Lessons learnt conducting minimally invasive autopsies in private mortuaries as part of HIV and tuberculosis research in South Africa

Current estimates of the burden of tuberculosis (TB) disease and cause-specific mortality in human immunodeficiency virus (HIV) positive people rely heavily on indirect methods that are less reliable for ascertaining individual-level causes of death and on mathematical models. Minimally invasive autopsy (MIA) is useful for diagnosing infectious diseases, provides a reasonable proxy for the gold standard in cause of death ascertainment (complete diagnostic autopsy) and, used routinely, could improve cause-specific mortality estimates. From our experience in performing MIAs in HIV-positive adults in private mortuaries in South Africa (during the Lesedi Kamoso Study), we describe the challenges we faced and make recommendations for the conduct of MIA in future studies or surveillance programmes, including strategies for effective communication, approaches to obtaining informed consent, risk management for staff and efficient preparation for the procedure.

What causes symptoms suggestive of tuberculosis in HIV-positive people with negative initial investigations?

OBJECTIVE:

To identify the causes of symptoms suggestive of tuberculosis (TB) among people living with the human immunodeficiency virus (PLHIV) in South Africa.

METHODS:

A consecutive sample of HIV clinic attendees with symptoms suggestive of TB (⩾1 of cough, weight loss, fever or night sweats) at enrolment and at 3 months, and negative initial TB investigations, were systematically evaluated with standard protocols and diagnoses assigned using standard criteria. TB was ‘confirmed’ if Mycobacterium tuberculosis was identified within 6 months of enrolment, and ‘clinical’ if treatment started without microbiological confirmation.

RESULTS:

Among 103 participants, 50/103 were preantiretroviral therapy (ART) and 53/103 were on ART; respectively 68% vs. 79% were female; the median age was 35 vs. 45 years; the median CD4 count was 311 vs. 508 cells/mm³. Seventy-two (70%) had ⩾5% measured weight loss and 50 (49%) had cough. The most common final diagnoses were weight loss due to severe food insecurity (n = 20, 19%), TB (n = 14, 14%: confirmed n = 7; clinical n = 7), other respiratory tract infection (n = 14, 14%) and post-TB lung disease (n = 9, 9%). The basis for TB diagnosis was imaging (n = 7), bacteriological confirmation from sputum (n = 4), histology, lumbar puncture and other (n = 1 each).

CONCLUSION:

PLHIV with persistent TB symptoms require further evaluation for TB using all available modalities, and for food insecurity in those with weight loss.

Isoniazid preventive therapy use among patients on antiretroviral therapy: a missed opportunity

Isoniazid preventive therapy (IPT) with antiretroviral therapy (ART) reduces incident tuberculosis among patients infected with the human immunodeficiency virus. We describe IPT use among patients on ART at two primary care clinics in South Africa. Of 597 participants interviewed, 100 (16.8%) reported IPT use; 73.4% (365/497) with no reported IPT use were eligible for IPT. IPT use was associated with age <35 years (aOR 1.90, 95%CI 1.18-3.06), and receiving care at one clinic as opposed to the other (aOR 4.72, 95%CI 2.69-7.93). The high proportion of patients on ART eligible for IPT represents a missed opportunity for IPT scale-up.

Spectrum of non-tuberculous mycobacteria identified using standard biochemical testing vs. 16S sequencing

Non-tuberculous mycobacterial isolates from gold miners were speciated using standard biochemical testing (SBT) and 16S rDNA sequencing. Of 237 isolates tested, SBT identified 126, compared with all 237 identified using sequencing. Of 111 isolates unspeciated by SBT but identified by sequencing, 38 (34.2%) were identified as Mycobacterium gordonae and 8 (7.2%) were new species. Of 126 isolates speciated by both methods, 37 were discordant, with 14/17 M. gordonae isolates incorrectly identified as M. scrofulaceum using SBT. The majority of these were the potentially pathogenic strain D, M. gordonae. Sequencing is preferable where available to guide treatment.

Trends in drug-resistant tuberculosis in a gold-mining workforce in South Africa, 2002-2008

SETTING AND OBJECTIVE

To describe trends in drug-resistant tuberculosis (TB) in two gold-mining workforces, South Africa, 2002-2008.

DESIGN

TB programme data analysis.

RESULTS

TB case notification rates decreased between 2002 and 2008 from 4006 to 3018 per 100,000 and from 3192 to 2468/100,000 for Companies A and B, respectively. Human immunodeficiency virus (HIV) prevalence exceeded 80% in TB episodes with known status. The proportion of TB episodes with multidrug-resistant TB (MDR-TB) increased from 6/129 (4.7%) to 17/85 (20.0%) among previously treated cases, and from 4/38 (10.4%) to 7/28 (25.0%) in Companies A and B, respectively (tests for trend, Company A, P < 0.001; Company B, P = 0.304). Case notifications of MDR-TB increased during 2002-2008 from 39.8 to 122.9/100,000/year in Company A and from 7.8 to 96.8/100,000/year in Company B. Coverage of second-line drug susceptibility testing (DST) among MDR-TB episodes was low. Previous treatment exposure was a strong risk factor for MDR-TB (prevalence ratio 8.78, 95%CI 5.94-12.97 in previously treated vs. untreated individuals).

CONCLUSION

Despite decreasing TB notifications overall, MDR-TB notifications and proportions of episodes with MDR-TB increased in the larger company. Cure must be ensured in first episodes to prevent acquired resistance. Improved coverage of culture, DST and HIV testing is required to allow treatment to be optimised.

Liquid vs. solid culture for tuberculosis: performance and cost in a resource-constrained setting

SETTING

National Health Laboratory Services tuberculosis (TB) laboratory, South Africa.

OBJECTIVES

To compare Mycobacterium Growth Indicator Tube (MGIT) with Löwenstein-Jensen (LJ) medium with regard to Mycobacterium tuberculosis yield, time to positive culture and contamination, and to assess MGIT cost-effectiveness.

DESIGN

Sputum from gold miners was cultured on MGIT and LJ. We estimated cost per culture, and, for smear-negative samples, incremental cost per additional M. tuberculosis gained with MGIT using a decision-tree model.

RESULTS

Among 1267 specimens, MGIT vs. LJ gave a higher yield of mycobacteria (29.7% vs. 22.8%), higher contamination (16.7% vs. 9.3%) and shorter time to positive culture (median 14 vs. 25 days for smear-negative specimens). Among smear-negative samples that were culture-positive on MGIT but negative/contaminated on LJ, 77.3% were non-tuberculous mycobacteria (NTM). Cost per culture on LJ, MGIT and MGIT+LJ was respectively US$12.35, US$16.62 and US$19.29. The incremental cost per additional M. tuberculosis identified by standard biochemical tests and microscopic cording was respectively US$504.08 and US$328.10 using MGIT vs. LJ, or US$160.80 and US$$109.07 using MGIT+LJ vs. LJ alone.

CONCLUSION

MGIT gives higher yield and faster results at relatively high cost. The high proportion of NTM underscores the need for rapid speciation tests. Minimising contaminated cultures is key to cost-effectiveness.

Clonal expansion of a globally disseminated lineage of Mycobacterium tuberculosis with low IS6110 copy numbers

Knowledge of the clonal expansion of Mycobacterium tuberculosis and accurate identification of predominant evolutionary lineages in this species remain limited, especially with regard to low-IS6110-copy-number strains. In this study, 170 M. tuberculosis isolates with </=6 IS6110 insertions identified in Cape Town, South Africa, were characterized by principal genetic grouping, restriction fragment length polymorphism analysis, spoligotyping, IS6110 insertion site mapping, and variable-number tandem repeat (VNTR) typing. These analyses indicated that all but one of the isolates analyzed were members of principal genetic group 2 and of the same low-IS6110-copy-number lineage. The remaining isolate was a member of principal genetic group 1 and a different low-IS6110-copy-number lineage. Phylogenetic reconstruction suggests clonal expansion through sequential acquisition of additional IS6110 copies, expansion and contraction of VNTR sequences, and the deletion of specific direct-variable-repeat sequences. Furthermore, comparison of the genotypic data of 91 representative low-IS6110-copy-number isolates from Cape Town, other southern African regions, Europe, and the United States suggests that certain low-IS6110-copy-number strain spoligotypes and IS6110 fingerprints were acquired in the distant past. These clones have subsequently become widely disseminated and now play an important role in the global tuberculosis epidemic.

Dysentery in patients infected with human immunodeficiency virus in Zimbabwe: an emerging role for Schistosoma mansoni and Escherichia coli O157?

Information on bloody diarrhoea in HIV-positives is scarce. A prospective study was therefore performed, in Zimbabwe, to determine and compare the pathogens associated with bloody diarrhoea in 25 antiretroviral-naïve HIV-infected patients and 15 non-HIV-infected patients. Stool cultures and colonic biopsies were performed. Shigella was isolated from 18 (45%) of the subjects, Schistosoma mansoni from eight (16%), Escherichia coli H7:O157 from three (8%) and Campylobacter jejunii from two (5%). There was no evidence of Salmonella, Entamoeba histolytica or cytomegalovirus infection. Shigella dysenteriae type-1 occurred more often in the HIV-negatives than the HIV-positives (P = 0.02). Although HIV-associated bloody diarrhoea in Zimbabwe appears to be most frequently caused by Shigella, it may also be commonly the result of infection with Sc. mansoni or shiga-toxin-producing E. coli. A larger study specifically to examine the role of Sc. mansoni and E. coli O157 is warranted.

TB infection: an exploratory study of BCG protective properties and the possible role of environmental mycobacteria

OBJECTIVE

To evaluate the presence of environmental mycobacterial strains and explore the implications for BCG vaccination against TB.

DESIGN

Multimethod approach which included structured interviews and medical records examination. Soil and water samples were analysed using standard microbiology methods.

SETTING

Beatrice Infectious Diseases Hospital, Public Health laboratories, University of Zimbabwe Medical School and several residential areas in Harare.

SUBJECTS

129 tuberculosis inpatients at Beatrice Infectious Diseases Hospital, 26 Public Health Laboratory technicians handling TB specimens and 51 fourth year medical students.

MAIN OUTCOME MEASURES

Vaccination status of TB inpatients, medical students and laboratory technicians, protective efficacy of BCG in all subjects, presence of environmental mycobacterium in the environment.

RESULTS

The type of tuberculosis did not differ significantly between vaccinated and non-vaccinated TB patients x2(df = 1) = 0.171 p > 0.05. There was no apparent difference between the revaccinated and non-vaccinated laboratory technicians. One respondent out of each of the revaccinated and non-vaccinated laboratory technicians had developed pulmonary tuberculosis. Among the fourth year medical students, four had positive tuberculin test results, even though they had not been vaccinated at the University clinic. Environmental mycobacteria presumptively identified as Mycobacterium scrofulaceum and Mycobacterium intracellulare were isolated from both the water and soil samples taken from a few selected areas in Harare. Of the 129 TB in-patients, 88 (68.2%) had previously been vaccinated against TB. Similarly among the 51 medical students 44(86.3%) had been vaccinated. Laboratory technicians re-vaccinated on the job were nine out of 26.

CONCLUSION

The results obtained seemed to indicate that BCG protective efficacy did wane with time and revaccination appeared not to be useful. Environmental mycobacterium that could influence the BCG efficacy do exist in our environment.