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bioRxiv2018

MISSED OPPORTUNITIES OF CHLAMYDIA AND GONORRHEA DETECTION WHEN NOT USING EXTRA GENITAL SCREENING AMONG MALES

BackgroundThrough extra genital screening methods, Health Departments and community clinics can increase detection of sexually transmitted diseases (STDs) through the application of urethral testing. The Long Beach Department of Health and Human Services (LBDHHS) works on preventing cases of chlamydia (CT) and gonorrhea (GC) from being undiagnosed, by providing extra genital screening. MethodsRetrospective medical review of 1,571 patient health records, who received CT/GC testing, based on at least 1-visit to the Long Beach Department of Health & Human Services, STD Clinic, between 2012 to 2015. All male patients ages 18 years or older with positive CT/GC results (242 cases) for any of the three sites (e.g. urethral, rectal, and pharyngeal); regardless of their sexual behaviors, were included in the study. Females, those under the age of 18, and patients who tested negative for all three anatomical sites were excluded (1,412 controls). ResultsAt time of collection, study participants had a mean age of 37 years. Reported ethnicity indicated 56% Caucasian, 21% Hispanic or Latino, 9% Asian or Pacific Islander, 7% Other, 5% Black, and 2% More than one race. The use of extra genital screening detected 15% (242) of the 1,571 patients tested positive for at least 1-type of CT/GC infection. Our findings demonstrated that if urine was the only specimen collected, then over 29.7% of CT and 46.8% of GC cases would have been missed. ConclusionsTesting of all three anatomical sites should continue to be performed for CT/GC detection. Cases of CT/GC are underreported if performing urethral screening alone. These results highlight the need for clinicians to perform extra genital screening among male patients for prevention and control. These testing measures may reduce the potential for missing a diagnosis and mitigating transmission. Short SummaryThe number of Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (GC) infections missed were determined using extra genital screening procedures among male patients from the Long Beach Department of Health and Human Services (LBDHHS), STD/Family Planning Clinic. This method tests urethral, pharyngeal, and rectal sites for CT and GC infection. In this retrospective review of 1,571 patient files, of which 242 tested positive, we determined the proportion of cases that would have remained undetected if only using urethral screening.

epidemiology↗

bioRxiv2018

DNA methylation links prenatal smoking exposure to later life health outcomes in offspring.

Maternal smoking during pregnancy is associated with adverse offspring health outcomes across their life course. We hypothesize that DNA methylation is a potential mediator of this relationship. To test this, we examined the association of prenatal maternal smoking with DNA methylation in 2,821 individuals (age 16 to 48 years) from five prospective birth cohort studies and perform Mendelian randomization and mediation analyses to assess, whether methylation markers have causal effects on disease outcomes in the offspring. We identify 69 differentially methylated CpGs in 36 genomic regions (P < 1x10-7), and show that DNA methylation may represent a biological mechanism through which maternal smoking is associated with increased risk of psychiatric morbidity in the exposed offspring.

epidemiology↗

bioRxiv2018

Chelation therapy using static magnetic field

Static magnetic field (SMF) is reported to mimic chelation agents. In thalassemia blood, SMF minimizes iron overloading effect. In such cells ROS level is reduced, in presence of moderate strength (70mT). Pilot study on transfusion dependent thalassemia, thalassemia carriers and normal red blood clearly indicate the differential effects of SMF on thalassemia, thalassemia carrier and normal cells. SMF also reduces ROS induced DNA damage in lymphocytes. A comparative study on the iron chelating drug deferasirox and SMF treated lymphocytes further confirm our main thesis. This non-invasive therapeutic regime for hemochromatosis may serve the dual purpose of treating, iron overloading and minimizing, cellular damage by lowering the ROS level.

epidemiology↗

bioRxiv2018

Deep learning facilitates rapid cohort identification using human and veterinary clinical narratives

ObjectiveCurrently, dedicated tagging staff spend considerable effort assigning clinical codes to patient summaries for public health purposes, and machine-learning automated tagging is bottlenecked by availability of electronic medical records. Veterinary medical records, a largely untapped data source that could benefit both human and non-human patients, could fill the gap. Materials and MethodsIn this retrospective study, we trained long short-term memory (LSTM) recurrent neural networks (RNNs) on 52,722 human and 89,591 veterinary records. We established relevant baselines by training Decision Trees (DT) and Random Forests (RF) on the same data. We finally investigated the effect of merging data across clinical settings and probed model portability. ResultsWe show that the LSTM-RNNs accurately classify veterinary/human text narratives into top-level categories with an average weighted macro F1, score of 0.735/0.675 respectively. The evaluation metric for the LSTM was 7 and 8% higher than that of the DT and RF models respectively. We generally did not find evidence of model portability albeit moderate performance increases in select categories. DiscussionWe see a strong positive correlation between number of training samples and classification performance, which is promising for future efforts. The use of LSTM-RNN models represents a scalable structure that could prove useful in cohort selection, which could in turn better address emerging public health concerns. ConclusionDigitization of human and veterinary health information will continue to be a reality. Our approach is a step forward for these two domains to learn from, and inform, one another.

epidemiology↗

bioRxiv2018

A theoretical foundation for state-transition cohort models in health decision analysis

Following its introduction over three decades ago, the cohort model has been used extensively to model population trajectories over time in decision-analytic modeling studies. However, the stochastic process underlying cohort models has not been properly described. In this study, we explicate the stochastic process underlying a cohort model, by carefully formulating the dynamics of populations across health states and assigning probability rules on these dynamics. From this formulation, we explicate a mathematical representation of the system, which is given by the master equation. We solve the master equation by using the probability generation function method to obtain the explicit form of the probability of observing a particular realization of the system at an arbitrary time. The resulting generating function is used to derive the analytical expressions for calculating the mean and the variance of the process. Secondly, we represent the cohort model by a difference equation for the number of individuals across all states. From the difference equation, a continuous-time cohort model is recovered and takes the form of an ordinary differential equation. To show the equivalence between the derived stochastic process and the cohort model, we conduct a numerical exercise. We demonstrate that the population trajectories generated from the formulas match those from the cohort model simulation. In summary, the commonly-used cohort model represent the average of a continuous-time stochastic process on a multidimensional integer lattice governed by a master equation. Knowledge of the stochastic process underlying a cohort model provides a theoretical foundation for the modeling method.

epidemiology↗

bioRxiv2018

Disrespect and abuse of women during childbirth in public health facilities in Arba Minch town, South Ethiopia - a cross-sectional study

IntroductionDisrespect and abuse during childbirth is the main deterring factor to skilled birth utilization as compared to other more commonly known factors such as financial and physical inaccessibility.\n\nObjectiveTo assess the occurrence of womens disrespect and abuse during childbirth in public health facilities in Arba Minch town, south Ethiopia.\n\nMethodsInstitution based cross-sectional study design was employed at all public health institutions in Arba Minch town, south Ethiopia. Systematic sampling method was used to include 281 women who had given birth at public health institutions between January 01 and February 28, 2017. Data were collected by face to face interview by four midwife tutors and supervised by the principal investigator on daily bases. Semi-structured pretested questionnaire was used to collect data. Epi info version 7.1.2.0 and SPSS version 24 were used to enter and analyze the data respectively.\n\nResultsA total of 281 women were participated in this study. The overall prevalence of non-respectful care was 98.9%. The womens right to information and informed consent was the most frequently violated right with a prevalence of 92.5% (95% CI: 90.9, 94.1) followed by non-dignified care (36.7, 95% CI: 34.9, 38.5), physical abuse (29.5%, 95% CI: 24.2, 34.8), discrimination (18.1%, 95% CI: 13.6, 22.6), non-confidential care (17.1%,95% CI: 12.7, 21.5) and abandonment of care (4.3%, 95% CI: 3.1, 5.5). However, there is no woman who had been kept in detention in the health facilities. Being rural resident, giving birth in hospital, having no or low educational status and giving birth by cesarean route were factors which were significantly associated with specific womens rights violations.\n\nConclusions and recommendationsThe status of non-respectful and abusive care in the health care facilities in this study area is unacceptably high and needs serious attention by the health managers to tackle the problem.

epidemiology↗

bioRxiv2018

Interrelationships among key Reproductive Health indicators in Sub-Saharan Africa

IntroductionIndicators of reproductive health (RH) services, outputs, outcomes and impacts are expected to be related with each other and with key social determinants. As the provision of RH services is usually integrated, the effort expended to improve one component is also expected to affect the other components. There is a lack of evidence-based models demonstrating the interrelationships among these indicators and between RH indicators and social determinants.\n\nObjectiveTo examine interrelationships among key RH indicators and their relationship with key social determinants in Sub-Saharan Africa (SSA).\n\nMethodThis study used data from the most recent demographic and health survey conducted during the period from 2010 to 2016 in 391 provinces of 29 SSA countries. We focused on seven RH indicator -- antenatal care, skilled birth attendance, postnatal care, contraceptive prevalence rate (CPR), ideal number of children, birth interval and total fertility rate (TFR), along with selected socio-demographic indicators. The unit of analysis was sub-national, at provincial level. Structural equation modelling was used to examine the strength of interrelationships among the indicators based on the total standardized effect sizes. Significance tests and 95% confidence intervals for the total effects were presented using a bias-corrected bootstrap method.\n\nResultsWomens literacy rate, at the centre of the model, has direct connections with all the RH indicators included in the final model. The strongest relationship was observed between womens literacy rate and CPR with a total standardized (std.) effect size of 0.79 (95% CI: 0.74, 0.83). RH indicators are interrelated directly and/or indirectly. A strong direct effect was also observed in the relationship between CPR and birth interval ({beta}=0.63, 95%: 0.50, 0.77) and the model suggests that the reported ideal number of children is a key predictor of birth interval (Std. effect size=-0.58, 95% CI: -0.69, -0.48) and TFR (Std. effect size=0.52, 95% CI: 0.38, 0.62).\n\nConclusionRH indicators are strongly interrelated and are all associated with womens literacy. The model of interrelationships developed in this study may guide the design, implementation and evaluation of RH policies and programs.

epidemiology↗

bioRxiv2018

Managing Marek’s disease in the egg industry

The industrialization of farming has had an enormous impact. To most, this impact is viewed solely in the context of productivity, but the denser living conditions and shorter rearing periods of industrial livestock farms provide pathogens with an ideal opportunity to spread and evolve. For example, the industrialization of poultry farms drove the Mareks disease virus (MDV) to evolve from causing a mild paralytic syndrome to causing a highly contagious, globally prevalent, disease that can have up to a 100% mortality rate. Fortunately, the economic catastrophe that would occur from MDV evolution has been prevented through widespread use of live imperfect vaccines that limit disease symptoms, but fail to prevent transmission. Unfortunately, the continued rollout of such imperfect vaccines is steering the evolution of MDV towards an even greater virulence and an ability to evade vaccine protection. Thus, there is a need to investigate alternative economically viable control measures for their ability to inhibit MDV spread and evolution. In what follows we examine the economic viability of standard husbandry practices for their ability to inhibit the spread of both virulent MDV and very virulent MDV throughout an industrialized egg farm. To do this, we parameterized a dynamic MDV transmission model and calculate the loss in egg production due to disease. We find that the MDV strain as well as the cohort duration had the greatest influence on disease burden and hence egg production. Additionally, we find that the standard husbandry practice involving conventional cages, often referred to as \"battery cages\", results in the least per capita loss in egg production due to MDV infection when compared to alternative enriched or aviary (free-run) systems for virulent MDV, but not very virulent MDV, in which case the Aviary system performs the best. These results highlight an important cost that managers will face when implementing new hen husbandry practices.

epidemiology↗

bioRxiv2018

Malaria control dynamics may explain inconsistent outcomes from bednet trials: a modeling study

BACKGROUNDLong-lasting insecticidal bednets have unparalleled efficacy in reducing malaria burden. However, insecticidal resistance and bednet avoidance behaviors among the mosquito vectors are now widespread.\n\nMETHODSReviewing the relevant field and semi-field studies highlights the ubiquity of zoophagic and spatiotemporal (biting outdoors or at different times of day) plasticity among vectors in response to bednet deployment. Transmission models coupled with the population genetics of vectors are developed to assess the impact on malaria control caused by insecticide resistance and the avoidance behaviors of mosquitoes.\n\nRESULTSInteractions between physiological resistance and behavioral resilience among mosquito vectors can significantly impact malaria control efforts both in the short- and long-term. The possibility of misleading observations from injudiciously timed assessments of malaria control programs is demonstrated through simulation.\n\nCONCLUSIONSCurrently, there are no guidelines to inform when during a bednet trial its effectiveness should be measured. The importance of this oversight is described in the context of recent randomized controlled bednet trials.

epidemiology↗

bioRxiv2018

Prevalence of TMD and level of chronic pain in a group of Brazilian adolescents

ObjectivesTo determine the prevalence of temporomandibular disorder and associated factors in an adolescent sample from Recife, Brazil.\n\nMaterials and MethodsA cross-sectional study was conducted with 1342 adolescents aged 10-17 years. The Research Diagnostic Criteria for Temporomandibular Disorder (RDC/TMD) was used by calibrated examiners to evaluate the presence and levels of chronic pain. To evaluate the socioeconomic conditions, the Brazilian Economic Classification Criteria (CCEB) questionnaire was answered by the subjects. Data were analyzed by means of binary logistic regression in SPSS.\n\nResultsThe results showed that 33.2% of the subjects had TMD irrespective of age (p= 0.137) or economic class (p=0.507). Statistically significant associations were found between TMD and gender (p= 0.020), headache/migraine in the past six months (p=0,000) and the presence of chronic pain (p=0,000). In final model, logistic regression showed that chronic pain contributes to the presence of TMD.\n\nConclusionsThe prevalence of TMD was considered high (33.2%) and adolescents with chronic pain were more likely to have TMD.\n\nClinical RelevanceThe data contribute to the understanding of TMD among adolescents and to the development of preventive measures and polices to identify the dysfunction promptly.

epidemiology↗

bioRxiv2018

A meta-analysis of Entamoeba histolytica/dispar in Iraq

BackgroundAmebiasis is a major health problem caused by the protozoan parasite Entamoeba histolytica with a worldwide distribution, especially in developing countries. The aim of this systematic review and meta-analysis was to estimate the proportion prevalence of E. histolytica/dispar in human in Iraq. Methodology/Principal FindingsPublished studies on human infection with E. histolytica/dispar in Iraq were searched in electronic databases using Google scholar, Iraqi Academic Scientific Journals (IASJ), PubMed, ScienceDirect and WHO Global Health Library (GHL). Eligible studies were cross-sectional and used fecal and/or serological methods to diagnose E. histolytica/dispar infection in human in Iraq, and published between 1970 and July 2017. The pooled prevalence was calculated using random effect model meta-analyses with 95% confidence interval (CI). Ninety nine studies were eligible for the meta-analysis that included 117694 individuals. The pooled proportion for E. histolytica/dispar infection in Iraq was estimated at 20.61% with a 95% confidence interval (CI) of 17.83, 23.53. A high level of heterogeneity was found among the studies. The prevalence among Iraqi population ranged between 1.66 and 90.5% per study (mean: 22.36%). The pooled prevalence of infection was 58.43% (95% CI: 54.71%?62.1%) and 43.10% (95% CI: 39.66%-46.6%) for males and females respectively. Parasite screening using microscopy did not differentiate between the pathogenic and nonpathogenic species of Entamoeba resulted in higher proportion prevalence than PCR proportion prevalence, (20.32%, 95% CI: 17.80%-22.96%) (17.57%, 95% CI: 8.07%-29.75%) respectively. Hospital based studies recorded the highest prevalence of E. histolytica/dispar infection at 22.69% (95% CI: 19.55%-25.99%). The prevalence decreased into 18.46 (95% CI: 14.28%-23.04%) between 2010 and 2017. Conclusions/SignificanceAlthough there was a reduction in prevalence of amebiasis since 2010, the prevalence of amebiasis is still considerable in population of Iraq. Therefore, prevention strategies of fecal contamination are required to reduce the infection. Author summaryAmebiasis is the infection with Entamoeba histolytica an invasive parasite dwelling the intestine or other organs such as liver, lungs, or skin of human. Infection with this parasite could be acquired by consumption of contaminated water, vegetables, and fruits with feces of infected human. The infection may be asymptomatic or symptomatic causing dysentery. We performed this meta-analysis to estimate the prevalence of amebiasis in the population of Iraq between 1970 and 2017. Ninety nine published studies were identified and the data were extracted from them to use in our meta-analysis and the total included individuals were 117694. The prevalence of population infection in Iraq was evaluated at 20.61%. The infection prevalence was higher in males than in females. The infection prevalence decreased during the period 2010 to 2017 in Iraqi population. This level of infection needs further efforts to eradicate amebiasis, these efforts begin with the prevention of the disease transmission through water and food and treatment of infected people. So awareness of simple hygienic principles can control the disease by boiling water and washing vegetables and fruits thoroughly.

epidemiology↗

bioRxiv2018

The design and evaluation of a Bayesian system for detecting and characterizing outbreaks of influenza

1The prediction and characterization of outbreaks of infectious diseases such as influenza remains an open and important problem. This paper describes a framework for detecting and characterizing outbreaks of influenza and the results of testing it on data from ten outbreaks collected from two locations over five years. We model outbreaks with compartment models and explicitly model non-influenza influenza-like illnesses.

epidemiology↗

bioRxiv2018

Transmission dynamics and between-species interactions of multidrug-resistant Enterobacteriaceae

Widespread resistance to antibiotics is among the gravest threats to modern medicine, and controlling the spread of multi-drug resistant Enterobacteriaceae has been given priority status by the World Health Organization. Interventions to reduce transmission within hospital wards may be informed by modifiable patient-level risk factors for becoming colonised, however understanding of factors that influence a patients risk of acquisition is limited. We analyse data from a one year prospective carriage study in a neonatal intensive care unit in Cambodia using Bayesian hierarchical models to estimate the daily probability of acquiring multi-drug resistant organisms, while accounting for patient-level time-varying covariates, including interactions between species, and interval-censoring of transmission events. We estimate the baseline daily probability for becoming colonised with third generation cephalosporin resistant (3GC-R) Klebsiella pneumoniae as 0.142 (95% credible interval [CrI] 0.066, 0.27), nearly ten times higher than the daily probability of acquiring 3GC-R Escherichia coli (0.016 [95% CrI 0.0038, 0.049]). Prior colonization with 3GC-R K. pneumoniae was associated with a greatly increased risk of a patient acquiring 3GC-R E. coli (odds ratio [OR] 6.4 [95% CrI 2.8, 20.9]). Breast feeding was associated with a reduced risk of colonization with both 3GC-R K. pneumoniae (OR 0.73 [95% CrI 0.38, 1.5]) and E. coli (OR 0.62 [95% CrI 0.28, 1.6]). The use of an oral probiotic (Lactobacillus acidophilus) did not show clear evidence of protection against colonization with either 3GC-R K. pneumoniae (OR 0.83 [95% CrI 0.51, 1.3]) or 3GC-R E. coli (OR 1.3 [95% CrI 0.77, 2.1]). Antibiotic consumption within the past 48 hours did not strongly influence the risk of acquiring 3GC-R K. pneumoniae. For 3GC-R E. coli, ceftriaxone showed the strongest effect for increasing the risk of acquisition (OR 2.2 [95% CrI 0.66, 6.2]) and imipenem was associated with a decreased risk (OR 0.31 [95% CrI 0.099, 0.76). Using 317 whole-genome assemblies of K. pneumoniae, we determined putatively related clusters and used a range of models to infer transmission rates. Model comparison strongly favored models with a time-varying force of infection term that increased in proportion with the number of colonized patients, providing evidence of patient-to-patient transmission, including among a cluster of Klebsiella quasipneumoniae. Our findings provide support for the hypothesis that K. pneumoniae can be spread person-to-person within ward settings. Subsequent horizontal gene transfer within patients from K. pneumoniae provides the most parsimonious explanation for the strong association between colonization with 3GC-R K. pneumoniae and acquisition of 3GC-R E. coli.

epidemiology↗

bioRxiv2018

Adjustment for index event bias in genome-wide association studies of subsequent events

Following numerous genome-wide association studies of disease susceptibility, there is increasing interest in genetic associations with disease prognosis, survival or other subsequent events. Such associations are vulnerable to index event bias, by which selection of subjects according to their disease status creates biased associations if common causes of incidence and prognosis are not accounted for. We propose a novel adjustment for index event bias using the residuals from the regression of genetic effects on prognosis on genetic effects on incidence. Our approach eliminates this bias when direct genetic effects on incidence and prognosis are independent, and otherwise reduces bias in realistic situations. In a study of idiopathic pulmonary fibrosis, we resolved a paradoxical association of the strong susceptibility gene MUC5B with increased survival, identifying instead a significant association with decreased survival. In re-analysis of a study of Crohns disease prognosis, four regions remained associated at genome-wide significance albeit with increased P-values.

epidemiology↗

bioRxiv2018

Drinking motives and alcohol use among college students with the alcohol flush reaction: A nationwide study

BackgroundThis study investigated the relationship between drinking motives and alcohol use among a nationally representative sample of college students with the alcohol flush reaction (AFR). We surveyed and analyzed the data of 2,245 male and 2,326 female college students in a nationally representative sample of 82 colleges in South Korea.\n\nMethodsOf our study population, 725 males (32.3%) and 812 females (34.9%) reported to currently suffering from AFR. Multiple regression analysis was used to identify the association between drinking motives and drinking behavior, measured via the AUDIT.\n\nResultsRelative to drinking because of peer pressure, students drinking for pleasure (males: {beta} = 2.622, p <.0001; females {beta} = 2.769, p <.0001) or stress/depression (males: {beta} = 2.479, p <.0001; females {beta} = 2.489, p <.0001) had higher AUDIT scores. Among students drinking because of stress/depression, seniors (males: {beta} = 3.603, p<.0001; females: {beta} = 3.791, p = 0.000), smokers (males: {beta} = 1.564, p = 0.000; females {beta} = 1.816, p = 0.007) and/or liberal arts students (males: {beta} = 6.1136, p<.0001; females {beta} = 4.2105, p <.0001) consumed more alcohol than their peers. Relative to conformity motives, enhancement and coping motives were found to have a greater influence on alcohol intake among college students with alcohol flush reaction.\n\nConclusionConsidering that the flush reaction can occur in AFR individuals after just one sip of wine, our results show that educators and policymakers must take action to deal with this problem.

epidemiology↗

bioRxiv2018

Rabies prevention and control practice and associated factors among dog owners in Aksum town and Laelay-Machew district, north Ethiopia: community based comparative cross-sectional study

BackgroundRabies is nearly 100% fatal zoonotic disease. One thousand seven hundred suspected rabies exposures reported in north Ethiopia, Tigray region in 2017, which has the highest rabies prevalence from Ethiopia. Almost half of them were from Central zone only. Of these 38% were in Aksum town and Laelay-Machew. Though Rabies exposure is prevalent in Tigray, there is scanty information on rabies prevention and control practices among dog owners. Thus, this deals with rabies prevention and control practice and associated factors among dog owners.\n\nMethods and materialsComparative community based cross-sectional study was conducted in Aksum town and Laelay-Machew district from March 01 to 20, 2018. A multi stage sampling was employed to recruit 558 households. Data were collected via structured and pretested questionnaire. Data were entered into Epi_info_7 and then exported to SPSS_20 for analysis. Both descriptive and inferential analysis was done with 95% confidence intervals at p value of 5% for the final model.\n\nResultThe overall prevalence of poor rabies prevention and control practice was 56% [95%CI (50, 61.9)] in urban and 62% [95% CI (57.2, 67.7)] in rural dog owners. In urban; being government employee [AOR (95%CI) = 0.35 (0.13, 0.94)], private employee [AOR (95%CI) =0.39(0.16, 0.97)] and having poor attitude [(AOR (95%CI) =1.84 (1.04, 3.25)] were significantly associated with outcome variable. Whereas in rural dwellers; having no formal education [AOR (95%CI)=6.41(1.1,38.6)], poor attitude [AOR (95%CI)= 2.19 (1.18,4.05)], having one dog [AOR (95%CI)=3.31(1.34,8.15)], travel [≥]30 minute to get vaccine [AOR (95%CI)= 4.26 (2.14,8.47]), no history of dog bite exposure [AOR (95%CI)= 4.16(1.49,11.6)] and neighbors as their source of information [AOR (95%CI) =3.64 (1.31,10.1)] have statistical significance with the outcome variable.\n\nConclusion and RecommendationThe prevalence of poor rabies prevention and control practice was higher among rural dog owners. Thus; interventions should be implemented both to urban and rural residents based on the identified findings so as to promote effective rabies prevention and control activities.

epidemiology↗

bioRxiv2018

What drives mortality among HIV patients in a conflict setting? A prospective cohort study in the Central African Republic

BackgroundProvision of antiretroviral therapy (ART) during conflict settings is rarely attempted and little is known about the expected patterns of mortality. The Central African Republic (CAR) continues to have a low coverage of ART despite an estimated 120,000 people living with HIV and 11,000 AIDS-related deaths in 2013. We present results from a cohort in Zemio, Haut-Mboumou prefecture. This region had the highest prevalence of HIV nationally (14.8% in 2010) and was subject to repeated attacks by armed groups on civilians during the observed period.\n\nMethodsConflict from armed groups can impact cohort mortality rates i) directly if HIV patients are victims of armed conflict, or ii) indirectly if population displacement or fear of movement reduces access to ART. Using monthly counts of civilian deaths, injuries and abductions, we estimated the impact of the conflict on patient mortality. We also determine patient-level risk factors for mortality and how this varies with time spent in the cohort. Model-fitting was performed in a Bayesian framework, using generalised-linear models with terms accounting for temporal autocorrelation.\n\nResultsPatients were recruited and observed from October 2011 to May 2017. Overall 1631 patients were enrolled, giving 4107 person-years and 148 deaths. Our first model shows that patient mortality did not increase during periods of heightened conflict. The monthly risk (probability) of mortality was markedly higher at the beginning of the program (0.047 in November 2011 [95% credible interval; CrI 0.0078, 0.21]) and had declined greater than ten-fold by the end of the observed period (0.0016 in June 2017 [95% CrI 0.00042, 0.0036]). Our second model shows the risk of mortality for individual patients was highest in the first five months spent in the cohort. Male sex was associated with a higher mortality (odds ratio; OR 1.7 [95% CrI 1.2, 2.8]) along with the severity of opportunistic infections at baseline.\n\nConclusionsOur results show that chronic conflict did not appear to adversely affect rates of mortality in this cohort, and that mortality was driven predominantly by patient specific risk factors. In areas initiating ART for the first time, particular attention should be focussed on stabilising patients with advanced symptoms.\n\nFundingMedecins Sans Frontieres

epidemiology↗

bioRxiv2018

Gini coefficients for measuring the distribution of sexually transmitted infections among individuals with different levels of sexual activity

ObjectivesGini coefficients have been used to describe the distribution of Chlamydia trachomatis (CT) infections among individuals with different levels of sexual activity. The objectives of this study were to investigate Gini coefficients for different sexually transmitted infections (STIs), and to determine how STI control interventions might affect the Gini coefficient over time.\n\nMethodsWe used population-based data for sexually experienced women from two British National Surveys of Sexual Attitudes and Lifestyles (Natsal-2: 1999-2001; Natsal-3: 2010-2012) to calculate Gini coefficients for CT, Mycoplasma genitalium (MG), and human papillomavirus (HPV) types 6, 11, 16 and 18. We applied bootstrap methods to assess uncertainty and to compare Gini coefficients for different STIs. We then used a mathematical model of STI transmission to study how control interventions affect Gini coefficients.\n\nResultsGini coefficients for CT and MG were 0.33 (95% confidence interval (CI): 0.18-0.49) and 0.16 (95% CI: 0.02-0.36), respectively. The relatively small coefficient for MG suggests a longer infectious duration compared with CT. The coefficients for HPV types 6, 11, 16 and 18 ranged from 0.15-0.38. During the decade between Natsal-2 and Natsal-3, the Gini coefficient for CT did not change. The transmission model shows that higher STI treatment rates are expected to reduce prevalence and increase the Gini coefficient of STIs. In contrast, increased condom use reduces STI prevalence but does not affect the Gini coefficient.\n\nConclusionsGini coefficients for STIs can help us to understand the distribution of STIs in the population, according to level of sexual activity, and could be used to inform STI prevention and treatment strategies.\n\nKey messagesO_LIThe Gini coefficient can be used to describe the distribution of STIs in a population, according to different levels of sexual activity.\nC_LIO_LIGini coefficients for Chlamydia trachomatis (CT) and human papillomavirus (HPV) type 18 appear to be higher than for Mycoplasma genitalium and HPV 6, 11 and 16.\nC_LIO_LIMathematical modelling suggests that CT screening interventions should reduce prevalence and increase the Gini coefficient, whilst condom use reduces prevalence without affecting the Gini coefficient.\nC_LIO_LIChanges in Gini coefficients over time could be used to assess the impact of STI prevention and treatment strategies.\nC_LI

epidemiology↗