Discordant rifampicin susceptibility results are associated with Xpert® MTB/RIF probe B and probe binding delay.

SETTING: Xpert® MTB/RIF is the first-line diagnostic test for Mycobacterium tuberculosis and rifampicin (RIF) resistance in South Africa. OBJECTIVE: To describe the rates of Xpert RIF resistance not confirmed on follow-up testing, as well as the patient and test characteristics associated with discordant results. DESIGN: Retrospective review of patients with isolates showing Xpert RIF resistance. Line-probe assay, phenotypic drug susceptibility testing or repeat Xpert were all considered confirmatory tests of RIF resistance. 'Discordance' was defined as a patient with RIF resistance identified on initial Xpert testing, with a subsequent confirmatory test indicating RIF susceptibility. Associations were analysed using Pearson χ² difference of proportions and modified Poisson regression. RESULTS: RIF discordance occurred in 22/263 subjects and was associated with Xpert probe B, probe binding delay, as opposed to probe dropout, and probe binding delays (ΔCt) of between 4 and 4.9. CONCLUSION: Discordant RIF resistance was common in our cohort and was associated with Xpert probe delay and use of probe B.

Delay to diagnosis and breast cancer stage in an urban South African breast clinic.

BACKGROUND: Breast cancer is the most common cancer in women in many low- and middle-income countries, and often presents at an advanced stage that affects prognosis irrespective of the care available. Although patient-related delay is commonly cited, the reasons for delay and the relationship of delay to stage are still poorly documented, especially in Africa. OBJECTIVES: To identify where patient-related socioeconomic delays occur and how these relate to stage at presentation. METHODS: Consecutive women with a new breast cancer diagnosis were prospectively invited to complete a questionnaire on their socioeconomic characteristics and ability to access care. Clinical stage at presentation was documented. RESULTS: Over 14 months, 252 women completed the questionnaire (response rate 71.6%). Their median age was 55 years (interquartile range 44 - 65), with 26.5% aged <45 years. Stage at presentation was stage 1 in 15.5% of patients, stage 2 in 28.5% and stage 3 in 56.0%. Almost a third of the patients (30.4%) presented with a T4 tumour (6.1% inflammatory). Total delay in presenting to the breast clinic was significantly associated with locally advanced stage at presentation (p=0.021). Average delay differed between early stage (1.5 months) and locally advanced (2.5 months), and most delay occurred between acknowledging a breast symptom and seeking care. The least delay was between attending a health service and presenting at the open-access breast clinic, with 75.0% presenting within 1 month. Factors associated with delay were difficulties with transport, low level of education and fear of missing appointments due to work. CONCLUSIONS: Most women delayed in seeking breast care. Facilitating direct access to specialist breast clinics may reduce delays in presentation and improve time to diagnosis and care.

Estimating the burden of cervical disease among HIV-infected women accessing screening services in South Africa: A model-based analysis.

BACKGROUND: Cervical cancer remains the second most common cancer among women worldwide, with much of the global burden occurring in low- and middle-income countries. HIV-infected women are at increased risk of human papillomavirus infection, preinvasive cervical disease and invasive cervical cancer (ICC). Funded through the United States President's Emergency Plan for AIDS Relief (PEPFAR) and working in collaboration with the South African (SA) Department of Health, our team supports cervical screening integrated within public sector HIV clinics in SA. OBJECTIVES: To estimate the burden of cervical disease among HIV-infected women accessing screening services supported through our programme. METHODS: We constructed conditional probability models to estimate the burden of grade 1 and grades 2/3 cervical intraepithelial lesions (CIN1 and CIN2/3) and ICC among two cohorts: one consisting of 3 190 HIV-infected women for whom only cytology results were available for analysis, and another consisting of 75 358 HIV-infected women for whom neither cytology nor histology results were available. Parameter estimates for the models were derived from routinely collected programmatic data and published clinical trials. RESULTS: Between January 2009 and November 2015, 75 358 HIV-infected women underwent Pap smear screening in public sector clinics supported by our cervical cancer prevention programme. Based on modelling analysis, we estimate that 46 123 cases of CIN1 (range 45 500 - 49 608), 13 598 cases of CIN2/3 (range 12 749 - 14 828), and 104 cases of ICC (range 61 - 186) occurred in this population. CONCLUSIONS: Our findings highlight the magnitude of cervical disease among HIV-infected women in SA.

Can patients afford the cost of treatment for multidrug-resistant tuberculosis in Ethiopia?

SETTING: Ethiopia has a high prevalence of tuberculosis (TB) and is one of the countries with the highest burden of multidrug-resistant TB (MDR-TB). OBJECTIVE: To understand the costs that patients incur in obtaining diagnosis and treatment for MDR-TB. DESIGN: In March 2013, interviews were conducted with 169 MDR-TB patients at three hospitals in Ethiopia to identify the cost to patients and the impact on employment and family income. RESULTS: The average MDR-TB patient incurred a total cost of US$1378, which represented 25 months of a mid-treatment household income of US$54. The impact on the patient's employment and on overall patient and family income was generally catastrophic: 74% of all respondents reported losing their jobs, 66% of patients lost household income, and household income was reduced by 38%. To help cover the costs, 38% of patients sold some type of property, while 7% leased out property and 41% took out loans, any of which could jeopardize their future financial situation even further. CONCLUSION: Despite services being officially free of charge, most patients incurred catastrophic costs and suffered significant income loss as a result of obtaining diagnosis and treatment for MDR-TB.

Impact of adverse drug reactions on the incremental cost-effectiveness of bedaquiline for drug-resistant tuberculosis.

BACKGROUND: Adverse drug reactions (ADRs) are common during standard, long-course treatment for multidrug-resistant and rifampicin-resistant tuberculosis (MDR-/RR-TB). In particular, second-line injectables (SLIs) are associated with permanent hearing loss, acute renal injury and electrolyte imbalance. We adapted an established Markov model for ambulatory treatment to estimate the impact of the toxicity profile on the incremental cost-effectiveness ratio (ICER) for a proposed MDR-/RR-TB regimen replacing the SLI with bedaquiline (BDQ). METHODS: Treatment effectiveness was evaluated in disability-adjusted life-years (DALYs). Clinical outcomes and ingredient costs from a provider perspective were derived from the South African public-sector treatment program or extracted from the literature. Costs and effectiveness were discounted at 3% per year over 10 years. RESULTS: A BDQ-based MDR-/RR-TB regimen compared with the SLI regimen had a mean ICER of US$516 per DALY averted using the standard Markov model. Costs for both regimens increased and effectiveness decreased for the SLI regimen once adjusted for toxicity. The resulting ICER for the BDQ-based regimen was cost saving (US$96/patient) and more effective (0.96 DALYs averted) after adjusting for ADRs. CONCLUSION: Decision-analysis models of treatment for MDR-/RR-TB, including new drug regimens, should consider the costs of managing ADRs and their sequelae.

Direct costs of managing adverse drug reactions during rifampicin-resistant tuberculosis treatment in South Africa.

OBJECTIVE: To estimate the provider costs of managing adverse drug reactions (ADRs) to standard long-course treatment for multidrug- and rifampicin-resistant tuberculosis (MDR/RR-TB) according to South African guidelines. METHODS: We parameterised a published Markov health state model for MDR/RR-TB with guidelines-based, bottom-up public-sector provider costing of ADR management. Frequency of ADR occurrence was extracted from the literature. Costs were estimated over 10 years, discounted 3% annually and tested using probabilistic sensitivity analysis. RESULTS: On average, guidelines-based costing of moderate ADRs weighted by the frequency of occurrence was US$135.76 (standard deviation [SD] US$17.18) and the cost of serious ADRs was US$521.29 (SD US$55.99). We estimated that the incremental costs of ADR management were US$380.17 annually per patient initiating MDR/RR-TB treatment. The incremental costs of ADR management for the public health sector in South Africa was US$4.76 million, 8.3% of the estimated cohort costs of MDR/RR-TB treatment ($57.55 million) for the 2015 cohort of 12 527 patients. CONCLUSIONS: Management of multiple ADRs and serious ADRs, which are common during the first 6 months of standard, long-course MDR/RR-TB treatment, substantially increases provider treatment costs. These results need to be taken into account when comparing regimen costs, and highlight the urgent need to identify drug regimens with improved safety profiles.

A two-step quality-improvement intervention to address Pap smear quality at public health facilities in South Africa.

BACKGROUND: The endocervical component of a Pap smear is an important indicator of sample quality - or 'adequacy'. However, only 6 of 52 districts in South Africa (SA) meet the Department of Health (DoH) performance benchmark: a 70% adequacy rate. We implemented a quality-improvement (QI) intervention to address suboptimal Pap smear quality in Tshwane District, Gauteng Province, SA. OBJECTIVES: To determine whether training with the wooden Ayre spatula (step 1) or introduction of the cytobroom (step 2) resulted in greater improvements in Pap smear adequacy rates. METHODS: Two Tshwane District health facilities participated in our QI project between May 2016 and February 2017. In step 1, staff received training on the Ayre spatula. In step 2, the spatula was replaced with the cytobroom. Pap smear volumes, adequacy rates and results are reported for the pre-intervention period and after each QI step. We compared adequacy rates using Fisher's exact test, with a significance level of p=0.05. RESULTS: In the pre-intervention period, 304 of 965 Pap smears were deemed adequate (32%; 95% confidence interval (CI) 29 - 35%). After step 1, the proportion increased to 109 of 191 (57%; 95% CI 50 - 64%; p<0.01). Similarly, after step 2, the proportion increased to 155 of 192 (81%; 95% CI 74 - 86%; p<0.01). The proportion of abnormal smears increased from 13% before the QI intervention to 17% after step 1 and 22% after step 2. CONCLUSION: Although training in Pap smear collection using the Ayre spatula resulted in modest improvements in quality, facilities only achieved the DoH benchmark of a 70% adequacy rate after the introduction of the cytobroom.

Persistently high early mortality despite rapid diagnostics for drug-resistant tuberculosis cases in South Africa.

OBJECTIVE: To describe the timing and predictors of mortality among multidrug- and rifampicin-resistant tuberculosis (MDR/RR-TB) patients reported in the South African electronic drug-resistant TB register (EDRweb), 2012-2014. DESIGN: We present time-to-event survival analysis and Cox proportional hazards regression. Identity numbers were matched to the National Vital Statistics Register. RESULTS: Of the 20 653 patients included in the analysis (median age 35 years, interquartile range 28-43), over half were male (n = 10 944, 53.0%). Most were human immunodeficiency virus (HIV) positive (n = 14 174, 68.9%), most of whom were on antiretroviral therapy (ART; n = 12 471, 88.0%). At 24 months, 4689 patients had died (22.7%); 2072 deaths (44.2%) were reported within 12 weeks of initiating treatment for MDR/RR-TB. From week 12 to week 24, there were 717 deaths/18 048 persons; 59.5% of mortality occurred within the first 24 weeks. During the first 12 weeks, the adjusted hazard rate (aHR) for mortality was highest among patients with a missing baseline culture result (aHR 3.78, 95%CI 2.94-4.86) and among HIV-positive, ART-naïve patients (aHR 3.40, 95%CI 2.90-3.99). Patients initiating MDR/RR-TB treatment within 4 weeks of diagnosis had higher mortality than those with delayed initiation (aHR 1.57, 95%CI 1.41-1.75). CONCLUSION: In EDRweb, mortality is highest in the first few weeks after MDR/RR-TB treatment initiation.

Awareness, perceived risk and practices related to cervical cancer and Pap smear screening: A cross-sectional study among HIV-positive women attending an urban HIV clinic in Johannesburg, South Africa.

BACKGROUND: Cervical cancer is a major cause of cancer-related deaths, especially in the context of the HIV epidemic. OBJECTIVE: To examine awareness, perceived risk and practices related to cervical cancer screening among HIV-positive women. METHODS: Interviewer-administered structured questionnaires were administered to HIV-positive women (aged ≥18 years) enrolled in a cervical cancer screening study at the Themba Lethu Clinic, Johannesburg, South Africa, from November 2009 to December 2011. Modified Poisson regression with robust standard errors was used to identify factors at enrolment associated with awareness, perceived risk and adequate practice related to cervical screening. Adjusted relative risks (aRRs) with 95% confidence intervals (CIs) are presented. RESULTS: Of the 1 202 women enrolled, 71.3% and 18.2% were aware of the Pap smear and HPV, respectively. Of the 1 192 participants with data evaluated, 76.5% were worried and 23.5% were not worried about cervical cancer; 28.6% of the women had adequate screening practice. Older age (40 - 49 years or ≥50 years v. 18 - 29 years) (aRR 1.63, 95% CI 1.12 - 2.37; aRR 2.22, 95% CI 1.44 - 3.41), higher education (tertiary v. less than grade 10) (aRR 1.39, 95% CI 1.00 - 1.93), initiation on combination antiretroviral therapy (aRR 1.36, 95% CI 1.00 - 1.85) and awareness of Pap smear screening (aRR 16.18, 95% CI 7.69 - 34.01) were associated with adequate screening practice. CONCLUSIONS: High levels of Pap smear awareness and low levels of Pap smear screening uptake were observed. However, Pap smear awareness was associated with adequate screening practice. More research into effective health education programmes to address these gaps is needed.

International neurocognitive normative study: neurocognitive comparison data in diverse resource-limited settings: AIDS Clinical Trials Group A5271.

Infrastructure for conducting neurological research in resource-limited settings (RLS) is limited. The lack of neurological and neuropsychological (NP) assessment and normative data needed for clinical interpretation impedes research and clinical care. Here, we report on ACTG 5271, which provided neurological training of clinical site personnel and collected neurocognitive normative comparison data in diverse settings. At ten sites in seven RLS countries, we provided training for NP assessments. We collected normative comparison data on HIV- participants from Brazil (n = 240), India (n = 480), Malawi (n = 481), Peru (n = 239), South Africa (480), Thailand (n = 240), and Zimbabwe (n = 240). Participants had a negative HIV test within 30 days before standardized NP exams were administered at baseline and 770 at 6 months. Participants were enrolled in eight strata, gender (female and male), education (<10 and ≥10 years), and age (<35 and ≥35 years). Of 2400 enrolled, 770 completed the 6-month follow-up. As expected, significant between-country differences were evident in all the neurocognitive test scores (p < 0.0001). There was variation between the age, gender, and education strata on the neurocognitive tests. Age and education were important variables for all tests; older participants had poorer performance, and those with higher education had better performance. Women had better performance on verbal learning/memory and speed of processing tests, while men performed better on motor tests. This study provides the necessary neurocognitive normative data needed to build infrastructure for future neurological and neurocognitive studies in diverse RLS. These normative data are a much-needed resource for both clinicians and researchers.

Seroprevalence of HPV vaccine types 6, 11, 16 and 18 in HIV-infected women from South Africa, Brazil and Botswana.

BACKGROUND: Many resource limited settings (RLS) suffer from high rates of both cervical cancer and HIV. Limited HPV serology data are available from RLS; such data could help describe local patterns of HPV infection and predict vaccine efficacy. OBJECTIVES: To determine seropositivity to HPV types 6, 11, 16 and 18 in HIV-infected women from South Africa (SA), Botswana and Brazil. STUDY DESIGN: HPV serotyping for high-risk types 6, 11, 16 and 18 was performed on samples collected from HIV-infected women from 2003-2010 using competitive Luminex Immuno Assay (HPV-4cLIA). We examined the association between seropositivity to these HPV types and country of enrollment, CD4, HIV-1 RNA level, and Pap smear. RESULTS: HPV serology results were available for 487 HIV-infected women (157, 170 and 160 from SA, Botswana and Brazil respectively). Approximately 65% of women had serum antibodies to one of the 4 HPV types and less than 3% of women had antibodies all 4 serotypes. Approximately 30% women demonstrated antibodies to type 16 HPV. Rates of seropositivity to HPV 11, and HPV 16+18 varied significantly between countries. Statistical difference was also shown in women in different age categories in the different countries. There was no difference in serology results compared by CD4 count, HIV viral load or Pap smear results. CONCLUSIONS: These data suggest that the quadrivalent vaccine may be effective in preventing HPV infection in these countries.

Human papillomavirus types in HIV seropositive men with penile warts in Johannesburg, South Africa.

Few data exist regarding the human papillomavirus (HPV) types in penile warts (PW) of HIV-infected men in Africa. Nurses collected penile swabs for HPV typing from 74 HIV-positive men with PW. HPV genotyping was performed using the Roche Linear Array Test. Analysis was performed on data relating to 74 samples. The mean age of the men was 36.0 years and 78.5% (51/65) were uncircumcised. Of the 73/74 validated results, all tested positive for HPV; 42.5% (31/73) and 32.9% (24/73) had HPV types 6 and 11, respectively. 84.9% of men tested positive for any oncogenic type: 20/73 (27.4%) were positive for type 16, 11/73 (15.1%) were positive for type 18 and 8/73 (11.0%) men had both types. Our study shows a high prevalence (68.5%) of HPV type 6 and/or 11 in this male population with PW. Given the poor availability of treatment, a quadrivalent vaccine for men may have significant benefit.

Tree-Based Methods for Discovery of Association between Flow Cytometry Data and Clinical Endpoints.

We demonstrate the application and comparative interpretations of three tree-based algorithms for the analysis of data arising from flow cytometry: classification and regression trees (CARTs), random forests (RFs), and logic regression (LR). Specifically, we consider the question of what best predicts CD4 T-cell recovery in HIV-1 infected persons starting antiretroviral therapy with CD4 count between 200 and 350 cell/muL. A comparison to a more standard contingency table analysis is provided. While contingency table analysis and RFs provide information on the importance of each potential predictor variable, CART and LR offer additional insight into the combinations of variables that together are predictive of the outcome. In all cases considered, baseline CD3-DR-CD56+CD16+ emerges as an important predictor variable, while the tree-based approaches identify additional variables as potentially informative. Application of tree-based methods to our data suggests that a combination of baseline immune activation states, with emphasis on CD8 T-cell activation, may be a better predictor than any single T-cell/innate cell subset analyzed. Taken together, we show that tree-based methods can be successfully applied to flow cytometry data to better inform and discover associations that may not emerge in the context of a univariate analysis.

Nitric oxide and superoxide in cultured cells: limited production and influence on DNA synthesis.

The ability of superoxide (O2-) and NO to influence DNA synthesis, as estimated by [3H]thymidine incorporation in logarithmically growing cells, was evaluated in three human cell types: embryonic lung fibroblasts, skin fibroblasts, and mesangial cells. Nontoxic rates of O2- generation (0.2 nM/min-0.2 microM/min) only slightly stimulated DNA synthesis in mesangial cells (10-13% increase) and did not affect fibroblast DNA synthesis. Nontoxic rates of NO generation (0.1-10 microM/min) also had only limited effects, inhibiting DNA synthesis in lung and skin fibroblasts slightly (10-20% decrease) but not affecting mesangial cells. In all three cell types, neither O2- nor NO was generated at high enough endogenous rates to support an autocrinic regulation of DNA synthesis. This and other lines of evidence indicate that a reaction between O2- and NO is unlikely to account for their opposing effects on DNA synthesis.

Regional localization of chromosome 3-specific DNA fragments by using a hybrid cell deletion mapping panel.

A series of human chromosome 3-specific DNA fragments isolated and characterized from a lamda phage genomic library were regionally localized on human chromosome 3. This was accomplished using filter hybridization blot analysis of a human chromosome 3 hybrid cell deletion mapping panel. Twenty-three new anonymous DNA fragments were assigned to one of four physical regions of chromosome 3. Seventeen DNA fragments were mapped to the long arm of chromosome 3, including one DNA fragment that demonstrated a restriction fragment length polymorphism (RFLP). Five DNA fragments were assigned to 3p14.2----pter, including one highly polymorphic fragment sublocalized at 3p25----pter by in situ hybridization. This DNA fragment is the second reported distal 3p polymorphic probe. One DNA fragment was localized to 3p14----p14.2. In addition, three fragments previously assigned to chromosome 3 were confirmed. Polymorphic DNA probes DNF15S2 (formerly D1S1) and D3S2 were mapped to 3p14.2----pter. The previous 3p25 in situ localization of the c-raf-1 oncogene was supported by deletion panel mapping. The physical localization of these twenty-three new DNA fragments has more than doubled the number of cloned DNA fragments assigned to chromosome 3. These and future regional assignments of DNA fragment probes will facilitate construction of both a physical and genetic linkage map of chromosome 3. They may also be useful in characterizing the chromosomal and molecular aberrations involved in small-cell lung cancer (SCLC), renal cell carcinoma, other malignancies, and the 3p14.2 common fragile site.