Tracking missed opportunities for an early HIV diagnosis in a population of people living with HIV with known time of infection.

PURPOSE: The goal of 90-90-90 first requires the expansion of access to HIV testing. Our aim was to record frequencies of HIV indicator conditions (ICs) and identify missed opportunities for an early HIV diagnosis. METHODS: We retrospectively identified ICs in a population of 231 people living with HIV with known infection dates who attended our clinic. The study population was divided into four groups: (1) those self-tested pre-emptively (47/231, 20.3%), (2) those offered targeted testing based on risk factors (67/231, 29%), (3) those tested after an IC (73/231, 31.6%) and (4) those who were not offered testing after an IC (44/231, 19%). HIV acquisition dates were estimated by molecular clock analysis. RESULTS: A total of 169 healthcare contacts (HCCs) were recorded. The most frequent HCC was mononucleosis-like syndrome (20.1%), unexplained weight loss (10.7%) and STIs (10.1%). AIDS-defining conditions were detected in 11.8%. Only 62.4% (73/117) of those with an IC were offered testing after their first HCC. Patients in group 4 had statistically significant delay in diagnosis compared with group 3 (109.1 weeks (IQR 56.4-238.6) vs 71.6 weeks (IQR 32.3-124.6)). The proportion of patients diagnosed as late presenters in each group was: (1) 16/47 (34%), (2) 37/67 (55.2%), (3) 43/73 (58.9%) and (4) 27/44 (61.4%) (p=0.027). CONCLUSIONS: Our study uses a combination of molecular and clinical data and shows evidence that late presentation occurs in a high proportion of patients even in the presence of an IC. Given that risk-based targeted testing has low coverage, IC-guided testing provides a reasonable alternative to facilitate earlier HIV diagnosis and to improve late diagnosis across Europe and globally.

Prevalence of anal cytological abnormalities and high-risk human papillomavirus prevalence in kidney transplant recipients: A cross-sectional study.

BACKGROUND: Transplant recipients are at high-risk of anal squamous cell cancer. We aimed to estimate the prevalence of high-risk human papillomavirus (HPV) and high-grade squamous intraepithelial lesion (HSIL) and assess characteristics associated with results METHODS: We recruited kidney transplant recipients in a single-center, 2015-2018. Participants completed a clinical questionnaire and received an anal-swab sent for HPV-DNA and cytological testing RESULTS: A total of 97 (74%) of 125 recipients approached consented to participate. Participants were median 47 (IQR 40-55) years, 60% male and median 4.5 (IQR .9-13) months-since-transplant. Of 86 assessable samples, at least one HPV genotype was detected in 15 (17%) participants; 1 (1%) HPV16, 8 (9%) other high-risk HPV. Of 76 assessable cytology samples, 9 (12%) showed evidence of abnormality; 1 (1%) HSIL, 1 (1%) atypical-squamous-cells, cannot exclude HSIL. Both HSIL recipients had high-risk HPV and biopsy confirmed HSIL. High-risk HPV was detected in six (9%) recipients with normal cytology. History of sexually transmitted infection, and abnormal cervical pap smear in women, was associated with high-risk HPV and HSIL CONCLUSIONS: High-risk HPV and HSIL testing may identify kidney transplant recipients at higher risk of anal cancer. Longitudinal studies are needed to describe the natural history of anal cancer in transplant recipients.

Ethnically diverse urban transmission networks of Neisseria gonorrhoeae without evidence of HIV serosorting.

OBJECTIVE: We aimed to characterise gonorrhoea transmission patterns in a diverse urban population by linking genomic, epidemiological and antimicrobial susceptibility data. METHODS: Neisseria gonorrhoeae isolates from patients attending sexual health clinics at Barts Health NHS Trust, London, UK, during an 11-month period underwent whole-genome sequencing and antimicrobial susceptibility testing. We combined laboratory and patient data to investigate the transmission network structure. RESULTS: One hundred and fifty-eight isolates from 158 patients were available with associated descriptive data. One hundred and twenty-nine (82%) patients identified as male and 25 (16%) as female; four (3%) records lacked gender information. Self-described ethnicities were: 51 (32%) English/Welsh/Scottish; 33 (21%) white, other; 23 (15%) black British/black African/black, other; 12 (8%) Caribbean; 9 (6%) South Asian; 6 (4%) mixed ethnicity; and 10 (6%) other; data were missing for 14 (9%). Self-reported sexual orientations were 82 (52%) men who have sex with men (MSM); 49 (31%) heterosexual; 2 (1%) bisexual; data were missing for 25 individuals. Twenty-two (14%) patients were HIV positive. Whole-genome sequence data were generated for 151 isolates, which linked 75 (50%) patients to at least one other case. Using sequencing data, we found no evidence of transmission networks related to specific ethnic groups (p=0.64) or of HIV serosorting (p=0.35). Of 82 MSM/bisexual patients with sequencing data, 45 (55%) belonged to clusters of ≥2 cases, compared with 16/44 (36%) heterosexuals with sequencing data (p=0.06). CONCLUSION: We demonstrate links between 50% of patients in transmission networks using a relatively small sample in a large cosmopolitan city. We found no evidence of HIV serosorting. Our results do not support assortative selectivity as an explanation for differences in gonorrhoea incidence between ethnic groups.

Molecular epidemiology of norovirus GⅡ.15 in Qingdao City / 中华传染病杂志

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.

Molecular epidemiology of norovirus GⅡ.15 in Qingdao City / 中华传染病杂志

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.

Characterization and primary resistance mutations in gag-pol gene of human immunodeficiency virus-1 CRF07_BC strain in Guangdong Province / 中华传染病杂志

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.

Distribution,molecular epidemiology and resistance genes of carbapenem resistant Klebsiella pneumoniae in Zhejiang Province / 中华传染病杂志

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.

Characteristics of hepatitis C virus infection and genotype distribution among entry travelers at Tengchong Port / 中华传染病杂志

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.

Molecular epidemiological characterization of human immunodeficiency virus-1 CRF01 AE strains in China / 中华传染病杂志

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.

Use of Chlamydia trachomatis high-resolution typing: an extended case study to distinguish recurrent or persistent infection from new infection.

OBJECTIVES: Repeated infections of Chlamydia trachomatis may be new infections or persistent infections due to treatment failure or due to unresolved infections in sexual partners. We aimed to establish the value of using high-resolution multilocus sequence typing (CT-MLST) to discriminate repeated C trachomatis infections. METHODS: Paired C trachomatis positive samples (baseline (T0) and after 6 months (T1)) were selected from two Dutch screening implementation studies among young heterosexual people. Typing with six CT-MLST loci included the ompA gene. The uniqueness of strains was assessed using 256 reference CT-MLST profiles. RESULTS: In 27 out of 34 paired cases, full sequence types were obtained. A multilocus (13 cases) or single locus variant (4 cases) was seen, indicating 17 new C trachomatis infections at T1. The ompA genovar was identical for 5 of 17 discordant cases. The 10 cases with concordant typing results were categorised as treatment failure (5 cases) versus persistent or recurrent infections (5 cases). Surprisingly, these concordant cases had C trachomatis strains that were either unique or found in small clusters. The median time between T0 and T1 did not differ between the concordant and discordant cases. CONCLUSIONS: High-resolution typing was superior in discriminating new infections compared with only using ompA genovar typing. Many cases (37%) showed exactly the same C trachomatis strain after 6 months. CT-MLST is not conclusive in distinguishing recurrent infections from treatment failure.

Molecular epidemiological study of Cryptococcus neoformans and Cryptococcus gattii in Shenzhen / 中华传染病杂志

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.

Characteristics of laboratory routine tests and molecular epidemiology for child mycoplasma pneumoniae infection in Shenzhen area / 国际检验医学杂志

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 .

The etiology, molecular epidemiology and clinical characteristics of Clostridium difficile infections in Xiangya Hospital / 中华检验医学杂志

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.

Genetic diversity in Trichomonas vaginalis.

Recent advances in genetic characterisation of Trichomonas vaginalis isolates show that the extensive clinical variability in trichomoniasis and its disease sequelae are matched by significant genetic diversity in the organism itself, suggesting a connection between the genetic identity of isolates and their clinical manifestations. Indeed, a high degree of genetic heterogeneity in T vaginalis isolates has been observed using multiple genotyping techniques. A unique two-type population structure that is both local and global in distribution has been identified, and there is evidence of recombination within each group, although sexual recombination between the groups appears to be constrained. There is conflicting evidence in these studies for correlations between T vaginalis genetic identity and clinical presentation, metronidazole susceptibility, and the presence of T vaginalis virus, underscoring the need for adoption of a common standard for genotyping the parasite. Moving forward, microsatellite genotyping and multilocus sequence typing are the most robust techniques for future investigations of T vaginalis genotype-phenotype associations.

The rarity of Trichomonas vaginalis in urban Australia.

OBJECTIVES: Infection with Trichomonas vaginalis has declined dramatically in urban Australia but remains endemic in some predominantly indigenous rural regions. The objective was to determine T vaginalis positivity rates in clinical specimens by PCR detection, from a large community-based private pathology laboratory servicing rural and urban Australian populations. METHODS: Retrospective analysis of data from 44 464 specimens referred for T vaginalis PCR testing over 8 years from 2004 to 2011. RESULTS: 44 464 consecutive specimens (37 137 female, 7242 male, 85 sex-unspecified) were analysed: T vaginalis was detected in 633 specimens. The overall community T vaginalis positivity rate was 1.4% (95% CI 1.3% to 1.5%). Overall rates were 2.1-fold higher in women than in men (1.5% vs 0.7%). Positivity rates were highest in the 10-14 year age group (p<0.0001). Referrals from urban areas of South-East Queensland accounted for 52% of specimens (23 121): the T vaginalis positivity rate in this urban cohort was 0.7% (95% CI 0.6% to 0.8%). Referrals identified to be from indigenous patients accounted for 48% of positive cases (304/633), and came from predominantly rural and regional areas of northern Queensland. Where follow-up testing was available 21% of patients (14/66) remained T vaginalis PCR positive when tested again within 3 months and 25% (26/101) within 6 months of the initial diagnosis. CONCLUSIONS: This study confirms that T vaginalis is rare in the urban non-indigenous Australian setting. Guidelines need to be developed to allow targeted testing. Follow-up testing 3 months after treatment should be considered.

Virulence characteristics and multilocus sequence type of Vibrio parahaemolyticus isolated from clinic / 中华检验医学杂志

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.

Molecular epidemiology of human Parechovirus infections in central nervous system-related disease and spsis in children / 中华传染病杂志

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.

Molecular epidemiology study on group A Rotavirus in hospitalized children with diarrhea in Shanghai during 2006-2008 / 中华传染病杂志

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.

The molecular epidemiology of a local dengue fever outbreak in Shenzhen / 中华传染病杂志

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.

Molecular epidemiology and antimicrobial susceptibility of Salmonella isolates recovered from children with diarrhea / 中华检验医学杂志

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.