The vaginal microbiome plays an important role in urogenital health. Quantitative real time Polymerase Chain Reaction (qPCR) assays for the most prevalent vaginal Lactobacillus species and bacterial vaginosis species G. vaginalis and A. vaginae exist, but qPCR information regarding variation over time is still very limited. We set up qPCR assays for a selection of seven species and defined the temporal variation over three menstrual cycles in a healthy Caucasian population with a normal Nugent score. We also explored differences in qPCR data between these healthy women and an ‘at risk’ clinic population of Caucasian, African and Asian women with and without bacterial vaginosis (BV), as defined by the Nugent score.

In endemic regions, asymptomatic Leishmania infection is common. In HIV patients, detection of asymptomatic Leishmania infection could potentially identify those at risk of visceral leishmaniasis (VL). However, data on the prevalence, incidence, and determinants of asymptomatic infection, and the risk of VL are lacking. We conducted a cross-sectional survey at a single ART centre, followed by a prospective cohort study amongst HIV-infected adults in HIV care in a district hospital in a VL-endemic area in North-West Ethiopia (9/2015-8/2016). Asymptomatic Leishmania infection was detected using the direct agglutination test (DAT), rK39-rapid diagnostic test (RDT)), PCR on peripheral blood and the KAtex urine antigen test, and defined as positivity on any Leishmania marker. All individuals were followed longitudinally (irrespective of the Leishmania test results). Risk factors for asymptomatic Leishmania infection were determined using logistic regression. A total of 534 HIV-infected individuals enrolled in HIV care were included in the study. After excluding 13 patients with a history of VL and an 10 patients with incomplete baseline Leishmania tests, 511 were included in analysis. The median age was 38 years (interquartile range (IQR) 30–45), 62.6% were male. The median follow-up time was 12 months (IQR 9–12). No deaths were reported during the study period. Most (95.5%) were on antiretroviral treatment at enrolment, for a median of 52 months (IQR 27–79). The median CD4 count at enrolment was 377 cells/mm3 (IQR 250–518). The baseline prevalence of Leishmania infection was 12.8% in males and 4.2% in females. Overall, 7.4% tested positive for rK39, 4.3% for DAT, 0.2% for PCR and 0.2% for KAtex. Independent risk factors for a prevalent infection were male sex (odds ratio (OR) 3.2; 95% confidence intervals (CI) 14–7.0) and concurrent malaria infection (OR 6.1; 95% CI 1.9–18.9). Amongst the 49 prevalent (baseline) infections with further follow-up, the cumulative incidence of losing the Leishmania markers by one year was 40.1%. There were 36 incident infections during the course of the study, with a cumulative one-year risk of 9.5%. Only one case of VL was detected during follow-up. We found a high prevalence of asymptomatic Leishmania infection, persisting in most cases. The incidence was more modest and overt VL was rare. Larger and longer studies with more complete follow-up may help to decide whether a test and treat strategy would be justified in this context. ClinicalTrials.gov NCT02839603 As visceral leishmaniasis (VL) in HIV patients is difficult to treat and associated with high mortality, strategies to detect and treat asymptomatic Leishmania infection in HIV patients should be explored. However, data on the prevalence, incidence, determinants of asymptomatic infection and risk of VL are lacking. We conducted a longitudinal study, including HIV-infected adult patients in HIV care in a district hospital in a VL-endemic area in North-West Ethiopia. Asymptomatic Leishmania infection was evaluated by Leishmania antibody tests (DAT and rK39), urine antigen tests (KAtex) and PCR, and was defined as positivity on any Leishmania marker. We also looked for independent risk factors for asymptomatic Leishmania infection at study recruitment. A total of 511 patients were included in the analysis. The median age was 38 years, 62.6% were male. The median time of residence in a VL-endemic area was 18 years. Most (95.5%) were on antiretroviral treatment at enrolment, for a median of 52 months. The median CD4 count at enrolment was 377 cells/mm³. The baseline prevalence of Leishmania infection was 12.8% in males and 4.2% in females. Overall, 7.4% tested positive for rK39, 4.3% for DAT, 0.2% for PCR and 0.2% for KAtex. Independent risk factors for a prevalent infection were male sex and concurrent malaria infection. Amongst the 49 prevalent infections that were present upon enrolment in the study, the probability of losing the Leishmania markers by one year was 40.1%. There were 36 new infections during the course of the study, with an overall risk of 9.5% by one year of follow-up. One case of VL was detected during follow-up. In conclusion, we found a high prevalence of asymptomatic Leishmania infection, which persisted in most cases. The incidence was more modest. Larger and longer studies would be needed to decide whether a test and treat strategy would be justified in this context.

In this study, we characterized all oropharyngeal and anorectal isolates of Neisseria spp. in a cohort of men who have sex with men. This resulted in a panel of pathogenic Neisseria (N. gonorrhoeae [n = 5] and N. meningitidis [n = 5]) and nonpathogenic Neisseria (N. subflava [n = 11], N. mucosa [n = 3] and N. oralis [n = 2]). A high proportion of strains in this panel were resistant to azithromycin (18/26) and ceftriaxone (3/26). Whole genome sequencing (WGS) of these strains identified numerous mutations that are known to confer reduced susceptibility to azithromycin and ceftriaxone in N. gonorrhoeae. The presence or absence of these known mutations did not explain the high level resistance to azithromycin (>256 mg/L) in the nonpathogenic isolates (8/16). After screening for antimicrobial resistance (AMR) genes, we found a ribosomal protection protein, Msr(D), in these highly azithromycin resistant nonpathogenic strains. The complete integration site originated from Streptococcus pneumoniae and is associated with high level resistance to azithromycin in many other bacterial species. This novel AMR resistance mechanism to azithromycin in nonpathogenic Neisseria could be a public health concern if it were to be transmitted to pathogenic Neisseria. This study demonstrates the utility of WGS-based surveillance of nonpathogenic Neisseria.

Diagnosis of a first-time visceral leishmaniasis (VL) infection in Ethiopia is established by use of a rapid diagnostic test (RDT) detecting antibodies against rK39, direct agglutination test (DAT) and microscopy according to the national algorithm. The performance of individual tests and algorithm is variable and depends on several factors, one being HIV status. Limited data are available on the performance of tests in VL-HIV coinfected patients. Assessment of the performance of DAT (ITM-A), rK39 ELISA (Serion) and six RDT (Onsite Leishmania Ab CTK, Antigen ICT Xinjier, IT Leish Biorad, Kalazar Detect Inbios, rK39 IgG1 Coris, rk28 IgG1 Coris) for the diagnosis of VL was done on a panel of 91 stored serum and plasma samples of ‘first-episode’ suspected VL patients, with HIV coinfection (n = 51) and without (n = 40). A combined reference standard was used: either positive microscopy on tissue aspirates, or in case of negative microscopy, positive PCR results on the aspirate slide. Additionally, endemic healthy controls (n = 20), non-endemic controls (n = 10) and patients with confirmed malaria infection (n = 10) were tested for specificity evaluation. Sensitivities ranged from 69.2% for DAT (applied cut-off ≥ 1/3200) to 92.2% for the Onsite RDT, whereas specificities ranged from 20.0% for Kalazar Antigen ICT to 100% for IT Leish and rK39 IgG1. Sensitivities from all assays decreased upon stratification according to HIV status but was only significantly different for rK39 Serion ELISA (p-value 0.0084) and the Onsite RDT (p-value 0.0159). In conclusion, performance of commercially available assays for VL on samples from Northern-Ethiopian patients varied widely with a substantial decrease in sensitivity in the VL-HIV coinfected group. Clear guidelines on minimal performance criteria of individual tests and algorithms are needed, as well as which reference standard should be used to determine the performance.

In addition to antimicrobial resistance, bacteria contain other mechanisms to survive antibiotic exposure such as tolerance, defined as the ability to slow metabolism by the extension of the lag phase without altering antimicrobial susceptibility. In a number of bacterial species, tolerance has been associated with treatment failure and infection chronicity and is found to precede and facilitate antimicrobial resistance. It is unknown if tolerance can be induced in Neisseria gonorrhoeae. In this study, we determined if tolerance to ceftriaxone (CRO) can be induced in N. gonorrhoeae and detected in clinical isolates. To induce tolerance, WHO P N. gonorrhoeae reference strain samples were grown under daily 3 h intermittent CRO exposure (10× the MIC), partitioned by overnight growth in GC broth. This cyclic exposure was performed for 7 consecutive days in sextuplicate, with two control cultures to which GC medium without antibiotics was added. To detect tolerance and assess CRO susceptibility, modified Tolerance Disc (TD) and Epsilometer tests were performed on isolates after each CRO exposure cycle. Additionally, this experiment was carried out on 18 clinical N. gonorrhoeae isolates. Tolerance was first detected after two CRO exposure cycles in five out of six samples. The phenotype differed per cycle with no clear pattern. No tolerance was found in control samples but was detected in 10 out of 18 clinical isolates. The present study is the first to demonstrate the induction of tolerance to CRO in N. gonorrhoeae through antibiotic exposure. In addition, tolerance to CRO was found in clinical samples.

Objectives: Pre-exposure prophylaxis (PrEP) users are screened bi-annual for sexually transmitted infections (STIs). A novel device, called the Colli-Pee, collects first-void urine in a standardised way and the collector tube can be easily delivered by regular post to a certified laboratory. The aim of the study was a one-to-one comparison between the STI test results obtained with the urine collected in the clinic, versus urine collected at home in a real-life setting by Men who have Sex with Men (MSM) in Belgium. The user-friendliness and acceptability of the Colli-Pee device by the users was also evaluated.Design: A single-site nested substudy in a prospective PrEP demonstration project (Be-PrEP-ared) among MSM in Belgium.Participants: A total of 473 home-based samples from 213 MSM were received with a mean age of 38.5 years.Interventions: Participants were requested to collect a urine sample at home using the Colli-Pee device and to send it to the laboratory via regular mail.Primary and secondary outcome measures: The presence ofChlamydia trachomatis(CT), Neisseria gonorrhoeae(NG), Mycoplasma genitalium(MG) andTrichomonas vaginalis(TV) was determined using molecular amplification assays. Agreement between test results of samples collected at the clinic and collected at home were evaluated using Cohen’s kappa statistic.Results: TV was not detected. A very good to almost perfect agreement was found for CT, NG and MG of κ=0.75, 0.87 and 0.85, respectively. Using the Colli-Pee device only one low positive CT and two MG infections were missed, however, three additional CT, two NG and six MG infections were detected.Conclusions: The Colli-Pee device is a feasible and convenient way to collect urine at home for STI testing. This may be particularly relevant for populations that need frequent STI testing, such as PrEP users and patients who prefer home-sampling.Trial registration number: NCT02552914; Pre-results.