Combining epidemiological data and whole genome sequencing to understand SARS-CoV-2 transmission dynamics in a large tertiary care hospital during the first COVID-19 wave in The Netherlands focusing on healthcare workers.

BACKGROUND: Healthcare facilities have been challenged by the risk of SARS-CoV-2 transmission between healthcare workers (HCW) and patients. During the first wave of the COVID-19 pandemic, infections among HCW were observed, questioning infection prevention and control (IPC) measures implemented at that time. AIM: This study aimed to identify nosocomial transmission routes of SARS-CoV-2 between HCW and patients in a tertiary care hospital. METHODS: All SARS-CoV-2 PCR positive HCW and patients identified between 1 March and 19 May 2020, were included in the analysis. Epidemiological data were collected from patient files and HCW contact tracing interviews. Whole genome sequences of SARS-CoV-2 were generated using Nanopore sequencing (WGS). Epidemiological clusters were identified, whereafter WGS and epidemiological data were combined for re-evaluation of epidemiological clusters and identification of potential transmission clusters. HCW infections were further classified into categories based on the likelihood that the infection was acquired via nosocomial transmission. Secondary cases were defined as COVID-19 cases in our hospital, part of a transmission cluster, of which the index case was either a patient or HCW from our hospital. FINDINGS: The study population consisted of 293 HCW and 245 patients. Epidemiological data revealed 36 potential epidemiological clusters, with an estimated 222 (75.7%) HCW as secondary cases. WGS results were available for 195 HCW (88.2%) and 20 patients (12.8%) who belonged to an epidemiological cluster. Re-evaluation of the epidemiological clusters, with the available WGS data identified 31 transmission clusters with 65 (29.4%) HCW as secondary cases. Transmission clusters were all part of 18 (50.0%) previously determined epidemiological clusters, demonstrating that several larger outbreaks actually consisted, of several smaller transmission clusters. A total of 21 (7.2%) HCW infections were classified as from confirmed nosocomial, of which 18 were acquired from another HCW and 3 from a patient. CONCLUSION: The majority of SARS-CoV-2 infections among HCW could be attributed to community-acquired infection. Infections among HCW that could be classified as due to nosocomial transmission, were mainly caused by HCW-to-HCW transmission rather than patient-to-HCW transmission. It is important to recognize the uncertainties of cluster analyses based solely on epidemiological data.

Role of IgM testing in the diagnosis and post-treatment follow-up of syphilis: a prospective cohort study.

OBJECTIVES: The diagnosis of repeat syphilis and its follow-up remains challenging. We aimed to investigate if IgM testing may assist in the diagnosis of syphilis reinfection/relapse and its treatment follow-up. METHODS: This substudy was conducted in the context of a syphilis biomarker discovery study (ClinicalTrials.gov Nr: NCT02059525). Sera were collected from 120 individuals with a new diagnosis of syphilis (72 with repeat infections) and 30 syphilis negative controls during a cohort study investigating syphilis biomarkers conducted at a sexually transmitted infection/HIV clinic in Antwerp, Belgium. Syphilis was diagnosed based on a simultaneous positive treponemal and non-treponemal assay result and/or positive serum PCR targeting polA. Specimens collected at visit of diagnosis, and 3 and 6 months post-treatment were tested by two enzyme immunoassays (EIAs), recomWell (Mikrogen; MI) and Euroimmun (EU), to detect anti-treponemal IgM. Baseline specimens were also tested for anti-treponemal IgM using a line immunoassay (LIA) recomLine (MI). Quantitative kinetic decay curves were constructed from the longitudinal quantitative EIA results. RESULTS: An overall sensitivity for the diagnosis of syphilis of 59.8% (95% CI: 50.3%-68.7%), 75.0% (95% CI: 66.1%-82.3%) and 63.3% (95% CI: 54.8%-72.6%) was obtained for the EU, MI EIAs and MI LIA, respectively. When only considering repeat syphilis, the diagnostic sensitivity decreased to 45.7% (95% CI: 33.9%-58.0%), 63.9% (95% CI: 51.7%-74.6%) and 47.2% (95% CI: 35.5%-59.3%), respectively. IgM seroreverted in most cases 6 months after treatment. Post-treatment IgM concentrations decreased almost 30% faster for initial syphilis compared with repeat infection. The IgM EIAs and IgM LIA agreed from fairly to moderately (Cohen's kappa (κ): 0.36 (EU EIA); κ: 0.53 (MI EIA); κ: 0.40 (MI LIA)) with the diagnosis of syphilis. CONCLUSIONS: IgM detection was not a sensitive method to diagnose syphilis and was even poorer in the diagnosis of syphilis repeat infections.

Take three, test one: a cross-sectional study to evaluate the molecular detection of Chlamydia trachomatis and Neisseria gonorrhoeae in pooled pharyngeal, anorectal and urine samples versus single-site testing among men who have sex with men in Belgium.

Objectives: To investigate the efficacy of performing a pooling strategy of triple-anatomical site samples (pharyngeal, anorectal and urine samples) for simultaneous Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) nucleic acid amplification detection.Methods: A total of 117 specimen sets (pharyngeal, anorectal and urine) were collected from 98 men between 2014 and 2016. Double sampling of pharyngeal, anorectal and urine samples allowed for pooled and unpooled analyses using a multiplex Abbott Real Time CT/NG assay, together with confirmatory PCR testing in case of CT/NG positivity. Clinical and demographic data were analyzed.Results: The positivity rate for the triple-site pooled testing for CT and NG was 8.5% (10/117) and 6.8%, (8/117), respectively, compared to the single-site testing total positivity rate, which was 9.4% (11/117) and 4.3% (5/117) for CT and NG, respectively. Pooled analysis missed one CT-positive urine sample and one CT-positive anorectal sample could not be confirmed. In addition, less PCR inhibition was reported for the pooled sample (PS) testing and ERV-3 qPCR testing revealed ineffective sampling of self-collected anorectal swabs in two cases. No pharyngeal samples were positive for CT, nor were any urine samples positive for NG.Conclusion: This small study showed that PS testing is a possible testing strategy for screening high-risk men who have sex with men attending pre-exposure prophylaxis (PrEP) clinics. However, due to the low positivity rate of CT/NG in this study, larger evaluations are needed to confirm the effectiveness of CT/NG screening with multiple-site PS nucleic acid amplification test (NAAT) screening practices.

Superimposing incident sexually transmitted infections on HIV phylogram to investigate possible misclassification of men who have sex with men as heterosexuals in a cohort in Antwerp, Belgium.

In this study, we assessed if the superimposition of incident sexually transmitted infections (STIs) on HIV phylogenetic analyses could reveal possible sexual behaviour misclassifications in our HIV-infected population. HIV-1 sequences collected between 1997 and 2014 from 1169 individuals attending a HIV clinic in Antwerp, Belgium were analysed to infer a partial HIV transmission network. Individual demographic, clinical and laboratory data collected during routine HIV follow-up were used to compare clustered and non-clustered individuals using logistic regression analyses. In total, 438 (37.5%) individuals were identified in 136 clusters, including 76 transmission pairs and 60 clusters consisting of three or more individuals. Individuals in a cluster were more likely to have a history of syphilis, Chlamydia and/or gonorrhoea (P < 0.05); however, when analyses were stratified by HIV transmission risk groups (heterosexual and men who have sex with men [MSM]), this association only remained significant for heterosexuals with syphilis (P = 0.001). Under closer scrutiny, this association was driven by six heterosexual men who were located in six almost exclusively MSM clusters. A parsimonious conclusion is that these six individuals were potentially misclassified as heterosexual. Improving the accuracy of sexual behaviour reporting could improve care.

Needle lost in the haystack: multiple reaction monitoring fails to detect Treponema pallidum candidate protein biomarkers in plasma and urine samples from individuals with syphilis.

Background: Current syphilis diagnostic strategies are lacking a sensitive manner of directly detecting Treponema pallidum antigens. A diagnostic test that could directly detect T. pallidum antigens in individuals with syphilis would be of considerable clinical utility, especially for the diagnosis of reinfections and for post-treatment serological follow-up. Methods: In this study, 11 candidate T. pallidum biomarker proteins were chosen according to their physiochemical characteristics, T. pallidum specificity and predicted abundance. Thirty isotopically labelled proteotypic surrogate peptides (hPTPs) were synthesized and incorporated into a scheduled multiple reaction monitoring assay. Protein extracts from undepleted/unenriched plasma (N = 18) and urine (N = 4) samples from 18 individuals with syphilis in various clinical stages were tryptically digested, spiked with the hPTP mixture and analysed with a triple quadruple mass spectrometer. Results: No endogenous PTPs corresponding to the eleven candidate biomarkers were detected in any samples analysed. To estimate the Limit of Detection (LOD) of a comparably sensitive mass spectrometer (LTQ-Orbitrap), two dilution series of rabbit cultured purified T. pallidum were prepared in PBS. Polyclonal anti- T. pallidum antibodies coupled to magnetic Dynabeads were used to enrich one sample series; no LOD improvement was found compared to the unenriched series. The estimated LOD of MS instruments is 300 T. pallidum/ml in PBS. Conclusions: Biomarker protein detection likely failed due to the low (femtomoles/liter) predicted concentration of T. pallidum proteins. Alternative sample preparation strategies may improve the detectability of T. pallidum proteins in biofluids.

Could differences in implicit attitudes to sexual concurrency play a role in generalized HIV epidemics?

Background: Sexual partner concurrency has been implicated in the genesis of generalized HIV epidemic in South Africa. Most South Africans, however, disapprove of concurrency in surveys. These surveys test individuals' explicit attitudes which are susceptible to a number of important biases such as the social desirability bias. Assessment of implicit cognitions have been found to be better predictors of behaviour in socially sensitive domains. We hypothesized that South Africans may have implicit attitudes more tolerant of concurrency than lower concurrency prevalence populations. Methods: To test this hypothesis, we developed a concurrency-implicit association test (C-IAT) and compared the C-IATs of samples of South African and Belgian university students. Results: We found a large and statistically significant difference in the C-IAT between the South Africans (D600-score = -0.009, indicating absence of preference for concurrency or monogamy) and Belgians (D600-score = 0.783, indicating a strong preference for monogamy; t-test = 13.3; P < 0.0001). The effect size measure, Cohen's d, was found to be 0.88, which is considered a large effect size in this field. Conclusions: Our results are compatible with the thesis that differences in implicit attitudes to concurrency play a role in the genesis of generalised HIV epidemics.

Candidate Treponema pallidum biomarkers uncovered in urine from individuals with syphilis using mass spectrometry.

AIM: A diagnostic test that could detect Treponema pallidum antigens in urine would facilitate the prompt diagnosis of syphilis. MATERIALS & METHODS: Urine from 54 individuals with various clinical stages of syphilis and 6 controls were pooled according to disease stage and interrogated with complementary mass spectrometry techniques to uncover potential syphilis biomarkers. RESULTS & CONCLUSION: In total, 26 unique peptides were uncovered corresponding to four unique T. pallidum proteins that have low genetic sequence similarity to other prokaryotes and human proteins. This is the first account of direct T. pallidum protein detection in human clinical samples using mass spectrometry. The implications of these findings for future diagnostic test development is discussed. Data are available via ProteomeXchange with identifier PXD009707.

Syphilis reinfection is associated with an attenuated immune profile in the same individual: a prospective observational cohort study.

BACKGROUND: Ascertaining if the clinical and immunological response to repeat syphilis differs from that in initial syphilis may assist in designing optimal syphilis screening strategies and vaccine design. METHODS: We prospectively recruited 120 patients with a new diagnosis of (baseline) syphilis. During a 24-month follow-up period, 11 of these patients had a further diagnosis of (repeat) syphilis. We conducted a paired comparison of their plasma cyto-chemokines at baseline and repeat syphilis. RESULTS: Comparing to their baseline infection, paired analyses of the 11 individuals with repeat infections during follow-up revealed that these reinfections had lower concentrations of Interferon (IFN)α (0.8 [Interquartile range (IQR) 0.8-0.8 vs. 12.2 [IQR 1.6-24.2], P = 0.004) and Chemokine (C-C motif) ligand (CCL) 4 (0.9 [IQR 0.9-12.2 vs. 17.5 [IQR 4.9-32.8], P = 0.022]. CONCLUSION: In this small study of 11 individuals, repeat syphilis was found to present with an attenuated immune response. The relevance of these findings to the design of optimal syphilis screening programs is discussed.

Repeat Syphilis Is More Likely to Be Asymptomatic in HIV-Infected Individuals: A Retrospective Cohort Analysis With Important Implications for Screening.

There is conflicting evidence as to whether repeat syphilis is more likely to present asymptomatically than initial syphilis. If it is, then this would motivate more frequent and long-term syphilis screening in persons with a history of multiple episodes of syphilis. We conducted detailed folder reviews of all individuals with 4 or more diagnoses of syphilis between 2000 and 2017 at the Institute of Tropical Medicine, Antwerp, and assessed if there was a difference in the proportion presenting with symptomatic (primary and secondary) vs asymptomatic (latent) syphilis in initial vs repeat syphilis. Forty-five clients with 4 or more episodes of syphilis were included in the study. All were HIV-infected. Repeat episodes of syphilis were less likely to be symptomatic than initial episodes (35/160 [21.9%] vs 28/45 [62.2%]; P < .001). Frequent screening in those with HIV infection may be the only way to diagnose repeat episodes of syphilis. Care providers can use this information to motivate persons with multiple episodes of syphilis to be screened every 3 to 6 months.

Functional insights from proteome-wide structural modeling of Treponema pallidum subspecies pallidum, the causative agent of syphilis.

BACKGROUND: Syphilis continues to be a major global health threat with 11 million new infections each year, and a global burden of 36 million cases. The causative agent of syphilis, Treponema pallidum subspecies pallidum, is a highly virulent bacterium, however the molecular mechanisms underlying T. pallidum pathogenesis remain to be definitively identified. This is due to the fact that T. pallidum is currently uncultivatable, inherently fragile and thus difficult to work with, and phylogenetically distinct with no conventional virulence factor homologs found in other pathogens. In fact, approximately 30% of its predicted protein-coding genes have no known orthologs or assigned functions. Here we employed a structural bioinformatics approach using Phyre2-based tertiary structure modeling to improve our understanding of T. pallidum protein function on a proteome-wide scale. RESULTS: Phyre2-based tertiary structure modeling generated high-confidence predictions for 80% of the T. pallidum proteome (780/978 predicted proteins). Tertiary structure modeling also inferred the same function as primary structure-based annotations from genome sequencing pipelines for 525/605 proteins (87%), which represents 54% (525/978) of all T. pallidum proteins. Of the 175 T. pallidum proteins modeled with high confidence that were not assigned functions in the previously annotated published proteome, 167 (95%) were able to be assigned predicted functions. Twenty-one of the 175 hypothetical proteins modeled with high confidence were also predicted to exhibit significant structural similarity with proteins experimentally confirmed to be required for virulence in other pathogens. CONCLUSIONS: Phyre2-based structural modeling is a powerful bioinformatics tool that has provided insight into the potential structure and function of the majority of T. pallidum proteins and helped validate the primary structure-based annotation of more than 50% of all T. pallidum proteins with high confidence. This work represents the first T. pallidum proteome-wide structural modeling study and is one of few studies to apply this approach for the functional annotation of a whole proteome.

Implicit attitudes to sexual partner concurrency vary by sexual orientation but not by gender-A cross sectional study of Belgian students.

High rates of sexual partner concurrency have been shown to facilitate the spread of various sexually transmitted infections. Assessments of explicit attitudes to concurrency have however found little difference between populations. Implicit attitudes to concurrency may vary between populations and play a role in generating differences in the prevalence of concurrency. We developed a concurrency implicit associations test (C-IAT) to assess if implicit attitudes towards concurrency may vary between individuals and populations and what the correlates of these variations are. A sample of 869 Belgian students (mean age 23, SD 5.1) completed an online version of the C-IAT together with a questionnaire concerning sexual behavior and explicit attitudes to concurrency. The study participants C-IATs demonstrated a strong preference for monogamy (-0.78, SD = 0.41). 93.2% of participants had a pro-monogamy C-IAT. There was no difference in this implicit preference for monogamy between heterosexual men and women. Men who have sex with men and women who have sex with women were more likely to exhibit implicit but not explicit preferences for concurrency compared to heterosexual men and women. Correlates of the C-IAT varied between men and women.

What Is the Role of Paired Rapid Plasma Reagin Testing (Simultaneous Testing of Acute and Convalescent Samples) in the Diagnosis of Repeat Syphilis and the Follow-up of Syphilis?

BACKGROUND: Repeat syphilis is playing an increasing role in syphilis transmission in several populations. The assessment of repeat syphilis and response to treatment depends on accurately measuring intraindividual changes in non-treponemal tests. For a 0- to 6-month delta rapid plasma reagin (RPR) to be determined by routine individual RPR testing, samples are tested 6 months apart with differences in reagent batches, environmental conditions, and observers all leading to measurement errors. We hypothesized that conducting paired RPR testing (simultaneous testing of acute and convalescent samples) would enable a more accurate determination of delta RPR compared with individual testing. METHODS: A total of 120 study participants with a new diagnosis of syphilis were followed up at 0, 3, 6, 9, 12, 18, and 24 months, with RPR testing performed via individual testing at each study visit and at any suspected repeat syphilis. Rapid plasma reagin paired testing was performed on samples from 0 and 6 months and at any suspected repeat syphilis. RESULTS: The quantitative agreement ±1 dilution among paired and individual testing was 97.2%. There was no difference in the proportion with serofast status at 6 months: 21 (19.4%) and 19 (17.6%) according to paired and individual testing, respectively (P = 0.726). There was no statistically significant difference between 0- and 6-month delta RPR as determined by paired and individual testing in predicting seroresponse at 12 months (86.1% and 91.6% agreement with 12-month serofast/nonserofast classification, respectively; P = 0.262). CONCLUSIONS: In our setting, individual testing performed equally well compared with paired testing. Follow-up of syphilis will remain onerous for the patient and the health care provider until new tests that can more accurately assess the response to therapy and repeat syphilis/treatment failure are developed.

Repeat syphilis has a different immune response compared with initial syphilis: an analysis of biomarker kinetics in two cohorts.

OBJECTIVE: We aimed to asses if there are differences in the clinical presentation and immune response of repeat as compared with initial syphilis. METHODS: Prospective study: we prospectively recruited all patients with a new diagnosis of syphilis and tested their plasma for a range of cytochemokines and rapid plasma reagin (RPR) at baseline pretreatment and 6 months following therapy. Retrospective study: we compared RPR assay response kinetics between initial and repeat syphilis in persons attending our HIV/STI clinic from 1993 to 2016. RESULTS: Prospective study: a total of 91 individuals, 36 with initial syphilis and 55 with repeat syphilis, were included in the study. At baseline visit, those with initial syphilis were more likely to be symptomatic and have higher levels of interleukin-10 than repeaters. At baseline, median RPR titres were higher in the repeat than the initial infection groups. Repeaters were less likely than those with initial infections to serorevert to a negative RPR and be serofast (<4-fold RPR titre decline) at 6 months.Retrospective study: syphilis was diagnosed in 1027/43 870 individuals tested. At diagnosis, repeaters had higher RPR titres and a stepwise increase in RPR titre with number of syphilis episodes. They had a different RPR test response kinetic: they were less likely to be serofast and to serorevert than initial syphilis at 6 and 12 months. No individuals with four or more previous episodes of syphilis seroreverted. CONCLUSION: Repeat syphilis has a different clinical presentation and immunological response to initial infection.

Evaluation of an automated quantitative latex immunoturbidimetric non-treponemal assay for diagnosis and follow-up of syphilis: a prospective cohort study.

Purpose. We evaluated the Sekure rapid plasma reagin (RPR-S) (Sekisui Diagnostics) automated quantitative latex immunoturbidimetric assay performed on the SK500 clinical chemistry system for clinical appropriateness.Methodology. Syphilis-infected individuals and controls were recruited into a prospective cohort study conducted at a sexually transmitted infection clinic in Antwerp, Belgium. Sera collected at diagnosis (baseline) and at 3, 6, 9 and 12 months post-treatment were tested with RPR-S and Macro-Vue RPR card (RPR-C) (Becton Dickinson) assays; RPR-C was considered the reference test. IgG/IgM enzyme immunoassay and Treponema pallidum polA serum PCR results were consulted by discordancy at baseline. Categorical analyses were performed and correlations were assessed with (non)-linear regression. Post-treatment longitudinal serological evolution was evaluated.Results. A total of 463 samples from 120 new syphilis cases from a variety of clinical stages and 30 syphilis-negative controls were tested. Initially, there was a weak correlation between quantitative RPR-C/S (r=0.15). In 70 samples there was a strong suspicion of hook effect. Of these, 57/70 sera were retested with an extra dilution step, resulting in an average 12-fold increase in quantitative RPR-S results. After the extra dilution, the overall qualitative RPR-C/S agreement was 78.89 %, (κ-coefficient: 0.484). Of the 92 discordant samples, 9 were from the baseline visit (RPR-C titre: 1-8), which could have led to possible missed diagnoses using the RPR-S.Conclusions. The sensitivity and accuracy of the RPR-S test requires improvement before it can be used to diagnose syphilis and evaluate treatment efficacy in clinical practice.

Molecular Typing of Syphilis-Causing Strains Among Human Immunodeficiency Virus-Positive Patients in Antwerp, Belgium.

Centers for Disease Control and Prevention and sequencing-based treponeme typing was used to analyze 72 blood samples, collected from human immunodeficiency virus and syphilis co-infected patients during 2014 to 2015 in Antwerp, Belgium. Twenty-nine (40.3%) isolates were polymerase chain reaction positive for Treponema pallidum, and all tested were macrolide-resistant. Four genotypes were identified by sequencing-based typing including two new genotypes, U4NR8 and SU9R8, whereas enhanced Centers for Disease Control and Prevention typing revealed 7 subtypes.

The immunological response to syphilis differs by HIV status; a prospective observational cohort study.

BACKGROUND: It is not known if there is a difference in the immune response to syphilis between HIV-infected and uninfected individuals. METHODS: We prospectively recruited all patients with a new diagnosis of syphilis and tested their plasma for IFNα, IFNγ, IL-1ß, IL-12p40, IL-12p70, IP-10, MCP-1, MIP-1α, MIP-1ß, IL-4, IL-5, IL-6, IL-7, IL-8, IL-10 and IL-17A at baseline pre-treatment and 6 months following therapy. RESULTS: A total of 79 HIV-infected [44 primary/secondary syphilis (PSS) and 35 latent syphilis (LS)] and 12 HIV-uninfected (10 PSS and 2 LS) cases of syphilis and 30 HIV-infected controls were included in the study. At the baseline visit, compared to the control group, concentrations of IL-10 were significantly elevated in the HIV-infected and uninfected groups. The level of IL-10 was significantly higher in the HIV-infected compared to the HIV-uninfected PSS group (25.3 pg/mL (IQR, 4.56-41.76) vs 2.73 pg/mL (IQR, 1.55-9.02), P = 0.0192). In the HIV-infected PSS group (but not the HIV-infected LS or HIV-uninfected PSS groups) the IP-10, MIP-1b, IL-6 and IL-8 were raised compared to the controls. IL-10 levels decreased but did not return to control baseline values by 6 months in HIV infected PSS and LS and HIV uninfected PSS. CONCLUSION: PSS and LS in HIV-infected individuals is characterized by an increase in inflammatory and anti-inflammatory cytokines such as IL-10. The increase of IL-10 is greater in HIV-infected than uninfected individuals. Further work is required to ascertain if this is part of an immunological profile that correlates with adverse outcomes such as serofast syphilis and neurosyphilis, in HIV-infected individuals.

HIV infection rather than concurrent opportunistic infections drives most systemic procoagulant, vascular and damage responses - a prospective cohort study in central Africa.

BACKGROUND: HIV infection is accompanied by various systemic host responses, including activation of coagulation and the vascular endothelium. We sought to determine the impact of opportunistic coinfections in a central African setting. METHODS: This prospective study included 98 HIV-infected individuals in Gabon initiating combination antiretroviral therapy (cART) and followed them up for 6 months. Patients were stratified according to the presence of active tuberculosis (TB; n=19), mucocutaneous opportunistic infection (n=9) or no opportunistic infection (n=70). HIV-uninfected subjects were included as controls (n=32). Plasma concentrations of 14 markers of coagulation, endothelial activation, extracellular matrix formation and tissue damage were measured with a multiplex assay at baseline and months 3 and 6 after cART initiation. RESULTS: HIV-infected patients showed elevated plasma levels of all biomarkers measured with exception of protein C, which was reduced. Concurrent TB was only associated with elevated concentrations of D-dimer, metallopeptidase inhibitor 1 and Tenascin-C. Mucocutaneous coinfection did not alter HIV-associated responses. Most markers measured declined but remained elevated despite response to cART. CONCLUSIONS: HIV infection is associated with systemic pro-coagulant, vascular and damage responses. In an ambulatory setting, concurrent opportunistic infections have little if any influence on these responses and normalization is incomplete after response to cART. This suggests that these responses are mainly driven by HIV-associated immune activation and less so by opportunistic infections.

Characterizing the Syphilis-Causing Treponema pallidum ssp. pallidum Proteome Using Complementary Mass Spectrometry.

BACKGROUND: The spirochete bacterium Treponema pallidum ssp. pallidum is the etiological agent of syphilis, a chronic multistage disease. Little is known about the global T. pallidum proteome, therefore mass spectrometry studies are needed to bring insights into pathogenicity and protein expression profiles during infection. METHODOLOGY/PRINCIPAL FINDINGS: To better understand the T. pallidum proteome profile during infection, we studied T. pallidum ssp. pallidum DAL-1 strain bacteria isolated from rabbits using complementary mass spectrometry techniques, including multidimensional peptide separation and protein identification via matrix-assisted laser desorption ionization-time of flight (MALDI-TOF/TOF) and electrospray ionization (ESI-LTQ-Orbitrap) tandem mass spectrometry. A total of 6033 peptides were detected, corresponding to 557 unique T. pallidum proteins at a high level of confidence, representing 54% of the predicted proteome. A previous gel-based T. pallidum MS proteome study detected 58 of these proteins. One hundred fourteen of the detected proteins were previously annotated as hypothetical or uncharacterized proteins; this is the first account of 106 of these proteins at the protein level. Detected proteins were characterized according to their predicted biological function and localization; half were allocated into a wide range of functional categories. Proteins annotated as potential membrane proteins and proteins with unclear functional annotations were subjected to an additional bioinformatics pipeline analysis to facilitate further characterization. A total of 116 potential membrane proteins were identified, of which 16 have evidence supporting outer membrane localization. We found 8/12 proteins related to the paralogous tpr gene family: TprB, TprC/D, TprE, TprG, TprH, TprI and TprJ. Protein abundance was semi-quantified using label-free spectral counting methods. A low correlation (r = 0.26) was found between previous microarray signal data and protein abundance. CONCLUSIONS: This is the most comprehensive description of the global T. pallidum proteome to date. These data provide valuable insights into in vivo T. pallidum protein expression, paving the way for improved understanding of the pathogenicity of this enigmatic organism.

Tuberculosis Treatment Outcome and Drug Resistance in Lambaréné, Gabon: A Prospective Cohort Study.

Despite overall global progress in tuberculosis (TB) control, TB remains one of the deadliest communicable diseases. This study prospectively assessed TB epidemiology in Lambaréné, Gabon, a Central African country ranking 10th in terms of TB incidence rate in the 2014 World Health Organization TB report. In Lambaréné, between 2012 and 2014, 201 adult and pediatric TB patients were enrolled and followed up; 66% had bacteriologically confirmed TB and 95% had pulmonary TB. The human immunodeficiency virus (HIV) coinfection rate was 42% in adults and 16% in children. Mycobacterium tuberculosis and Mycobacterium africanum were identified in 82% and 16% of 108 culture-confirmed TB cases, respectively. Isoniazid (INH) and streptomycin yielded the highest resistance rates (13% and 12%, respectively). The multidrug resistant TB (MDR-TB) rate was 4/91 (4%) and 4/13 (31%) in new and retreatment TB cases, respectively. Treatment success was achieved in 53% of patients. In TB/HIV coinfected patients, mortality rate was 25%. In this setting, TB epidemiology is characterized by a high rate of TB/HIV coinfection and low treatment success rates. MDR-TB is a major public health concern; the need to step-up in-country diagnostic capacity for culture and drug susceptibility testing as well as access to second-line TB drugs urgently requires action.