Clinical application of whole-genome sequencing in the management of extensively drug-resistant tuberculosis: a case report.

BACKGROUND: Whole-genome sequencing (WGS)-based prediction of drug resistance in Mycobacterium tuberculosis has the potential to guide clinical decisions in the design of optimal treatment regimens. METHODS: We utilized WGS to investigate drug resistance mutations in a 32-year-old Tanzanian male admitted to Kibong'oto Infectious Diseases Hospital with a history of interrupted multidrug-resistant tuberculosis treatment for more than three years. Before admission, he received various all-oral bedaquiline-based multidrug-resistant tuberculosis treatment regimens with unfavourable outcomes. RESULTS: Drug susceptibility testing of serial M. tuberculosis isolates using Mycobacterium Growth Incubator Tubes culture and WGS revealed resistance to first-line anti-TB drugs, bedaquiline, and fluoroquinolones but susceptibility to linezolid, clofazimine, and delamanid. WGS of serial cultured isolates revealed that the Beijing (Lineage 2.2.2) strain was resistant to bedaquiline, with mutations in the mmpR5 gene (Rv0678. This study also revealed the emergence of two distinct subpopulations of bedaquiline-resistant tuberculosis strains with Asp47f and Glu49fs frameshift mutations in the mmpR5 gene, which might be the underlying cause of prolonged resistance. An individualized regimen comprising bedaquiline, delamanid, pyrazinamide, ethionamide, and para-aminosalicylic acid was designed. The patient was discharged home at month 8 and is currently in the ninth month of treatment. He reported no cough, chest pain, fever, or chest tightness but still experienced numbness in his lower limbs. CONCLUSION: We propose the incorporation of WGS in the diagnostic framework for the optimal management of patients with drug-resistant and extensively drug-resistant tuberculosis.

Antimicrobial usage in cattle and poultry production in Dar es Salaam, Tanzania: pattern and quantity.

BACKGROUND: Antimicrobials are extensively used in cattle and poultry production in Tanzania. However, there is dearth of information on its quantitative use. A questionnaire-based cross-sectional study was conducted from August to September 2019 in randomly selected poultry and small-scale dairy farms, in three districts of Dar es Salaam City eastern, Tanzania, to assess the practice and quantify antimicrobial use. Descriptive and statistical analyses were performed at a confidence interval of 95%. The ratio of Used Daily Dose (UDD) and Defined Daily Dose (DDD) were used to determine whether the antimicrobial was overdosed or under dosed. RESULTS: A total of 51 poultry and 65 small-scale dairy farms were involved in the study. The route of antimicrobial administration was 98% orally via drinking water and 2% in feeds for poultry and for small-scale dairy farms, all through parenteral route. Seventeen types of antimicrobials comprising seven classes were recorded in poultry farms while nine belonging to six classes in the small dairy farms. Majority of the farms (poultry, 87.7% and small scale dairy, 84.3%) used antimicrobials for therapeutic purposes. About 41% of the poultry and one third (34%) of the dairy farmers' were not compliant to the drug withdrawal periods. Beta-lactams, fluoroquinolones, sulphonamides, tetracyclines and macrolides were the commonly used antimicrobials on these farms. In the poultry farms both those with records and those which relied on recall, antimicrobials were overdosed whereas in the small dairy farms, sulfadimidine, oxytetracycline and neomycin were within the appropriate dosing range (0.8-1.2). The majority (58.6%) of farmers had adequate level of practices (favorable) regarding antimicrobial use in cattle and poultry production. This was associated with the age and level of education of the cattle and poultry farmers. CONCLUSION: The study revealed a widespread misuse of antimicrobials of different types and classes in both poultry and small-scale dairy farming in Dar es Salaam, Tanzania. This result gives insight into the antimicrobial use practices and its quantification. The information obtained can guide and promote prudent use of antimicrobials among the farmers by developing mitigate strategies that reduce antimicrobial resistance risk potentials.

Whole genome sequencing of Mycobacterium tuberculosis isolates and clinical outcomes of patients treated for multidrug-resistant tuberculosis in Tanzania.

BACKGROUND: Tuberculosis (TB), particularly multi- and or extensive drug resistant TB, is still a global medical emergency. Whole genome sequencing (WGS) is a current alternative to the WHO-approved probe-based methods for TB diagnosis and detection of drug resistance, genetic diversity and transmission dynamics of Mycobacterium tuberculosis complex (MTBC). This study compared WGS and clinical data in participants with TB. RESULTS: This cohort study performed WGS on 87 from MTBC DNA isolates, 57 (66%) and 30 (34%) patients with drug resistant and susceptible TB, respectively. Drug resistance was determined by Xpert® MTB/RIF assay and phenotypic culture-based drug-susceptibility-testing (DST). WGS and bioinformatics data that predict phenotypic resistance to anti-TB drugs were compared with participant's clinical outcomes. They were 47 female participants (54%) and the median age was 35 years (IQR): 29-44). Twenty (23%) and 26 (30%) of participants had TB/HIV co-infection BMI < 18 kg/m2 respectively. MDR-TB participants had MTBC with multiple mutant genes, compared to those with mono or polyresistant TB, and the majority belonged to lineage 3 Central Asian Strain (CAS). Also, MDR-TB was associated with delayed culture-conversion (median: IQR (83: 60-180 vs. 51:30-66) days). WGS had high concordance with both culture-based DST and Xpert® MTB/RIF assay in detecting drug resistance (kappa = 1.00). CONCLUSION: This study offers comparison of mutations detected by Xpert and WGS with phenotypic DST of M. tuberculosis isolates in Tanzania. The high concordance between the different methods and further insights provided by WGS such as PZA-DST, which is not routinely performed in most resource-limited-settings, provides an avenue for inclusion of WGS into diagnostic matrix of TB including drug-resistant TB.

The potential of CBC-derived ratios (monocyte-to-lymphocyte, neutrophil-to-lymphocyte, and platelet-to-lymphocyte) to predict or diagnose incident TB infection in Tanzanian adolescents.

BACKGROUND: Ratios of different immune cell populations (i.e., monocyte-to-lymphocyte, neutrophil-to-lymphocyte, and platelet-to-lymphocyte ratios) have been studied as a means of predicting future tuberculosis (TB) disease risk or to assist in the diagnosis of incident TB disease. No studies to-date, however, have evaluated the potential of these ratios to predict or assist in the diagnosis of incident TB infection - the first step in the natural history of TB disease. METHODS: In this prospective study, we evaluated the complete blood count (CBC)-derived metrics of monocyte-to-lymphocyte ratio (MLR), neutrophil-to-lymphocyte ratio (NLR), and platelet-to-lymphocyte ratio (PLR) as predictors of future TB infection risk or aids in the diagnosis of TB infection among 145 Tanzanian adolescents enrolled in the DAR-901 vaccine trial, using paired CBCs and interferon-gamma release assays (IGRAs) obtained at 0, 60 and 720 days after study enrollment. RESULTS: At baseline, there were no significant differences between study participants who remained persistently IGRA negative throughout the study period and those who subsequently converted to IGRA positive with respect to MLR (0.18 vs 0.17, p = 0.10), NLR (0.88 vs 1.02, p = 0.08), or PLR (115 vs 120, p = 0.28). Similarly, no significant differences were noted with respect to MLR, NLR, and PLR between IGRA converters and time-matched negative controls at the time of IGRA conversion. With respect to other blood cell measures, however, there were modest but significant differences between IGRA negatives and IGRA converters with respect to red blood cell count (4.8 vs 4.6 ×  106 cells/mcL, p = 0.008), hemoglobin (12.6 vs 12.3 g/dL, p = 0.01), and hematocrit (38.8 vs 37.8%, p = 0.005). CONCLUSIONS: In contrast to prior studies that have suggested that the ratios of different immune cell populations are associated with development of TB disease, our present findings do not demonstrate an association between these ratios and the development of TB infection. However, decreased red blood cell measures were associated with the subsequent development of TB infection, suggesting either that dysregulation of iron metabolism may play a role in TB pathogenesis or that following TB infection, iron dysregulation may precede IGRA positivity. TRIAL REGISTRATION: Clinicaltrials.gov NCT02712424 . Date of registration: March 14, 2016.

High prevalence of human immunodeficiency virus, hepatitis B and C viral infections among people who inject drugs: a potential stumbling block in the control of HIV and viral hepatitis in Tanzania.

BACKGROUND: Tanzania has witnessed a significant decrease in the prevalence of human immunodeficiency virus (HIV) and viral hepatitis in the general population attributed to several interventional measures. It is uncertain whether this decline has also occurred among people who inject drugs (PWID). This study aimed to determine the seroprevalence of HIV, Hepatitis B and C viruses infection among PWID recruited from their hotspot sites in Dar es Salaam, Tanzania. METHODS: A cross-sectional study conducted between June and September 2017 recruited PWID from pre-identified hotspot sites using a snowball referral sampling technique. A structured questionnaire was used to obtain information regarding socio-demographic characteristics, behaviour and drug use. Blood was tested for the presence of IgG antibodies against HIV and Hepatitis C virus (HCV) and hepatitis B surface antigen (HBsAg). Data were entered in the computer using excel software and analysed using Statistical Package for Social Sciences version 20. RESULTS: A total of 219 PWID were recruited, the majority of whom were males (74.9%), unmarried (60.7%), had low education (62.6%) and low income (57.1%). The median age was 39 years, with an inter-quartile range of 35-43. Approximately 32.0% had a history of drug injection for more than 3 years, 79.9% were injecting drugs more than 3 times per day and 47.5% were sharing needles. The overall prevalence of HIV, HBsAg, and HCV was 33.8, 7.8, and 50.2%, respectively. There was serologic evidence of at least one infection for 68.9%, while 22.4% had two or more infections. HIV infection was independently associated with being married, while HCV was associated with injecting drugs for more than 3 years and unprotected sex. CONCLUSION: Over two-third of PWID had serologic evidence of infection with at least one virus while 22.4% having at least two infections. The high prevalence of HIV and viral hepatitis infections among PWID may hamper initiatives of ending HIV and viral hepatitis epidemics in Tanzania.

A chromosome 5q31.1 locus associates with tuberculin skin test reactivity in HIV-positive individuals from tuberculosis hyper-endemic regions in east Africa.

One in three people has been infected with Mycobacterium tuberculosis (MTB), and the risk for MTB infection in HIV-infected individuals is even higher. We hypothesized that HIV-positive individuals living in tuberculosis-endemic regions who do not get infected by Mycobacterium tuberculosis are genetically resistant. Using an "experiment of nature" design that proved successful in our previous work, we performed a genome-wide association study of tuberculin skin test positivity using 469 HIV-positive patients from prospective study cohorts of tuberculosis from Tanzania and Uganda to identify genetic loci associated with MTB infection in the context of HIV-infection. Among these individuals, 244 tested were tuberculin skin test (TST) positive either at enrollment or during the >8 year follow up, while 225 were not. We identified a genome-wide significant association between a dominant model of rs877356 and binary TST status in the combined cohort (Odds ratio = 0.2671, p = 1.22x10-8). Association was replicated with similar significance when examining TST induration as a continuous trait. The variant lies in the 5q31.1 region, 57kb downstream from IL9. Two-locus analyses of association of variants near rs877356 showed a haplotype comprised of rs877356 and an IL9 missense variant, rs2069885, had the most significant association (p = 1.59x10-12). We also replicated previously linked loci on chromosomes 2, 5, and 11. IL9 is a cytokine produced by mast cells and TH2 cells during inflammatory responses, providing a possible link between airway inflammation and protection from MTB infection. Our results indicate that studying uninfected, HIV-positive participants with extensive exposure increases the power to detect associations in complex infectious disease.

A Locus at 5q33.3 Confers Resistance to Tuberculosis in Highly Susceptible Individuals.

Immunosuppression resulting from HIV infection increases the risk of progression to active tuberculosis (TB) both in individuals newly exposed to Mycobacterium tuberculosis (MTB) and in those with latent infections. We hypothesized that HIV-positive individuals who do not develop TB, despite living in areas where it is hyperendemic, provide a model of natural resistance. We performed a genome-wide association study of TB resistance by using 581 HIV-positive Ugandans and Tanzanians enrolled in prospective cohort studies of TB; 267 of these individuals developed active TB, and 314 did not. A common variant, rs4921437 at 5q33.3, was significantly associated with TB (odds ratio = 0.37, p = 2.11 × 10(-8)). This variant lies within a genomic region that includes IL12B and is embedded in an H3K27Ac histone mark. The locus also displays consistent patterns of linkage disequilibrium across African populations and has signals of strong selection in populations from equatorial Africa. Along with prior studies demonstrating that therapy with IL-12 (the cytokine encoded in part by IL12B, associated with longer survival following MTB infection in mice deficient in CD4 T cells), our results suggest that this pathway might be an excellent target for the development of new modalities for treating TB, especially for HIV-positive individuals. Our results also indicate that studying extreme disease resistance in the face of extensive exposure can increase the power to detect associations in complex infectious disease.

Laboratory confirmed puerperal sepsis in a national referral hospital in Tanzania: etiological agents and their susceptibility to commonly prescribed antibiotics.

BACKGROUND: In most developing countries, puerperal sepsis is treated empirically with broad spectrum antibiotics due to lack of resources for culture and antibiotics susceptibility testing. However, empirical treatment does not guarantee treatment success and may promote antimicrobial resistance. We set to determine etiological agents and susceptibility pattern to commonly prescribed antimicrobial agents, among women suspected of puerperal sepsis, and admitted at Muhimbili National Hospital. METHODS: Hospital based cross-sectional study conducted at tertiary hospital from December 2017 to April 2018. The study recruited post-delivery women suspected with puerperal sepsis. Socio- demographic, clinical and obstetric information were collected using structured questionnaire. Blood and endocervical swab samples were collected for aerobic culture. Blood culture bottles were incubated in BACTEC FX40 (Becton-Dickinson, Sparks, MD, USA). Positive blood cultures and cervical swabs were inoculated onto sheep blood agar, MacConkey agar, chocolate agar and Sabouraud's dextrose agar, incubated aerobically at 37 °C for 18-24 h. Antimicrobial susceptibility was determined by Kirby-Bauer disc diffusion method. RESULTS: A total of 197women were recruited, of whom 50.3% had spontaneous vaginal delivery, while 49.2% had caesarean section. Bacteraemia was detected in 22 (11.2%) women, along with 86 (43.6%) isolated from endocervical swabs. Gram-negative bacilli were the predominant isolates detected in 92(46.7%) cases. Majority of the isolates were E. coli 68(61.8%) followed by Klebsiella spp. 22(20.0%). E. coli were highly susceptible to meropenem (97.0%), while resistance to ceftriaxone, ampicillin and ceftazidime was 64.7, 67.6 and 63.2%, respectively. Klebsiella spp. were susceptible to meropenem (86.4%) and resistant to ceftriaxone (77.3%), gentamicin (86.4%), ampicillin (81.8%) and ceftazidime (86.4%). Staphylococcus aureus isolates were 100% susceptible to clindamycin. The proportion of extended spectrum beta lactamase producers among gram-negative bacilli was 64(69.6%) and 53.8% of S. aureus isolates were resistant to methicillin. CONCLUSION: In this study puerperal sepsis was mostly caused by E. coli and Klebsiella spp. Causative agents exhibited very high levels of resistance to most antibiotics used in empiric treatment calling for review of treatment guidelines and strict infection control procedures.

Effects of isoniazid resistance on TB treatment outcomes under programmatic conditions in a high-TB and -HIV setting: a prospective multicentre study.

Objectives: The scale and impact of background isoniazid resistance in TB- and HIV-endemic countries requires definition to improve treatment success and guide the scale-up of isoniazid preventive therapy (IPT). We describe the effects of isoniazid resistance on TB treatment outcomes among patients with or without HIV infection in Dar es Salaam, Tanzania. Methods: A multicentre, prospective observational study was conducted among TB patients commencing WHO-recommended first-line TB treatment. In multivariate analysis we ascertained the relationship between isoniazid resistance at presentation with a composite of poor treatment outcomes (death, failure or default from TB therapy). Results: Of 861 patients, 250 (29.0%) were HIV infected and 23 (2.7%) had isoniazid resistance. Seven hundred and ninety-seven (92.6%) of the patients were successfully treated and 25 (2.9%) died. Isoniazid resistance [relative risk (RR) = 6.0; 95% CI = 1.9-18.7; P < 0.01] and HIV infection with (RR = 2.3; 95% CI = 1.0-5.2; P = 0.05) or without (RR = 3.1; 95% CI = 1.5-6.2; P < 0.01) ART were independent predictors of poor treatment outcomes. Conclusions: Background isoniazid resistance and HIV infection adversely affected TB treatment outcomes. Early laboratory detection of isoniazid resistance is important for successful TB therapy. Studies on the impact of background isoniazid resistance on the efficacy of isoniazid prophylaxis are recommended.

Improved performance of Xpert MTB/RIF assay on sputum sediment samples obtained from presumptive pulmonary tuberculosis cases at Kibong'oto infectious diseases hospital in Tanzania.

BACKGROUND: The introduction of Xpert MTB/RIF assay (Xpert) has significantly improved diagnosis of Tuberculosis (TB) in resource limited human immunodeficiency virus (HIV) endemic settings. We aimed to modify the Xpert protocol to improve the detection of Mycobacterium tuberculosis (MTB). METHODS: This cross sectional study was conducted among presumptive pulmonary tuberculosis (PTB) patients at Kibong'oto Infectious Diseases Hospital between August and November 2015. Each patient consented to provide 2 samples of raw sputa. One-sputum sample was sedimented using the Petroff's method and divided into two portions. One portion of sediment was inoculated on Lowenstein-Jensen culture media and observed for any growth for up to 8 weeks. Both, raw sputum and the portions of sediments were tested separately using Xpert with a sample reagent ratio of 1:2. Mean age of patients, prevalence of MTB, Xpert sensitivity, specificity, positive and negative predictive value were calculated. An incremental sensitivity was determined. Pearson chi-square and either an independent T or Mann-Whitney U-test were used to compared categorical and continuous variables respectively. A p- value of ≤0.05 was considered significant. RESULTS: Of the 270 presumptive PTB cases, 262 were eligible for analysis. Eight (3%) were excluded due to contaminated culture. Patients' mean age was 42.9 (±SD 15.1) years of which 173 (66%) were female. The overall prevalence of PTB was 112 (43%), of which the Xpert detected 105 (40%) in sediments and 98 (37%) in raw sputa as compared to culture which detected 85 (32%) cases of PTB. Sensitivity, specificity, positive and negative predictive values of Xpert on sputum sediments were 92%, 85%, 74% and 96% respectively. Overall, the incremental sensitivity of Xpert on sediment over raw sputum was 6%. In HIV infected Presumptive PTB, the incremental sensitivity was 12%. CONCLUSION: Lowering the sample reagent to sediment dilution ratio increases sensitivity of Xpert on MTB detection among presumptive PTB cases, especially in HIV infected individuals.

Identification and antimicrobial resistance patterns of bacterial enteropathogens from children aged 0-59 months at the University Teaching Hospital, Lusaka, Zambia: a prospective cross sectional study.

BACKGROUND: Bacterial diarrhoeal disease is among the most common causes of mortality and morbidity in children 0-59 months at the University Teaching Hospital in Lusaka, Zambia. However, most cases are treated empirically without the knowledge of aetiological agents or antimicrobial susceptibility patterns. The aim of this study was, therefore, to identify bacterial causes of diarrhoea and determine their antimicrobial susceptibility patterns in stool specimens obtained from the children at the hospital. METHODS: This hospital-based cross-sectional study involved children aged 0-59 months presenting with diarrhoea at paediatrics wards at the University Teaching Hospital in Lusaka, Zambia, from January to May 2016. Stool samples were cultured on standard media for enteropathogenic bacteria, and identified further by biochemical tests. Multiplex polymerase chain reaction was used for characterization of diarrhoeagenic Escherichia coli strains. Antimicrobial susceptibility testing was performed on antibiotics that are commonly prescribed at the hospital using the Kirby-Bauer disc diffusion method, which was performed using the Clinical Laboratory Standards International guidelines. RESULTS: Of the 271 stool samples analysed Vibrio cholerae 01 subtype and Ogawa serotype was the most commonly detected pathogen (40.8%), followed by Salmonella species (25.5%), diarrhoeagenic Escherichia coli (18%), Shigella species (14.4%) and Campylobacter species (3.5%). The majority of the bacterial pathogens were resistant to two or more drugs tested, with ampicillin and co-trimoxazole being the most ineffective drugs. All diarrhoeagenic Escherichia coli isolates were extended spectrum ß-lactamase producers. CONCLUSION: Five different groups of bacterial pathogens were isolated from the stool specimens, and the majority of these organisms were multidrug resistant. These data calls for urgent revision of the current empiric treatment of diarrhoea in children using ampicillin and co-trimoxazole, and emphasizes the need for continuous antimicrobial surveillance as well as the implementation of prevention programmes for childhood diarrhoea.

Predictors of blaCTX-M-15 in varieties of Escherichia coli genotypes from humans in community settings in Mwanza, Tanzania.

BACKGROUND: Extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae commonly cause infections worldwide. Bla CTX-M-15 has been commonly detected in hospital isolates in Mwanza, Tanzania. Little is known regarding the faecal carriage of ESBL isolates and bla CTX-M-15 allele among humans in the community in developing countries. METHODS: A cross-sectional study involving 334 humans from the community settings in Mwanza City was conducted between June and September 2014. Stool specimens were collected and processed to detect ESBL producing enterobacteriaceae. ESBL isolates were confirmed using disc approximation method, commercial ESBL plates and VITEK-2 system. A polymerase chain reaction and sequencing based allele typing for CTX-M ESBL genes was performed to 42 confirmed ESBL isolates followed by whole genome sequence of 25 randomly selected isolates to detect phylogenetic groups, sequence types plasmid replicon types. RESULTS: Of 334 humans investigated, 55 (16.5 %) were found to carry ESBL-producing bacteria. Age, history of antibiotic use and history of admission were independent factors found to predict ESBL-carriage. The carriage rate of ESBL-producing Escherichia coli was significantly higher than that of Klebsiella pneumoniae (15.1 % vs. 3.8 %, p = 0.026). Of 42 ESBL isolates, 37 (88.1 %) were found to carry the bla CTX-M-15 allele. Other transferrable resistance genes were aac(6')Ib-cr, aac(3)-IIa, aac(3)-IId, aadA1, aadA5, strA, strB and qnrS1. Eight multi-locus sequence types (ST) were detected in 25 E. coli isolates subjected to genome sequencing. ST-131 was detected in 6 (24 %), ST-38 in 5 (20 %) and 5 (20 %) clonal complex - 10(ST-617, ST-44) of isolates. The pathogenic phylogenetic groups D and B2 were detected in 8/25 (32 %) and 6/25 (24 %) of isolates respectively. BlaCTX-M-15 was found to be located in multiple IncY and IncF plasmids while in 13/25(52 %) of cases it was chromosomally located. CONCLUSION: The overlap of multi-drug resistant bacteria and diversity of the genotypes carrying CTX-M-15 in the community and hospitals requires an overall approach that addresses social behaviour and activity, rationalization of the antibiotic stewardship policy and a deeper understanding of the ecological factors that lead to persistence and spread of such alleles.

Auditory Impairments in HIV-Infected Children.

OBJECTIVES: In a cross-sectional study of human immunodeficiency virus (HIV)-infected adults, the authors showed lower distortion product otoacoustic emissions (DPOAEs) in HIV+ individuals compared with controls as well as findings consistent with a central auditory processing deficit in HIV+ adults on antiretroviral therapy. The authors hypothesized that HIV+ children would also have a higher prevalence of abnormal central and peripheral hearing test results compared with HIV- controls. DESIGN: Pure-tone thresholds, DPOAEs, and tympanometry were performed on 244 subjects (131 HIV+ and 113 HIV- subjects). Thirty-five of the HIV+, and 3 of the HIV- subjects had a history of tuberculosis treatment. Gap detection results were available for 18 HIV- and 44 HIV+ children. Auditory brainstem response results were available for 72 HIV- and 72 HIV+ children. Data from ears with abnormal tympanograms were excluded. RESULTS: HIV+ subjects were significantly more likely to have abnormal tympanograms, histories of ear drainage, tuberculosis, or dizziness. All audiometric results were compared between groups using a two-way ANOVA with HIV status and ear drainage history as grouping variables. Mean audiometric thresholds, gap detection thresholds, and auditory brainstem response latencies did not differ between groups, although the HIV+ group had a higher proportion of individuals with a hearing loss >25 dB HL in the better ear. The HIV+ group had reduced DPOAE levels (p < 0.05) at multiple frequencies compared with HIV- subjects. No relationships were found between treatment regimens or delay in starting treatment and audiological parameters. CONCLUSIONS: As expected, children with HIV+ were more likely to have a history of ear drainage, and to have abnormal tympanograms. Similar to the adult findings, the HIV+ group did not show significantly reduced audiometric thresholds, but did have significantly lower DPOAE magnitudes. These data suggest that (1) HIV+ children often have middle ear damage which complicates understanding the direct effects of HIV on the hearing system, and (2) even when corrected for confounders DPOAEs were lower in the HIV+ group. Previous studies suggest ototoxicity from antiretroviral drugs is an unlikely cause of the reduced DPOAE magnitudes. Other possibilities include effects on efferent pathways connecting to outer hair cells or a direct effect of HIV on the cochlea.

Prevalence of HIV and syphilis infections among pregnant women attending antenatal clinics in Tanzania, 2011.

BACKGROUND: The occurrence of HIV-1 and syphilis infections during pregnancy poses major health risks to the foetus due to mother-to-child transmission. We conducted surveillance of HIV and syphilis infections among pregnant women attending antenatal clinics (ANCs) in Mainland Tanzania in 2011. METHODS: This surveillance was carried out in 133 ANCs selected from 21 regions in Tanzania. In each region, six ANC sites were selected, with urban, semi-urban, and rural areas contributing two each. All pregnant women who were attending selected sentinel ANC sites for the first time at any pregnancy between September and December 2011 were enrolled. Serial ELISA assays were performed to detect HIV infection in an unlinked anonymous manner using dried blood spot (DBS) after routine syphilis testing. Data analysis was conducted using Stata v.12 software. RESULTS: A total of 39,698 pregnant women representing 2.4 % of all pregnant women (1.68 million) attending ANCs in the Mainland Tanzania were enrolled. The overall HIV prevalence was found to be 5.6 % (95 % CI: 5.4-5.8 %). The risk for HIV infection was significantly higher among women aged 25-34 (cOR = 1.97, 95 % CI: 1.79-2.16; p < 0.05), older than 35 years (cOR = 1.88, 95 % CI: 1.62-2.17; p < 0.05) and those having 1-2 and 3-4 previous pregnancies. HIV infection was less prevalent among women attending rural ANC clinics (cOR = 0.46, 95 % CI 0.4-0.52; p < 0.05). The overall syphilis prevalence was 2.5 % (95 % CI: 2.3, 3.6). The risk for syphilis infection was significantly higher among women attending semi-urban and rural clinics and those having 3-4, and 5 previous pregnancies (p < 0.05). Marital status and level of education were not statistically significant with either of the two infections. HIV and syphilis co-infections occurred in 109 of 38,928 (0.3 %). CONCLUSION: The overall prevalence of HIV infection (5.6 %) and syphilis (2.5 %) found among pregnant women attending ANC clinics in Tanzania calls for further strengthening of current intervention measures, which include scaling up the integration of prevention of mother to child transmission (PMTCT) services in Reproductive and Child Health (RCH) clinics.

Development of a One Health National Capacity in Africa : the Southern African Centre for Infectious Disease Surveillance (SACIDS) One Health Virtual Centre Model.

Among the many challenges to health, infectious diseases stand out for their ability to have a profound impact on humans and animals. The recent years have witnessed an increasing number of novel infectious diseases. The numerous examples of infections which originated from animals suggest that the zoonotic pool is an important and potentially rich source of emerging diseases. Since emergence and re-emergence of pathogens, and particularly zoonotic agents, occur at unpredictable rates in animal and human populations, infectious diseases will constitute a significant challenge for the public health and animal health communities in the twenty-first century. The African continent suffers from one of the highest burdens of infectious diseases of humans and animals in the world but has the least capacity for their detection, identification and monitoring. Lessons learnt from recent zoonotic epidemics in Africa and elsewhere clearly indicate the need for coordinated research, interdisciplinary centres, response systems and infrastructures, integrated surveillance systems and workforce development strategies. More and stronger partnerships across national and international sectors (human health, animal health, environment) and disciplines (natural and social sciences) involving public, academic and private organisations and institutions will be required to meet the present and future challenges of infectious diseases. In order to strengthen the efficiency of early warning systems, monitoring trends and disease prediction and timely outbreak interventions for the benefit of the national and international community, it is essential that each nation improves its own capacity in disease recognition and laboratory competence. The SACIDS, a One Health African initiative linking southern African academic and research institutions in smart partnership with centres of science excellence in industrialised countries as well as international research centres, strives to strengthen Africa's capacity to detect, identify and monitor infectious diseases of humans and animals, to better manage health and socio-economic risks posed by them, and to improve research capacity in investigating the biologic, socio-economic, ecologic and anthropogenic factors responsible for emergence and re-emergence of infectious diseases.

Species diversity of non-tuberculous mycobacteria isolated from humans, livestock and wildlife in the Serengeti ecosystem, Tanzania.

BACKGROUND: Non-tuberculous mycobacteria (NTM), which are ubiquitous micro-organisms occurring in humans, animals and the environment, sometimes receive public health and veterinary attention as opportunistic disease-causing agents. In Tanzania, there is limited information regarding the diversity of NTM species, particularly at the human-livestock-wildlife interface such as the Serengeti ecosystem, where potential for cross species infection or transmission may exist. METHODS: Mycobacterial DNA was extracted from cultured isolates obtained from sputum samples of 472 suspect TB patients and 606 tissues from wildlife species and indigenous cattle. Multiplex PCR was used to differentiate NTM from Mycobacterium tuberculosis complex (MTBC) members. NTM were further identified to species level by nucleotide sequencing of the 16S rRNA gene. RESULTS: A total of fifty five (55) NTM isolates representing 16 mycobacterial species and 5 isolates belonging to the MTBC were detected. Overall, Mycobacterium intracellulare which was isolated from human, cattle and wildlife, was the most frequently isolated species (20 isolates, 36.4%) followed by M. lentiflavum (11 isolates, 20%), M. fortuitum (4 isolates, 7.3%) and M. chelonae-abscessus group (3 isolates, 5.5%). In terms of hosts, 36 isolates were from cattle and 12 from humans, the balance being found in various wildlife species. CONCLUSION: This study reveals a diversity of NTM species in the Serengeti ecosystem, some of which have potential for causing disease in animals and humans. The isolation of NTM from tuberculosis-like lesions in the absence of MTBC calls for further research to elucidate their actual role in causing disease. We are also suggesting a one health approach in identifying risk factors for and possible transmission mechanisms of the NTM in the agro-pastoral communities in the Serengeti ecosystem.

Auditory impairments in HIV-infected individuals in Tanzania.

OBJECTIVES: Abnormal hearing tests have been noted in human immunodeficiency virus (HIV)-infected patients in several studies, but the nature of the hearing deficit has not been clearly defined. The authors performed a cross-sectional study of both HIV+ and HIV- individuals in Tanzania by using an audiological test battery. The authors hypothesized that HIV+ adults would have a higher prevalence of abnormal central and peripheral hearing test results compared with HIV- controls. In addition, they anticipated that the prevalence of abnormal hearing assessments would increase with antiretroviral therapy (ART) use and treatment for tuberculosis (TB). DESIGN: Pure-tone thresholds, distortion product otoacoustic emissions (DPOAEs), tympanometry, and a gap-detection test were performed using a laptop-based hearing testing system on 751 subjects (100 HIV- in the United States, plus 651 in Dar es Salaam, Tanzania, including 449 HIV+ [130 ART- and 319 ART+], and 202 HIV-, subjects. No U.S. subjects had a history of TB treatment. In Tanzania, 204 of the HIV+ and 23 of the HIV- subjects had a history of TB treatment. Subjects completed a video and audio questionnaire about their hearing, as well as a health history questionnaire. RESULTS: HIV+ subjects had reduced DPOAE levels compared with HIV- subjects, but their hearing thresholds, tympanometry results, and gap-detection thresholds were similar. Within the HIV+ group, those on ART reported significantly greater difficulties understanding speech in noise, and were significantly more likely to report that they had difficulty understanding speech than the ART- group. The ART+ group had a significantly higher mean gap-detection threshold compared with the ART- group. No effects of TB treatment were seen. CONCLUSIONS: The fact that the ART+/ART- groups did not differ in measures of peripheral hearing ability (DPOAEs, thresholds), or middle ear measures (tympanometry), but that the ART+ group had significantly more trouble understanding speech and had higher gap-detection thresholds indicates a central processing deficit. These data suggest that: (1) hearing deficits in HIV+ individuals could be a CNS side effect of HIV infection, (2) certain ART regimens might produce CNS side effects that manifest themselves as hearing difficulties, and/or (3) some ART regimens may treat CNS HIV inadequately, perhaps due to insufficient CNS drug levels, which is reflected as a central hearing deficit. Monitoring of central hearing parameters could be used to track central effects of either HIV or ART.

Management of neonatal sepsis at Muhimbili National Hospital in Dar es Salaam: diagnostic accuracy of C-reactive protein and newborn scale of sepsis and antimicrobial resistance pattern of etiological bacteria.

BACKGROUND: We determined the accuracy of Rubarth's newborn scale of sepsis and C- reactive protein in diagnosing neonatal sepsis and assessed antimicrobial susceptibility pattern of etiological bacteria. METHODS: This cross sectional study was conducted at Muhimbili National Hospital in Dar es Salaam, Tanzania between July 2012 and March 2013. Neonates suspected to have sepsis underwent physical examination using Rubarth's newborn scale of sepsis (RNSOS). Blood was taken for culture and antimicrobial sensitivity testing, full blood picture and C - reactive protein (CRP) performed 12 hours apart. The efficacy of RNSOS and serial CRP was assessed by calculating sensitivity, specificity, negative and positive predictive values, receiver operating characteristics (ROC) analysis as well as likelihood ratios (LHR) with blood culture result used as a gold standard. RESULTS: Out of 208 blood samples, 19.2% had a positive blood culture. Single CRP had sensitivity and specificity of 87.5% and 70.9% respectively, while RNSOS had sensitivity of 65% and specificity of 79.7%. Serial CRP had sensitivity of 69.0% and specificity of 92.9%. Combination of CRP and RNSOS increased sensitivity to 95.6% and specificity of 56.4%. Combination of two CRP and RNSOS decreased sensitivity to 89.1% but increased specificity to 74%. ROC for CRP was 0.86; and for RNSOS was 0.81. For CRP the LHR for positive test was 3 while for negative test was 0.18, while for RNSOS the corresponding values were 3.24 and for negative test was 0.43. Isolated bacteria were Klebsiella spp 14 (35%), Escherichia coli 12 (22.5%), Coagulase negative staphlococci 9 (30%), Staphylococcus aureus 4 (10%), and Pseudomonas spp 1 (2.5%). The overall resistance to the WHO recommended first line antibiotics was 100%, 92% and 42% for cloxacillin, ampicillin and gentamicin, respectively. For the second line drugs resistance was 45%, 40%, and 7% for ceftriaxone, vancomycin and amikacin respectively. CONCLUSIONS: Single CRP in combination with RNSOS can be used for rapid identification of neonates with sepsis due to high sensitivity (95.6%) but cannot exclude those without sepsis due to low specificity (56.4%). Serial CRP done 12hrs apart can be used to exclude non-cases. This study demonstrated very high levels of resistance to the first-line antibiotics.

Greater preexisting interferon γ responses to mycobacterial antigens and lower bacillary load during HIV-associated tuberculosis.

The role of preexisting interferon (IFN) γ responses in controlling bacillary burden in human immunodeficiency virus (HIV)-associated tuberculosis is not known. Among BCG-immunized HIV-infected adults who developed tuberculosis in a phase III trial of an investigational tuberculosis vaccine, greater baseline IFN-γ responses to early secretory antigenic target 6 and Mycobacterium tuberculosis whole-cell lysate were associated with reduced bacillary burden on sputum smear grade, days to culture positivity on agar, and sputum culture grade during subsequent tuberculosis. This association was most consistent among recipients of the investigational vaccine. When HIV-associated tuberculosis develops, greater preexisting IFN-γ responses to mycobacterial antigens are associated with reduced tuberculosis bacillary burden. ClinicalTrials.gov Identifier. NCT0052195.

Evidence of Human-designated Antiretroviral (ARV) Drug Residues in Broiler Chicken, Domestic Pigs, and Animal Feeds in Tanzania.

Background : Recent reports have indicated the use of antiretroviral (ARV) drugs to boost animal production in neighboring Uganda, with further reports of use in several African countries. Methods: This cross-sectional study was conducted in nine districts in Tanzania, and involved screening for the presence of three first-line ARVs (lamivudine, nevirapine, and efavirenz) residues in the muscle and blood of domestic pigs and broiler chickens, and in sampled animal feed and water. Residues were determined using liquid chromatography and mass spectrometry (LC-MS/MS). The method involved calibration of the lower limit of quantitation (LLOQ) and limit of detection (LOD). ARVs were detected and quantified using the Multiple Reaction Monitoring (MRM) system. Results: 131 (66.8%) of the 196 samples of muscle, blood, and animal feed were found to contain lamivudine residues, with the highest concentration detected in domestic pig blood and muscle (7.58mg/kg) and the lowest concentration (0.01 mg/kg) in broiler chicken feed. There was a significant relationship between the presence of lamivudine by sample type and sample origin (p=0.000). Nevirapine and efavirenz drugs were not detected in any of the collected samples. No ARV residues were detected in water samples (n=37). Conclusion: This study confirms the use of ARVs in animal production in Tanzania as evidenced by the presence of residues in animal feeds. We found lamivudine residues in domestic pigs and broiler chickens at concentrations higher than those recently reported in other East African studies. Farmers living with HIV may be using ARVs from their prescribed medications, which may lead to poor adherence and the emergence of drug resistance. Besides direct human and animal health issues, these residues in animal feeds and animal excreta can lead to environmental contamination leading to several negative impacts. We recommend a total ban on human-designated ARVs in animal production and advocate for comprehensive studies and monitoring systems across African countries to reveal potential societal and other reasons for their use and provide comprehensive solutions using One Health approaches.