Nationwide and regional incidence of microbiologically confirmed pulmonary tuberculosis in South Africa, 2004-12 : a time series analysis

BACKGROUND : South Africa has the highest incidence of tuberculosis in the world, largely resulting from a high population prevalence of HIV infection. We investigated the incidence of microbiologically confirmed pulmonary tuberculosis, and new cases of pulmonary tuberculosis registered for treatment, nationally and provincially in South Africa from 2004 to 2012, during which time there were changes in antiretroviral therapy (ART) coverage among individuals with HIV infection. METHODS : We identifi ed cases of microbiologically confi rmed pulmonary tuberculosis from 2004 to 2012 from the National Health Laboratory Service Corporate Data Warehouse. New cases registered for treatment were identifi ed from National Department of Health electronic registries. A time series analysis, using autoregressive models, was undertaken on incidence of microbiologically confi rmed pulmonary disease nationally and provincially; this trend was also examined relative to ART coverage of adults with HIV infection. FINDINGS : During the 9-year period, 3 523 371 cases of microbiologically confirmed pulmonary tuberculosis were recorded nationally. Annual incidence (per 100 000 population) increased from 650 (95% CI 648–652) in 2004 to 848 (845–850) in 2008, declining to 774 (771–776) by 2012 (9% decrease from 2008 to 2012). Incidence varied by age group, sex, and province. There was an inverse association between incidence of microbiologically confirmed disease and ART coverage among HIV-infected individuals nationally and provincially. Trends in incidence of tuberculosis cases registered for treatment mirrored those of microbiologically confirmed cases nationally and provincially; however, incidence of microbiologically confirmed cases was consistently higher than cases registered for treatment nationally and in seven of nine provinces. INTERPRETATION : Since its peak in 2008, the incidence of microbiologically confirmed pulmonary tuberculosis in South Africa had declined by 2012; this decline is associated with an increase in ART coverage. Future integration of registries for microbiologically confirmed cases and new cases registered for treatment would improve the assessment of the burden of pulmonary tuberculosis in South Africa. FUNDING : National Institute for Communicable Diseases: Division of the National Health Laboratory Service, South Africa.SAM has received grants and personal fees from GlaxoSmithKline, Pfizer, and Sanofi Pasteur, and grants from Novartis.http://www.thelancet.com/infectionhb2017Medical Microbiolog

The Epidemiology of Meningitis among Adults in a South African Province with a High HIV Prevalence, 2009-2012.

INTRODUCTION:Meningitis is a major cause of mortality in southern Africa. We aimed to describe the aetiologies and frequencies of laboratory-confirmed fungal and bacterial meningitis among adults in a South African province with an 11% HIV prevalence, over 4 years. METHODS:We conducted a retrospective, observational study of secondary laboratory data, extracted on all cerebrospinal fluid (CSF) specimens submitted to public-sector laboratories in Gauteng province from 2009 through 2012. We calculated cause-specific incidence rates in the general and HIV-infected populations and used Poisson regression to determine if trends were significant. RESULTS:We identified 11,891 (10.7%) incident cases of meningitis from 110,885 CSF specimens. Cryptococcal meningitis, tuberculous meningitis and pneumococcal meningitis accounted for 62.3% (n = 7,406), 24.6% (n = 2,928) and 10.1% (n = 1,197) of cases over the four-year period. The overall incidence (cases per 100,000 persons) of cryptococcal meningitis declined by 23% from 24.4 in 2009 to 18.7 in 2012 (p <0.001) and decreased by 19% among HIV-infected persons from 178.2 to 144.7 (p <0.001). Tuberculous meningitis decreased by 40% from 11.3 in 2009 to 6.8 in 2012 (p <0.001) and decreased by 36% among HIV-infected persons from 54.4 to 34.9 (p <0.001). Pneumococcal meningitis decreased by 41% from 4.2 in 2009 to 2.5 in 2012 (p <0.001) and decreased by 38% among HIV-infected persons from 28.0 to 17.5 (p <0.001). Among cases of other bacterial meningitis (248/11,891, 2.1%), Neisseria meningitidis (n = 93), Escherichia coli (n = 72) and Haemophilus influenzae (n = 20) were the most common organisms identified. CONCLUSIONS:In this high HIV-prevalence province, cryptococcal meningitis was the leading cause of laboratory-confirmed meningitis among adults. Over a 4-year period, there was a significant decrease in incidence of cryptococcal, tuberculous and pneumococcal meningitis. This coincided with expansion of the national antiretroviral treatment programme, enhanced tuberculosis control programme and routine childhood immunisation with pneumococcal conjugate vaccines

Number and percentage of major pathogenic organisms isolated from all CSF specimens tested, as recorded in the NHLS CDW, in Gauteng province, South Africa, by year 2009 through 2012 (n = 11,891).

<p>Number and percentage of major pathogenic organisms isolated from all CSF specimens tested, as recorded in the NHLS CDW, in Gauteng province, South Africa, by year 2009 through 2012 (n = 11,891).</p

Population incidence of cryptococcal, tuberculous and pneumococcal meningitis among adults in Gauteng province, South Africa, showing key treatment interventions, 2009–2012 (n = 11,531).

<p>PCV-7 = seven-valent pneumococcal conjugate vaccine introduction. PCV-13 = thirteen-valent pneumococcal conjugate vaccine introduction. GeneXpert = GeneXpert MTB/Rif assay introduction. CrAg screening = introduction of cryptococcal antigen screening and treatment intervention.</p

Demographic characteristics of patients with laboratory-confirmed fungal and bacterial meningitis in Gauteng province, South Africa, 2009 through 2012 (n = 11,891).

<p>Demographic characteristics of patients with laboratory-confirmed fungal and bacterial meningitis in Gauteng province, South Africa, 2009 through 2012 (n = 11,891).</p

Incidence of cryptococcal meningitis and pneumococcal meningitis, by age group and gender, 2012.

<p>CM = cryptococcal meningitis, PM = pneumococcal meningitis.</p