Operational research within the national tuberculosis control programme in Benin.

OBJECTIVE: To document whether the placement of operational research (OR) fellows within disease control programmes in low and middle income countries leads to the implementation of operational research and improvements in policy and practice. RESULT: In 2012, an OR fellow was placed within the National TB Programme, Benin, to strengthen the implementation of operational research. From 2012 to 2015, eight OR projects were implemented, of which three contributed to changes in programme practice and five provided information which was not previously available from quarterly/annual reports. Two of these projects-one on the burden and treatment outcomes of childhood TB and one on tracing patients who had discontinued treatment-are discussed in more detail. OR should be strongly encouraged within national TB programme settings and an OR fellow facilitates this process

Tuberculosis Case Finding in Benin, 2000-2014 and Beyond: A Retrospective Cohort and Time Series Study.

Objective. To determine any changes in tuberculosis epidemiology in the last 15 years in Benin, seasonal variations, and forecasted numbers of tuberculosis cases in the next five years. Materials and Methods. Retrospective cohort and time series study of all tuberculosis cases notified between 2000 and 2014. The "R" software version 3.2.1 (Institute for Statistics and Mathematics Vienna Austria) and the Box-Jenkins 1976 modeling approach were used for time series analysis. Results. Of 246943 presumptive cases, 54303 (22%) were diagnosed with tuberculosis. Annual notified case numbers increased, with the highest reported in 2011. New pulmonary bacteriologically confirmed tuberculosis (NPBCT) represented 78%  ± SD 2%. Retreatment cases decreased from 10% to 6% and new pulmonary clinically diagnosed cases increased from 2% to 8%. NPBCT notification rates decreased in males from 2012, in young people aged 15-34 years and in Borgou-Alibori region. There was a seasonal pattern in tuberculosis cases. Over 90% of NPBCT were HIV-tested with a stable HIV prevalence of 13%. The ARIMA best fit model predicted a decrease in tuberculosis cases finding in the next five years. Conclusion. Tuberculosis case notifications are predicted to decrease in the next five years if current passive case finding is used. Additional strategies are needed in the country

National profile and treatment outcomes of patients with extrapulmonary tuberculosis in Bénin.

BACKGROUND: In sub-Saharan Africa, there is a dearth of published literature on extrapulmonary tuberculosis (EPTB). OBJECTIVE: To describe demographic, diagnostic and HIV-status characteristics of patients with EPTB in Bénin, their treatment outcomes, and among those who completed their treatment in the Centre National Hospitalier de Pneumo-Phtisiologie (CNHP-P), the proportion whose bodyweight increased during treatment. MATERIAL AND FINDINGS: This was a retrospective cohort study with comparisons made between EPTB and new smear-positive pulmonary tuberculosis (NPTB) patients diagnosed in the country from January to December 2011. There were 383 EPTB patients (9% of all TB cases) with a mean age of 35 years, male/female ratio of 1.3 and important regional variation. There were significantly more females (p = 0.001), children <15 years (p<0.001) and HIV-positive patients (p = 0.005) with EPTB compared with NPTB. Pleural effusion, spinal and lymph node tuberculosis accounted for 66% of all EPTB. Children <15 years represented 16% of cases, with lymph node disease being most common among them (p<0.001). Of 130 EPTB patients registered in CNHP-P, 7% had a confirmed bacteriological/histological diagnosis. There were 331 (86%) patients who successfully completed treatment. More patients with EPTB were lost-to-follow-up compared with NPTB (p<0.001) with all these patients from one region. The best treatment completion rates were in children <15 years (OR:3.5, 95%CI:1.0-14.8) while patients with pleural effusion and ascites had the worst outcomes. Of 72 HIV-coinfected patients, 88% were on antiretroviral therapy (ART). HIV-positive status was associated with poor outcomes while those on ART fared better. In the CNHP-P, more than 80% who completed their treatment showed an increase in bodyweight and this was more evident in HIV-positive compared with HIV-negative patients (p = 0.03). CONCLUSION: Patients with EPTB generally do well in Bénin, although the TB Programme would benefit through more attention to accurate diagnosis and earlier start of ART in HIV-infected patients

Follow-up and programmatic outcomes of HIV-exposed infants registered in a large HIV centre in Lilongwe, Malawi: 2012-2014.

OBJECTIVE: To assess follow-up and programmatic outcomes of HIV-exposed infants at Martin Preuss Centre, Lilongwe, from 2012 to 2014. METHODS: Retrospective cohort study using routinely collected HIV-exposed infant data. Data were analysed using frequencies and percentages in Stata v.13. RESULTS: Of 1035 HIV-exposed infants registered 2012-2014, 79% were available to be tested for HIV and 76% were HIV-tested either with DNA-PCR or rapid HIV test serology by 24 months of age. Sixty-five infants were found to be HIV-positive and 43% were started on antiretroviral therapy (ART) at different ages from 6 weeks to 24 months. Overall, 48% of HIV-exposed infants were declared lost-to-follow-up in the database. Of these, 69% were listed for tracing; of these, 78% were confirmed as lost-to-follow-up through patient charts; of these, 51% were traced; and of these, 62% were truly not in care, the remainder being wrongly classified. Commonest reasons for being truly not in care were mother/guardian unavailability to bring infants to Martin Preuss Centre, forgetting clinic appointments and transport expenses. Of these 86 patients, 36% were successfully brought back to care and 64% remained lost-to-follow-up. CONCLUSION: Loss to follow-up remains a huge challenge in the care of HIV-exposed infants. Active tracing facilitates the return of some of these infants to care. However, programmatic data documentation must be urgently improved to better follow-up and link HIV-positive children to ART

Characteristics and Treatment Outcomes of Retreatment Tuberculosis Patients in Benin.

Objective. To determine among retreatment tuberculosis patients in Benin baseline characteristics, culture, and drug sensitivity testing (DST) results and treatment outcomes. Materials and Methods. A retrospective national cohort study of all retreatment tuberculosis patients in Benin in 2013 using registers and treatment cards. Results. Of 3957 patients with tuberculosis, 241 (6%) were retreatment cases. Compared to new pulmonary bacteriologically confirmed tuberculosis (NPBCT) patients, there were significantly higher numbers of males (P = 0.04), patients from "Atlantique-Littoral" (P = 0.006), patients aged 45-64 years (P = 0.007), and HIV-positive patients (P = 0.04) among those retreated. Overall, 171 (71%) patients submitted sputum for DST, of whom (163) 95% were positive for Mycobacterium tuberculosis on Xpert MTB/RIF and/or culture and 17 (10%) were rifampicin resistant (9 with MDR-TB and 8 monoresistant to rifampicin). For those without MDR-TB (n = 224), treatment success was 93%. Worse outcomes occurred in those with unknown HIV status (RR: 0.27; 0.05-1.45; P < 0.01) while better outcomes occurred in those who relapsed (RR: 1.06, 95 CI: 1.02-1.10, P = 0.04). Conclusion. In 2013, a high proportion of retreatment patients received DST. Treatment success was good although more needs to be done to systematically increase the final follow-up smear examination. Reasons of high losses to follow-up from "Oueme-Plateau" should be investigated

Risk of obstructive sleep apnea and quality of sleep among adults with type 2 diabetes mellitus in a subSaharan Africa city

Introduction:&nbsp;diabetes mellitus (DM) and Obstructive Sleep Apnea (OSA) are two major and interconnected non-communicable diseases. Both negatively impact on sleep quality. This study aimed to determine among persons with type 2 DM, the proportions at high risk of OSA and of self-reported poor sleep quality along with their associated-factors in Parakou city, Benin. Methods:&nbsp;this was a cross-sectional prospective study of 100% (n=383) outpatient adults with type 2 DM, conducted between April and August 2019 in the three top centres managing diabetic persons in Parakou city. They were interviewed, examined and investigated using capillary fasting blood glucose tests. The STOP-Bang Questionnaire (SBQ) was used to determine the risk of OSA. Results:&nbsp;overall, their mean age was 57.37 (11.45) years. They were 61.62% (n=236) females and 38.38% (n=147) males. Sleep duration was insufficient in 26.89% (n=103). Nocturia was reported in 49.35% (n=189). The risk of OSA was high in 14.10% (n=54), intermediate in 24.80% (n=95) and low in 61.10% (n=234). Friedman Position Tongue Grade 3 (Adjusted Odds Ratio, aOR=2.48; 95%CI=1.11 - 5.55; p=0.025) and 4 (aOR=4.65; 95%CI=1.26 - 15.90; p=0.015) were independently associated with a high risk of OSA. The prevalence of reported poor sleep quality was 27.42% (n=105). Female gender (aOR=2.08; 95%CI=1.18-3.83; p=0.014), diabetic foot (aOR=5.07; 95%CI=1.15-23.63; p=0.031), nocturia (aOR=1.96; 95%CI=1.18-3.29; p=0.010), tiredness (aOR=2.77; 95%CI=1.26-6.23; p=0.012) and a high risk of OSA (aOR=3.31; 95%CI=1.28-8.93; p=0.015) were independently associated with a greater risk of reported poor sleep quality. Conclusion:&nbsp;in Parakou, the proportions of patients with type 2 DM at increased risk of OSA and with poor quality of sleep are relatively high. There is need for better systematic screening of OSA in persons with DM

HIV Viral Load Estimation Using Hematocrit Corrected Dried Blood Spot Results on a BioMerieux NucliSENS® Platform.

While reporting human immunodeficiency virus (HIV) viral load (VL) using dried blood spot (DBS) in the BioMerieux NucliSENS platform, application of the hematocrit correction factor has been suggested. In this cross-sectional study from the National Microbiology Reference Laboratory of Zimbabwe, we assessed whether hematocrit correction (individual and/or mean) in DBS results improved the correlation with plasma VL and prediction of VL non-suppression (≥1000 copies per ml in plasma). Of 517 specimens during August-December 2018, 65(12.6%) had non-suppressed plasma VL results. The hematocrit correction factor ranged from 1.3 to 2.0 with a mean of 1.6, standard deviation (SD: 1.5, 1.7). The intraclass correlation (ICC) for mean (0.859, 95% CI: 0.834, 0.880) and individual (0.809, 95% CI: 0.777, 0.837) hematocrit corrected DBS results were not significantly different. The uncorrected DBS results had a significantly lower ICC (0.640, 95% CI: 0.586, 0.688) when compared to corrected DBS results. There were no significant differences in validity, predictive values, and areas under the receiver operating characteristics curves for all three DBS results when predicting VL non-suppression. To conclude, hematocrit correction of DBS VL results improved agreement with the plasma results but did not improve prediction of VL non-suppression. The results were not significantly different for individual and mean corrected results

Antimicrobial resistance among migrants in Europe: a systematic review and meta-analysis

BACKGROUND: Rates of antimicrobial resistance (AMR) are rising globally and there is concern that increased migration is contributing to the burden of antibiotic resistance in Europe. However, the effect of migration on the burden of AMR in Europe has not yet been comprehensively examined. Therefore, we did a systematic review and meta-analysis to identify and synthesise data for AMR carriage or infection in migrants to Europe to examine differences in patterns of AMR across migrant groups and in different settings. METHODS: For this systematic review and meta-analysis, we searched MEDLINE, Embase, PubMed, and Scopus with no language restrictions from Jan 1, 2000, to Jan 18, 2017, for primary data from observational studies reporting antibacterial resistance in common bacterial pathogens among migrants to 21 European Union-15 and European Economic Area countries. To be eligible for inclusion, studies had to report data on carriage or infection with laboratory-confirmed antibiotic-resistant organisms in migrant populations. We extracted data from eligible studies and assessed quality using piloted, standardised forms. We did not examine drug resistance in tuberculosis and excluded articles solely reporting on this parameter. We also excluded articles in which migrant status was determined by ethnicity, country of birth of participants' parents, or was not defined, and articles in which data were not disaggregated by migrant status. Outcomes were carriage of or infection with antibiotic-resistant organisms. We used random-effects models to calculate the pooled prevalence of each outcome. The study protocol is registered with PROSPERO, number CRD42016043681. FINDINGS: We identified 2274 articles, of which 23 observational studies reporting on antibiotic resistance in 2319 migrants were included. The pooled prevalence of any AMR carriage or AMR infection in migrants was 25·4% (95% CI 19·1-31·8; I2 =98%), including meticillin-resistant Staphylococcus aureus (7·8%, 4·8-10·7; I2 =92%) and antibiotic-resistant Gram-negative bacteria (27·2%, 17·6-36·8; I2 =94%). The pooled prevalence of any AMR carriage or infection was higher in refugees and asylum seekers (33·0%, 18·3-47·6; I2 =98%) than in other migrant groups (6·6%, 1·8-11·3; I2 =92%). The pooled prevalence of antibiotic-resistant organisms was slightly higher in high-migrant community settings (33·1%, 11·1-55·1; I2 =96%) than in migrants in hospitals (24·3%, 16·1-32·6; I2 =98%). We did not find evidence of high rates of transmission of AMR from migrant to host populations. INTERPRETATION: Migrants are exposed to conditions favouring the emergence of drug resistance during transit and in host countries in Europe. Increased antibiotic resistance among refugees and asylum seekers and in high-migrant community settings (such as refugee camps and detention facilities) highlights the need for improved living conditions, access to health care, and initiatives to facilitate detection of and appropriate high-quality treatment for antibiotic-resistant infections during transit and in host countries. Protocols for the prevention and control of infection and for antibiotic surveillance need to be integrated in all aspects of health care, which should be accessible for all migrant groups, and should target determinants of AMR before, during, and after migration. FUNDING: UK National Institute for Health Research Imperial Biomedical Research Centre, Imperial College Healthcare Charity, the Wellcome Trust, and UK National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infections and Antimictobial Resistance at Imperial College London

Surgical site infection after gastrointestinal surgery in high-income, middle-income, and low-income countries: a prospective, international, multicentre cohort study

Background: Surgical site infection (SSI) is one of the most common infections associated with health care, but its importance as a global health priority is not fully understood. We quantified the burden of SSI after gastrointestinal surgery in countries in all parts of the world. Methods: This international, prospective, multicentre cohort study included consecutive patients undergoing elective or emergency gastrointestinal resection within 2-week time periods at any health-care facility in any country. Countries with participating centres were stratified into high-income, middle-income, and low-income groups according to the UN's Human Development Index (HDI). Data variables from the GlobalSurg 1 study and other studies that have been found to affect the likelihood of SSI were entered into risk adjustment models. The primary outcome measure was the 30-day SSI incidence (defined by US Centers for Disease Control and Prevention criteria for superficial and deep incisional SSI). Relationships with explanatory variables were examined using Bayesian multilevel logistic regression models. This trial is registered with ClinicalTrials.gov, number NCT02662231. Findings: Between Jan 4, 2016, and July 31, 2016, 13 265 records were submitted for analysis. 12 539 patients from 343 hospitals in 66 countries were included. 7339 (58·5%) patient were from high-HDI countries (193 hospitals in 30 countries), 3918 (31·2%) patients were from middle-HDI countries (82 hospitals in 18 countries), and 1282 (10·2%) patients were from low-HDI countries (68 hospitals in 18 countries). In total, 1538 (12·3%) patients had SSI within 30 days of surgery. The incidence of SSI varied between countries with high (691 [9·4%] of 7339 patients), middle (549 [14·0%] of 3918 patients), and low (298 [23·2%] of 1282) HDI (p < 0·001). The highest SSI incidence in each HDI group was after dirty surgery (102 [17·8%] of 574 patients in high-HDI countries; 74 [31·4%] of 236 patients in middle-HDI countries; 72 [39·8%] of 181 patients in low-HDI countries). Following risk factor adjustment, patients in low-HDI countries were at greatest risk of SSI (adjusted odds ratio 1·60, 95% credible interval 1·05–2·37; p=0·030). 132 (21·6%) of 610 patients with an SSI and a microbiology culture result had an infection that was resistant to the prophylactic antibiotic used. Resistant infections were detected in 49 (16·6%) of 295 patients in high-HDI countries, in 37 (19·8%) of 187 patients in middle-HDI countries, and in 46 (35·9%) of 128 patients in low-HDI countries (p < 0·001). Interpretation: Countries with a low HDI carry a disproportionately greater burden of SSI than countries with a middle or high HDI and might have higher rates of antibiotic resistance. In view of WHO recommendations on SSI prevention that highlight the absence of high-quality interventional research, urgent, pragmatic, randomised trials based in LMICs are needed to assess measures aiming to reduce this preventable complication

Planck 2015 results VII. High Frequency Instrument data processing: Time-ordered information and beams

The Planck High Frequency Instrument (HFI) has observed the full sky at six frequencies (100, 143, 217, 353, 545, and 857 GHz) in intensity and at four frequencies in linear polarization (100, 143, 217, and 353 GHz). In order to obtain sky maps, the time-ordered information (TOI) containing the detector and pointing samples must be processed and the angular response must be assessed. The full mission TOI is included in the Planck 2015 release. This paper describes the HFI TOI and beam processing for the 2015 release. HFI calibration and map making are described in a companion paper. The main pipeline has been modified since the last release (2013 nominal mission in intensity only), by including a correction for the nonlinearity of the warm readout and by improving the model of the bolometer time response. The beam processing is an essential tool that derives the angular response used in all the Planck science papers and we report an improvement in the effective beam window function uncertainty of more than a factor of 10 relative to the2013 release. Noise correlations introduced by pipeline filtering function are assessed using dedicated simulations. Angular cross-power spectra using data sets that are decorrelated in time are immune to the main systematic effects