bluuebunny/crossref_metadata_2025_split huggingface dataset:
P4-S1.06 High-resolution Multilocus Sequence Typing (MLST) ofChlamydia trachomatisfrom three catchment areas in North and Central Norway
Authors: Herrmann B , Christerson L , Gravningen K , Stahlsten A , Ödman K , Nguyen D , Isaksson J , Furberg A S , Simonsen G S 
Published: July 2011

BackgroundTheC trachomatisincidence rate in the county of Finnmark in North Norway is twice as high as in the rest of the country. This study genetically characterises theC trachomatisstrains in Finnmark and compares them with strains from two other counties in Norway.MethodsDNA sequencing of ompA, which encodes the major outer membrane protein MOMP, and a high-resolution multilocus sequence typing (MLST) system, which is based on PCR amplification and DNA sequencing of five highly variable genetic regions (not housekeeping genes as in conventional MLST), were used. In total, 80 specimens from adolescents mainly aged 15–19 were collected in five high schools (n=60) and in the laboratory routine (n=20) in Finnmark (extended county with sparse population in minor municipalities) and compared to 80 laboratory specimens from Tromsø county (capital of North Norway) and 88 laboratory specimens from Trondheim in Central Norway.ResultsSequencing of ompA detected 11 genotypes in these 248 specimens. The MLST analysis displayed 50 sequence types (STs), providing five times higher resolution than ompA. Thirty-one (62%) of the STs were novel. The study revealed overlapping STs between the different counties, but 64% of the STs were unique for specific counties (Abstract P4-S1.06 figure 1). The MLST genetic diversity was lower in Finnmark (0.26 ST per specimen compared to 0.34 in Tromsø and 0.32 in Trondheim, respectively), but the geographical differences were not statistically significant.The common ompA genovar E predominated in Tromsø and Trondheim (55%) whereas genovar G (36%) was most frequent in Finnmark.Abstract P4-S1.06 Figure 1Distribution of sequence types (n=50) of 248C trachomatiscases in the counties of Finnmark (n=80), Tromsø (n=80), and Trondheim (n=88).ConclusionsOur MLST provided a significantly higher differentiation capacity than conventional ompA typing, which has predominated genotyping ofC trachomatisfor decades. Thus high-resolution MLST is a useful tool for molecular epidemiology of chlamydial infections.
P4-S2.01 A cross-sectional survey of Hepatitis B virus infections and natural immunity against Hepatitis B virus infections among HIV discordant heterosexual couples in Kisumu, Kenya
Authors: Ondondo R 
Published: July 2011

BackgroundHIV and hepatitis B virus (HBV) share transmission modes. HIV infected people are thought to be at increased risk of HBV acquisition, chronic HBV infection and HBV disease. Chronic HBV infection may pose a challenge among HIV infected individuals' eligible for antiretroviral therapy, increasing their risk of rapid HIV-disease progression. Early prevention of HBV infection by vaccinating HIV infected people is recommended. However, in most poor countries HBV vaccination is not routine and those opting for vaccination are rarely tested before vaccination. We sought to determine the prevalence of HBV infection and natural immunity against HBV infection among HIV discordant couples.MethodsThe first 949 discordant heterosexual couples screened for eligibility into an HIV pre-exposure prophylaxis study had HBV surface antigen (HBsAg) and anti-HBs status determined. CD4 count was also performed for HIV infected potential subjects. None of these participants reported HBV vaccination history. SPSS version 17 software was used for statistical analysis.ResultsOf 949 HIV positive subjects, 34.7% (329) were men thus women were more likely to be the HIV-positive spouse in these HIV-discordant relationships (p<0.001). 99 of 1898 subjects were positive for HBVsAg, resulting to 5.2% HBV prevalence, with men being more likely to be HBV infected compared to women (p<0.05). 40% (758) of 1898 subjects tested for anti-HBs were immune to HBV, with men being more likely to possess natural protective antibodies against HBV compared to women (p<0.05). Among HIV infected subjects, those with a CD4 count >250 cells/ml were more likely to possess immunity against HBV compared to those with a CD4 count <250 cells/ml (p<0.001). However, HIV status was not associated with either HBV infection (p=0.302) or immunity against HBV (p=0.512).ConclusionScaling-up routine vaccination after anti-HBs screening in resource limited settings could be cost-effective and easy to roll-out in HIV endemic Sab-Sahara Africa. This is because 40% of individuals are already immune to HBV. Validation of Anti-HBs rapid screening tests is urgently needed in this population.
P4-S2.02 Regulatory T cells and Fox P3 levels in naive and HAART treated HIV-1 infected patients in Thailand
Authors: Sukwit S , Srisurapanon S , Chuenchitra T , Horthongkham N , Sutthent R 
Published: July 2011

BackgroundThe frequency and expression levels of FoxP3 in regulatory T-cells (T-regs) from advanced-stage HIV-infected patients are controversial. Thus, the aims of this study were to compare these parameters of T-regs from HIV infected patients and from healthy controls.MethodsT-reg population and expression levels of FoxP3 were assessed from 43 HIV-1 infected individuals and 12 healthy controls by using FACs flow cytometry.ResultsMinor decrease in frequencies of T-regs was found in both infected groups (naïve and treated) compared with those from healthy controls (p=0.02, p=0.01, respectively). In contrast, a significantly increase in the ratios of T-regs: CD4 cells from HIV-infected patients was observed (p=0.001). In addition, FoxP3 expression levels in both treated and untreated HIV-1 infected patients were significantly higher than those in healthy controls (p<0.001 and 0.01 respectively).ConclusionsThe decreased number of T-regulatory cells and the increased levels of FoxP3 in T-regs from HIV infected patients were associated with advanced stage of AIDS disease.
P4-S2.03 Calculating BMI in HIV+ female adolescents: a case of shaping the health of adolescents in Zimbabwe: Shaz! plus project
Authors: Nhamo D 
Published: July 2011

BackgroundBody Mass Index (BMI) is a statistical measure which compares a person's weight and height. It is used to estimate a healthy body weight based on a person's height. This measure is pertinent to use in HIV positives since weight loss is used as a proxy measure for clinical progression of HIV disease in that more weight loss is associated with advancing disease and often precedes clinical symptoms. We sought to measure BMI among HIV+ female adolescents to see if this is the best tool to use in immune-compromised populations.MethodsData were pulled out from an ongoing RCT entitled SHAZ! Plus. (N=650). It enrols HIV +ive female adolescents who are out of school. Data were collected at baseline, 6, 12 and 18-month follow-up visits, with the project facilitating ongoing care, ART and support to those in need of it. BMI was calculated using Adolphe Quetelet BMI calculator of weight in kg over height in m2(kg/m2). BMI prime 25 was also calculated and used to compare the BMI results. Sample of xx used.Results64.5% of the cohort had BMIs falling within normal ranges 18.5 to 25. 33.8% had BMIs of <18.5 and 0.16% had a BMI of >25. 64.5% had BMI prime that fell within normal ranges of 0.74 and 0.99. 33.8% had BMI prime of <0.74 and 0.16% had a BMI prime of >1.00. The average BMI at baseline was 19.35 Weight ranged from 25 to 70 at baseline, average was 47.71.ConclusionResults call for the need to come up with an adjusted BMI index for female adolescents who are immuno-compromised to use as a standard measure for optimal health. BMI however has it's shortcomings since it does not measure the actual body fat. In resource poor settings, a simple tool like weight lost or gained over time might be a good indicator of clinical progression of HIV as opposed to validated tools like the BMI.
P4-S3.02 Subtyping of Treponema pallidum strains by sequence analysis of tp0279 and tp0548
Authors: Pillay A , Chen C Y , Morshed M G , Philip S , Ballard R C 
Published: July 2011

BackgroundThe goal of the study was to evaluate two sequence-based subtyping methods for their ability to further differentiate Treponema pallidum strains characterised by the CDC typing system.Methods12 clinical specimens with the 14d strain type obtained from patients with GUD in Cape Town in 2000; 14 specimens with the 14d strain type from patients with primary or secondary syphilis in San Francisco collected between 2004 and 2007; and 12 clinical specimens with the 14d strain type collected between 2000 and 2002 from a syphilis outbreak in Vancouver were included in the study. Specimens were previously characterised using the CDC typing method which involves analysis of the sequence variability with tprE, G, and J and, the variable number of 60-bp tandem repeats within the arp gene. Subtyping was performed by PCR amplification of a homonucleotide G" tandem repeat within tp0279 and a variable region within tp0548. PCR amplicons were purified and directly sequenced using the BigDye® Terminator v3.1 cycle sequencing kit and an ABI 3130 sequencer.ResultsOf the 12 samples from South Africa, sequence analysis of tp0279 revealed three subtypes (9G, 10G, 11G) and combining this data with the CDC typing method produced strain subtypes 14d9, 14d10, and 14d11. Sequence analysis of the variable region within tp0548 resulted in five subtypes designated a, c, f, k, and l among these samples and, combination with strain type using the CDC method produced subtypes 14d/a, 14d/c, 14d/f, 14d/k, 14d/l. All 14 samples from San Francisco had 9G tandem repeats within tp0279 resulting in subtype 14d9. Sequence analysis of the variable region within tp0548 resulted in 3 subtypes designated f, g and j among these 14 samples and incorporation of the CDC typing method produced subtypes 14d/f, 14d/g, and 14d/j. Of the 12 samples from Vancouver, sequence analysis of tp0279 produced two subtypes (8G, 9G) resulting in strain subtypes 14d8 (1/12) and14d9 (11/12). Sequencing of tp0548 also produced two subtypes (e, f) resulting in strain subtypes 14d/e (1/12) and14d/f (11/12).ConclusionsThe tp0279 subtyping method further differentiated 14d strains into four subtypes while the tp0548 method differentiated 14d strains into eight subtypes. Subtyping of strains from the initial syphilis outbreak in Vancouver suggests clonal spread ofT pallidum. Both subtyping methods enhanced the original CDC typing method and appear to be promising tools for molecular epidemiological studies on syphilis.
P4-S3.03 Characterisation ofUreaplasma parvumfrom symptomatic and asymptomatic men attending a family practice in Pretoria, South Africa
Authors: Kock M , Maningi N , Adam A , Hoosen A 
Published: July 2011

BackgroundThe genus Ureaplasma colonises human mucosal surfaces such as urogenital tract of men and women. In men it has been implicated in the aetiology of non-gonococcal urethritis and infertility. Although its pathogenesis is not yet fully understood, it has been suggested that certain serotypes are associated with disease. This study undertook to detect genitalUreaplasma spp.and to characteriseUreaplasma parvumin men with and without urogenital symptoms.MethodsTwo hundred first void urine specimens were collected from symptomatic (100) and asymptomatic (100) men attending a private clinic. All specimens were cultured in U9 broth and subcultured on A2 agar medium for confirmation. All isolates were tested for susceptibility using the Mycofast Evolution 3 kit. DNA was extracted from all specimens and amplified using a multiplex TaqMan polymerase chain reaction assay targeting the multiple-banded antigen gene for the detection and serotyping ofU parvum.Ureaplasma urealyticumwas detected by a commercial real-time PCR kit.ResultsCultures were positive in 16/100 symptomatic and 12/100 asymptomatic men (p=NS). All isolates were susceptible to doxycycline, pristimycin, roxycycline and azithromycin. OneUreaplasma spp.from an asymptomatic male was resistant to ciprofloxacin and josamycin and intermediately resistant to ofloxacin and another was resistant to ofloxacin. An isolate from a symptomatic man was resistant to ciprofloxacin. There was no significant difference (p=0.16) between theU parvumisolated from symptomatic (11/100) and asymptomatic (18/100) men as well as forU urealyticumfrom symptomatic 16/100 and asymptomatic 15/100 men (p=0.86). Four men (two from each group) were colonised by bothUreaplasma spp.. The predominant serotype was six, followed by types 1, 14 and 3 with no significant difference between symptomatic and asymptomatic men (p=0.309).ConclusionsThere is no data of circulatingU parvumserotypes from South Africa. The prevalence rate was low and no significant differences were found between symptomatic and asymptomatic men for bothUreaplasma spp.. Serotype 6 was the most common type compared to reports from developed countries which suggests type 3 as being the most common. Macrolides and tetracyclines remain effective drugs for treatment of the Ureaplasma infections. Molecular techniques are valuable identification and characterisation of this fastidious group of bacteria.
P4-S3.04 Treponema pallidum molecular typing in China
Authors: Peng R R , Yin Y P , Wei W H , Wang H C , Chen X S 
Published: July 2011

BackgroundSyphilis is resurgent in China, but there have been limited data on molecular epidemiology. A novelTreponema Pallidum(T pallidum) typing method that uses tp0548 gene in addition to arp and tpr E, G, J genes with greater discriminatory power has recently been developed. This study aimed to analyseT pallidumstrain types across geographical areas in China using this novel method.MethodsFrom 2008 to 2010, genital specimens, including those from chancres, condyloma lata and mucosal patches, were collected from patients with clinically suspected primary or secondary syphilis in STI clinics in East China (Nanjing), South China (Guangzhou, Jiangmen and Fuzhou), Southwest China (Nanning and Chengdu), North China (Tianjin), and Northeast China (Harbin). All specimens were first amplified by PCR of polA gene to screen for positive DNA, followed by analysis of arp, tpr E,G, J and tp0548 genes for complete strain type. A χ2test was used to compare the distribution of strain types across the 5 geographical areas.ResultsTypeableT pallidumDNA was detected in 184 of 401 specimens, and 27 strain types were identified. Overall, 3 to 20 repeats (except 4, 11, and 19 repeats) and 25 repeats were found for the 60-bp arp gene. This was the first time 9 and 25 repeats for the arp gene have been detected. For the RFLP pattern of the tpr E, G, J genes, a, d, h, j and l were identified. For the sequence pattern of the tp0548 gene, c, e and f were identified. The distribution of strain types was significantly different across the geographical areas of China (χ2=29.2, p=0.008), but type 14d/f was most predominant within each geographical area (approximately 40% constituent ratio in each area). Taking all geographical areas into account, types 15d/f, 13d/f, 16d/f, and 14a/f were the next most common in descending order see Abstract P4-S3.04 figure 1.Abstract P4-S3.04 Figure 1Strain types ofT pallidumidentified in clinical specimens from five geographical areas in China.ConclusionsThere is substantial genetic diversity ofT pallidumin China. However, the overall predominance of a single 14d/f strain type may imply a potential link in sexual transmission of syphilis across geographical areas.
P1-S1.52 Incidence of Anal HPV and HPV-related sequelae in HIV-infected and uninfected US adolescents
Authors: Mullins T , Wilson C , Rudy B , Sucharew H , Kahn J 
Published: July 2011

BackgroundImmunodeficiency related to HIV infection may place HIV-infected youth at increased risk of human papillomavirus (HPV) infection and anal dysplasia. Our objective was to determine incidence of anal HPV infection and related sequelae, and factors associated with these outcomes, among adolescents who are HIV-infected or -uninfected but at-risk.MethodsWe analysed data from the Reaching for Excellence in Adolescent Care and Health Project. Adolescents age 12–18 years who were behaviourally HIV-infected (n=319) or -uninfected but at risk (n=177) were recruited at 15 US sites from 1996 to 1999. Incidence rates for anal HPV, high risk anal HPV, anogenital warts, and anal dysplasia were calculated using Poisson modelling. Factors associated with these outcomes were explored using Cox proportional hazards modelling.ResultsMean age at entry was 16.8 years, and mean follow-up time for detection of anal HPV infection was 22.4 months (SD 10.8). Most participants (76%) were female, and 70% were black non-Hispanic. HIV-infected women (vs -uninfected women) had higher incidence of anal HPV (30 vs 14 per 100 person-years; p=0.002), high risk anal HPV (12 vs 5.3 per 100 person-years; p=0.04), and anogenital warts (6.7 vs 1.6 per 100 person-years; p=0.002) but not anal dysplasia. Although incidence rates of these outcomes were consistently higher among HIV-infected vs -uninfected men, they did not achieve statistical significance. Factors associated with incident anal HPV, high risk anal HPV, anogenital warts, and anal dysplasia in women are shown in the Abstract P1-S1.52 table 1 below. No factors were associated with any outcome in men.Abstract P1-S1.52 Table 1Factors associated with incident anal HPV and HPV-related sequelae among womenOutcomeHIV-uninfectedHIV-infectedPredictorHR (95% CI)PredictorHR (95% CI)Anal HPVCervical HPV infection2.45 (1.01 to 5.92)NoneHigh risk anal HPVNoneSmoker3.46 (1.21 to 9.89)Late (vs early) CDC disease stage2.80 (1.18 to 6.67)Anogenital wartsNoneCervical HPV infection4.28 (1.29 to 14.19)HIV viral load1.55 (1.12 to 2.17)Anal dysplasiaNoneLate (vs early) CDC disease stage7.02 (2.18 to 22.59)Ever had high risk anal HPV infection3.72 (1.52 to 9.12)ConclusionsHIV-infected women, when compared to HIV-uninfected women, had higher rates of HPV and related sequelae. Because HIV-infected youth are at increased risk of HPV and related disease, enhanced HPV prevention efforts, such as vaccination, are warranted for this group.
P4-S3.08 Development of a novel chimeric protein construct for improved diagnosis of syphilis
Authors: Smith B , Cameron C 
Published: July 2011

ObjectivesTo develop a novel diagnostic protein in order to enhance early detection of syphilis infections and improve overall syphilis diagnosis.MethodsUsing pooled serum samples from patients infected with syphilis, immunoreactive regions of two previously identified diagnostic protein candidates, Tp0326 and Tp0453, were elucidated. Focusing on these regions, a chimeric protein construct was created for expression inEscherichia coliand expression conditions were optimised to produce soluble protein expression. This Tp0326/Tp0453 chimeric construct was screened against serum samples from; patients with primary, secondary, latent, and neurosyphilis and uninfected individuals. These results were directly compared to the rapid plasma regain (RPR) test, and the microhemagglutination assay forT pallidum(MHA-TP).ResultsScreening results show high degrees of sensitivity and specificity for the Tp0326/Tp0453 chimeric construct, identifying all stages of syphilis infection from early primary to late latent.ConclusionThe Tp0326/Tp0453 chimera shows promise as a new diagnostic antigen for detecting all stages of syphilis infection and for development into point-of-care diagnostic test formats.
P4-S3.09 The prevalence ofTrichomonas vaginalisvirus (TVV) in globally distributedTrichomonas vaginalisisolates
Authors: Lezeau L , Conrad M , Gorman A , Carlton J 
Published: July 2011

ObjectiveTrichomonas vaginalis, a highly prevalent non-viral sexually transmitted infection, has been shown to be infected by a double-stranded RNA virus known asT vaginalisvirus (TVV). The presence of this virus has been associated with increased trafficking of the immunogenic P270 to the surface of the parasite, and has therefore been hypothesised to be an important virulence factor in trichomoniasis. In the present study, we investigate the prevalence of TVV in globally distributedT vaginalisisolates and find an association between TVV infection and genetically distinctT vaginalispopulations.Methods150T vaginalisisolates from the USA, Mexico, Italy, Southern Africa, Papua New Guinea and Australia were screened for TVV infection by running total RNA extract on 1% agarose gels to detect the presence or absence of the diagnostic 4.5 kb dsRNA genome of the virus. The prevalence of TVV in genetically distinctT vaginalisphylotypes was compared using χ2tests.ResultsTVV was found to be present in 37% ofT vaginalisisolates. We find a difference in the prevalence of TVV infection between genetically distinct populations of parasites, with 3% of phylotype 1 isolates containing the virus vs 73% of phylotype 2 parasites (<0.001).ConclusionsTVV prevalence varies betweenT vaginalisphylotypes 1 and 2. This finding has implications suggesting that TVV is transmitted vertically among parasites, as more closely relatedT vaginalisstrains are infected with TVV. Preliminary data also suggests that phylotype 2 parasites may show greater virulence, and further studies will be required in determining the role of TVV in this increased pathology.
P4-S4.01 Investigation of the bacterial diversity in urine of urethritis patients and healthy controls using 454 high-throughput-sequencing
Authors: Ahrens P , Frølund M , Al-Soud W A , Wikström A , Lidbrink P , Cullberg M , Sørensen S J , Jensen J S 
Published: July 2011

BackgroundNon-gonococcal urethritis (NGU) is a common sexually transmitted disease in men but in 30–50% of NGU cases, no known organism is found. We have used 454 high throughput sequencing to analyse the micro flora in urine samples from cases of urethritis and from controls.MethodsUrine samples from men, 10 patients with urethritis and >5 PMNL/hpf and 10 healthy controls with <5 PMNL/hpf, were collected. All samples were tested forNeisseria gonorrhoeae,Chlamydia trachomatis,Mycoplasma genitalium,Ureaplasma urealyticum,U parvum,Trichomonas vaginalis, Herpes Simplex Virus type 1 and 2 and Adenovirus using specific PCR assays. The V3 and V4 regions of the 16S rRNA gene were PCR amplified, tagged and sequenced using the Titanium kit and GS FLX pyrose-quencing system (Roche) according to manufacturer's instructions. Sequences were analysed using the RDP Pyrosequencing Pipeline and CLC Genomics Workbench.ResultsFrom each of the 20 samples, 8150 quality filtered sequences were randomly selected. Sequences were assigned to the genus level using the RDP Classifier. A total of 172 gen-era were identified, 133 in patients and 104 in controls. The median number of genera was 35.5 (19–49) in patients with urethritis compared to 25 (16–43) in the controls. No single genus was present in all samples. Members of the genera Pseudomonas and Sphingomonas were present in all the controls and in most of the patient samples. Also, representatives of the genera Brevundimonas, Micrococcus, Bradyrhizobium and Chry-seobacterium were present in 15–18 of the samples. Of the 172 genera, 77 were only found in a single sample and 33 were found in two different samples. Rarefaction analysis at the 5 % level (comparable to genus) suggested that all the controls and most urethritis samples harboured each between 31 and 125 different groups. Four of the urethritis samples apparently contained between 150 and 300 different groups.ConclusionsUrine, even from healthy men, contains a very diverse micro-flora. Though not statistically significant, the total and median number of genera was found higher in patients with urethritis than in controls. Several widespread genera are likely to represent commensals and bacteria present in the environment.