 2019 to 2021, drug susceptibility test and whole genome sequencing were conducted for the isolates, and multilocus sequence typing, drug resistance gene, phenotype and virulence gene were analyzed for the data.Results:Ten pathogenic bacteria were isolated from 245 cooked food samples collected. The ST types of 7 Salmonella strains were ST40, ST198, ST14, ST13 and ST155. The two strains of Vibrio parahaemolyticus were ST647 and ST2622 respectively. One strain of Cronobacter sakazakii was ST8 type. All the 6 isolates were drug-resistant, and 3 of them were multidrug-resistant (MDR). A total of 63 drug-resistant genes were predicted in 10 isolates. Two Salmonella strains were ampicillin-chloramphenicol-streptomycin-sulfamethoxazole-tetracycline resistant (MDR-ACSSuT), and both Salmonella strains carried gyrA double mutations (S83F, D87N) and parC mutations (S80I). Vibrio parahaemolyticus mainly carries blaCARB and tet (35) genes, while Cronobacter sakazakii carries only one resistance gene blaCSA-1. A total of 163 virulence genes were predicted from 10 isolates. Conclusions:In this study, pathogenic bacteria are repeatedly detected in quail eggs, warning that other eggs besides chicken eggs should also pay special attention to the risk of contamination. The isolates in this study are all of the prevalent ST type with widespread drug resistance, and MDR-ACSSuT strains should be paid attention to. The key role of gyrA double mutation (S83F, D87N) and parC mutation (S80I) in the development of quinolone resistance should not be ignored. T3SS (typeⅢ secretory system) and T6SS (typeⅥ secretory system) are important virulence gene clusters of Salmonella and Vibrio parahemolyticus.

Objective:To analyze the whole genome traceability and variation analysis of SARS-CoV-2 in local COVID-19 outbreaks in Binhai New Area, Tianjin.Methods:The whole-genome high-throughput sequencing was performed on throat swab samples collected from one local asymptomatic infected person and five confirmed cases of COVID-19 in Binhai New Area of Tianjin from November 7 to December 5, 2020. The sequencing data were assembled by De novo. MAFFT v7.0 multiple sequence alignment program and MEGA X software were used to compare the above data and construct phylogenetic tree (Neighbor-joining method).Results:The genetic similarity between the sequences of 6 SARS-CoV-2 strains and Wuhan reference sequence (Wuhan-Hu-1) was greater than 99.9%. Two of six strains were genetically identical, conform to the L-Lineage European Branch Ⅱ.1(America Branch)/B.1; The other four strains had the same genes and were in line with the characteristics of L-Lineage European Branch Ⅰ/B.1.1.These six strains belonged to different evolutionary branches and two different transmission chains. There were 18 nucleotide mutation sites in sequences of six SARS-CoV-2 strains, eight of which were synonymous mutation sites, nine of which were missense mutation sites, resulting in nine amino acid mutation sites, and important mutation sites of RDRP-P323L and S-D614G were found in all of the six samples.Conclusions:In this study, there were two COVID-19 outbreaks in Binhai New Area of Tianjin, and the sequences of six SARS-CoV-2 strains belonged to different evolutionary branches and two different transmission chains. It might come from porters′ contact with imported cold chain items contaminated with SARS-CoV-2 from different sources. All the sequences of six SARS-CoV-2 strains had P323L and D614G mutations, which indicated that the virus mutation and transmission ability were stronger. The surveillance of important employees of the cold chain in Tianjin and local and imported cases should be continuously strengthened.

Objective:To retrospectively analyze the test results of novel coronavirus (2019-nCoV) in different samples (throat swab, sputum and feces) collected from recovered COVID-19 patients in order to provide a more reliable basis for discharge and reduce the risk of recurrence after discharge.Methods:Throat swabs and sputum were sampled in pairs from 78 patients before discharge and sampled in pairs twice from 54 cases with an interval of 1-5 d. Real-time fluorescence quantitative RT-PCR was used to detect the virus in the two types of samples. Throat swab, sputum and fecal samples of six patients were tested for 2019-nCoV during follow-up.Results:The detection rate of viral nucleic acid was 46.15% in throat swabs and 50.00% in sputum samples. Test results of the second paired samples showed that the detection rate of viral nucleic acid was 25.93% in throat swabs and 46.30% in sputum samples, and the difference between the two types of samples was statistically significant ( P<0.05). During follow-up, 2019-nCoV nucleic acid could be detected in the fecal samples of the six patients, but not in their throat swab and sputum samples. Their fecal samples remained positive up to 52 d. Conclusions:In the late convalescence, the respiratory symptoms of COVID-19 patients gradually disappeared with the improvement of clinical symptoms. Moreover, the virus might enter the gastrointestinal tract from respiratory tract, and could long-term exist in recovered patients and be excreted in feces. In order to reduce the rate of missed detection and avoid false negative results, it was suggested to test the viral nucleic acid in different types of samples before a COVID-19 patient was discharged.