Predominance of modern Mycobacterium tuberculosis strains and active transmission of Beijing sublineage in Jayapura, Indonesia Papua.

Mycobacterium tuberculosis genotype distribution is different between West and Central Indonesia, but there are no data on the most Eastern part, Papua. We aimed to identify the predominant genotypes of M. tuberculosis responsible for tuberculosis in coastal Papua, their transmission, and the association with patient characteristics. A total of 199 M. tuberculosis isolates were collected. Spoligotyping was applied to describe the population structure of M. tuberculosis, lineage identification was performed using a combination of lineage-specific markers, and genotypic clusters were identified using a combination of 24-locus-MIRU-VNTR and spoligotyping. A high degree of genetic diversity was observed among isolates based on their spoligopatterns. Strains from modern lineage 4 made up almost half of strains (46.9%), being more abundant than the ancient lineage 1 (33.7%), and modern lineage 2 (19.4%). Thirty-five percent of strains belonged to genotypic clusters, especially strains in the Beijing genotype. Previous TB treatment and mutations associated with drug resistance were more common in patients infected with strains of the Beijing genotype. Papua shows a different distribution of M. tuberculosis genotypes compared to other parts of Indonesia. Clustering and drug resistance of modern strains recently introduced to Papua may contribute to the high tuberculosis burden in this region.

Low cost HIV-1 quantitative RT-PCR assay in resource-limited settings: improvement and implementation.

Monitoring of HIV viral load in low and middle income settings is limited by high cost of the commercial assays. Therefore, we developed a novel RT-PCR quantitative assay was developed. This assay targets the HIV-1 pol integrase gene (INT). Subsequently, the performance of the INT assay, described previously as a Long Terminal Repeat (LTR) assay and a combined INT/LTR dual target RT-PCR assay was compared. The LTR-assay was found to be sensitive and cost-effective (50-70% cheaper than commercial assays) with the lowest coefficient of variation (%CV). Introduction of an internal standard further improved assay reliability. Therefore, this LTR assay was implemented in West Java, Indonesia. Linearity and precision of the LTR assay were good: %CV ranged from 1.0% to 10.4%. The limit of quantitation was 616 copies/ml. Performance was comparable with the commercial assay (Abbott assay) (r(2)=0.01), although on average the viral loads were 0.39 log(10)copies/ml lower. In clinical practice, it had excellent capability for monitoring treatment failure, the positive predictive value was 99% and the negative predictive value was 93%. In conclusion, the implementation of the improved HIV-1 viral load LTR-assay for routine diagnosis in resource poor settings can be a good alternative when commercial assays are unaffordable.

Comparison of real time IS6110-PCR, microscopy, and culture for diagnosis of tuberculous meningitis in a cohort of adult patients in Indonesia.

BACKGROUND: Bacteriological confirmation of tuberculous (TB) meningitis is difficult. Culture is slow and microscopy has insufficient sensitivity. We evaluated real time PCR targeting insertion sequence IS6110 among 230 consecutive adult patients with subacute meningitis in a referral hospital in Indonesia. METHODS: Cerebrospinal fluid (CSF) samples were examined using microscopy, solid and liquid culture, and real time IS6110-PCR with a fluorescence-labeled probe using DNA extracted from CSF. CSF samples from 40 non-infectious neurology patients were used as negative controls. IS6110-PCR results were linked with clinical and CSF characteristics. RESULTS: Most patients presented with subacute meningitis, after a median of 14 days of symptoms (range 7-30). After exclusion of cryptococcal and bacterial meningitis, 207 patients were classified as definite or probable TB meningitis; 17.9% with HIV infection. Among this group IS6110-PCR gave the highest positivity rate (68%, 95% CI 62-74%) compared with microscopy of ZN-stained slides (11%, 95% CI 7-15%), and mycobacterial culture using solid (36%, 95% CI 29-42%) and liquid (44%, 95% CI 37-51%) media. IS6110-PCR was positive in 92% of patients with culture-positive and 42% of patients with culture-negative probable TB meningitis. Among culture-negative patients, a positive PCR was associated with a history of TB treatment, a longer duration of illness, a higher CSF cell count and protein, and a lower CSF glucose. IS6110-PCR was negative in all CSF samples from non-meningitis control patients. CONCLUSIONS: Real time IS6110-PCR is a quick, sensitive, and specific test for diagnosing of TB meningitis in this setting. Its performance in other (less-developed) settings needs further study.