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1.  Innate Antibacterial Activity in Female Genital Tract Secretions Is Associated with Increased Risk of HIV Acquisition 
AIDS Research and Human Retroviruses  2015;31(11):1153-1159.
Abstract
Greater inhibitory activity against Escherichia coli and levels of human β defensin (HBD)-2 in genital tract secretions predicted HIV acquisition in women in the HPTN 035 trial. We investigated whether higher levels of E. coli inhibitory activity and antimicrobial peptides in cervicovaginal lavage (CVL) samples predicted HIV acquisition in women in the CAPRISA 002 Acute Infection Study. E. coli inhibitory activity and antimicrobial peptides were quantified in CVL from a subset of CAPRISA 002 participants who did not seroconvert (n=39) and from seroconverting women prior to infection (n=17) and during acute infection (n=11). Women who acquired HIV had significantly greater preinfection CVL E. coli inhibitory activity (p=0.01) and HBD-1 levels (p=0.02) compared to women who remained uninfected. Preinfection E. coli inhibitory activity remained significantly associated with seroconversion following adjustment for the presence of bacterial vaginosis (OR 1.45; 95% CI 1.07, 1.97). Partial least squares discriminant analysis confirmed that preinfection CVL E. coli inhibitory activity, together with higher CVL concentrations of HBD-1 and secretory leukocyte protease inhibitor, distinguished seroconverters from nonseroconverters with 67% calibration accuracy. CVL concentrations of human neutrophil peptides (HNP) 1–3 increased significantly with acute infection (p=0.001) and correlated with plasma viral set point (r=0.66, p=0.03). E. coli inhibitory activity in genital tract secretions could provide a biomarker of HIV risk. The correlation between HNP 1–3 and viral set point merits further investigation of the relationship between mucosal inflammation during early HIV infection and disease progression.
doi:10.1089/aid.2015.0011
PMCID: PMC4651017  PMID: 26061218
2.  Genomic and functional analyses of Mycobacterium tuberculosis strains implicate ald in D-cycloserine resistance 
Nature genetics  2016;48(5):544-551.
A more complete understanding of the genetic basis of drug resistance in Mycobacterium tuberculosis is critical for prompt diagnosis and optimal treatment, particularly for toxic second-line drugs like D-cycloserine. Here, we used whole-genome sequences from 498 strains of M. tuberculosis to identify novel resistance-conferring genotypes. By combining association and correlated evolution tests with strategies for amplifying signal from rare variants, we found that loss-of-function mutations in ald (Rv2780), encoding L-alanine dehydrogenase, were associated with unexplained drug resistance. Convergent evolution of this loss-of-function was observed exclusively among multidrug-resistant strains. Drug susceptibility testing established that ald loss-of-function conferred resistance to D-cycloserine, and susceptibility to the drug was partially restored by complementation of ald. Clinical strains with mutations in ald and alr exhibited increased resistance to D-cycloserine when cultured in vitro. Incorporation of D-cycloserine resistance in novel molecular diagnostics could allow for targeted utilization of this toxic drug among patients with susceptible infections.
doi:10.1038/ng.3548
PMCID: PMC4848111  PMID: 27064254
3.  Sequential Immunization with gp140 Boosts Immune Responses Primed by Modified Vaccinia Ankara or DNA in HIV-Uninfected South African Participants 
PLoS ONE  2016;11(9):e0161753.
Background
The safety and immunogenicity of SAAVI DNA-C2 (4 mg IM), SAAVI MVA-C (2.9 x 109 pfu IM) and Novartis V2-deleted subtype C gp140 (100 mcg) with MF59 adjuvant in various vaccination regimens was evaluated in HIV-uninfected adults in South Africa.
Methods
Participants at three South African sites were randomized (1:1:1:1) to one of four vaccine regimens: MVA prime, sequential gp140 protein boost (M/M/P/P); concurrent MVA/gp140 (MP/MP); DNA prime, sequential MVA boost (D/D/M/M); DNA prime, concurrent MVA/gp140 boost (D/D/MP/MP) or placebo. Peak HIV specific humoral and cellular responses were measured.
Results
184 participants were enrolled: 52% were female, all were Black/African, median age was 23 years (range, 18–42 years) and 79% completed all vaccinations. 159 participants reported at least one adverse event, 92.5% were mild or moderate. Five, unrelated, serious adverse events were reported. The M/M/P/P and D/D/MP/MP regimens induced the strongest peak neutralizing and binding antibody responses and the greatest CD4+ T-cell responses to Env. All peak neutralizing and binding antibody responses decayed with time. The MVA, but not DNA, prime contributed to the humoral and cellular immune responses. The D/D/M/M regimen was poorly immunogenic overall but did induce modest CD4+ T-cell responses to Gag and Pol. CD8+ T-cell responses to any antigen were low for all regimens.
Conclusions
The SAAVI DNA-C2, SAAVI MVA-C and Novartis gp140 with MF59 adjuvant in various combinations were safe and induced neutralizing and binding antibodies and cellular immune responses. Sequential immunization with gp140 boosted immune responses primed by MVA or DNA. The best overall immune responses were seen with the M/M/P/P regimen.
Trial Registration
ClinicalTrials.gov NCT01418235
doi:10.1371/journal.pone.0161753
PMCID: PMC5008759  PMID: 27583368
4.  Design, synthesis, and characterization of (1-(4-aryl)- 1H-1,2,3-triazol-4-yl)methyl, substituted phenyl-6-methyl-2-oxo-1,2,3,4-tetrahydropyrimidine-5-carboxylates against Mycobacterium tuberculosis 
The novel (1-(4-aryl)-1H-1,2,3-triazol-4-yl)methyl, substituted phenyl-6-methyl-2-oxo-1,2,3,4-tetrahydropyrimidine-5-carboxylate derivatives were synthesized by the click reaction of the dihydropyrimidinones, bearing a terminal alkynyl group, with various substituted aryl azides at room temperature using a catalytic amount of Cu(OAc)2 and sodium ascorbate in a 1:2 ratio of acetone and water as a solvent. The newly synthesized compounds were characterized by a number of spectroscopic techniques, such as infrared, liquid chromatography-mass spectrometry, 1H, and 13C nuclear magnetic resonance along with single crystal X-ray diffraction. The current procedure for the synthesis of 1,2,3-triazole hybrids with dihydropyrimidinones is appropriate for the synthesis of a library of analogs 7a-l and the method accessible here is operationally simple and has excellent yields. The title compounds 7a-l were evaluated for their in vitro antitubercular activity against H37RV and multidrug-resistant strains of Mycobacterium tuberculosis by resazurin microplate assay plate method and it was found that compound 7d was promising against H37RV and multidrug-resistant strains of M. tuberculosis at 10 and 15 μg/mL, respectively.
doi:10.2147/DDDT.S109760
PMCID: PMC5003518  PMID: 27601885
1; 2; 3-triazole; dihydropyrimidinone; click chemistry; antitubercular drug discovery; synthesis
5.  Primary capreomycin resistance is common, and associated with early mortality in extensively drug-resistant tuberculosis (XDR-TB) patients in KwaZulu-Natal, South Africa 
Background
Capreomycin is a key antimycobacterial drug in treatment of extensively drug-resistant tuberculosis (XDR-TB). Drug susceptibility testing (DST) for capreomycin is not routinely performed in newly diagnosed XDR-TB in South Africa. We performed this study to assess the prevalence, clinical significance, and molecular epidemiology of capreomycin resistance in newly diagnosed XDR-TB patients in KwaZulu-Natal, South Africa.
Methods
Retrospective cohort study of consecutive XDR-TB patients admitted to a TB referral hospital without prior XDR-TB treatment. A subset of isolates had extended DST (including capreomycin), mutational analysis and IS6110 restriction fragment length polymorphism (RFLP) assays.
Results
216 eligible XDR-TB patients were identified. The majority were treated with capreomycin (72%), were young (median age 35.5) and female (56%). 165 (76%) were HIV+, and 109 (66%) were on antiretroviral therapy. A subset of 52 patients had full DST. 47/52 (90.4%) XDR-TB patients were capreomycin resistant. Capreomycin-resistant patients experienced worse mortality and culture conversion than capreomycin susceptible though this difference was not statistically significant. The A1401G mutation in the rrs gene was associated with capreomycin resistance. The majority of capreomycin resistant strains were F15/LAM4/KZN lineage (80%), and clustering was common in these isolates (92.5%).
Conclusions
Capreomycin resistance is common in patients with XDR-TB in KwaZulu-Natal, is predominantly due to ongoing province-wide transmission of a highly resistant strain, and is associated with high mortality. Capreomycin should be included in routine DST in all XDR-TB patients. New drug regimens that do not include injectable agents should be operationally tested as empiric treatment in XDR-TB.
doi:10.1097/QAI.0000000000000650
PMCID: PMC4501864  PMID: 25886924
extensively drug-resistant tuberculosis (XDR-TB); capreomycin resistance; South Africa; drug susceptibility testing
6.  Lower concentrations of chemotactic cytokines and soluble innate factors in the lower female genital tract associated with use of injectable hormonal contraceptive 
Progesterone-based injectable hormonal contraceptives (HCs) potentially modulate genital barrier integrity and regulate the innate immune environment in the female genital tract, thereby enhancing risk for STIs or HIV infection. We investigated the effects of injectable HC use on concentrations of inflammatory cytokines and other soluble factors associated with genital epithelial repair and integrity. The concentrations of 42 inflammatory, regulatory, adaptive, growth factors and hematopoetic cytokines, five matrix metalloproteinases (MMPs), and four tissue inhibitors of metalloproteinases (TIMPs) were measured in cervicovaginal lavages (CVLs) from 64 HIV negative women using injectable HCs and 64 control women not using any HCs, in a matched case-control study. There were no differences between groups in the prevalence of bacterial vaginosis (BV; nugent score ≥7), or common sexually transmitted infections (STIs). In multivariate analyses adjusting for condom use, sex work status, marital status, BV and STIs, median concentrations of chemokines (eotaxin, MCP-1, MDC), adaptive cytokines (IL-15), growth factors (PDGF-AA) and a metalloproteinase (TIMP-2) were significantly lower in CVLs from women using injectable HCs than controls. In addition, pro-inflammatory cytokine IL-12p40 and chemokine fractalkine were less likely to have detectable levels in women using injectable HCs compared to those not using HCs. We conclude that injectable HC use was associated with an immunosuppressive female genital tract innate immune profile. While the relationship between injectable HC use and STI or HIV risk is yet to be resolved, our data suggest that injectable HCs effects were similar between STI positive and STI negative participants.
doi:10.1016/j.jri.2015.03.007
PMCID: PMC4779161  PMID: 25956139
hormonal contraceptives; DMPA; Net-EN; cytokines; MMP; TIMP
7.  Risk factors for HIV acquisition in high risk women in a generalised epidemic setting 
AIDS and behavior  2015;19(7):1305-1316.
In South Africa young women bear a disproportionate burden of HIV infection however, risk factors for HIV acquisition are not fully understood in this setting. In a cohort of 245 women, we used proportional hazard regression analysis to examine the association of demographic, clinical and behavioural characteristics with HIV acquisition. The overall HIV incidence rate (IR) was 7.20 per 100 women years (wy), 95% Confidence Interval (CI) 4.50–9.80]. Women 18–24 years had the highest HIV incidence [IR 13.20 per 100 wy, 95% CI 6.59–23.62] and were almost three times more likely to acquire HIV compared to women 25 years and older [adjusted Hazard Ratio (aHR) 2.61, 95% CI 1.05–6.47]. Similarly, women in relationships with multiple sex partners had more than twice the risk of acquiring HIV when compared to women who had no partner or who had a husband or stable partner (aHR 2.47, 95% CI 0.98–6.26). HIV prevention programmes must address young women's vulnerability and sex partner reduction in this setting.
doi:10.1007/s10461-015-1002-5
PMCID: PMC4506252  PMID: 25662962
Risk factors; HIV acquisition; women
8.  Demonstrating the Efficacy of the FoneAstra Pasteurization Monitor for Human Milk Pasteurization in Resource-Limited Settings 
Breastfeeding Medicine  2015;10(2):107-112.
Abstract
Human milk provides crucial nutrition and immunologic protection for infants. When a mother's own milk is unavailable, donated human milk, pasteurized to destroy bacteria and viruses, is a lifesaving replacement. Flash-heat pasteurization is a simple, low-cost, and commonly used method to make milk safe, but currently there is no system to monitor milk temperature, which challenges quality control. FoneAstra, a smartphone-based mobile pasteurization monitor, removes this barrier by guiding users through pasteurization and documenting consistent and safe practice. This study evaluated FoneAstra's efficacy as a quality control system, particularly in resource-limited settings, by comparing bacterial growth in donor milk flash-heated with and without the device at a neonatal intensive care unit in Durban, South Africa.
Materials and Methods: For 100 samples of donor milk, one aliquot each of prepasteurized milk, milk flash-heated without FoneAstra, and milk pasteurized with FoneAstra was cultured on routine agar for bacterial growth. Isolated bacteria were identified and enumerated.
Results: In total, 300 samples (three from each donor sample) were analyzed. Bacterial growth was found in 86 of the 100 samples before any pasteurization and one of the 100 postpasteurized samples without FoneAstra. None of the samples pasteurized using FoneAstra showed bacterial growth.
Conclusions: Both pasteurization methods were safe and effective. FoneAstra, however, provides the additional benefits of user-guided temperature monitoring and data tracking. By improving quality assurance and standardizing the pasteurization process, FoneAstra can support wide-scale implementation of human milk banks in resource-limited settings, increasing access and saving lives.
doi:10.1089/bfm.2014.0125
PMCID: PMC4352695  PMID: 25668396
9.  Rapid Disease Progression in HIV-1 Subtype C–Infected South African Women 
This study shows that one-third of HIV subtype C–infected women require antiretroviral therapy within 12 months of infection, increasing to 69% if the initiation CD4 count is 500 cells/µL. This has significant implications for program implementation, resource allocation, and HIV prevention.
Background. Whereas human immunodeficiency virus (HIV) subtype B–infected individuals generally progress to AIDS within 8–10 years, limited data exist for other clades, especially from Africa. We investigated rates of HIV disease progression of clade C–infected South African women.
Methods. Prospective seroincidence cohorts in KwaZulu-Natal were assessed for acute HIV infection monthly (n = 245) or every 3 months (n = 594) for up to 4 years. Rapid disease progression was defined as CD4 decline to <350 cells/µL by 2 years postinfection. Serial clinical and laboratory assessments were compared using survival analysis and logistic regression models.
Results. Sixty-two women were identified at a median of 42 days postinfection (interquartile range, 34–59), contributing 282 person-years of follow-up. Mean CD4 count dropped by 39.6% at 3 months and 46.7% at 6 months postinfection in women with preinfection measurements. CD4 decline to <350 cells/µL occurred in 31%, 44%, and 55% of women at 1, 2, and 3 years postinfection, respectively, and to <500 cells/µL in 69%, 79%, and 81% at equivalent timepoints. Predictors of rapid progression were CD4 count at 3 months postinfection (hazard ratio [HR], 2.07; 95% confidence interval [CI], 1.31–3.28; P = .002), setpoint viral load (HR, 3.82; 95% CI, 1.51–9.67; P = .005), and hepatitis B coinfection (HR, 4.54; 95% CI, 1.31–15.69; P = .017). Conversely, presence of any of HLAB*1302, B*27, B*57, B*5801, or B*8101 alleles predicted non–rapid progression (HR, 0.19; 95% CI, .05–.74; P = .016).
Conclusions. Nearly half of subtype C–infected women progressed to a CD4 count <350 cells/µL within 2 years of infection. Implementing 2013 World Health Organization treatment guidelines (CD4 count <500 cells/µL) would require most individuals to start antiretroviral therapy within 1 year of HIV infection.
doi:10.1093/cid/ciu573
PMCID: PMC4271037  PMID: 25038116
HIV disease progression; acute HIV infection; subtype C; viral load; women
10.  The successful use of amphotericin B followed by oral posaconazole in a rare case of invasive fungal sinusitis caused by co-infection with mucormycosis and aspergillus 
IDCases  2015;2(4):116-117.
We report on an unusual case of oro-rhinocerebral disease caused by mucormycosis and aspergillus co-infection in a 54-year-old insulin dependent diabetic patient. Although she was successfully treated with parenteral amphotericin B followed by oral posaconazole, she was left with irreversible blindness of the right eye and multiple cranial nerve palsies.
doi:10.1016/j.idcr.2015.10.001
PMCID: PMC4712212  PMID: 26793475
Mucormycosis; Aspergillus; Co-infection; Amphotericin B; Posaconazole
12.  Evolution of Extensively Drug-Resistant Tuberculosis over Four Decades: Whole Genome Sequencing and Dating Analysis of Mycobacterium tuberculosis Isolates from KwaZulu-Natal 
PLoS Medicine  2015;12(9):e1001880.
Background
The continued advance of antibiotic resistance threatens the treatment and control of many infectious diseases. This is exemplified by the largest global outbreak of extensively drug-resistant (XDR) tuberculosis (TB) identified in Tugela Ferry, KwaZulu-Natal, South Africa, in 2005 that continues today. It is unclear whether the emergence of XDR-TB in KwaZulu-Natal was due to recent inadequacies in TB control in conjunction with HIV or other factors. Understanding the origins of drug resistance in this fatal outbreak of XDR will inform the control and prevention of drug-resistant TB in other settings. In this study, we used whole genome sequencing and dating analysis to determine if XDR-TB had emerged recently or had ancient antecedents.
Methods and Findings
We performed whole genome sequencing and drug susceptibility testing on 337 clinical isolates of Mycobacterium tuberculosis collected in KwaZulu-Natal from 2008 to 2013, in addition to three historical isolates, collected from patients in the same province and including an isolate from the 2005 Tugela Ferry XDR outbreak, a multidrug-resistant (MDR) isolate from 1994, and a pansusceptible isolate from 1995. We utilized an array of whole genome comparative techniques to assess the relatedness among strains, to establish the order of acquisition of drug resistance mutations, including the timing of acquisitions leading to XDR-TB in the LAM4 spoligotype, and to calculate the number of independent evolutionary emergences of MDR and XDR. Our sequencing and analysis revealed a 50-member clone of XDR M. tuberculosis that was highly related to the Tugela Ferry XDR outbreak strain. We estimated that mutations conferring isoniazid and streptomycin resistance in this clone were acquired 50 y prior to the Tugela Ferry outbreak (katG S315T [isoniazid]; gidB 130 bp deletion [streptomycin]; 1957 [95% highest posterior density (HPD): 1937–1971]), with the subsequent emergence of MDR and XDR occurring 20 y (rpoB L452P [rifampicin]; pncA 1 bp insertion [pyrazinamide]; 1984 [95% HPD: 1974–1992]) and 10 y (rpoB D435G [rifampicin]; rrs 1400 [kanamycin]; gyrA A90V [ofloxacin]; 1995 [95% HPD: 1988–1999]) prior to the outbreak, respectively. We observed frequent de novo evolution of MDR and XDR, with 56 and nine independent evolutionary events, respectively. Isoniazid resistance evolved before rifampicin resistance 46 times, whereas rifampicin resistance evolved prior to isoniazid only twice. We identified additional putative compensatory mutations to rifampicin in this dataset. One major limitation of this study is that the conclusions with respect to ordering and timing of acquisition of mutations may not represent universal patterns of drug resistance emergence in other areas of the globe.
Conclusions
In the first whole genome-based analysis of the emergence of drug resistance among clinical isolates of M. tuberculosis, we show that the ancestral precursor of the LAM4 XDR outbreak strain in Tugela Ferry gained mutations to first-line drugs at the beginning of the antibiotic era. Subsequent accumulation of stepwise resistance mutations, occurring over decades and prior to the explosion of HIV in this region, yielded MDR and XDR, permitting the emergence of compensatory mutations. Our results suggest that drug-resistant strains circulating today reflect not only vulnerabilities of current TB control efforts but also those that date back 50 y. In drug-resistant TB, isoniazid resistance was overwhelmingly the initial resistance mutation to be acquired, which would not be detected by current rapid molecular diagnostics employed in South Africa that assess only rifampicin resistance.
Editors' Summary
Background
Tuberculosis (TB)—a contagious bacterial disease that usually infects the lungs—is a global public health problem. Every year, about 9 million people develop active TB disease, and 1.5 million people die from the disease. Mycobacterium tuberculosis, the organism that causes TB, is spread in airborne droplets when people with TB cough. The symptoms of TB include cough, weight loss, and fever. Diagnostic tests for the disease include sputum smear microscopy (microscopic analysis of mucus coughed up from the lungs) and chest X-rays. TB can be cured by taking a regimen of multiple antibiotics daily for 6 mo. However, the emergence of multidrug-resistant tuberculosis (MDR-TB, TB with resistance to both isoniazid and rifampicin) and extensively drug-resistant tuberculosis (XDR-TB, MDR-TB with additional resistance to both quinolones and second-line injectable agents), together with the spread of HIV (which increases susceptibility to TB), is now threatening TB control efforts. MDR-TB is caused by M. tuberculosis strains that have acquired mutations (genetic changes) that make them resistant to isoniazid, rifampicin, and sometimes other anti-TB drugs; XDR-TB is caused by bacteria that are resistant to isoniazid, rifampicin, one or more fluoroquinolones (for example, ofloxacin), and at least one injectable second-line drug (for example, kanamycin).
Why Was This Study Done?
A better understanding of the origins of drug-resistant TB is essential for effective control of TB. Public health experts need to know whether the emergence of drug-resistant TB is caused by inadequacies in TB control or related to other factors such as the spread of HIV and whether new resistant strains of M. tuberculosis repeatedly emerge during XDR-TB outbreaks or whether the transmission of a single drug-resistant strain drives these outbreaks. Here, the researchers use whole genome sequencing and dating analysis to investigate the origin and evolution of an XDR-TB outbreak identified in 2005 in Tugela Ferry, KwaZulu-Natal, South Africa. The predominant strain of XDR M. tuberculosis isolated during this large XDR-TB outbreak belongs to a subfamily called LAM4. Since the outbreak began, XDR-TB has also been reported in hospitals across KwaZulu-Natal, and some of these outbreaks have been caused by bacterial strains not falling within the LAM4 spoligotype (“spoligotyping” characterizes M. tuberculosis strains based on the presence of unique DNA sequences in a specific region of the bacterial genome).
What Did the Researchers Do and Find?
The researchers tested the antibiotic susceptibility of 337 clinical isolates of M. tuberculosis collected in KwaZulu-Natal between 2008 and 2013 and of three historical isolates—two collected in the province in the mid-1990s and a third from the Tugela Ferry XDR outbreak. They sequenced the whole genome of these isolates and used comparative techniques to assess the isolates’ relatedness and to investigate the acquisition of drug resistance. This analysis revealed a 50-member clone of XDR bacteria among the isolates collected across KwaZulu-Natal that was highly related to the LAM4 strain (a clone is defined here as a set of strains in which each member differs by no more than ten single nucleotide polymorphisms [SNPs] from at least one other member; an SNP is a type of genetic variant). Mutations that conferred isoniazid resistance in this clone were acquired in about 1957; MDR and XDR strains emerged in about 1984 and 1995, respectively. The analysis also indicates that MDR and XDR evolved de novo 56 times and nine times, respectively, and that isoniazid resistance nearly always evolved before rifampicin resistance.
What Do These Findings Mean?
These findings provide new information about the ordering and timing of the acquisition of drug-resistance mutations by M. tuberculosis in KwaZulu-Natal but do not necessarily represent the evolution of XDR-TB in other settings. Most notably, these findings indicate that the ancestral precursor of the Tugela Ferry XDR outbreak strain gained resistance to first-line antibiotics shortly after these antibiotics became available for clinical use. Subsequent stepwise accumulation of additional resistance mutations that occurred over decades led to the emergence of MDR and XDR strains. Importantly, the emergence of these strains occurred before the explosion of HIV in KwaZulu-Natal. Thus, these findings highlight the dire repercussions of the failure of historic attempts to control resistance to first-line anti-TB drugs and draw attention to the need for new anti-TB drugs to be used prudently to prevent early fixation of resistance and to protect the useful lifespan of these agents. Finally, the finding that isoniazid resistance is a key initiation event for progression to MDR and XDR suggests that TB control programs should test routinely for both isoniazid and rifampicin resistance to ensure early detection of drug-resistant TB.
Additional Information
This list of resources contains links that can be accessed when viewing the PDF on a device or via the online version of the article at http://dx.doi.org/10.1371/journal.pmed.1001880.
The World Health Organization (WHO) provides information (in several languages) on TB and on MDR-TB; the Global Tuberculosis Report 2014 provides information about TB around the world; a supplement to the report entitled “Drug-Resistant TB—Surveillance and Response” is available
The Stop TB Partnership is working towards TB elimination and provides personal stories about TB (in English and Spanish)
The United States Centers for Disease Control and Prevention provides information about TB and about drug-resistant TB (in English and Spanish)
The US National Institute of Allergy and Infectious Diseases also has detailed information on TB, including a drug-resistant TB visual tour
TB & Me, a collaborative blogging project run by patients being treated for MDR-TB and Mèdecins sans Frontiéres, provides more patient stories
The not-for-profit organization Global Health Education provides information about TB in South Africa
MedlinePlus has links to further information about TB (in English and Spanish)
doi:10.1371/journal.pmed.1001880
PMCID: PMC4587932  PMID: 26418737
13.  Continued Follow-Up of Phambili Phase 2b Randomized HIV-1 Vaccine Trial Participants Supports Increased HIV-1 Acquisition among Vaccinated Men 
PLoS ONE  2015;10(9):e0137666.
Background
The Phase 2b double-blinded, randomized Phambili/HVTN 503 trial evaluated safety and efficacy of the MRK Ad5 gag/pol/nef subtype B HIV-1 preventive vaccine vs placebo in sexually active HIV-1 seronegative participants in South Africa. Enrollment and vaccinations stopped and participants were unblinded but continued follow-up when the Step study evaluating the same vaccine in the Americas, Caribbean, and Australia was unblinded for non-efficacy. Final Phambili analyses found more HIV-1 infections amongst vaccine than placebo recipients, impelling the HVTN 503-S recall study.
Methods
HVTN 503-S sought to enroll all 695 HIV-1 uninfected Phambili participants, provide HIV testing, risk reduction counseling, physical examination, risk behavior assessment and treatment assignment recall. After adding HVTN 503-S data, HIV-1 infection hazard ratios (HR vaccine vs. placebo) were estimated by Cox models.
Results
Of the 695 eligible, 465 (67%) enrolled with 230 from the vaccine group and 235 from the placebo group. 38% of the 184 Phambili dropouts were enrolled. Enrollment did not differ by treatment group, gender, or baseline HSV-2. With the additional 1286 person years of 503-S follow-up, the estimated HR over Phambili and HVTN 503-S follow-up was 1.52 (95% CI 1.08–2.15, p = 0.02, 82 vaccine/54 placebo infections). The HR was significant for men (HR = 2.75, 95% CI 1.49, 5.06, p = 0.001) but not for women (HR = 1.12, 95% CI 0.73, 1.72, p = 0.62).
Conclusion
The additional follow-up from HVTN 503-S supported the Phambili finding of increased HIV-1 acquisition among vaccinated men and strengthened the evidence of lack of vaccine effect among women.
Trial Registration
clinicaltrials.gov NCT00413725
SA National Health Research Database DOH-27-0207-1539
doi:10.1371/journal.pone.0137666
PMCID: PMC4569275  PMID: 26368824
14.  High Prevalence of inhA Promoter Mutations among Patients with Drug-Resistant Tuberculosis in KwaZulu-Natal, South Africa 
PLoS ONE  2015;10(9):e0135003.
Background
Drug-resistant tuberculosis (TB) remains extremely difficult to treat because there are often few remaining active medications and limited diagnostic options to detect resistance. Resistance to isoniazid is typically caused by mutations in either katG or the inhA promoter. inhA mutations confer low-level resistance to isoniazid and cross-resistance to ethionamide while katG mutations confer high-level isoniazid resistance and no cross-resistance. Line Probe Assays (LPAs) that detect mutations in katG and inhA are currently performed on all positive TB cultures in KwaZulu-Natal province, South Africa, but the frequency of inhA mutations in drug-resistant TB patients has not been examined.
Methods
We sought to determine the proportion of patients who could potentially benefit from high-dose isoniazid and who may be resistant to ethionamide. We reviewed 994 LPA (Hain MTBDRplus) results at the TB reference laboratory in KwaZulu-Natal to determine the frequency of mutations in either katG or the inhA promoter. We stratified these results by drug-resistance category (i.e., MDR-TB, pre-XDR-TB, and XDR-TB) as determined by phenotypic drug-susceptibility testing.
Results
Among MDR- and XDR-TB isolates, the prevalence of inhA mutations without a concurrent katG mutation was 14.8% and 10.3% respectively. The prevalence of inhA mutations with OR without a katG mutation was 30.3% and 82.8%, respectively.
Conclusion
More than 10% of patients with MDR- and XDR-TB may benefit from high-dose isoniazid. Although ethionamide is empirically included in all MDR- and XDR-TB regimens, nearly a third of MDR-TB patients and a majority of XDR-TB patients likely have resistance to ethionamide. Laboratories performing line probe assays should report specific band patterns so that clinicians may adjust treatment regimens accordingly.
doi:10.1371/journal.pone.0135003
PMCID: PMC4557915  PMID: 26332235
15.  Impact of Antiretroviral Therapy on Health-Related Quality of Life among South African Women in the CAPRISA 002 Acute Infection Study 
AIDS and behavior  2014;18(9):1801-1807.
Concerns are often raised regarding potentially adverse effects of antiretroviral therapy (ART) on health-related quality of life (HRQoL), but there is limited longitudinal data to prove this. Building on our prior investigation, we examined the impact of ART on HRQoL among HIV-infected South African women with extensive follow-up in the CAPRISA 002 Acute Infection Cohort Study. Overall HRQoL and five sub-domains [physical well-being (PWB), emotional well-being (EWB), functional and global well-being (FGWB), social well-being (SWB) and cognitive functioning (CF)] were assessed using the Functional Assessment of HIV Infection (FAHI) instrument. Our analyses comparing FAHI scores between pre-ART (established infection) and ART phases using paired Wilcoxon signed-rank tests and adjusted mixed-effects regression models revealed improvements on ART in overall HRQoL, and in PWB, EWB, and SWB, but not in FGWB and CF. No long-term adverse impact of ART on HRQoL was detected, providing additional non-biomedical support to early treatment strategies.
doi:10.1007/s10461-014-0800-5
PMCID: PMC4127113  PMID: 24849623
Health-related quality of life; South Africa; Acute HIV infection; Functional assessment of HIV infection; ART
16.  Incidence and Geographic Distribution of Extensively Drug-Resistant Tuberculosis in KwaZulu-Natal Province, South Africa 
PLoS ONE  2015;10(7):e0132076.
South Africa is experiencing a widespread drug-resistant tuberculosis epidemic, although data are limited regarding the current situation. This study finds that the extensively drug-resistant tuberculosis (XDR-TB) incidence in KwaZulu-Natal increased to 3.5 cases/100,000 (776 cases) in 2011-2012. XDR-TB cases are widely distributed geographically, with the majority of districts experiencing a rise in incidence.
doi:10.1371/journal.pone.0132076
PMCID: PMC4493033  PMID: 26147963
17.  Health-Related Quality of Life Dynamics of HIV-positive South African Women up to ART Initiation: Evidence from the CAPRISA 002 Acute Infection Cohort Study 
AIDS and behavior  2014;18(6):1114-1123.
Few studies have investigated the long-term dynamics in health-related quality of life (HRQoL) among HIV-positive persons from acute infection. From 2004, 160 women were enrolled into the CAPRISA 002 Acute Infection study at two sites in the province of KwaZulu-Natal and underwent 3–6 monthly HRQoL assessments using the functional assessment of HIV infection (FAHI) instrument. Overall and 5 sub-scale FAHI scores [physical well-being (PWB), emotional well-being (EWB), functional and global well-being (FGWB), social well-being (SWB) and cognitive functioning (CF)] were calculated up to antiretroviral therapy (ART) initiation and scores at enrollment were compared to the acute, early and established infection phases. Mixed-effects regression models adjusting for behavioral and clinical factors were applied to assess HRQoL trends and the proportion of women meeting minimally important differences was calculated. Our analyses revealed that overall/sub-scale scores improved over time, except from PWB and CF. A higher educational status, contraceptive use and a higher BMI were the strongest predictors of higher overall/sub-scale FAHI scores. CD4 count and HIV viral load were strongly associated with PWB and CF, but not overall FAHI and other sub-scales. Women newly diagnosed with acute HIV infection face profound HRQoL challenges. While early ART delivery may be important for PWB and CF, factors such as education, contraception provision and good nutritional status should be promoted to maximize HRQoL in HIV positive individuals.
doi:10.1007/s10461-013-0682-y
PMCID: PMC4020968  PMID: 24368630
Health-related quality of life; South Africa; Acute HIV infection; Functional assessment of HIV infection
18.  The phase 2b HVTN 503/Phambili study test-of-concept HIV vaccine study, investigating a recombinant adenovirus type 5 HIV gag/pol/nef vaccine in South Africa: unblinded, long-term follow-up 
The Lancet. Infectious diseases  2014;14(5):388-396.
Background
The Phambili study, conducted in South Africa amongst a predominantly heterosexual population, evaluated the efficacy of the MRK Ad5 gag/pol/nef subtype B HIV-1 preventive vaccine. Enrollment and vaccinations were stopped, participants unblinded, and follow-up extended when the Step study evaluating the same vaccine in the Americas, Caribbean and Australia was unblinded for non-efficacy with more HIV infections amongst vaccinee than placebo recipients [ZM1]. Extensive analyses over the complete follow-up period, most of which was unblinded, are reported.
Methods
Phambili participants were HIV-1 uninfected, sexually active men and women aged 18–35 years, followed for 3.5 years. HIV testing and risk reduction counseling occurred at weeks 0, 12, 30 and were switched to a 3 monthly schedule after unblinding. Cox proportional hazards models were used to estimate HIV-1 infection hazard ratios (HR) comparing vaccine to placebo recipients, overall and within subgroups. Long-term vaccine efficacy was evaluated in participants who were unblinded early in follow-up.
Results
Of the 801 participants enrolled (400 vaccine, 401 placebo), 112 (28%) received 1 vaccination, 259 (65%) 2 vaccinations and 29(7%) 3 vaccinations. More infections occurred in vaccinees (n=63) as compared to placebo (n=37) (adjusted HR (vaccine:placebo) 1.70, 95% CI 1.13–2.55, p = 0.01). We found no increase in infections with the number of vaccinations received and that the HRs did not differ by gender, circumcision, or Ad5 serostatus. Differences in risk behavior at baseline or during the study, or differential drop-out (p=0.40) are unlikely explanations for the increased rate of HIV-1 infections seen in vaccinees.
Conclusion
The increased HR of HIV-1 acquisition, irrespective of number of doses received, warrants further investigation to understand the biological mechanism. Further use of the Ad5 vector for HIV vaccines is not warranted
doi:10.1016/S1473-3099(14)70020-9
PMCID: PMC4174314  PMID: 24560541
HIV; rAd5 HIV vaccines; HIV-1 vaccine efficacy studies; South Africa
19.  Posttraumatic Brain Abscess Caused by Aeromonas hydrophila 
Journal of Clinical Microbiology  2014;52(5):1796-1797.
Posttraumatic brain abscesses are usually caused by Gram-negative bacilli, notably Enterobacteriaceae and Staphylococcus aureus. Although Aeromonas hydrophila is a recognized cause of trauma-related sepsis, it has not been previously isolated from posttraumatic brain abscesses. We describe the first case of Aeromonas hydrophila brain abscess.
doi:10.1128/JCM.00267-14
PMCID: PMC3993702  PMID: 24622098
20.  TRIM5α and TRIM22 Are Differentially Regulated According to HIV-1 Infection Phase and Compartment 
Journal of Virology  2014;88(8):4291-4303.
ABSTRACT
The antiviral role of TRIM E3 ligases in vivo is not fully understood. To test the hypothesis that TRIM5α and TRIM22 have differential transcriptional regulation and distinct anti-HIV roles according to infection phase and compartment, we measured TRIM5α, TRIM22, and type I interferon (IFN-I)-inducible myxovirus resistance protein A (MxA) levels in peripheral blood mononuclear cells (PBMCs) during primary and chronic HIV-1 infection, with chronic infection samples being matched PBMCs and central nervous system (CNS)-derived cells. Associations with biomarkers of disease progression were explored. The impact of IFN-I, select proinflammatory cytokines, and HIV on TRIM E3 ligase-specific expression was investigated. PBMCs from individuals with primary and chronic HIV-1 infection had significantly higher levels of MxA and TRIM22 than did PBMCs from HIV-1-negative individuals (P < 0.05 for all comparisons). PBMCs from chronic infection had lower levels of TRIM5α than did PBMCs from primary infection or HIV-1-uninfected PBMCs (P = 0.0001 for both). In matched CNS-derived samples and PBMCs, higher levels of MxA (P = 0.001) and TRIM5α (P = 0.0001) in the CNS were noted. There was a negative correlation between TRIM22 levels in PBMCs and plasma viral load (r = −0.40; P = 0.04). In vitro, IFN-I and, rarely, proinflammatory cytokines induced TRIM5α and TRIM22 in a cell type-dependent manner, and the knockdown of either protein in CD4+ lymphocytes resulted in increased HIV-1 infection. These data suggest that there are infection-phase-specific and anatomically compartmentalized differences in TRIM5α and TRIM22 regulation involving primarily IFN-I and specific cell types and indicate subtle differences in the antiviral roles and transcriptional regulation of TRIM E3 ligases in vivo.
IMPORTANCE Type I interferon-inducible TRIM E3 ligases are a family of intracellular proteins with potent antiviral activities mediated through diverse mechanisms. However, little is known about the contribution of these proteins to antiviral immunity in vivo and how their expression is regulated. We show here that TRIM5α and TRIM22, two prominent members of the family, have different expression patterns in vivo and that the expression pattern depends on HIV-1 infection status and phase. Furthermore, expression differs in peripheral blood versus central nervous system anatomical sites of infection. Only TRIM22 expression correlated negatively with HIV-1 viral load, but gene silencing of both proteins enhances HIV-1 infection of target cells. We report subtle differences in TRIM5α and TRIM22 gene induction by IFN-I and proinflammatory cytokines in CD4+ lymphocytes, monocytes, and neuronal cells. This study enhances our understanding of antiviral immunity by intrinsic antiviral factors and how their expression is determined.
doi:10.1128/JVI.03603-13
PMCID: PMC3993776  PMID: 24478420
21.  Effects of introducing Xpert MTB/RIF test on multi-drug resistant tuberculosis diagnosis in KwaZulu-Natal South Africa 
BMC Infectious Diseases  2014;14:442.
Background
An algorithm instituted following Xpert MTB/RIF (Xpert) introduction in South Africa advocates for treating all Xpert rifampicin resistant patients as MDR-TB cases while awaiting confirmation by phenotypic or genotypic drug susceptibility testing. This study evaluates how the Xpert has influenced the diagnosis and management of drug resistant TB in the highest burdened district of KwaZulu-Natal Province.
Methods
Data was retrospectively collected from all patients with rifampicin resistance on Xpert performed between March 2011 and April 2012. Xpert results were compared with those of phenotypic and/genotypic drug susceptibility testing. Patients’ records were used to determine the time to treatment initiation.
Results
Out of 637 patients tested by Xpert, 50% had confirmatory results, of which a third were sent on the same day as Xpert test. The rate of rifampicin discordance and monoresistance was 8.8% and 13.4% respectively and there was no difference between phenotypic and genotypic confirmation. Among those who had been initiated on treatment, 28%, 40%, 21% and 8% of patients commenced within 2 weeks, 1 month, 2 months and 3 months of Xpert testing respectively, while the remaining 3% were observed without treatment.
Conclusion
This study emphasizes the importance of complying with the algorithm in confirming all Xpert rif resistant cases so as to ensure proper management of these patients. Despite the rapidity of the Xpert results, only about 70% of patients had been initiated treatment at one month. Therefore there is a definite need to improve the health systems in order to improve on these delays.
doi:10.1186/1471-2334-14-442
PMCID: PMC4141089  PMID: 25129689
Xpert; Rifampicin; Resistant; MTB; South Africa
22.  Predictors of HVTN 503 MRK-AD5 HIV-1 gag/pol/nef Vaccine Induced Immune Responses 
PLoS ONE  2014;9(8):e103446.
Background
Phambili, the Merck (MRK)-Adenovirus Type 5 (Ad5) HIV-1 gag/pol/nef subtype B vaccine study, conducted in South Africa, suspended enrollment and vaccination when companion study, Step, was found non-efficacious. Although the vaccine did not prevent HIV-1 infection or lower viral-load setpoint, immune responses recognized clades B and C HIV-1 subtypes. We investigated predictors of the vaccine-induced antigen-specific immune responses.
Methods
Vaccine-induced immunogenicity was ascertained by interferon-γ ELISpot assays on the first 186 enrolled participants receiving two vaccinations. Analyses, stratified by study arm/sex, were performed on baseline demographics [sex, age, Body Mass Index (BMI), site, Adenovirus Type-5 (Ad5) titer, Herpes Simplex Virus Type-2 (HSV2) status, heavy drinking]. Multivariate logistic regression determined predictors.
Results
Of the 186 participants, 53.7% (n = 100) were female, median BMI was 22.5 [IQR: 20.4–27.0], 85.5% (n = 159) were Ad5 seropositive, and 18.8% (n = 35) drank heavily. All vaccine recipients responded to both clade B (n = 87; 47%) and/or C (n = 74; 40%), p = 0.17. In multivariate analysis, female sex [Adjusted Odds Ratio (AOR): 6.478; p = 0.0159], overweight/obese BMI (AOR: 0.186; p = 0.0452), and heavy drinking (AOR: 0.270; p = 0.048) significantly predicted immune response to clade C for any antigens. A marginally significant predictor of clade C-pol antigen was female sex (AOR: 3.182; p = 0.0500).
Conclusions
Sex, BMI, and heavy drinking affected vaccine-induced HIV-1 specific immune responses to clade C antigens. The role of female sex and overweight/obese BMI boosting and suppressing vaccine-induced HIV-1 specific immune responses, respectively, requires elucidation, including any effect on HIV vaccine efficacy, especially in the era of colliding epidemics (HIV and obesity).
doi:10.1371/journal.pone.0103446
PMCID: PMC4121165  PMID: 25090110
23.  Differential Impact of Magnitude, Polyfunctional Capacity, and Specificity of HIV-Specific CD8+ T Cell Responses on HIV Set Point 
Journal of Virology  2014;88(3):1819-1824.
Defining the characteristics of HIV-specific CD8+ T cell responses that lead to viral control is crucial for vaccine development. We evaluated the differential impact of magnitude, polyfunctional capacity, and specificity of the CD8+ response at approximately 6 months postinfection on the viral set point at 12 months in a cohort of HIV-infected individuals. High frequencies of Gag and Nef responses endowed with four functions were the best predictors of a low viral set point.
doi:10.1128/JVI.02968-13
PMCID: PMC3911608  PMID: 24227857
24.  The HVTN503/Phambili HIV vaccine trial: a comparison of younger and older participants 
By comparing younger to older participants enrolled in a HIV vaccine efficacy trial, we aimed to gain insights into the inclusion of adolescents in future trials. This was a sub-analysis of a multisite HIV vaccine randomized clinical trial in South Africa, conducted January-September, 2007. Motivations for trial enrollment, social harms, adverse events, and loss to follow-up were compared between younger (18-20 years old) and older participants (21-35 years old). Both younger (n=238) and older participants (n=563) were equally likely to report enrolling for altruistic reasons. Younger females were less likely than older participants to join for trial reimbursement (p=0.005), while younger males were more likely to enroll because the vaccine may provide protection from HIV-acquisition (p<0.001). There were no significant differences in the number of social harms reported. Compared to males over 20 years-old, 18-20-year-old females were less likely to experience adverse events (OR=0.1, CI 0.01-0.80) and no more likely to be lost to follow up (OR=0.7, CI 0.39-1.25), while 18-20-year-old males were no more likely to experience adverse events (OR=1.3, CI 0.58-2.83) or loss to follow-up (OR=0.8, CI 0.51-1.41). Our data support the inclusion of younger participants who are at risk for HIV in future HIV vaccine efficacy trials.
doi:10.1177/0956462413506892
PMCID: PMC3968181  PMID: 24104693
HIV; vaccine trials; clinical trials; youth; South Africa
25.  Rapid, complex adaption of transmitted HIV-1 full-length genomes in subtype C-infected individuals with differing disease progression 
AIDS (London, England)  2013;27(4):507-518.
Objective(s)
There is limited information on full-length genome sequences and the early evolution of transmitted HIV-1 subtype C viruses, which constitute the majority of viruses spread in Africa. The purpose of this study was to characterize the earliest changes across the genome of subtype C viruses following transmission, to better understand early control of viremia.
Design
We derived the near full-length genome sequence responsible for clinical infection from five HIV subtype C-infected individuals with different disease progression profiles and tracked adaption to immune responses in the first six months of infection.
Methods
Near full-length genomes were generated by single genome amplification and direct sequencing. Sequences were analyzed for amino acid mutations associated with cytotoxic T-lymphocyte (CTL) or antibody (Ab)-mediated immune pressure, and for reversion.
Results
Fifty-five sequence changes associated with adaptation to the new host were identified with 38% attributed to CTL pressure; 35% to antibody pressure; 16% to reversions and the remainder were unclassified. Mutations in CTL epitopes were most frequent in the first 5 weeks of infection, with the frequency declining over time with the decline in viral load. CTL escape predominantly occurred in nef, followed by pol and env. Shuffling/toggling of mutations was identified in 81% of CTL epitopes with only 7% reaching fixation within the six month period.
Conclusions
There was rapid virus adaptation following transmission, predominantly driven by CTL pressure, with most changes occurring during high viremia. Rapid escape and complex escape pathways provide further challenges for vaccine protection.
doi:10.1097/QAD.0b013e32835cab64
PMCID: PMC3720865  PMID: 23370465
HIV-1; Africa; genome; acute infection; cytotoxic T-lymphocytes; progression

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