Evaluation of gene xpert for routine diagnosis of HIV-associated tuberculosis in Nigeria: A prospective cohort study.

BACKGROUND: Xpert MTB/Rif (Xpert) is described as a game changer in tuberculosis (TB) control. We evaluated the impact of Xpert on diagnosis, time to treatment, and treatment outcome among patients with HIV associated TB in Nigeria. METHODS: Adults with HIV being evaluated for pulmonary TB (PTB) were consecutively enrolled into the study cohort. At baseline, expectorated sputa were examined using Xpert and smear microscopy for Mycobacterium tuberculosis (MTB) and acid fast bacilli, respectively. Patients diagnosed with TB were followed-up until 6 months post TB diagnosis. TB was defined as sputum positive by smear microscopy, Xpert detection of MTB (bacteriologically confirmed case), or clinician diagnosed TB with initiation of full TB treatment (clinical diagnosis). Time to treatment was time from first clinic presentation for TB evaluation to initiation of TB treatment. We examined the proportion PTB patients with a positive Xpert result and compared time to TB treatment and outcome of TB treatment in patients based on sputum test results. RESULTS: A total of 310 adults with HIV were enrolled. The median CD4 cell count was 242 (interquartile range (IQR) 120-425) cells/mm3 and 88.1% were receiving antiretroviral therapy (ART). PTB was diagnosed in 76 (24.5%) patients, with 71 (93.4%) being bacteriologically confirmed. Among patients with PTB, 56 (73.7%) were Xpert positive. Median time to treatment was 5 (IQR 2-8) days and 12 (IQR 5-35) days in patient with and without Xpert positive results, respectively; p = 0.005. Overall 73.1% had symptom free survival at 6 months post PTB treatment initiation with no significant differences observed based on TB test method. 10 (14.9%) died within 6 months of TB treatment initiation. In analysis adjusted for age, sex, and mode of diagnosis (Xpert positive or negative), only ART use independently predicted mortality (AOR 0.10; 95% CI 0.01-0.93). CONCLUSION: The use of Xpert for routine care reduced time to PTB treatment, but did not improve survival in patients with HIV treated for susceptible PTB.

Sputum smear concentration may misidentify acid-fast bacilli as Mycobacterium tuberculosis in HIV-infected patients.

BACKGROUND: Tuberculosis (TB) diagnosis in most resource-limited settings still depends on smear microscopy for identification of acid-fast bacilli (AFB). However, recently developed molecular diagnostics that test for the presence of Mycobacterium tuberculosis (Mtb) DNA have been shown to be superior for confirmation of TB diagnosis. METHODS: At regular clinical visits over a 12-month period, we collected sputa from HIV-infected patients presenting with signs or symptoms of TB at 2 Nigerian clinics. Sputa were stained for AFB and tested using the Genotype MTBDRplus to confirm the presence of Mtb. Other species were identified using 16S rRNA sequence. RESULTS: In 56% (233/415) of AFB-positive patients, Mtb was confirmed. The patients on antiretroviral therapy were less likely than those not on antiretroviral therapy to be infected with Mtb [odds ratio (OR) = 0.25, P = 0.003]. In a multivariate logistic regression model using clinical features and diagnostic results, abnormal respiratory findings on auscultation (OR = 3.28, P = 0.03) and a direct sputum smear grade >3/100 (OR = 6.4, 4.6, P < 0.02) were significant predictors of Mtb infection. Concentrated sputum smear was predictive of Mtb infection only at the highest grades (2+, 3+). Interestingly, among 65 samples that could not be confirmed for Mtb, 32 (49%) were found to contain other, possibly novel, actinomycetes, including atypical Mycobacteria, Rhodococcus spp, Nocardia spp, and Corynebacterium spp. CONCLUSIONS: We conclude that concentrated sputum smears may misidentify other bacteria as Mtb in HIV-infected patients. The use of molecular diagnostics could reduce unnecessary or inappropriate treatment and improve identification of pathogens in resource-limited settings with high HIV burden.

Genetic determinants of drug-resistant tuberculosis among HIV-infected patients in Nigeria.

Tuberculosis (TB) is the most common opportunistic infection in human immunodeficiency virus (HIV)-infected patients and the emergence of drug-resistant tuberculosis (DR-TB) is a growing problem in resource-limited settings. Adequate infrastructure for testing drug sensitivity and sufficient evidence of first-line resistance are currently unavailable in Nigeria. We collected sputum samples from HIV-infected patients enrolled in the Harvard PEPFAR/APIN Plus program over 12 months at two PEPFAR antiretroviral therapy (ART) clinics in the southwest and north central regions in Nigeria. Smear-positive sputum samples were submitted for GenoType MTBDRplus testing (n = 415); mutations were confirmed through sequencing. Our results show high rates of DR-TB in Nigerian HIV-infected individuals (7.0% for rifampin [RIF] and 9.3% for RIF or isoniazid [INH]). Total RIF resistance indicative of MDR-TB in treatment-naive patients was 5.52%, far exceeding the World Health Organization predictions (0 to 4.3%). RIF resistance was found in 6/213 (2.8%) cases, INH resistance was found in 3/215 (1.4%) cases, and MDR-TB was found in 8/223 (3.6%) cases. We found significantly different amounts of DR-TB by location (18.18% in the south of the country versus 3.91% in the north central region [P < 0.01]). Furthermore, RIF resistance was genetically distinct, suggesting possible location-specific strains are responsible for the transmission of drug resistance (P < 0.04). Finally, GenoType MTBDRplus correctly identified the drug-resistant samples compared to sequencing in 96.8% of cases. We found that total DR-TB in HIV-infection is high and that transmission of drug-resistant TB in HIV-infected patients in Nigeria is higher than predicted.

Genetic diversity of Mycobacterium tuberculosis Complex in Jos, Nigeria.

BACKGROUND: Nigeria has a high tuberculosis incidence, and genotyping studies of Mycobacterium tuberculosis Complex (MTC) in the country are necessary in order to improve our understanding of the epidemic. METHODS: Isolates of MTC were isolated from cases of pulmonary tuberculosis in Jos, North Central region of Nigeria during 2006-2008. Drug susceptibility test (DST) was performed on 77 of 111 isolates by proportion method on Lowenstein Jensen (LJ) slope while genotyping of mycobacterial DNA was performed by spoligotyping. The SpolDB4 database and the model-based program 'spotclust' were used to assign isolates to families, subfamilies and variants. RESULTS: A total of 111 pulmonary isolates from consecutive tuberculosis patients in the city of Jos, Plateau State, Nigeria were spoligotyped. A total of 84 (76%) of the isolates belonged to the Latin American Mediterranean (LAM) family. Of these, 78 isolates were assigned to the LAM10 lineage. Among these, 66 exhibited identical spoligopatterns. Drug susceptibility profiles obtained were not consistently associated with any spoligopattern. CONCLUSIONS: The dominance of few M. tuberculosis lineages suggests either a high rate of transmission, frequent import of closely related strains, or a highly conserved genotype. It remains to be confirmed whether the predominance of identical LAM10 represent an outbreak.Spoligotyping was useful to gain an overall understanding of the local TB epidemic. This study demonstrated that the incidence of TB in Jos, Nigeria may be caused by a few successful M. tuberculosis families, dominated by the LAM10 family.

Comparison of a DNA based PCR method with conventional methods for the detection of M. tuberculosis in Jos, Nigeria.

BACKGROUND: To achieve early diagnosis and effective treatment of pulmonary tuberculosis, simple and sensitive methods that enhance the detection of Mycobacterium tuberculosis (M. tuberculosis) from clinical specimens are needed. This study compared the effectiveness and suitability of an insertion sequence (IS 6110) based polymerase chain reaction (PCR) assay with conventional methods for the detection of M. tuberculosis from clinical specimens in a resource-limited setting. METHODS: Sputa from 101 HIV-positive patients and 40 clinical specimens (sputa, gastic wash out, ascitic fluid, pleural fluid and cerebrospinal fluid) collected from children (HIV status unknown), all suspected for pulmonary tuberculosis at the Jos University Teaching Hospital, Jos, (JUTH) Nigeria, were examined by Ziehl Neelsen (ZN) smear microscopy, Lowenstein Jensen's (LJ) egg-based culture, and PCR methods for the detection of M. tuberculosis. RESULTS: Mycobacteria was detected in 45/101 (44.6%) of the specimens from the HIV-positive patients and comprised of 6% ZN(+)culture(+)PCR(+), 4% ZN(-)culture(+)PCR(-), 16% ZN(-)culture(+)PCR(+) and 19% ZN(-)culture(-)PCR(+). Twenty-two of forty (55%) children were positive with 0% smear microscopy; 4/40 (10%) culture(+)PCR(+); and 18/40 (45%) culture(-)PCR(+). The sensitivity and specificity of the PCR for the HIV-positive patients were 85% and 74% respectively against 23% and 100% for ZN smear microscopy. CONCLUSION: The IS6110 PCR is a rapid and sensitive method that is specific for the M. tuberculosis complex group. It is simple in our experience and increased the detection of M. tuberculosis from the specimens examined. We suggest its use for the detection of M. tuberculosis in high TB and HIV burden areas.

Drug susceptibility test of Mycobacterium tuberculosis by nitrate reductase assay.

BACKGROUND: Drug susceptibility testing for Mycobacterium tuberculosis (M. tuberculosis) is especially required in difficult cases of tuberculosis (TB) chemotherapy and in cases of multidrug resistance (MDR-TB; combined resistance to isonizid and rifampicin with or without resistance to any other drug). The methods for in vitro cultivation and drug susceptibility testing (DST) of M. tuberculosis are cumbersome and not readily adaptable in most routine laboratories, particularly those in the developing world due to limited resources and lack of political will in those countries. A simple and cost effective method, the nitrate reductase assay (NRA), was compared with the gold standard proportion (egg bases Lowenstein Jensen's [LJ]) method for DST of M. tuberculosis in order to substantiate its suitability for routine use in Nigeria and in other countries of the developing world with high TB endemicity. METHOD: Drug susceptibility test was performed for 70 pulmonary isolates of M. tuberculosis (Indirect DST) and 20 sputum (10 acid fast bacilli [AFB] positive and 10 AFB negative) specimens (direct DST) by the NRA and the proportion method using 0.2microg isoniazid (INH), 2microg ethambutol (EMB), 40 microg rifampicin (RIF) and 4 microg streptomycin STR). RESULTS: The indirect NRA showed sensitivity and specificity for INH: 100% and 100%, EMB: 75% and 100% RIF: 90% and 96.6%, STR: 66.6% and 91.8%. The results of direct NRA and proportion method for INH, EMB RIF and STR agreed 10/10 (100%) for AFB negative specimens and 9/10 (90%) with AFB positive specimens. CONCLUSION: Drug susceptibility test of M. tuberculosis by the NRA is simple and sensitive with shorter turn around time of 10 to 1 4 days compared to 42 days by the LJ proportion method. The direct use of AFB positive sputum specimens is likewise reproducible and excludes about 3 - 8 weeks period required for isolation of M. tuberculosis .

Helicobacter pylori: pathogen and symbiont.

There are puzzles in defining the exact role of Helicobacter pylori infection in humans. The bacterium, which is associated with human disease of the upper gastrointestinal tract, may otherwise exist as a commensal with probable symbiotic association in some human hosts. Although virulence associated genes have been detected in some strains which explain their pathogenicity, their pathogenic effect and subsequent clinical manifestations seem to vary in different human populations or geographical locations. Some human hosts remain predominantly asymptomatic in spite of the "virulent" H. pylori strain(s) they harbour. There are probable benefits of H. pylori colonisation of the human gastric mucosa. Thus the recommendation of eradication therapy in patients with known peptic ulcer disease may be more advantageous than the "test and treat policy", which suggests treatment of uninvestigated dyspeptic patients, who may not have any lesions.