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Objective@#To analyze the molecular epidemiology of norovirus (NoV) genotype GⅡ.15 in Qingdao City.@*Methods@#One thousand four hundred and twelve stool samples were collected from suspected NoV infected patients and detected by real-time polymerase chain reaction (PCR). Open reading frame (ORF)1-ORF2 and VP1 gene were amplified by reverse transcription (RT)-PCR and sequenced for genotyping, evolutionary analysis and homology modeling.@*Results@#Seven cases of GⅡ.15 type were detected including four sporadic cases and one outbreak.The VP1 gene was highly homologous and had little variation compared with early strain J23/US/1999. The differences of amino acids between strains in Qingdao City were mainly asparagine/asparticacid(N/D)300 and proline/serine(P/S)302.Homology modeling suggested that VP1 of GⅡ.15 strain was composed of S domain and P domain (P1 subdomain included 224-276 and 431-555, P2 subdomain included 277-430). S domain contained eight anti-parallel β-sandwiches and two α-helixes, and P1 subdomain contained one α-helix and seven β-strands, and the P2 subdomain folded into a compact barrel-like structure consisting of six β-strands.Argnine (R)-glycine (G)-valine (V)-motif (289-291) and three specific loci including glutarnine (Q)313, asparagine (N)349 and Q389 were located in the P2 subdomain, with NGR-motif (265-267) located at 22nd upstream of RGV-motif.Site I (SNR-alanine(A)- histidine(H)357-361), Site Ⅱ (D388) and Site Ⅲ (G454, G455) were the main characteristic sites of histo-blood group antigens (HBGA) binding interface, which may be similar to the binding pattern of GⅡ.4 type VA387 and HBGA.@*Conclusion@#Although GⅡ.15 type NoV evolves very slowly, it may still have the risk to become an epidemic strain, which needs to be monitored and further studied.
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Objective To analyze the molecular epidemiology of norovirus (NoV) genotype G Ⅱ.15 in Qingdao City.Methods One thousand four hundred and twelve stool samples were collected from suspected NoV infected patients and detected by real-time polymerase chain reaction (PCR).Open reading frame (ORF) I-ORF2 and VP1 gene were amplified by reverse transcription (RT)-PCR and sequenced for genotyping,evolutionary analysis and homology modeling.Results Seven cases of GⅡ.15 type were detected including four sporadic cases and one outbreak.The VP1 gene was highly homologous and had little variation compared with early strain J23/US/1999.The differences of amino acids between strains in Qingdao City were mainly asparagine/asparticacid(N/D) 300 and proline/serine (P/S) 302.Homology modeling suggested that VP1 of GⅡ.15 strain was composed of S domain and P domain (P1 subdomain included 224-276 and 431-555,P2 subdomain included 277-430).S domain contained eight anti-parallel β3-sandwiches and two α-helixes,and P1 subdomain contained one α-helix and seven β3-strands,and the P2 subdomain folded into a compact barrel-like structure consisting of six β-strands.Argnine (R)-glycine (G)-valine (V)-motif (289-291) and three specific loci including glutarnine (Q)313,asparagine (N)349 and Q389 were located in the P2 subdomain,with N GR-motif (265-267) located at 22nd upstream of RGV-motif.Site Ⅰ (SNR-alanine (A)-histidine (H)357-361),Site Ⅱ (D388) and Site IⅢ (G454,G455) were the main characteristic sites of histo-blood group antigens (HBGA) binding interface,which may be similar to the binding pattern of G Ⅱ.4 type VA387 and HBGA.Conclusion Although G Ⅱ.15 type NoV evolves very slowly,it may still have the risk to become an epidemic strain,which needs to be monitored and further studied.
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Objective To investigate the genetic variations of gag-pol gene in human immunodeficiency virus-1(HIV-1) CRF07_BC strain in Guangdong Province.Methods From February to September in 2015,plasma samples of 78 cases with HIV 1 CRF07_BC infection in Guangdong were collected before antiretroviral treatment.Viral RNA was extracted from plasma.Gene (gag and pol) sequences were amplified by reverse transcriptase and nested-PCR using specific primers.Phylogenetic tree,genic dispersion rate,nucleotide polymorphism,selection pressure and variation characteristics were analyzed.Results The main transmission route of the enrolled patients was homosexual transmission (80.77％,63/78).The gag pol gene phylogenetic tree was divided into two sub-clusters.The strains from different transmission routes were not in cluster.The average genetic dispersion rate and average entropy of gag gene were both higher than those of pol gene.The average genetic dispersion and average entropy of p17 and p6 regions of gag gene were both higher than those of p24.The average genetic dispersion and average entropy of pol gene were higher than those of rt region.The average ds/dn values of gag and pol genes were greater than one.Compared with the common HIV-related antigenic epitopes (A2,A11,B39,B60,Cw1,Cw3,Cw8),the cytotoxic lymphocyte (CTL) epitope mutations in the P17 region were more in the consensus of GAG region than those in the P24 region.The epitope conserved rates were 26.92％,0,1.28％,0,96.15％,82.05％,84.62％ and 98.72％,respectively.The drug resistance rate of pol gene was 2.56％ (2/78).Conclusions The gag and pol genes of CRF07_BC strain in Guangdong are all mutated.Diversity of gag gene is greater than that of pol gene,and gag gene variation is mainly in p17 and p6 regions.gag and pol genes are both affected by negative selection pressure.P17 protein CTL epitope variability is greater than P24 protein epitope.The prevalence of drug resistance mutation is lower than the threshold.It's important to monitor the spread of drug-resistant strains.
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Objective To retrospectively investigate the distribution,molecular epidemiology and carbapenemases-encoding genes of carbapenem resistant K lebsiella pneumoniae(CRKP)in Zhejiang Province.Methods A total of 772 clinical isolates of K.pneumoniae isolated from 9 hospitals in Zhejiang Province in 2011 were selected,and antimicrobial susceptibility testings were carried out with disk diffusion or broth microdilution method.Polymerase chain reaction(PCR)was used to detect resistant genes,and molecular typing was performed by multilocus sequence typing(MLST)and pulsed field gel electrophoresis(PFGE).Results A total of 48 CRKP(6.2%)were screened in 9 hospitals. Carbapenemase-encoding genes were detected in 39 isolates by PCR,among which 37(77.1%)were identified as blaKPC-2and 2 were blaIMP-4.MLST showed that ST11 was the dominant ST type(30, 62.5%).Results of PFGE showed that 48 CRKP can be divided into 15 types.CRKP was found in 6 hospitals except hospitals in Wenzhou,Jiaxing and Shaoxing.Conclusions In 2011,CRKP is distributed in most areas of Zhejiang Province.The production of KPC-2 is the most important carbapenem resistance mechanism and ST11 is the most prevalent ST type.
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Objective To investigate the characteristics of epidemic and genotype/subtype distribution of hepatitis C virus (HCV) among entry travelers at Tengchong port,to provide references for HCV prophylaxis and treatment.Methods A total of 54 serum samples were collected from anti-HCV positive travelers at Tengchong port from June 2009 to June 2016.HCV NS5B gene was amplified using reverse transcription polyonerase chain reation (RT-PCR) and subsequently sequenced.Based on the obtained sequences and retrieved reference sequences,phylogenetic analysis was conducted to determine HCV genotype/subtype.Results HCV infection rate among entry travelers at Tengchong ports was 0.45 ％ (54/12 059).Forty five samples were successfully genotyped.Phylogenetically,HCV genotype 3b was revealed to be the predominant subtype (28.89 ％,13/45) in this population,followed by genotype 6n (20.0％,9/45),genotype 1b (17.78％,8/45),genotype 3a (13.33％,6/45),genotype 2a (11.11％,5/45),genotype 1a (2.22％,1/45) and genotype 6a (2.22％,1/45).The major genotype in Myanmar travelers was genotype 6,while in Chinese population,genotype 1 predominated.Genotype 6 in the population showed close phylogenetic relationship with strains prevalent in China and Southeast Asia.Genotype 3 was closely clustered with strains prevalent in China.Conclusions The distribution of HCV genotypes among entry travelers at Tengchong port is impacted by HCV epidemic strains both in Yunnan province and neighboring regions.This population serves as a transmitting media which may influence the epidemiological characteristics of HCV in Tengchong and neighboring areas.
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Objective To understand the molecular epidemiological characterization of human immunodeficiency virus (HIV)-1 CRF01 AE strains in China.Methods Data were extracted by a systematic search in the databases combined with literature review.Data were then grouped according to the sites and risk groups for a Meta-analysis.Sequences of CRF01 AE pol genes from China were downloaded from Los Alamos database to build phylogenetic trees by means of FastTree2.1 .The Bayes factor test was calculated by BEAST V1 .6.2 package and Spread to explore spatial transmission links. Results Meta-analysis demonstrated that CRF01 AE strains accounted for more than 45 .0% of all subtypes among men who have sex with men (MSM)in six areas of China.Among heterosexuals in eastern,northern,southwestern and south-central China,the proportions of CRF01 AE strains exceeded 30.0%. The strains were also prevalent among intravenous drug users in south-central regions, accounting for 57.3% (95 %CI :35 .1 %-79.6%),and were only detected among blood donors in south-central China (10.6%,95 %CI :6.2% - 14.9%).Seven distinct phylogenetic clusters of CRF01 AE strains which were transmitted independently were identified.Clusters 1 ,3 and 5 were prevalent among heterosexuals,while clusters 2 and 6 were found primarily among MSM,and clusters 4 was detected chiefly among sexual contact people.Geographically,clusters 1,2,3,4 and 5 were prevalent in southwestern areas. Clusters 1 and 7 were circulating in south-central areas.Clusters 2 and 6 were prevalent in northern areas,while clusters 2 and 4 were dominant in eastern regions and cluster 6 was prevalent in northeastern China.The Bayes factor test reveals the complexity of transmission links among eastern,south-central,southwestern, northern,and northeastern provinces.Conclusion CRF01 AE strains are prevalent in most high risk groups in multiple regions of China and the transmission between different regions is complicated.
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Objective To study the epidemiological features of Cryptococcus neoformans and Cryptococcus gattii isolated from clinical samples in Shenzhen and to elucidate the distribution of species,varieties,genotypes and mating types within the strains tested.Methods The strains involved in this study were 55 cryptococcal strains isolated from our clinical samples.The canavanine-glycine bromthymolblue (CGB) culture was performed to distinguish Cryptococcus neoformans from Cryptococcus gattii.The genotype was characterized by polymerase chain reaction (PCR) fingerprinting with primer M13.The Cryptococcus gattii species and varieties of grubii and neoformans together with two opposite mating type α and a were identified by PCR with variety-specific and mating type-specific primers.The GEF1-restriction fragment length polymorphism analysis was conducted to simultaneously determine the genotype and mating types of strains tested.The sequence type of IGS1 region was analyzed for the VG Ⅱ genotype.Results Of the 55 tested cryptococcal strains,52 were Cryptococcus neoformans,all of which were var.grubii,genotype VN Ⅰ and mating type α.The remaining 3 strains were Cryptococcus gattii,among which,one was genotype VG Ⅰ and mating type α,and two were genotype VG Ⅱ and mating type α.The two VGⅡ genotype strains belonged to the sequence type Ⅱ.Conclusions The strains belonging to the Cryptococcus neoformans var.grubii,genotype VN Ⅰ and mating type α predominate in causative pathogens of cryptococcosis in Shenzhen.Cryptococcus gattii accounts for minority of the cryptococcal isolates,and the highly pathogenic VG Ⅱ genotypes in foreign countries are also characterized.The sequence types of IGS1 region of the two VG Ⅱ strains are in accord with VG Ⅱb sub-genotype.
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Objective To analyze the epidemiological characteristics of mycoplasma pneumoniae (MP) infection among the out-patients and inpatients children in Shenzhen area during 2010-2012 and to explore the significance of the results of the laboratory routine tests in the diagnosis of MP infection .Methods The children patients with respiratory tract infection from 2010 to 2012 were selected and the MP infection and the non-MP infection were screened out .The epidemiological characteristics of gender ,age , etc .,among the children patients with MP infection during these 3 years were analyzed .The differences in the laboratory routine tests and high sensitivity C reactive protein (hsCRP) were compared between the MP infection and the non-MP infection .Results The positive detection rate of MP-DNA in males was slightly higher than that in females ,the difference had no statistical signifi-cance (P>0 .05);MP infection occurred in different age groups ,the positive detection rate of MP-DNA was lowest in the children patients aged <1 year old and highest in the children patients aged 3 - < 6 years (P< 0 .05);the routine laboratory tests and hsCRP level had no specificity in the diagnosis of MP infection .Conclusion The MP molecular epidemiology in Shenzhen area shows that MP infection has the seasonality ,the laboratory routine tests and hsCRP level can not be used as the basis of the MP la-boratory diagnosis .
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Objective A preliminary study on the etiology , the gene typing , the PCR-ribotyping and the clinical features of Clostridium difficile from clinical isolates at Xiangya Hospital could improve the isolation rate and provide the basis for effectively prevention of C.difficile.Methods A prospective observational study was performed.A total of 452 stool samples were collected during June to December 2012 at Xiangya Hospital.All stools were anaerobic cultured by selective medium and identified by API 20A for C.difficile.The positive isolates were detected the toxin genes ( tcdA, tcdB, cdtA, cdtB ) and ribotyping (16S-23S internal spacer region ) by PCR.The clinical data of all patients were collected and analyzed through Logistic regression to discover the risk factors for the development of C.difficile infection ( CDI ) . Results The rate of CDI occurrence was 13.94%(63/452), among them, 42.86%(36/63) were A-B+strains and only 14.29%(9/63) were obtained from community acquired-CDI.No binary toxin was detected in any of the isolates.Eleven different PCR ribotypes were identified , the dominant ribotype CD017 accounted for 22.22%(14/63).Logistic regression analysis showed that the risk factors for CDI included age>55(P=0.016;OR=4.45;95%CI:1.33-14.91), diarrhea frequency(P=0.007, OR=0.03;95%CI:0.002 -0.38 ) and the duration of diarrhea ( P =0.015; OR =7.86; 95%CI: 1.50 -41.16 ) . Conclusions C.difficile is the main pathogens of diarrhea patients and is mainly from hospital infections with higher detection rate of A -B+ in Xiangya Hospital.Ribotyping exist comparative advantages type CD017.No evidence suggests outbreak of C.difficile infection.
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Objective To study on virulence characteristics and multilocus sequence type of Vibrio parahaemolyticus isolated from clinic in Beijing Tongren hospital.Methods Total 152 strains of Vibrio parahaemolyticus isolates were collected from diarrheal patients of outpatients in Beijing Tongren Hospital,Capital Medical University from 2009 to 2011.PCR was used to detect hemolysin gene thermo stable direct themolysin gene (tdh),TDH-related hemolysin gene (trh),type Ⅲ secretion system 2 (T3SS2α,T3SS2β)and systematic functional gene (toxRS/new,orf8) for pandemic 03∶ K6 clone and its derivatives.The genetic features of these strains were determined by multilocus sequence typing (MLST).Results 96％ (146/152) VP harbored tdh gene,2％ (3/152) VP harbored trh gene and 100％ (152/152) VP harbored T3SS2 gene.In this study there were 107 pandemic strains (both tdh and toxRS/new positive and trh negative),38 pathogenic strains (tdh positive and/or trh positive) and 6 nonpathogenic strains (both tdh and trh negative).All nonpathogenic strains harbored systematic functional gene (toxRS/new,orf8).Only one pathogenic strains harbored orf8 gene.One clone harbored all virulence gene.In this study there were 16 sequence types,and ST3 is the pandemic sequence type,including 113 strains,and four new sequence types were found.Conclusions In this study more than 90％ Vibrio haemolyticus harbored tdh gene and ST3 was the pandemic sequence type in Beijing.One can get bacterial pathogenic charateristic and population genetics information by virulence gene testing and MLST.
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Objective To investigate the dynamic characteristic of molecular epidemiology of group A Rotavirus (RV) by analyzing viral genotypes,disease seasonality,and the patients' age distribution,so that to provide theoretical basis for preyention and control of RV diarrhea in children.MethodsA total of 380 RV antigen positive samples were selected from 5176 stool specimens collected from ＜5 year-old patients with acute diarrhea who were admitted to Children's Hospital of Fudan University during January 2006 to December 2008. Multiplex nested reverse transcription polymerase chain reaction (RT-PCR) was used to analyze the RV genotypes.ResultsDuring 2006-2008,the incidence of RV related diarrhea peaked from October to December and about 96.8％ of all RV episodes occurred in patients younger than 3 years old,The predominant genotype was G3 which accounted for 58.4％ (222/380),G9 was an emerging genotype with the prevalence rate as high as 10.8％ (41/380).G1 and G2 types were rarely found during the three years.Infections with both G3 and G9 were the major mixed genotype G infection. Genotype P [8] was predominant with the prevalence rates of 64.6％ (53/82) and 46.8％ (58/124) in 2006 and 2008,respectively,whereasgenotype P[4] was predominant in 2007 (38,5％,67/174).P[6] and P[9] were found as minor types.The major mixed genotype P infection were genotype P[4] and P[8]. The proportion of undetermined genotype G and genotype P strains tended to increasing during 2006-2008.Genotype P [8]G3 was the major RV strain (20.5％) in Shanghai during 2006-2008 and the other prevalent genotypes included P[4]G3 and P[m]G3.Conclusion The infection of group A RV in Shanghai presents some new molecular epidemiology characteristics during 2006-2008,such as switch of predominant genotypes and diversification of prevalent genotypes.
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Objective To determine the pathogen of a local dengue fever outbreak in Shenzhen city in 2010,and to analyze the molecular characteristics of the epidemic dengue virus strain as well as explore the possible origin.Methods The serum samples collected from the suspect dengue fever cases were detected for IgM, IgG by enzyme-linked immunosorbent assay ( ELISA ),immunochromatography and dengue virus nucleic acid by real-time polymerase chain reaction (PCR).Serum samples from patients with early stage dengue fever were used to isolate virus with C6/36 and BHK-21 cell lines.The type of isolated virus strain was determined by RT-semi-nested-PCR and realtime PCR.E gene of isolated virus strain was amplified by RT-PCR and sequenced.Homology and phylogenetic tree of E gene of Shenzhen dengue virus with the strains isolated from other areas were constructed.Results IgM,IgG and RNA of type 1 dengue virus were detected in serum samples from dengue fever suspected patients.Type 1 dengue virus named DEV1-SZ1029 was successfully isolated from the serum sample.The homology of nucleotide sequence of E gene of SZ1029 strain with standard type 1 dengue virus HAWAII 45,Fj231/04,GD14/97 and GD05/99 were 94.8％,99.6％,97.7％ and 98.5 ％,respectively.The phylogenetic tree indicated that SZ1029 had the greatest similarity with the D1/Malaysia/36000/05 strain,SG(EHI)DED142808 strain and Fj231/04 strain and they lied in the same branch of the phylogenetic tree.The isolated dengue virus type 1 belonged to genetype Ⅰ with GZ/80,Taiwan87,All patients lived in a certain construction site in Shenzhen and had no recent travel history outside the area in one month before infection.Conclusions The virological,serological and molecular features all identify that the local dengue fever outbreak in Shenzhen in 2010 is caused by type 1 dengue virus and SZ1029 strain may be transferred from Southeast Asian region,and there may be a plague focus in Shenzhen.
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Objective To obtain the molecular epidemiology of human Parechovirus (HPeV)infections m children with central nervous system (CNS)-related disease and sepsis,as well as understand the pathogenic properties of HPeV infections by detecting HPeV in cerebrospinal fluid (CSF) and blood samples.Methods From January to December in the year of 2009,a total of 359enterovirus-negative specimens including 210 CSF and 149 blood samples were collected from 328children ＜14 years of age who were hospitalized for CNS-related disease and sepsis at Children's Hospital,Fudan University,Shanghai,China.HPeV was detected by nested reverse transcription polymerase chain reaction (RT-PCR),and then directly genotyped by sequencing nested RT-PCR product of VP3/VP1 region.Ninty-nine blood samples from healthy children were collected as controls during the same period.Results Twenty-seven children (8.2％) were HPeV positive in 328 children.HPeV infections were found in all age groups of children and the highest frequency was seen in children ＜3 months old (18.2％,12/66).HPeV was detected in several months,with the peak in December (18.8％,9/48).Of all the positive samples,20 were genotyped successfully and identified to be HPeV1.No HPeV infections were found in blood of healthy controls.ConclusionsHPeV is the pathogen of CNS infections and sepsis in children.HPeV screening should be enrolled in the routine virus testing in specimens obtained from children.HPeV1 is the prevalent type in children in the year of 2009 in Shanghai.
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Objective To investigate molecular epidemiology and antimicrobial susceptibility of Salmonella spp. isolates recovered from the stool samples of children with diarrhea. Methods Seventy-two isolates of Salmonella spp. were collected from children with diarrhea. The serum type of Salmonella spp.was determined by serology agglutinating method. Antimicrobial susceptibility was determined by K-B disk diffusion method and MICs of cefotaxime and ceftazidime were measured by agar dilution method for Salmonella spp. isolates. PCR and DNA sequencing were used for detecting ESBL, ISEcpl and AmpC genes; The transfer of cefotaxime resistance was determined by conjugation experiments. PFGE was performed for determining the homogeneity of the S. typhimurium isolates. Results A total of 72 isolates of Salmonella spp. were collected, among which S. typhimurium accounted for 86 % (62/72) and was the main serum type. S. typhimurium isolates and S. thompson isolates were often resistant to most of clinically used antimicrobial agents. Resistance of S. thompson isolates to ampicillin was the highest (90%, 56/62),followed by tetracycline (81%, 50/62), trimethoprim/sulfamethoxazole (74%, 46/62) and chloramphenicol (66%, 41/62). Seventeen S. typhimurium isolates (27%, 17/62) and two S. thompson isolates were resistant to cefotaxime. Forty-nine S. typhimurium isolates and two S. thompson isolates were positive for blaTEB-1b and resistant to ampicillin. Thirteen ESBL-producing S. typhimurium isolates (21%, 13/62) were positive for blaCTX-M (eight for blaCTX-M-14, three for blaCTX-M-15, one for blaCTX-M-55, one for both blaCTX-M-14 and blaCTX-M-55). All isolates harboring blaCTX-M genes were positive for upstream insert sequence ISEcpl. blaDHA-1was detected in a cefoxitin-resistant S. thompson isolate. Two main clones (PFGE type A and D) accounting for 19% (12/62) and 50% (31/62) respectively were found among 62 S. typhimurium isolates. Seven CTXM-producing isolates belonged to PFGE type D. Conclusions The multi-resistance to antimicrobial agents and high prevalence of blaCTX-M genes are found among S. typhimurium and S. thompson clinical isolates. blaCTX-M-55 is first found in S. typhimurium isolates and blaDHA-1 is found in S. thompson isolates. Clonal spread is responsible for the dissemination of S. typhimurium isolates.
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Objective To determine the possible genetic background and the source of our hospital's 43 clinical isolates of multidrug-resistant Acinetobacter baumannii, and the category of gene cassettes in type 1 integrons of all strains.Methods Restriction enzyme Apa I was chosed for all strains in pulsed-field gel electrophoresis (PFGE) methods.Multilocus sequence typing ( MLST) was used to compare the allelic profiles of all the strains. PCR method was used for amplify the integrons of all strains. Results PFGE results showed that 43 strains were divided into four types. A-type and B-type were divided into 4 and 2 subtypes, respectively. The MLST results showed the existing of three allelic profiles; 1-3-3-2-2-7-3, 1-3-3-2-2-11-3, and 1-3-3-2-2-14-3.B-type and D-type of PFGE have the same allelic profile(1-3-3-2-2-11-3).A-type strains were detected mainly in ICU, and in burn unit only found B- and D-type.The same integron was detected in 62.8% of the strains.The constituent ratio of A1,A2,A3,A4,B1,B2,C and D-type was 40.7% , 18.5% , 7.4% , 3.7% , 14.8% , 3.7% , 3.7% and 7.4% , respectively.Conclusions The coexistence of multiple cloning system in this region was proved by the PFGE and MLST, and the same clone can evolve to different subtypes when stimulated by different environmental conditions; and the different carrying-situationt of the same integron in strains prove the possibility of the change during the evolution of resistance mechanisms.
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Objective To investigate the molecular epidemiology of CRAB isolated from children in wuhan. Methods Forty non-repetitive strains of CRAB were collected from hospitalized children of emergency department, neonatal medicine, cardiothoracic surgery, bone surgery, respiratory medicine and renal medicine in Wuhan children's hospital during December 2008 and May 2009. MIC values were PFGE; KPC, IMP, GIM, SPM, SIM, OXA-23, VIM genes and integrase gene were amplified by PCR and then sequenced to confirm the genotypes.; Plasmid conjugation experiment was used to study the transfer method of bacterial resistance and southern blot hybridization was used to target the resistance genes. Results Susceptible rates of 40 strains to gentamicin, tobramycin, amikacin, ciprofloxacin, levofloxacin, trimoxazole were 20%, 5%, 93%, 93%, 95%, and 23% respectively. Eleven types of clone were detected by PFGE,including 29 strains of type A clone, 2 strains of type B clone, and 1 strain for each type of C to K clone. Eleven isolates produced both IMP-4 and OXA-23 carbapemase. Twenty-six isolates only possessed OXA-23 carbapemase. Thirty-six strains carried class Ⅰ integron. The results of southern blot hybridization showed that Intl, IMP-4 and OXA-23 type were located on chromosome. Conclusions Type A clone of CRAB is the most common. OXA-23 and IMP-4 type are the major acquired carbapemases, especially the OXA-23 is the most common type. The horizontal transmission of OXA-23 and IMP-4 gene mediated by Int1 and the spread of type A resistant clone is the major way of the spread of carbapenem-resistant Acinetobacter baumannii in the region.
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El Colera es una diarrea infecciosa aguda producida por Vibrio cholerae. La transmision se produce predominantemente a traves de agua o alimentos contaminados. La administracion de antibioticos puede disminuir la severidad de los sintomas. A partir de 1977, se han caracterizado cepas de V.cholerae O1 con resistencia multiple a los antibioticos. Los determinantes de resistencia han sido reportados principalmente asociados a plasmidos e integrones. Historicamente, solo las cepas del serogrupo O1 habian sido asociadas con epidemias de Colera. En 1992, un nuevo serogrupo, O139, emergio como la cepa causante de un gran brote de Colera. La diarrea masiva es causada por la toxina colerica (CT). El operon que codifica CT forma parte del genoma de un bacteriofago lisogenizado en la bacteria el cual permite interconversion de cepas. Se ha demostrado que el "quorum-sensing" regula negativamente la expresion de los genes de viru len cia en V. cholerae. El genoma de V. cholerae El Tor consiste en dos cromosomas circulares y con una pronunciada asimetria en la distribucion de los genes, en el cual se han detectado varias islas patogenicas (PAIs). Se ha reportado la existencia de V.cholerae "viable no cultivable" en ambientes acuaticos. Este fenomeno representa una nueva perspectiva en la vision de la "sobrevivencia" de V.cholerae en el ambiente e incorpora nuevas implicaciones epidemiologicas. El Colera ha sido catalogado como una "enfermedad emergente y reemergente", que amenaza a los paises en desarrollo. Los resultados de distintos grupos de investigadores han establecido que la transferencia horizontal de genes tiene influencia en la patogenicidad y ha sido importante en la evolucion de V. cholerae. Todavia permanecen sin descifrar algunos misterios en el origen de las cepas patogenas, pero, con las nuevas tecnologias seguro se develaran datos significativos que puedan dar luces sobre el origen de la patogenicidad de este organismo, que fue en ...
The Cholera is an acute infectious diarrhea produced by Vibrio cholerae. Mainly the transmission takes place through contaminated water or foods. Antibiotic administration during the acute phase of the disease can reduce the severity of the symptoms. Since 1977, strains of V. cho lerae O1 with multiple antibiotic resistances have been characterized. The resistance determinants have been reported mainly associated to plasmids and integrones. Historically, the serogrupo O1 had been associated with epidemics of Cholera. In 1992, a new serogrupo, designated O139, emerged as the strain of cause from a big Cholera outbreak. The massive diarrhea is caused by the choleric toxin (CT). Operon ctxAB, that codifies the CT, is carried in lisogenic filamentous bacteriophage in the bacterium. "Quorum-sensing" negatively regulates the expression of the virulence genes in V.cholerae. The genome of V.cholerae El Tor consists of two circular chromosomes with a pronounced asymmetry in the distribution of the genes. Several patogenics islands (PAIs) have been detected in the genome of V.cholerae. In aquatic environments the existence of "viable but non cultivable" V.cholerae, has been reported. This phenomenon represents a new perspective in the role in survival in the natural environment with new epidemiological implications. The Cho lera has been catalogued as an "emergent, re-emergent disease" that threatens developing countries. The results of different investigators groups have established that horizontal transference of genes had influence in the pathogenicity and has been important in the evolution of V.cholerae. Several mysteries in the origin of the pathogenics clones still remain, but, the new technologies will reveal significant data about the origin of this pathogen, former an estuary innocuous bacterium.
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OBJECTIVE: To determine genetic relatedness of clone Colombia5 ST289 with invasive Streptococcus pneumoniae serotype 5 isolates recovered in nine Latin American countries. METHODS: Forty-four invasive S. pneumoniae serotype 5 isolates recovered from children under 5 years of age in Bolivia, Chile, Dominican Republic, Ecuador, Nicaragua, Panama, Paraguay, Peru, and Venezuela were studied. Pulsed-field gel electrophoresis patterns of DNA treated with SmaI restriction enzyme were classified using Tenover's criteria and analyzed with the Fingerprinting II program to determine their genetic relatedness with the Colombian clone. RESULTS: All isolates had a genetic similarity of 78.5 percent or more with the Colombian clone. Thirteen electrophoretic subtypes derived of pattern A were identified, and five of them (A5, A6, A8, A13, A27) comprised 61.4 percent of the isolates. CONCLUSIONS: Clone Colombia5 ST289 is disseminated in Latin America. This is important because S. pneumoniae serotype 5 frequently causes invasive disease in the region and is associated with trimethoprim-sulfamethoxazole resistance.
OBJETIVO: Determinar la relación genética del clon Colombia5 ST289 con los aislamientos invasores de Streptococcus pneumoniae serotipo 5 provenientes de nueve países latinoamericanos. MÉTODOS: Se estudiaron 45 aislamientos invasores de Streptococcus pneumoniae serotipo 5 procedentes de niños menores de 5 años de Bolivia, Chile, Ecuador, Nicaragua, Panamá, Paraguay, Perú, República Dominicana y Venezuela. Los patrones en electroforesis en gel de campo pulsante del ADN tratado con la enzima de restricción SmaI se clasificaron mediante el criterio de Tenover y se analizaron con el programa Fingerprinting II para determinar su relación genética con el clon colombiano. RESULTADOS: Todos los aislamientos tuvieron una similitud genética de 78,5 por ciento o mayor con el clon colombiano. Se identificaron 13 subtipos electroforéticos derivados del patrón A y cinco de ellos (A5, A6, A8, A13 y A27) constituyeron 61,4 por ciento de los aislamientos. CONCLUSIONES: El clon Colombia5 ST289 está diseminado por América Latina. Esto es importante ya que S. pneumoniae serotipo 5 es causa frecuente de enfermedades invasoras en la Región y está asociado con la resistencia a trimetoprim-sulfametoxazol.
Subject(s)
Humans , Streptococcus pneumoniae/genetics , Streptococcus pneumoniae/isolation & purification , Colombia , Latin AmericaABSTRACT
Objective To study the prevalent status of human immunodeficiency virus-1 (HIV-1) subtypes in IDU (injecting drug users) population in Shenzhen and to study their source of infection in order to predict the epidemic trend and evolution. Methods 166 HIV-1 positive plasma from the IDUs was collected from 1996 to 2008. HIV-1 env genes were amplified by nested-PCR from RNA. The C2-V3 regions (450 bp) of HIV-1 env were sequenced for analyses. Phylogenetic analyses were performed on the nucleotide sequence data. Results Among 166 samples, there were 6 HIV-1 strains including CRF01_AE, CRF08_BC, CRF07_BC 3 circulating recombinant forms (CRFs) and B',C, A1 3 subtypes. Data from the genotype analyses showed that 65.06% (108/166) were CRF01_AE, 19.88% (33/166) were CRF07 BC_6.02% (10/166) were CRF08_BC, 7.23%(9/166) were subtype B', 0.60% (1/166) were subtype C and 1.20% (2/166) were subtype A1. Phylogenetic tree analysis showed that some of HIV-1 clusters defined in CRF01_AE, CRF07_BC and subtype B' in different time groups. Significant increase of gene distance in CRF01_AE and CRF07_BC strains in the three different periods. Conclusion CRF01_AE and CRF07_BC were the major epidemic CRF strains among the IDU population in Shenzhen while the subtype B', C, A1 and CRF08_BC were also circulating in IDU population in this region. The variation of all different subtypes was increasing through these years.
ABSTRACT
Objective To investigate the characteristic of rotavirus(RV) molecular epidemiology among infants and young children with nosoeomial diarrhea in Shanghai area. Methods Two hundred and twenty-six stool specimens collected from inpatients with nosocomial diarrhea from November 2006 to January 2008 were measured by colloidal gold assay and nested polymerase chain reaction (PCR). The positive samples were typed to investigate the clinical characteristics of patients. The data were shown with constituent ratio and positive detection rate. The analysis was done by using t test. Results RV was detected in 108 of 226 specimens (47.8%) by colloidal gold assay. The incidence was highest in infants younger than one year old. Neonatal cases with RV accounted for 32.4 % of all RV nosocomial infections recruited. The peak seasons were October and November. RV serotyping in 67 cases older than 1 year old by nested PCR showed that G3 was predominant and accounted for 46.3%, followed by G1 (23.9%), G2 (3.0%), G9 (1.5%), seven cases were coinfections with G1 and G3 (10.40%) and 10 couldn't be typed. Based on P typing, P [8] was predominant genotype with 90.0%, P[4] accounted for only 6.0% and 3 couldn't be typed. P[6], P[9] and P[10] haven't been detected. G3P[8] was the maior isolates which accounted for 61.2%, followed by G1P[8] (17.9 %), G1 and G3P[8] coinfection accounted for 9.5%. Two cases were infected with G2P[4] and G8P[9], respectively. Ten out of 32 neonatal specimens were typed successfully which were G1P [8]. Nosocomial RV diarrhea resulted in prolonged hospital stay and increased medical cost. Conclusions RV is the major etiological agent of nosoeomial diarrhea among infants and young children in Shanghai area. G3P[8] is the predominant serotype. And the outbreak of G1 epidemic strain infection should be monitored.