Resistance, molecular epidemiology and virulence gene of non-A-F group serotype isolates of Salmonella enterica enteric subspecies isolated from children / 中华检验医学杂志

Objective:To analyze the anti-drug resistance, molecular epidemiology and virulence gene distribution of non-A-F group serotype isolates of Salmonella enterica enteric subspecis, so as to provide epidemiological basis for clinical diagnosis and treatment.Methods:Serotyping, antimicrobial susceptibility test and whole genome sequencing were performed on 11 isolates of non-A-F group serotype isolates of Salmonella enterica enteric subspecies that were isolated from The Children′s Hospital, Zhejiang University School of Medicine between 2017 and 2020. The serotype, multilocus sequence typing and virulence gene of the whole genome sequencing results were analyzed. Results:In our hospital, the detection rate of non-A-F group serotype isolates of Salmonella enterica enteric subspecies was low (1.13%). Among the 11 strains, there were 3 strains belong to Jangwani serotype, 2 strains of Hvittingfoss serotype, and Wandsworth, Pomona, Kedougou, Urbana, Poona and Kumasi serotypes have 1 strain each. Except for the two multi-drug resistant strains, the other strains were sensitive to most antibiotics, and the MICs were at low levels. A total of 9 ST types were detected in the 11 strains, the 3 Jangwani serotype strains were ST3918, and the other isolates were of different ST types. The phylogenetic tree shown that the three strains of Jangwani serotype were closely related. A total of 103 virulence genes were detected in the 11 strains, including 78 genes related to secretion system, 21 genes related to adherence, 2 genes related to magnesium uptake, 1 gene related to resistance to antimicrobial peptides and 1 gene related to typhoid toxin. Conclusions:The detection rate of the non-A-F group serotype isolates of Salmonella enterica enteric subspecies was low, and the sensitivity of the isolates to common antibiotics was high. The ST types and genetic relationship showed diversity. Clinical laboratory should pay attention to the detection of the non-A-F group serotype isolates of Salmonella enterica enteric subspecies, and the changes in drug resistance and virulence genes of the isolates should be closely monitored.

Real-time recombinase polymerase amplification for detection of Vibrio parahaemolyticus / 预防医学

Objective@# To establish real-time recombinase polymerase amplification（RPA）for the rapid detection of Vibrio parahaemolyticus（VP）.@*Methods@#An exo probe and primers were designed according to the conserved sequence of thermolabile hemolysin（tlh）gene of VP and then RPA for detection of VP was established. The sensitivity of the assay was evaluated by detecting different concentration of VP;the specificity was evaluated by detecting different bacteria;the stability was evaluated by repeat trials;the application effect was evaluated by detecting food samples which were simultaneously tested with traditional culture method according to GB 4798.7-2013 Detection of VP.@*Results@#A real-time RPA was established to complete VP amplification within 20 min at a constant temperature of 39 ℃. The analytical sensitivity of the assay was five pg per reaction and no cross-reactivity with other pathogenic bacteria observed. The RPA detection results with different concentration of VP and E. coli DNA templates at three time points were consistent. The detection results of 51 food samples by RPA were the same as those by traditional culture method.@*Conclusion@#The established real-time RPA can qualitatively detect VP,with simple operation and interpretation of results,which is suitable for rapid detection of VP in public health emergencies and food safety supervision.

Establishment and evaluation of identification method for Yersinia pestis and Yersinia pseudotuberculosis / 中华流行病学杂志

<p><b>OBJECTIVE</b>To establish a gene identification method of Yersinia pestis and Yersinia pseudotuberculosis for plague surveillance.</p><p><b>METHODS</b>According to the specific genomic sequences of Y. pestis and Y. pseudotuberculosis, i.e. "pestis Island (PeI)" and "pseudotuberculosis Island (PsI)" and the published genomic sequences of 12 strains of Y. pestis and 4 strains of Y. pseudotuberculosis, the specific identification primers of these sequences were designed.</p><p><b>RESULTS</b>A total of 52 strains of Y. pestis and 57 strains of Y. pseudotuberculosis and other intestinal bacteria strains were tested with PCR. Of the 5 pairs of Y. pestis identification primers, PeI2 and PeI11 were specific for Y. pestis. Besides Y. pestis, the primers PeI1, PeI3 and PeI12 could detect part of 57 Y. pseudotuberculosis strains. Of the 5 pairs of Y. pseudotuberculosis identification primers, PsI1 could detect all the 52 strains of Y. pestis and 57 strains of Y. pseudotuberculosis. PsI7, PsI16, PsI18 and PsI19 were specific for Y. pseudotuberculosis.</p><p><b>CONCLUSION</b>The primers PsI1, PeI 2 and PeI11, PsI7, PsI16, PsI18 and PsI19 can be used in the rapid identification of Y. pestis and Y. pseudotuberculosis, which can be also used to explore the circulation of atypical Y. pestis in quiescent plague foci.</p>

Analysis of molecular features of clinical Vibrio parahaemolyticus strains in China / 中华预防医学杂志

<p><b>OBJECTIVE</b>To explore the phenetic and genetic features of clinical Vibrio parahaemolyticus strains from 2007-2009 in China.</p><p><b>METHODS</b>A total of 135 clinical Vibrio parahaemolyticus strains, isolated from Zhejiang, Jiangsu, Sichuan, Guangxi, Liaoning Provinces during 2007 to 2009, were selected for the research. The occurrence of virulence genes thermostable direct hemolysin (tdh) and TDH-related hemolysin (trh), species-specific genes thermolabile hemolysin (tlh), toxR, VPM and gyrB, the pandemic clone gene markers(GS-PCR, PGS-PCR, orf8 and HU-α) in 135 Vibrio parahaemolyticus strains was detected by PCR. The antimicrobial susceptibilities to eight antimicrobial agents of the experimental strains were determined by the broth microdilution method. All strains were serotyped and underwent the cluster analysis with pulsed-field gel electrophoreses.</p><p><b>RESULTS</b>The results of PCR methods claim that all experiment strains carry species-specific genes such as tlh, toxR, gyrB, VPM. Among clinical strains, 85.9% (116/135) carry tdh and/or trh. 85.2% (115/135) were positive for tdh, and 3.0% (4/135) were positive for trh; while 3 strains carried both.66.7% (90/135) , 80.7% (109/135) , 65.2% (88/135) , 66.7% (90/135) clinical strains carried the genes of GS-PCR, PGS-PCR, orf8, HU-α, respectively. The results of antibiotics susceptibility test showed that 8.1% (11/135) strains were resistant to at least one agent, including 9 strains were resistant to ampicillin, 2 strains were resistant to trimethoprim and sulphamethoxazole, and 1 strain were resistant to tetracycline. All clinical strains were sensitive to cefotaxime, ceftazidime, gentamicin, ciprofloxacin and chloromycetin.Serological analysis of the O and K antigens claimed that a total of 29 serotypes were identified for clinical strains, predominantly O3, O4 and O1 groups, accounting for 89.6% (121/135). O3: K6 was dominant serotype, accounting for 56.3% (76/135). The pandemic flora in China included O3: K6, O4: K68, O1: K36, O1: K25, O1: K5 and O3: K29 serotypes.Genomic DNAs of 135 clinical strains were digested with SfiI and NotI, the molecular size of PFGE restriction fragments used for analysis mainly ranged from 30-700 kb.When subjected to UPGMA clustering, 6 and 9 clusters were grouped by SfiI and NotI, and the minimal similarity was 52.6% and 58.7%, and pandemic flora were located in C groups and D group, respectively.</p><p><b>CONCLUSION</b>Most of Vibrio parahaemolyticus strains isolated from clinical sources in China were pathogenic. The pandemic clone, especially O3: K6 was prevalent. The GS-PCR and HU-α genes were reliable markers to identify the pandemic flora. The serotype by PFGE was reliable to distinguish the pandemic flora and the sporadic strains.</p>

Antimicrobial resistance profiles and genetic diversity of bovine staphylococcus aureus isolated in 5 provinces of China in 2013 / 中华预防医学杂志

<p><b>OBJECTIVE</b>To investigate antimicrobial resistance profiles and genetic diversity of staphylococcus aureus isolated from lactating cows of 5 provinces in China, 2013.</p><p><b>METHODS</b>A total of 680 samples were collected from 15 herds (12 farms, 3 artels) in 5 provinces of China in 2013, including swabs of extramammary sites (bovine teat skin and milking machine liners) and quarter milk samples from lactating cows diagnosed with subclinical mastitis. The antimicrobial resistance of the isolates were tested by broth microdilution method and the genotypes were determined by PFGE (pulsed-field gel electrophoresis) method.</p><p><b>RESULTS</b>A total of 111 isolates were isolated and identified as staphylococcus aureus. Resistance to penicillin (90.1% (100/111)), erythromycin (48.6% (54/111)), ciprofloxacin (36.9% (41/111)), clindamycin (27.9% (31/111)), gentamycin (18.9% (21/111)), chloramphenicol (9.0% (10/111)), tetracycline (7.2% (8/111)) of these strains were observed. All isolates were sensitive to oxacillin, vancomycin and selectrin. 92.8% (103/111) staphylococcus aureus isolates were resistant to at least one antimicrobial. 38.7% (43/111) strains were multi-drug resistant isolates. The resistance rate of isolates in artels (100% (48/48)) was higher than it in farms (87% (55/63)) and the difference was statistically significant (χ(2) = 4.80, P < 0.05). The multi-resistance rate of isolates in artels (54% (26/48)) was higher than it in farms (27% (17/63)) and the difference was also statistically significant (χ(2) = 8.48, P < 0.05). The 111 strains were clustered into 8 types, 6 out of which were consisted of 98% isolates (109/111), and were prevalent in 2 to 9 herds. Every herd had 1 to 4 types, and tend to be comprised by one major type. Most swab isolates were indistinguishable from isolates infecting the mammary gland. There were no relationship between antimicrobial resistance profiles and genotypes of these isolates.</p><p><b>CONCLUSION</b>The drug resistance of staphylococcus aureus isolates associated with lactating cows of 5 provinces in China is serious, especially the isolates collected from artels. A few specialized clones were responsible for most of the cases of bovine mastitis in a single herd and some clones might have a broad geographic distribution.</p>

Sequence analyses of the Cps2J gene in 9 strains of Streptococcus suis serotype2 isolated in Zhejiang province / 中国人兽共患病学报

To explore the molecular characteristics of Streptococcus suis serotype 2(ss2) isolated in Zhejiang province by deciding the variation loci and its variation frequency of Cps2J gene.The total DNA of 9 strains of ss2 isolated in Zhejiang province were extracted and amplifed by PCR. Then,the Cps2J fragments were cloned into plasmid carrier and completely sequenced after purification.Finally,the sequence results of all 9 ss2 isolates were compared with those obtained by other studies around the world.It was found that the open reading fragments of Cps2J in 9 SS2 isolates encoding 333 amino acids were 999 bp in length.Comparisons of this region among ss2 isolates revealed a similarity of between 98.8% and 99.9%, while the homology to ss1 strains varied between 56.8% and 57.0%.Our study shows the sequences of complete Cps2J segment are fairly stable and all these 9 ss2 strains of different sources possibly have the same evolutionary origin.

Research on detection of Legionella pneumophila by real-time fluorescence PCR / 中华微生物学和免疫学杂志

Objective To develop a real-time fluorescence quantitative PCR method for detection of Legionella pneumophila as a tool for environmental and clinical examination. Methods A pair of degen-erated primers and one TaqMan-MGB probe were designed to test the conserved region at the macrophage in-fective potentiation (mip) gene of Legionella pneumophila. TaqMan MGB real-time quantitative PCR assay was developed with pMD-19T plasmid including mip gene of Legionella pneumophila as standard sample. The sensitivity and specificity of the real-time quantitative PCR was evaluated using the standard sample and dif-ferent strains. Results The detection limit of 0.71 copy/μl was obtained for the standard sample in a reac-tion system of 0.6μl of sense and antisense primers (20μmol/L), respectively, 0.4μl of probe (20μmol/L) and 6.0μl of DNA temple. Conditions for the PCR reactions were as follows. After an initial de-naturation at 95℃ for 20s, 40 amplification cycles were performed. Each cycle consisted of denaturation at 95℃ for 10 s, primer annealing at 50℃ for45s. The PCR Ct value of a standard strain and 12 isolates was in a scale of 13.23 and 16.04. However, the Ct values of the strains of Staphylococcus aureus, Salmonella typhimurium, Vibrio parahaemolyticus, Escherichia coli, Pseudomonas aeruginosa and Shigella sonnei were greater than 30. Conclusion The real-time quantitative PCR method has good sensitivity and specificity and the result has potentiality of applying for detecting Legionella pneumophila.

Severe acute respiratory syndrome-associated coronavirus genotype and its characterization / 中华医学杂志(英文版)

<p><b>OBJECTIVE</b>To study the severe acute respiratory syndrome (SARS)-associated coronavirus genotype and its characteristics.</p><p><b>METHODS</b>A SARS-associated coronavirus isolate named ZJ01 was obtained from throat swab samples taken from a patient in Hangzhou, Zhejing province. The complete genome sequence of ZJ01 consisted of 29,715 bp (GenBank accession: AY297028, version: gi: 30910859). Seventeen SARS-associated coronavirus genome sequences in GenBank were compared to analyze the common sequence variations and the probability of co-occurrence of multiple polymorphisms or mutations. Phylogenetic analysis of those sequences was done.</p><p><b>RESULTS</b>By bioinformatics processing and analysis, the 5 loci nucleotides at ZJ01 genome were found being T, T, G, T and T, respectively. Compared with other SARS-associated coronavirus genomes in the GenBank database, an A/G mutation was detected besides the other 4 mutation loci (C:G:C:C/T:T:T:T) involved in this genetic signature. Therefore a new definition was put forward according to the 5 mutation loci. SARS-associated coronavirus strains would be grouped into two genotypes (C:G:A:C:C/T:T:G:T:T), and abbreviated as SARS coronavirus C genotype and T genotype. On the basis of this new definition, the ZJ01 isolate belongs to SARS-associated coronavirus T genotype, first discovered and reported in mainland China. Phylogenetic analysis of the spike protein gene fragments of these SARS-associated coronavirus strains showed that the GZ01 isolate was phylogenetically distinct from other isolates, and compared with groups F1 and F2 of the T genotype, the isolates of BJ01 and CUHK-W1 were more closely related to the GZ01 isolate. It was interesting to find that two (A/G and C/T) of the five mutation loci occurred in the spike protein gene, which caused changes of Asp to Gly and Thr to Ile in the protein, respectively.</p><p><b>CONCLUSION</b>Attention should be paid to whether these genotype and mutation patterns are related to the virus's biological activities,epidemic characteristics and host clinical symptoms.</p>