ABSTRACT
Urinary schistosomiasis which is transmitted by schistosome species is the major cause of liver and bladder pathologies and still remains a serious threat in the underdeveloped and developing world. This study evaluates the prevalence of Schistosoma haematobiuminfection among school aged children in Biase, Obubra and Ogoja Local Government Areas of Cross River State. Five hundred (500) pupils were examined and selected randomly from a public primary and secondary schools in the study area. Freshly passed mid-day urine samples were collected and transferred to the laboratory where there were examined for the presence of Schistosoma haematobium eggs. Study participants were grouped into three age groups,8-10 years. 11-13 years, and 14-16 years old. Overall prevalence of S. heamatobium was (13.6%). Infection was more prevalent among the age group of 14-16years, the percentage of prevalence and intensity of infection were higher in males (14.1%) than in females (6.9%). Inter simple sequence repeats of PCR test performed for the collected urine samples using ISSR test of the Dral-1 gene reveals 73% study subjects had a polymorphism for UPA02 and UPA13 primers, while primer UPA13 showed 24% polymorphism. Total number of polymorphic bands were 2 each for primers UPA02 and UPA13 primers while UPA12 showed only one polymorphic band. Major allele frequencies (MAF) were 0.53 for each of UPA02 and UPA 13 primers but showed 0.71 frequency with UPA12 primer. Allele frequencies (AF) also varied slightly among the primers used. UPA02 and UPA 13 had allele frequencies of 8 each while UPA12 had 4 allele frequencies (Table 13). Nei抯 genetic diversity indices for the primers revealed variations among the different primers. UPA02 and UPA13 Nei抯 gene diversity of 0.64 each while primer UPA12 showed gene diversity of 0.28. Results of polymorphic information content showed that primers UPA02 and UPA13 discriminately revealed a PIC of 0.68 while UPA12 discriminated 0.28 PIC. This study therefore, revealed a critical need for targeting health campaign towards school age children and heads of households in order to empower them with the basic knowledge to recognize, treat and manage their health challenges.Applications of one to two doses of praziquantel considerably reduced the severity of urinary Schistosomiasis in the study area.
ABSTRACT
Objective:To evaluate the relationship between the Panton-Valentine leukocidin (pvl) strain and clinical characteristics, and to describe the molecular biological characteristics of invasive Staphylococcus aureus ( S. aureus) infected clinical isolates. Methods:The isolates of S. aureus caused by invasive infection were collected in Beijing Children's Hospital Affiliated to Capital Medical University from January 2016 to December 2019, and the clinical data of the corresponding children were collected retrospectively using electronic medical records. Multilocus sequence typing, spa typing and pvl gene were analyzed using the PCR. In addition, the minimum inhibitory concentrations (MIC) of antibiotics of all isolates were detected by the micro-broth dilution method, and the isolates were divided into the pvl+ and pvl- groups according to whether or not the S. aureus isolates carried pvl. The t test and the Mann-Whitney U test were used to compare the clinical symptoms between the pvl+ and pvl- groups. Chi-square test was used to compare the drug susceptibility between the two isolates. Results:A total of 127 cases of invasive S. aureus infection were collected during the study period. The white blood cell count, neutrophil count, and C-reaction protein level in the pvl+ group were significantly higher than those in the pvl- group ( P=0.001, P=0.001, P=0.005). The rate of pvl carrier was 44.9%. Among 57 pvl+ pathogenic strains, 64.9% (37/57) were MRSA. The multidrug resistance rate of pvl- isolates was higher than that of pvl+ isolates (70% vs. 49.12%, P=0.02). Conclusions:In invasive S. aureus infection, pvl+ strain is associated with elevated inflammatory markers in children. the positive rate of pvl is higher in clinical isolates, and the multidrug resistance rate of pvl- S. aureus is higher.
ABSTRACT
Objective:To analyze the molecular evolution characteristics of HA and NA genes of influenza B/Yamagata (BY) and influenza B/Victoria (BV) lineage viruses in Guizhou Province, aiming to provide reference for scientific prevention and control of influenza. Methods:The prevalence of various types of influenza viruses in Guizhou Province from 2017 to 2021 was analyzed. The nucleic acid of influenza B viruses was extracted, and then the HA and NA genes were amplified by RT-PCR. Fourteen strains were sequenced and the sequences of 83 strains were obtained from GISAID. Homologies between the 97 influenza B viruses as well as the phylogenetic characteristics and amino acid site variations were analyzed. Results:Influenza A, BY and BV lineage viruses co-circulated in Guizhou Province and BV lineage was the predominant type. The homologies of HA and NA genes were 98.7%-99.4% and 98.4%-99.6% between BY lineage viruses and the reference vaccine strain B/PHUKET/3073/2013. BV lineage viruses shared 98.3%-99.3% and 98.9%-99.6% homologies with the reference vaccine strain B/Colorado/06/2017. The BY lineage strains in Guizhou Province mainly belonged to Y3 genetic group with HA gene in two branches of Y3-H1-2 and NA gene in three branches of Y3-N1-3. Three reassortant strains were found in Y3 clade. The isolated BV lineage strains mainly belonged to V1A-2 genetic group with HA gene in four branches of V1A-2 H1-4 and NA gene in five branches of V1A-2 N1-5. Twenty reassortant strains were found in V1A-2 clade and no inter-lineage reassortants were found. Analysis of variations at key amino acid sites showed that there was no mutation at epitopes in Y3 genetic group. However, there were point mutations at four main epitopes and a shift mutation in 190 helix in V1A-2 genetic group. There was no mutation in drug resistance sites. Conclusions:Various types of influenza viruses circulated in Guizhou Province. The homology between influenza B viruses and vaccine strains was decreasing. Different branches of HA and NA genes had been evolved and various forms of mutations were detected in the sequences. Intra-lineage reassortant strains and new varieties emerged. Surveillance of influenza B viruses should be strengthened.
ABSTRACT
OBJECTIVE@#To investigate the molecular characteristics and intracellular growth ability of Legionella pneumophila (L. pneumophila) strains from 1989 to 2016 in Sichuan Province, China.@*METHODS@#Seventy-nine isolates of L. pneumophila were collected from environmental and clinical sources, including cooling towers, hot springs, bath water, fountains, and patients, and identified with 16S rRNA gene analysis and serum agglutination assay. The isolates were then typed by Sequence-Based Typing (SBT), and Genotyping of forty-two LP1 strains were analyzed by means of multiple-locus VNTR analysis with 8 loci (MLVA-8). All strains were further analyzed for two virulence genes: Legionella vir homologue (lvh) and repeats in structural toxin (rtxA). The intracellular growth ability of 33 selected isolates was determined by examining their interaction with J774 cells.@*RESULTS@#All isolates were identified to L. pneumophila including 11 serogroups, among which the main serogroup were LP1, accounting for 54.43%. Thirty-three different sequence types (STs) from five main clonal groups and five singletons were identified, along with 8 different MLVA patterns. Both the lvh and rtxA loci were found in all 79 strains. Thirty isolates showed high intracellular growth ability in J774 cells.@*CONCLUSION@#L. pneumophila is a potential threat to public health, and effective control and prevention strategies are urgently needed.
Subject(s)
Humans , Bacterial Proteins , Genetics , Bacterial Toxins , Genetics , China , Genotyping Techniques , Legionella pneumophila , Genetics , RNA, Ribosomal, 16S , Genetics , Water MicrobiologyABSTRACT
Purpose To describe the clinicopathologic features, diagnosis and differential diagnosis, and prognosis of secretory breast carcinoma (SBC). Methods Clinicopathological and follow-up data of six SBC patients were collected. Histopathologic analysis was performed on hematoxylin and eosinstained (HE) section. Immunohistochemical staining was performed by En Vision two-step method and ETV6 gene detected by fluorescence in situ hybridization (FISH), then relevant literatures were reviewed. Results The ages of the patients ranged from 6 to 76 years with a mean age of 38.7 years, including one male and five female patients. The right breast was involved in 4 cases, and the left, in 2 cases. Five cases showed painless breast mass while one presented with a nipple discharge. The tumor size ranged from 1.0 to 3.1 cm with a mean size of 2.0 cm. Most of the tumors were circumscribed, solid gray white to light brown. Histologically, tumor showed solid nested microcystic, glandular or papillary pattern separating by hyaline fibrous tissue and growed in multiple nodular from. The cytoplasm contains abundant eosinophilic secretions or secretory vesicles. Immunhistochemistry, all cases were positive for CK7, S-100 and CEA, but negative for estrogen and progesterone receptors (ER and PR) and HER-2, and the proliferation index Ki-67 ranged from 10％ to 40％. Molecular testing confirmed the presence of the EVT6 gene translocation in one case. Lumpectomy was performed in 2 cases and modified radical mastectomy in 4 cases, two of them had lymph node metastasis (3/15, 1/16). Five cases were followed up for 6 months to 20 years, 1 case had lung metastasis. Conclusion SBC is a rare breast tumor with relatively indolent clinical and good prognosis. It can be diagnosed according to typical pathological morphology and immunohistochemical characteristics. The characteristic EVT6 gene translocation also has important differential diagnostic value.
ABSTRACT
Objective@#To study the clinical and molecular characteristics of Staphylococcus aureus(S.aureus ) isolated from neonates of Beijng Children′s Hospital.@*Methods@#The clinical information of S. aureus infection in newborns of Beijing Children′s Hospital from February 2016 to January 2017 was collected.The molecular biological characteristics of S. aureus isolates were detected.Methicillin-resistant S. aureus (MRSA) and methicillin-susceptible S. aureus(MSSA)were identified, using the cefoxitin disc method and the detection of the mecA gene.Multilocus sequence typing(MLST)and spa typing were analyzed using the PCR, and the staphylococcal chromosomal cassette mec(SCCmec) type was analyzed for the MRSA isolates.Eleven adhesion gene and three virulence genes(pvl, psma, hlα )were also detected by PCR.Antimicrobial susceptibility testing was performed by agra dilution method or E-test method.@*Results@#The total of 57 cases of neonatal S. aureus infection were collected during the study.The most common clinical diagnosis was 38 cases (66.7%) of pneumonia and 28 cases (49.1%) of skin infection syndrome (SSTI). There were 31 cases (54.4%) with MRSA infection and 26 cases (45.6%) with MSSA infection.The proportion of SSTI in the MRSA group (64.5%) and the infection of more than 2 sites (61.3%, 19/31) were significantly higher than those in the MSSA group (30.8%, 8/26 and 23.1%, 6/31). There were 16 MLST types and 29 spa types, the most common ones were ST59 (40.4%) and t437 (33.33%), respectively.The most common popular clones of MRSA and MSSA were ST59-SCCmecIVa-t437 (54.8%) and ST22-t309, respectively(11.5%). The sdrE carrying rate of MRSA was higher than that of MSSA, while the sdrD and cna carrying rates were lower than those of MSSA (P<0.05). The other adhesion and virulence gene carrying rates were not significantly different between the two strains.The multi-drug resistance rate of all strains was 61.4%(35/57). Except for lactam antibiotics, the most common resistant phenotypes of MRSA and MSSA were ERY-CLI, accounting for 74.2% and 26.9%, respectively.@*Conclusion@#The main types of neonatal S. aureus infection in our hospital were pneumonia and SSTI.SSTI and multi-site infections of MRSA infection are more common.MRSA and MSSA isolates have clonal dissemination characteristics.The most common clones are ST59-SCCmecIVa-t43 and ST22-t309, which show no significant differences in the status of carrying virulence factors between them.The multi-drug resistance rate of neonatal S. aureus isolates is higher.
ABSTRACT
Objective This study aimed to analyze the differences in the molecular characteristics of transcriptome between esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma (EAC). Methods We obtained transcriptomic data on ESCC and EAC from the TCGA database, screened differentially expressed mRNAs, lncRNAs and miRNAs in cancer and the adjacent tissues, and constructed a network of ESCC- and EAC-related competitive endogenous RNA (ceRNA). We predicted the target genes and performed gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses on important miRNAs, and compared the molecular features of the transcriptomes between ESCC and EAC. Results The ceRNA network analysis showed that PVT1, LINC00524, miR-204, miR-383, HOXC8 and NTRK2 played important regulatory roles in both ESCC and EAC. Totally, 13 227 regulatory target genes were predicted with miR-204-5p via miRWalk and 232 target genes screened from the miRDB database. GO analysis revealed 38 enrichments, mainly involved in the regulation of cell-matrix adhesion, morphogenesis of cell membrane projection, and β-catenin combination, KEGG analysis showed 4 relevant pathways: the hedgehog, life-regulating, estrogen and relaxin signaling pathways, and survival analysis manifested LINC00261, MLIP-IT1 and LINC00504 as survival-related differentially expressed lncRNAs, hsa-mir-338 as differentially expressed miRNA, but no mRNA in ESCC. Survival-related differentially expressed lncRNAs in EAC included CYP1B1-AS1 and HOTAIR, and differentially expressed mRNAs included IL11, NTRK2, ANGPT2 and PBK. Of the differentially expressed lncRNAs in both ESCC and EAC, 150 (15.4%) were up-regulated and 158 (26.8%) down-regulated; of the miRNAs, 22 (24.2%) up-regulated and 8 (27.6%) down-regulated; and of the mRNAs, 234 (20.5%) up-regulated and 418 (23.7%) down-regulated. Conclusion There are significant molecular differences between ESCC and EAC, and the differentially expressed lncRNA, miRNA and mRNA may provide some new targets and molecular markers for the treatment and prognosis of esophageal carcinoma.
ABSTRACT
Rhizoctonia solani Kühn [teleomorph: Thanatephorus cucumeris (Frank) Donk.] is an important fungal pathogen widespread in all potato growing areas of the world that causes stem canker and black scurf of potato (Solanum tuberosum L.). The aim of this study was to find a simple and reliable technique for determining the pathogenicity of Rhizoctonia solani isolates. Sixty (60) isolates of R. solani obtained from sclerotia on potato tubers, collected from different market of Agadir and Casablanca regions (Morocco), were studied for their morphology, pathogenicity and molecular characteristics. They were morphologically characterised by the production of sclerotia and moniloïd cells, and by the mycelium growth capacity at 15, 20, 25, 30 and 35°C. This morphological characterisation leads to three groups of isolates. The first group contained P01 and P03 isolates, which were able to develop under 35°C. However, under 25°C, they did not develop sclerotia. The second group, only formed by L17.1 isolate, did not form sclerotia under 25°C and was not able to develop under 35°C. The third group, formed by several isolates, developed sclerotia under 25°C conditions and were not able to grow under 35°C. Also, a positive correlation was consistent between the production of sclerotia and moniloïd cell formation. The anastomosis reaction revealed that P01, P03, L17.1, and L4.1 isolates were identified as AG-4 and for the other isolates as AG-3. The pathogenic characterisation has shown that P01, P03, L4.1, and L17.1 isolates caused important damping off of radish, tomato, beans, zucchini, and melon. However, the other isolates showed only a minor damping off rate. Molecular characterisation confirmed the classical anastomosis grouping of the isolates into AG-3 and AG-4 Anastomosis Groups. The molecular characterisation is the most rapid and reliable technique to determine the anastomosis group of unknown isolates. The three tests including the pathogenicity, the cultural anastomosis grouping, and the molecular method helped to separate the studied isolates to two groups AG-3 and AG-4.
ABSTRACT
Objective To investigate the molecular characteristics,virulence genes and antimicrobial susceptibility to Staphylococcus aureus strains isolated from children with skin and soft tissue infections (SSTIs) in Beijing.Methods A total of 52 Staphylococcus aureus isolates were collected from children with SSTIs in Beijing Children's Hospital,Capital Medical University,and the clinical data were collected and analyzed.Methicillin-resistant Staphylococcus aureus(MRSA) and methicillin-susceptible Staphylococcus aureus(MSSA) were identified by using the cefoxitin disc method and the detection of mecA gene.Multilocus sequence typing (MLST) and staphylococcal protein A (spa) typing were analyzed by the PCR method,and the staphylococcal chromosomal cassette mec (SCCmec) type was analyzed for the MRSA isolates.The pvl,eta,etb,tsst-1 and hlg genes were also detected by PCR.The susceptibility strains to 16 antibiotics were evaluated by using the agar dilution method.Results A total of 52 Staphylococcus aureus SSTIs patients,30 with MRSA infections and 22 with MSSA infections were included in the study.There were 23 patients (44.2％) less than 1 year old.The most frequent infections were the newborn omphalitis (12/52 strains,23.1％)and abscess(11/52 strains,21.2％).ST59-MRSA-SCCmecⅣa-t437 was the most predominant clones of MRSA isolates.Among the MSSA isolates(14/30 strains,46.7％),no significant epidemic clone was found.Ten sequence types (STs) and 14 spa types were identified in MSSA,and the most common types were ST22(6/22 strains,27.3％)and t309 (5/22 strains,22.7％),respectively.Notably,the multidrug resistant rates of MRSA and MSSA isolates were all ＞ 85％.The percentages of the Staphylococcus aureus SSTIs strains resistant to Erythromycin,Penicillin,Chloramphenicol and Clindamycin were 100.0％,94.2％,69.2％ and 63.5％,respectively.The tested isolates were susceptible to Trimethoprim/Sulfamethoxazole,Mupirocin,Fusidic acid,Tigecycline,Linezolid and Vancomycin.The pvl gene's positive rate was 40.4％,and no significant difference between MRSA and MSSA was observed (P ＞ 0.05).Eta and etb genes were detected in 2 patients with staphylococcal scalded skin syndrome.Conclusions The Staphylococcus aureus SSTIs strains are most frequently isolated from newborn omphalitis and abscess in Beijing.The multidrug resistant rate is relatively high,so the erythromycin and clindamycin should not be preferred in empiric treatment of children with Staphylococcus aureus SSTIs.The prevalence of pvl gene is 40.1％.ST59-MRSA-SCCmecⅣa-t437 is the common clone of MRSA,while the MSSA isolates have a more diverse genetic background.
ABSTRACT
Objective To understand the circulation,drug resistance and molecular characteristics of Salmonella 1,4,[5],12:i:-in human in Guangdong province.Methods Salmonella 1,4,[5],12:i:-isolated from diarrhea patients in Guangdong during 2007-2016 were detected for drug resistance,genes and PFGE characteristics.Results A total of 2 960 strains Salmonella 1,4,[5],12:i:-were isolated from human diarrhea cases during this period.The positive rates of the isolation increased year by year.The male to female ratio of the infection cases was 1.58 ∶ 1,and the infection mainly occurred in infants and young children.Except imipenem,Salmonella 1,4,[5],12:i:-was resistant to other 17 antibiotics to some extent.The drug resistant rates to ceftazidime,cefotaxime and ciprofloxacin increased from 2011 to 2016.Multi-drug resistance was serious,for example,the multi-drug resistant strains with ASSuT accounted for 70.62％ (435/616) and the multi-drug resistant strains with ACSuGSTTm accounted for 27.11％ (167/616).The lack offljA,fljB and hin genes,as well as the retaining of iroB,STM2740,STM2757 genes,resulted in the unable expression of FljBenx gene with 8 different defection profiles.There were 934 different PFGE patterns observed in 2 347 strains,which displayed a relatively large fingerprint polymorphism.The major PFGE pattern was JPXX01.GD0226,which was found in 97 strains,accounting for 4.13％ (97/2 347).The PFGE patterns in 168 Salmonella 1,4,[5],12:i:-strains were consistent with that of Salmonella typhimurium.Conclusions Salmonella 1,4,[5],12:i:-strains has become the major serotype of Salmonella that cause diarrhea in human in Guangdong.The multi-drug resistance of Salmonella 1,4,[5],12:i:-was serious,and since the defection offljA,fljB and hin genes,the expression of FljBenx protein failed.The PFGE results were diverse,which displayed polymorphism in inheritance.
ABSTRACT
Objective To understand the circulation,drug resistance and molecular characteristics of Salmonella 1,4,[5],12:i:-in human in Guangdong province.Methods Salmonella 1,4,[5],12:i:-isolated from diarrhea patients in Guangdong during 2007-2016 were detected for drug resistance,genes and PFGE characteristics.Results A total of 2 960 strains Salmonella 1,4,[5],12:i:-were isolated from human diarrhea cases during this period.The positive rates of the isolation increased year by year.The male to female ratio of the infection cases was 1.58 ∶ 1,and the infection mainly occurred in infants and young children.Except imipenem,Salmonella 1,4,[5],12:i:-was resistant to other 17 antibiotics to some extent.The drug resistant rates to ceftazidime,cefotaxime and ciprofloxacin increased from 2011 to 2016.Multi-drug resistance was serious,for example,the multi-drug resistant strains with ASSuT accounted for 70.62％ (435/616) and the multi-drug resistant strains with ACSuGSTTm accounted for 27.11％ (167/616).The lack offljA,fljB and hin genes,as well as the retaining of iroB,STM2740,STM2757 genes,resulted in the unable expression of FljBenx gene with 8 different defection profiles.There were 934 different PFGE patterns observed in 2 347 strains,which displayed a relatively large fingerprint polymorphism.The major PFGE pattern was JPXX01.GD0226,which was found in 97 strains,accounting for 4.13％ (97/2 347).The PFGE patterns in 168 Salmonella 1,4,[5],12:i:-strains were consistent with that of Salmonella typhimurium.Conclusions Salmonella 1,4,[5],12:i:-strains has become the major serotype of Salmonella that cause diarrhea in human in Guangdong.The multi-drug resistance of Salmonella 1,4,[5],12:i:-was serious,and since the defection offljA,fljB and hin genes,the expression of FljBenx protein failed.The PFGE results were diverse,which displayed polymorphism in inheritance.
ABSTRACT
Objective@#To analyze the clinical manifestations and results of etiological examinations of 17 elderly patients with influenza A (H1N1) viral pneumonia, and to understand the clinical features of pneumonia and molecular characteristics of influenza A (H1N1) virus infection in the elderly.@*Methods@#The elderly patients with pneumonia who were hospitalized in the Department of Respiratory Diseases of Nanjing First Hospital from January 2018 to March were enrolled. The cases were confirmed by nucleic acid examination for influenza virus and the clinical data were collected. After the amplification of the whole genome of influenza virus, the high throughput sequencing and bioinformatics analysis were performed.@*Results@#The mean age of the 17 enrolled patients was 73.8±10.8. All of them had at least 1 underlying disease, and 7 cases had co-infection. Respiratory symptoms and fever were the most prominent clinical manifestations. Lesions in both lungs were found in 76.5% of the patients. The result of high throughput sequencing showed that all the viruses were highly homologous to the vaccine strain, and the HA gene belonged to the 6B.1 subgroup. Furthermore, three variations of antigenic locus (H138Y, S74R and S164T in HA) and a drug-resistant variation (H275Y in NA) were detected in the circulating strains.@*Conclusions@#Elderly patients with influenza A (H1N1) virus pneumonia often have underlying diseases and are prone to have co-infection. The molecular characteristics of the virus and the variation of key amino acid loci should be closely monitored in order to provide evidence for epidemic prevention and clinical antiviral treatment.
ABSTRACT
Objective Influenza A(H7N9) virus causes a relatively high mortality in humans and therefore it is of great sig-nificance to know its prevalence in China .This article aimed to study the genetic characteristics and evolution of the hemagglutinin (HA) gene of the influenza A(H7N9) virus prevailing in China between 2013 and 2017. Methods We downloaded the HA se-quences of the influenza A ( H7N9) virus prevailing in China between 2013 and 2017 from The Global Initiative on Sharing All Influen-za Data and National Center for Biotechnology Information .Using the bioinformatics software , we analyzed the homology , molecular characteristics , phyletic evolution , and selective pressure of the HA gene. Results The homology of the HA gene of the influenza A ( H7N9) virus and the reference strain was decreasing each year from 2013 to 2017, 99.0%-99.9%in 2013, 98.7%-99.5%in 2014, 98.4%-99.6%in 2015, 76.8%-99.4%in 2016, and 69.9%-98.2%in 2017.Compared with the reference strain , the HA gene of the influ-enza A(H7N9) virus underwent variations in 21 antigenic sites.The variation of N285D was the highest (23%) in 2015 and that of R148K increased yearly,reaching 65%in 2016 and 78.5% in 2017. Phylogenetic analysis showed a concentrative distribution of the influenza A ( H7N9) virus strains on the phylogenetic tree in the same year from 2013 to 2017.Amino acid substitution of T 140A was observed in most of the influenza A ( H7N9) virus strains from Guang-dong in 2013, and the widest distribution of the virus strains was found in 2014.Positive selective pressure site 65 was obtained in the sequence of 2015 using the FEL and IFEL models, but not in the strains of 2016 or 2017. Conclusion Influenza A(H7N9) virus constantly undergoes variation , which has increased the difficulty in its prevention and control .More importance should be attached to observation of the virus and response to its adaptive mutations .
ABSTRACT
Objective To study the molecular characteristics of the Staphylococcus aureus isolated from the intensive care units (ICUs) of children's hospital.Methods From January 2016 to December 2016,a total of 39 S.aureus strains were collected and identified from various clinical specimens that were obtained from patients who were confined in the neonatal and pediatric ICUs of Beijing Childreng Hospital.Methicillin-resistant S.aureus (MRSA) and methicillin-susceptible S.aureus (MSSA) were identified using the cefoxitin disc method and the detection of the mecA gene.Multilocus sequence typing (MLST) and spa typing were analyzed using the PCR,and the staphylococcal chromosomal cassette mec (SCCmec) type was analyzed for the MRSA isolates.Twenty-one superantigen genes and the Panton-Valentine leukocidin (pvl) gene were also detected by PCR.Their susceptibility to 12 antibiotics was evaluated using the E-test method.The differences in prevalence of virulence genes and antimicrobial resistance were compared between the MRSA and MSSA isolates by Fisherg exact test.Results All the S.aureus strains were isolated from secretion inside the airway of pneumonia (including severe pneumonia),the blood of patients with bacteremia,and exudate of skin and soft tissue infections.ST59-SCCmecⅣa-t437 (55.6％) and ST398-t571 (28.6％) were the most predominant clones of MRSA and MSSA,respectively.Of the 39 isolates,26 strains (66.7％) had at least one superantigen gene,and seb (38.5％),sek (30.8％),and seq (20.5％) were the most common genes;seb-sek-seq (18.0％) was the main virulence genotype.The pvl geneg positive rate was 25.6％,and no significant difference between MRSA and MSSA was observed (P ＞ 0.05).Notably,79.9％ of the S.aureus isolates were multidrug resistant,and 94.9％,53.8％,and 51.3％ of the isolates were resistant to erythromycin,clindamycin,and chloramphenicol,respectively.The tested isolates were susceptible to trimethoprim/sulfamethoxazole,rifampicin,and vancomycin.Conclusions The S.aureus strains from the ICUs of childreng hospital were isolated from the secretion inside the airway of pneumonia (including severe pneumonia),the blood of patients with bacteremia,and exudate of skin and soft tissue infections.ST59-SCCmecⅣa-t437 (55.6％) and ST398-t571 (28.6％) were the common clones of MRSA and MSSA,respectively.The prevalence of superantigen genes and the multidrug resistant rate were relatively high.
ABSTRACT
Objective Influenza A(H7N9) virus causes a relatively high mortality in humans and therefore it is of great sig-nificance to know its prevalence in China .This article aimed to study the genetic characteristics and evolution of the hemagglutinin (HA) gene of the influenza A(H7N9) virus prevailing in China between 2013 and 2017. Methods We downloaded the HA se-quences of the influenza A ( H7N9) virus prevailing in China between 2013 and 2017 from The Global Initiative on Sharing All Influen-za Data and National Center for Biotechnology Information .Using the bioinformatics software , we analyzed the homology , molecular characteristics , phyletic evolution , and selective pressure of the HA gene. Results The homology of the HA gene of the influenza A ( H7N9) virus and the reference strain was decreasing each year from 2013 to 2017, 99.0%-99.9%in 2013, 98.7%-99.5%in 2014, 98.4%-99.6%in 2015, 76.8%-99.4%in 2016, and 69.9%-98.2%in 2017.Compared with the reference strain , the HA gene of the influ-enza A(H7N9) virus underwent variations in 21 antigenic sites.The variation of N285D was the highest (23%) in 2015 and that of R148K increased yearly,reaching 65%in 2016 and 78.5% in 2017. Phylogenetic analysis showed a concentrative distribution of the influenza A ( H7N9) virus strains on the phylogenetic tree in the same year from 2013 to 2017.Amino acid substitution of T 140A was observed in most of the influenza A ( H7N9) virus strains from Guang-dong in 2013, and the widest distribution of the virus strains was found in 2014.Positive selective pressure site 65 was obtained in the sequence of 2015 using the FEL and IFEL models, but not in the strains of 2016 or 2017. Conclusion Influenza A(H7N9) virus constantly undergoes variation , which has increased the difficulty in its prevention and control .More importance should be attached to observation of the virus and response to its adaptive mutations .
ABSTRACT
Objective@#To understand epidemiological characteristics of the pathogens and evolution of the genotype associated with infectious diarrhea epidemic caused by norovirus in Hebei Province.@*Methods@#A total of 8 infectious diarrhea outbreaks caused by norovirus were reported from Jan 2015 to Dec 2016, of which epidemic treatment materials and specimens were collected at the same time. Norovirus nucleic acid was detected by using real-time PCR, and the partial ORF2 of the all positive specimens were amplified by RT-PCR and sequenced. Phylogenetic tree was constructed by using Mega5.2 based on partial ORF2 sequences of norovirus to perform phylogenetic analysis.@*Results@#A total of 8 norovirus outbreaks, involving 265 cases who were mainly for residential inhabitents, children and students, were reported during this period, and the overall attack rate ranged from 0.70% to 8.13%. The overall positive detection rate of norovirus was 66.25%. The PCR products were sequenced, and sequencing result were obtained for 28 samples, which included GⅠ.3, GⅡ.2, GⅡ.4, GⅡ.13 and GⅡ.17.@*Conclusions@#Multiple genotypes of infectious diarrhea outbreaks caused by norovirus were found in Hebei province.
ABSTRACT
Objective To analyze the genetic characteristics and the evolution of the influenza A (H3N2) virus strains circulating in Jiangsu province between 2013 and 2014.Methods This study analyzed thirty-one representative strains of influenza A (H3N2) virus, which were isolated in different regions of Jiangsu province and during different time periods from 2013 to 2014.Results Genetic distances in nucleic acid and amino acid between a strain used for vaccine production (A/Texas/50/2012) and the 31 strains were 0.010 5 and 0.012 4.Similarities between them in nucleic acid and amino acid sequences were 97.9%-99.6% and 97.2%-99.3%.Phylogenetic analysis showed that the hemagglutinin (HA) genes of the 31 strains were divided into three different groups.Three strains isolated in 2013 and three strains isolated in 2014 belonged to Group 1 and Group 2, respectively, while the others belonged to Group 3.Three positive selection sites (237, 366 and 367) in HA protein were observed by REL model.Compared with the strain used for vaccine production, the 31 strains were characterized by amino acid substitutions (N128A/T and P198S/A) in HA protein and all of the mutations located in B-cell epitopes.The total number of mutation sites reached 24.Compared with the A/Texas/50/2012 strain, seven strains presented the glycosylation site 126NWT, and three strains showed disappeared glycosylation sites of 45NSS and 144NNS.Evaluation of vaccine efficacy for A(H3N2) virus strains showed that the vaccine efficacy was not very well.Conclusion The HA gene of A(H3N2) virus had undergone a greater variation and the vaccine efficacy was not very well in Jiangsu province during 2013 to 2014, which made the influenza A(H3N2) virus become the circulating strain.
ABSTRACT
Objective To explore the molecular characteristics of community-associated Methicillin-resistant Staphylococcus aureus (CA-MRSA) from children with skin and soft tissue infection (SSTIs) in China.Methods CA-MRSA was collected from the outpatients in Department of Dermatology in 13 Children's Hospitals of China.Genotypic characteristics of CA-MRSA isolates were tested by adopting mnltilocus sequence typing (MLST),staphylococcal protein A (spa) typing and Staphyloccoccal cassette chromosome mec (SCCmec) typing.And the presence of Panton-Valentine leukocidin genes(pvl) was determined also.Results Overall,1 705 strains of Staphylococcus aureus were isolated from SSTIs children,and CA-MRSA accounted for 2.6％ (44/1 705 strains).Two types of SCCmec were detected in all the CA-MRSA strains,and the main types were SCCmec Ⅳ and SCCmec Ⅴ,accounting for 45.5 ％ (20/44 strains) and 54.5 ％ (24/44 strains),respectively.Thirteen MLST types (STs) and 15 spa types were detected among CA-MRSA.The most prevalent MLST was ST121 (18/44 strains,40.9％),followed by ST59 (9/44 strains,20.5％).Additionally,t437 was predominant,accounting for 40.9％ (18/44 strains).ST121 strain had 8 spa types,and t2086 was the most common type (6/18 strains,33.3％);while ST59 had only 1 spa type,t437.No ST121,ST59 and t437 strains were found in Central and Eastern region of China.Only 4 (9.1％) of the 44 CA-MRSA strains harbored pvl genes which were all from Southern region.Conclusions The most common clone of SSTIs CA-MRSA in children is MRSA-ST121-SCCmec Ⅳ/Ⅴ,as the molecular epidemiology of CA-MRSA strain has changed,ST121 has replaced ST59 to become the main epidemic strains.
ABSTRACT
Objective To analyze the evolutionary characteristics and predict the variation trend of neuraminidase (NA) gene of influenza A/H1N1 (09pdm) virus in China from 2009 to 2016 in order to provide the basis of assessment for flu vaccines.Methods A total of 1 141 sequences of NA gene of influenza A/H1N1 (09pdm) virus were screened out from the Global Initiative on Sharing All Influenza Data and National Center for Biotechnology Information.The phylogenetic trees and the mutations of amino acids sequences were constructed and analyzed by biological softwares.The prediction for epidemic trend of influenza was analyzed by Bayesian skyline Plot.Results Compared with the sequence of reference strain,the homology of nucleic acid sequence of NA gene decreased year by year from 2009 to 2016.The phylogenetic analysis showed that NA gene clustered nearly on the identical phylogenetic tree in one year.The positive selection pressure site of NA strain was observed by different models in each year except 2012.The dynamics analysis showed that the popularity of influenza A/H1N1 virus may continue to increase to a peak in 2017.Conclusion The amino acid encoded by NA gene of influenza A/H1N1 virus is varying gradually,so the importance of surveillance for influenza virus should be reinforced for every year.
ABSTRACT
The human calcium- and integrin-binding protein (CIB) family is composed of CIB1, CIB2, CIB3, and CIB4 proteins and the CIB4 gene affects fertility. Kermani sheep is one of the most important breeds of Iranian sheep breeds. The aim of this study was to analyze for the first time molecular characteristics of the CIB4 gene and protein in Kermani sheep. Different tissues were collected from the Kermani sheep and real time PCR was performed. The PCR products were sequenced, comparative analyses of the nucleotide sequences were performed, a phylogenetic tree was constructed, and different characteristics of CIB4 proteins were predicted. Real time PCR results showed that the CIB4 gene is expressed only in testis of Kermani sheep. The cDNA nucleotide sequence was identical with small tail Han sheep, cattle, goat, camel, horse, dog, mouse and human, respectively 100, 99, 99, 98, 98, 96, 96, and 96%. Hence, it can be suggested that the CIB4 gene plays a role in male fertility. Based on the phylogenetic analysis, sheep CIB4 gene has a close relationship with goat and cattle first, and then with camel and whale. Although we demonstrated that CIB4 is a testis-specific gene, expressed only in the testis and it interacts with other proteins, the mechanisms by which CIB4 expression is regulated need to be elucidated.