Advancing the case for microbial conservation

The majority of the biomass and biodiversity of life on the Earth is accounted for by microbes. They play pivotal roles in biogeochemical cycles and harbour novel metabolites that have industrial uses. For these reasons the conservation of microbial ecosystems, communities and even specific taxa should be a high priority. We review the reasons for including microorganisms in conservation agenda. We discuss some of the complications in this endeavour, including the unresolved argument about whether microorganisms have intrinsic value, which influences some of the non-instrumental motivations for their conservation and, from a more pragmatic perspective, exactly what it is that we seek to conserve (microorganisms, their habitats or their gene pools). Despite complications, priorities can be defined for microbial conservation and we provide practical examples of such priorities

Interpreting declines in HIV test positivity:an analysis of routine data from Zimbabwe's national sex work programme, 2009–2019

Introduction: Early diagnosis of HIV is critical for epidemic control. To achieve this, successful testing programmes are essential and test positivity is often used as a marker of their performance. The aim of this study was to analyse trends and predictors of HIV test positivity over time and explore how an understanding of seroconversion rates could build on our interpretation of this indicator among female sex workers in Zimbabwe. Methods: We analysed HIV test data from Zimbabwe's nationally scaled sex work programme between 2009 and 2019. We defined test positivity as the proportion of all tests that were HIV positive and measured new diagnoses by estimating seroconversion rates among women with repeat tests, defined as an HIV-positive test after at least one HIV-negative test in the programme. We used logistic regression to analyse test positivity over three time-periods: 2009–2013, 2014–2017 and 2018–2019, adjusting for potential confounding by demographic factors and the mediating effects of time since last HIV test. We calculated the seroconversion rates for the same time-periods. Results: During the 10-year study period, 54,503 tests were recorded in 39,462 women. Between 2009 and 2013, 18% of tests were among women who reported testing in the previous 6 months. By 2018–2019, this had increased to 57%. Between 2018 and 2019, test positivity was 9.6%, compared to 47.9% for 2009–2013 (aOR 6.08 95% CI 5.52–6.70) and 18.8% for 2014–2017 (aOR 2.17 95% CI 2.06–2.28). Adjusting for time since last test reduced effect estimates for 2009–2013 (aOR 4.03 95% CI 3.64–4.45) and 2014–2017 (aOR 1.97 95% CI 1.86–2.09) compared to 2018–2019. Among 7573 women with an initial HIV-negative test in the programme and at least one subsequent test, 464 tested HIV positive at a rate of 3.9 per 100 pyar (95% CI 3.5–4.2).Conclusions: Test positivity decreased among women testing through the programme over time, while seroconversion rates remained high. These declines were partly driven by changes in individual testing history, reflecting comprehensive coverage of testing services and greater knowledge of HIV status, but not necessarily declining rates of seroconversion. Understanding testing history and monitoring new HIV infections from repeat tests could strengthen the interpretation of test positivity and provide a better understanding of programme performance.</p

Interpreting declines in HIV test positivity:an analysis of routine data from Zimbabwe's national sex work programme, 2009–2019

Introduction: Early diagnosis of HIV is critical for epidemic control. To achieve this, successful testing programmes are essential and test positivity is often used as a marker of their performance. The aim of this study was to analyse trends and predictors of HIV test positivity over time and explore how an understanding of seroconversion rates could build on our interpretation of this indicator among female sex workers in Zimbabwe. Methods: We analysed HIV test data from Zimbabwe's nationally scaled sex work programme between 2009 and 2019. We defined test positivity as the proportion of all tests that were HIV positive and measured new diagnoses by estimating seroconversion rates among women with repeat tests, defined as an HIV-positive test after at least one HIV-negative test in the programme. We used logistic regression to analyse test positivity over three time-periods: 2009–2013, 2014–2017 and 2018–2019, adjusting for potential confounding by demographic factors and the mediating effects of time since last HIV test. We calculated the seroconversion rates for the same time-periods. Results: During the 10-year study period, 54,503 tests were recorded in 39,462 women. Between 2009 and 2013, 18% of tests were among women who reported testing in the previous 6 months. By 2018–2019, this had increased to 57%. Between 2018 and 2019, test positivity was 9.6%, compared to 47.9% for 2009–2013 (aOR 6.08 95% CI 5.52–6.70) and 18.8% for 2014–2017 (aOR 2.17 95% CI 2.06–2.28). Adjusting for time since last test reduced effect estimates for 2009–2013 (aOR 4.03 95% CI 3.64–4.45) and 2014–2017 (aOR 1.97 95% CI 1.86–2.09) compared to 2018–2019. Among 7573 women with an initial HIV-negative test in the programme and at least one subsequent test, 464 tested HIV positive at a rate of 3.9 per 100 pyar (95% CI 3.5–4.2).Conclusions: Test positivity decreased among women testing through the programme over time, while seroconversion rates remained high. These declines were partly driven by changes in individual testing history, reflecting comprehensive coverage of testing services and greater knowledge of HIV status, but not necessarily declining rates of seroconversion. Understanding testing history and monitoring new HIV infections from repeat tests could strengthen the interpretation of test positivity and provide a better understanding of programme performance.</p

Temporal trends in, and risk factors for, HIV seroconversion among female sex workers accessing Zimbabwe's national sex worker programme, 2009–19:a retrospective cohort analysis of routinely collected HIV testing data

Background: The frequency of new HIV infections among female sex workers in sub-Saharan Africa is poorly understood. We used routinely collected data that enable unique identification of repeat HIV testers to assess temporal trends in seroconversion and identify associated risk factors for female sex workers accessing Sisters with a Voice, Zimbabwe's national sex worker programme. Methods: We pooled HIV testing data gathered between Sept 15, 2009, and Dec 31, 2019, from 36 Sisters programme sites in Zimbabwe. We included female sex workers aged 16 years or older with an HIV-negative test and at least one subsequent programme test. We calculated HIV seroconversion rates (using the midpoint between the HIV-positive test and the last negative test as the seroconversion date) and estimated rate ratios to compare 2-year periods by using Poisson regression, with robust SEs to account for clustering by site and adjusting for age and testing frequency to assess temporal trends. We did sensitivity analyses to explore assumptions about seroconversion dates and the effects of variation in follow-up time on our conclusions. Findings: Our analysis included data for 6665 female sex workers, 441 (7%) of whom seroconverted. The overall seroconversion rate was 3·8 (95% CI 3·4–4·2) per 100 person-years at risk. Seroconversion rates fell with time since first negative HIV test. After adjustment, there was evidence of a decrease in seroconversion rates from 2009 to 2019 (p=0·0053). In adjusted analyses, being younger than 25 years, and having a sexually transmitted infection diagnosis at a previous visit, were significantly associated with increased seroconversion rates. Our findings were mostly robust to sensitivity analyses, but when 1 month before an HIV-positive test was used as the seroconversion date, seroconversion rates no longer fell with time. Interpretation: We identified high rates of seroconversion shortly after linkage to programme services, which emphasises the need to strengthen HIV prevention programmes from first contact with female sex workers in Zimbabwe. New infections among female sex workers remain challenging to measure, but longitudinal analysis of routine testing data can provide valuable insights into seroconversion rates and associated risk factors. Funding: UN Population Fund, Deutsche Gesellschaft für Internationale Zusammenarbeit, the Bill &amp; Melinda Gates Foundation, The Global Fund to Fight AIDS, Tuberculosis and Malaria, US President's Emergency Plan for AIDS Relief, US Agency for International Development, and the Elton John AIDS Foundation.</p

Suppression of basophil histamine release and other IgE-dependent responses in childhood Schistosoma mansoni/hookworm coinfection.

BACKGROUND: The poor correlation between allergen-specific immunoglobulin E (asIgE) and clinical signs of allergy in helminth infected populations suggests that helminth infections could protect against allergy by uncoupling asIgE from its effector mechanisms. We investigated this hypothesis in Ugandan schoolchildren coinfected with Schistosoma mansoni and hookworm. METHODS: Skin prick test (SPT) sensitivity to house dust mite allergen (HDM) and current wheeze were assessed pre-anthelmintic treatment. Nonspecific (anti-IgE), helminth-specific, and HDM-allergen-specific basophil histamine release (HR), plus helminth- and HDM-specific IgE and IgG4 responses were measured pre- and post-treatment. RESULTS: Nonspecific- and helminth-specific-HR, and associations between helminth-specific IgE and helminth-specific HR increased post-treatment. Hookworm infection appeared to modify the relationship between circulating levels of HDM-IgE and HR: a significant positive association was observed among children without detectable hookworm infection, but no association was observed among infected children. In addition, hookworm infection was associated with a significantly reduced risk of wheeze, and IgG4 to somatic adult hookworm antigen with a reduced risk of HDM-SPT sensitivity. There was no evidence for S. mansoni infection having a similar suppressive effect on HDM-HR or symptoms of allergy. CONCLUSIONS: Basophil responsiveness appears suppressed during chronic helminth infection; at least in hookworm infection, this suppression may protect against allergy

Experimental Validation of Specialised Questioning Techniques in Conservation

Conservation increasingly relies on social science tools to understand human behavior. Specialized questioning techniques (SQTs) are a suite of methods designed to reduce bias in social surveys and are widely used to collect data on sensitive topics, including compliance with conservation rules. Most SQTs have been developed in Western, industrialized, educated, rich, and democratic countries, meaning their suitability in other contexts may be limited. Whether these techniques perform better than conventional direct questioning is important for those considering their use. We designed an experiment to validate the performance of four SQTs (unmatched count technique, randomized response technique, crosswise model, and bean method) against direct questions when asking about a commonly researched sensitive behavior in conservation, wildlife hunting. We developed fictional characters, and for each method asked respondents to report the answers that each fictional character should give when asked if they hunt wildlife. We collected data from 609 individuals living close to protected areas in two different cultural and socioeconomic contexts (Indonesia and Tanzania) to quantify the extent to which respondents understood and followed SQT instructions and to explore the sociodemographic factors that influenced a correct response. Data were modeled using binomial general linear mixed models. Participants were more likely to refuse to answer questions asked using SQTs compared with direct questions. Model results suggested that SQTs were harder for participants to understand. Demographic factors (e.g., age and education level) significantly influenced response accuracy. When sensitive responses to sensitive questions were required, all SQTs (excluding the bean method) outperformed direct questions, demonstrating that SQTs can successfully reduce sensitivity bias. However, when reviewing each method, most respondents (59–89%) reported they would feel uncomfortable using them to provide information on their own hunting behavior, highlighting the considerable challenge of encouraging truthful reporting on sensitive topics. Our results demonstrate the importance of assessing the suitability of social science methods prior to their implementation in conservation contexts

Suppression of basophil histamine-release and other IgE-dependent responses in childhood Schistosoma mansoni hookworm co-infection

Background. The poor correlation between allergen-specific-IgE (asIgE) and clinical signs of allergy in helminth infected populations suggests that helminth infections could protect against allergy by uncoupling asIgE from its effector mechanisms. We investigated this hypothesis in Ugandan schoolchildren coinfected with Schistosoma mansoni and hookworm. Methods. Skin prick test (SPT) sensitivity to house dust mite allergen (HDM) and current wheeze were assessed pre-anthelmintic treatment. Non-specific (anti-IgE), helminth-specific and HDM-allergen-specific basophil histamine release (HR), plus helminth- and HDM-specific IgE and IgG4 responses were measured pre- and post-treatment. Results. Non-specific- and helminth-specific-HR, and associations between helminth-specific-IgE and helminth-specific-HR increased post-treatment. Hookworm infection appeared to modify the relationship between circulating levels of HDM-IgE and HR: a significant positive association was observed among children without detectable hookworm infection but no association was observed among infected children. In addition, hookworm infection was associated with a significantly reduced risk of wheeze, and IgG4 to somatic adult hookworm antigen with a reduced risk of HDM-SPT sensitivity. There was no evidence for S. mansoniinfection having a similar suppressive effect on HDM-HR or symptoms of allergy. Conclusions. Basophil responsiveness appears suppressed during chronic helminth infection; at least in hookworm infection, this suppression may protect against allergy

Suppression of basophil histamine release and other IgE-dependent responses in childhood Schistosoma mansoni/hookworm coinfection.

BACKGROUND: The poor correlation between allergen-specific immunoglobulin E (asIgE) and clinical signs of allergy in helminth infected populations suggests that helminth infections could protect against allergy by uncoupling asIgE from its effector mechanisms. We investigated this hypothesis in Ugandan schoolchildren coinfected with Schistosoma mansoni and hookworm. METHODS: Skin prick test (SPT) sensitivity to house dust mite allergen (HDM) and current wheeze were assessed pre-anthelmintic treatment. Nonspecific (anti-IgE), helminth-specific, and HDM-allergen-specific basophil histamine release (HR), plus helminth- and HDM-specific IgE and IgG4 responses were measured pre- and post-treatment. RESULTS: Nonspecific- and helminth-specific-HR, and associations between helminth-specific IgE and helminth-specific HR increased post-treatment. Hookworm infection appeared to modify the relationship between circulating levels of HDM-IgE and HR: a significant positive association was observed among children without detectable hookworm infection, but no association was observed among infected children. In addition, hookworm infection was associated with a significantly reduced risk of wheeze, and IgG4 to somatic adult hookworm antigen with a reduced risk of HDM-SPT sensitivity. There was no evidence for S. mansoni infection having a similar suppressive effect on HDM-HR or symptoms of allergy. CONCLUSIONS: Basophil responsiveness appears suppressed during chronic helminth infection; at least in hookworm infection, this suppression may protect against allergy

Farnesoid X receptor and liver X receptor ligands initiate formation of coated platelets

The liver X receptors (LXRs) and farnesoid X receptor (FXR) have been identified in human platelets. Ligands of these receptors have been shown to have nongenomic inhibitory effects on platelet activation by platelet agonists. This, however, seems contradictory with the platelet hyper-reactivity that is associated with several pathological conditions that are associated with increased circulating levels of molecules that are LXR and FXR ligands, such as hyperlipidemia, type 2 diabetes mellitus, and obesity. We, therefore, investigated whether ligands for the LXR and FXR receptors were capable of priming platelets to the activated state without stimulation by platelet agonists. Treatment of platelets with ligands for LXR and FXR converted platelets to the procoagulant state, with increases in phosphatidylserine exposure, platelet swelling, reduced membrane integrity, depolarization of the mitochondrial membrane, and microparticle release observed. Additionally, platelets also displayed features associated with coated platelets such as P-selectin exposure, fibrinogen binding, fibrin generation that is supported by increased serine protease activity, and inhibition of integrin αIIbβ3. LXR and FXR ligand-induced formation of coated platelets was found to be dependent on both reactive oxygen species and intracellular calcium mobilization, and for FXR ligands, this process was found to be dependent on cyclophilin D. We conclude that treatment with LXR and FXR ligands initiates coated platelet formation, which is thought to support coagulation but results in desensitization to platelet stimuli through inhibition of αIIbβ3 consistent with their ability to inhibit platelet function and stable thrombus formation in vivo