Usefulness of Xpert MTB/RIF Ultra for rapid diagnosis of extrapulmonary tuberculosis in Tunisia.

Extrapulmonary tuberculosis (EPTB) remains a challenging diagnosis. The purpose of this study was to assess the accuracy of Xpert MTB/RIF Ultra (Cepheid, USA) for rapid diagnosis of EPTB in Tunisia. Eight hundred and forty-seven extrapulmonary samples collected from 2017 to 2021, were subjected to Xpert MTB/RIF Ultra. Microscopy and culture were performed for all the specimens. The accuracy of Xpert Ultra was evaluated in comparison to the culture. Xpert Ultra diagnosed EPTB with a global sensitivity of 80.66% (74.3-85.75) and specificity of 70.87% (67.31-74.20). The molecular test was most accurate when performed in cerebrospinal fluids, bones and joints and cutaneous specimens showing a sensitivity of 100% and a specificity ranging from 70.60 to 91.11%. In lymph node samples comprising aspirates and biopsies, the sensitivity of Xpert Ultra was high 87.50% (77.23-93.53), however, the specificity was 51.08% (44.67-57.46). For pleural samples, the Xpert Ultra sensitivity was 77.50% (68.34-84.68) ranging from 71.43 to 80% in pleural biopsies and fluids respectively. The specificity in all pleural specimens was 79.56% (74.40-83.91). Xpert Ultra showed promise in the diagnosis of EPTB. The performances varied according to the site of the disease. The test may be more valuable if used in combination with other diagnostic modalities.

Performances of single tube nested polymerase chain reaction and GeneXpert ultra on Formalin fixed paraffin embedded tissues in the diagnosis of tuberculous spondylodiscitis.

INTRODUCTION: Tuberculous Spondylodiscitis is the most common form of musculoskeletal tuberculosis. Molecular techniques on fresh tissues are proved to improve the diagnosis of tuberculous spondylodiscitis and to allow a rapid diagnosis to initiate the treatment and prevent neurological complications. OBJECTIVES: The objective of the present study was to assess the diagnostic performances of single tube nested PCR and GeneXpert ultra in the diagnosis of tuberculous spondylodiscitis on formalin fixed paraffin embedded tissues. METHODS: This study included 63 tuberculous spondylodiscitis cases collected from June 2014 to January 2020 and corresponding to 27 definite tuberculous spondylodiscitis with positive microbiology, and 36 probable tuberculous spondylodiscitis, with histopathological, clinical and radiological findings consistent with tuberculous spondylodiscitis but with negative microbiology. The sensitivity, specificity, positive predictive value and negative predictive value of nested PCR and GeneXpert ultra were determined with reference to microbiology. RESULTS: Nested PCR was positive in 47 (75%) cases: 26/27 definite tuberculous spondylodiscitis and 21/36 probable tuberculous spondylodiscitis. GeneXpert ultra was positive in only 6 (10%) cases corresponding to definite tuberculous spondylodiscitis. The sensitivity, specificity, positive predictive value and negative predictive value of nested PCR on formalin fixed paraffin embedded tissues were 96%, 100%, 100%, 83% respectively. For GeneXpert ultra, these rates were 22%, 100%, 100% and 25% respectively. CONCLUSION: Nested PCR and GeneXpert ultra on formalin fixed paraffin embedded tissues are useful tools for the diagnosis of tuberculous spondylodiscitis, especially for cases where microbiological investigations were not carried out. Both techniques have excellent specificity but single tube nested PCR is more sensitive. Key Points • Molecular techniques are routinely performed on fresh tissues • GeneXpert and nested PCR on formalin fixed paraffin embedded tissues are reliable for the diagnosis of tuberculous spondylodiscitis • Nested PCR is more sensitive than Genexpert for diagnosing tuberculous spondylodiscitis.

Performance of the GenoType MTBDRsl V 2.0 for detecting second-line drugs resistance of Mycobacterium tuberculosis isolates in Tunisia.

Rapid detection of the second-line drug (SLD) resistant tuberculosis (TB) strains is challenging to prescribe an immediate adequate treatment and limit the transmission of SLD resistant strains. The study aimed to evaluate the performance of GenoType MTBDRsl V2.0 compared to phenotypic drug susceptibility testing (pDST:MGIT960) to detect resistance to SLD of Mycobacterium tuberculosis (MTB) isolates in Tunisia, between May 2015 and December 2019. As a matter of fact, 103 rifampicin-resistant and multidrug-resistant MTB strains were included. Discrepancies between pDST and MTBDRsl were solved by whole genome sequencing. Compared to pDST, MTBDRsl V2.0 showed a sensitivity of 92.8% (68.5%-98.7%) in detecting resistance to fluoroquinolones. As for second-line injectable drugs, it presented a sensitivity of 80.0% (49.0%-94.3%). MTBDRsl had sensitivities of 100.0% (67.5%-100.0%), 75.0% (40.9%-92.8%) and 100.0% (60.9%-100.0%) respectively for kanamycin, capreomycin and amikacin. The specificity was 100.0% for all the drugs evaluated. As for diagnosing XDR-TB, it had a sensitivity of 57.1% (25.0%-84.1%) and a specificity of 100.0% (96.1%-100.0%). MTBDRsl V2.0 showed a high performance in detecting SLD resistance with a short turnaround time compared with pDST, which made it possible to start an early treatment and to maintain a low prevalence of SLD resistance and XDR-TB in Tunisia.

The Value of Histology in the Diagnosis of Tuberculous Spondylodiscitis.

BACKGROUND: Tuberculous spondylodiscitis (TS) is the most common form of musculoskeletal tuberculosis. Currently, histology is widely used to distinguish tuberculous from nontuberculous disease. OBJECTIVES: The aim of the present study was to assess the accuracy of histology compared with bacteriology in the diagnosis of TS. METHODS: This is a single-center case series carried out from January 2014 to February 2018 in a pathology department. It included 121 discovertebral biopsies of infective spondylodiscitis. The measures of diagnostic accuracy of histology were determined taking bacteriology as criterion standard. RESULTS: Among the 121 cases, 55 (45.4%) were diagnosed as TS by histological and/or bacteriological findings, 17 (30.9%) were classified as definite TS by bacteriology, and the remaining 38 (69.1%) had positive histology and negative bacteriology. There were 2 false-negatives, which histologically displayed suppuration without granuloma, and 3 false-positives; in one case, histology displayed granulomas without necrosis and culture isolated Brucella. In the 2 others, histology revealed granulomas with caseous-like necrosis and microbiology isolated fungal species. The sensitivity, specificity, positive predictive value, negative predictive value, and accuracy of histology in the diagnosis of TS were 88.2%, 93.4%, 83.3%, 95.5%, and 92%, respectively. CONCLUSIONS: Histology is proved to be an accurate diagnostic tool in TS. Suppurative forms of TS without granuloma are rare and represent the main cause of false-negative histology. Suggestive histology of TS does not rule out fungal and brucellar spondylodiscitis. Caseous necrosis is not pathognomonic of tuberculosis. Fungal infection can also exhibit such type of necrosis.

Accuracy of the QIAxcel Automated System for MIRU-VNTR Genotyping of Mycobacterium tuberculosis in Two Limited Resource Settings.

Mycobacterial interspersed repetitive units variable number tandem repeat (MIRU-VNTR) typing of Mycobacterium tuberculosis complex (MTBC) isolates, based on 24 loci, is still widely used as the standard for routine molecular surveillance of tuberculosis (TB). QIAxcel system is proposed as an affordable tool that could replace conventional gel electrophoresis and provide high concordance with the reference methods regarding MIRU-VNTR typing of MTBC. We aimed to evaluate the QIAxcel accuracy for allele calling of MIRU-VNTR loci in two regional reference laboratories. A total of 173 DNA were used for the study. Results obtained with QIAxcel were compared to the reference results obtained with an ABI 3730 DNA analyzer. In Albania, the overall agreement with the reference method was 97.92%. A complete agreement result was obtained for 17 loci. In Tunisia, the overall agreement with the reference method was 98.95%. A complete agreement result was obtained for 17 loci. Overall agreement in both centers was 98.43%. In our opinion, use of QIAxcel technology has the potential to be reliable, given an optimized algorithm. Inaccuracies in sizing of long fragments should be solved, especially regarding locus 4052.

Diagnosis of lymph node tuberculosis using the GeneXpert MTB/RIF in Tunisia.

INTRODUCTION: GeneXpert MTB/RIF is a fully-automated diagnostic molecular test which simultaneously detects tuberculosis (TB) and rifampicin (RIF) drug resistance. The purpose of this study is to evaluate the performance of the GeneXpert MTB/RIF test for the detection of Mycobacterium tuberculosis complex (MTBC) in lymph node specimens and to show the place of Mycobacterium bovis as a major cause of TB lymphadenitis. MATERIAL AND METHODS: This study was conducted simultaneously in the National Reference Laboratory for Mycobacteria of Ariana and the Central Laboratory of Sfax, from January to December 2013. In total, 174 lymph node specimens were processed simultaneously for Ziehl-Neelsen, auramine and immuno-histochemical staining. Conventional culture on both Lowenstein-Jensen and liquid medium (Bactec MGIT 960 BD system) and the new molecular-based GeneXpert MTB/RIF assay system were performed. Positive cultures were confirmed using molecular identification (Genotype MTBC Hain Lifescience). RESULTS: Among the 174 samples tested, the GeneXpert detected the DNA of MTBC in 134 samples (77%). Standard bacteriological assays, including AFB microscopy and culture, were positive, respectively, in 41 (23.6%) and 79 (45.4%) specimens. M. bovis was isolated in 76% of positive cultures. GeneXpert sensitivity and specificity results were assessed according to smear and culture results, clinical and histological findings. The sensitivity and specificity of the Xpert assay were 87.5% (126/144) and 73.3%, respectively. CONCLUSION: The implementation of the GeneXpert MTB/RIF assay may dramatically improve the rapid diagnosis of lymph node TB.

Severe pneumococcal community-acquired pneumonia admitted to medical Tunisian ICU.

Streptococcus pneumoniae is the most common cause of community-acquired pneumonia (CAP). There are no available data about this disease in Tunisian intensive care patients. The objective of this study is to describe the clinical and microbiological features of pneumococcal CAP and determine the prognostic factors. This is a retrospective cohort study of all pneumococcal CAP cases hospitalized in the medical intensive care unit (ICU) of Hospital A. Mami of Ariana (Tunisia) between January 1999 and August 2008. Included were 132 patients (mean age, 49.5 years; 82.6% males); 30 patients had received antimicrobial treatment before hospital admission. The mean of the Simplified Acute Physiology Score II was 32.9. All patients had an acute respiratory failure; 34 patients (25.8%) had pneumococcal bacteremic CAP. Among the isolated strains, 125 antimicrobial susceptibility tests were performed. The use of the new Clinical and Laboratory Standards Institute breakpoints for susceptibility when testing penicillin against S. pneumoniae showed that all isolated strains were susceptible to penicillin. The mortality rate was 25%. The need of mechanical ventilation at admission [odds ratio (OR), 3.4; 95% confidence interval (CI), 1.67-6.94; P = 0.001), Sepsis-related Organ Failure Assessment (SOFA) score at admission ≥4 (OR, 3.1; 95% CI, 1.56-6.13; P = 0.001), and serum creatinine at admission ≥102 µmol/l (OR, 1.8; 95% CI, 1.02-3.17; P = 0.043) were independent factors related to ICU mortality. In conclusion, pneumococcal CAP requiring hospitalization in the ICU is associated with high mortality. All isolated stains were susceptible to penicillin.

Detection of isoniazid and rifampin resistance of Mycobacteriumtuberculosis by a multiplex allele-specific polymerase chain reaction (PCR) assay.

BACKGROUND: The use of molecular techniques is a major improvement for the rapid routine detection and control of multidrug-resistant tuberculosis (MDR-TB). MATERIALS: In this study, the multiplex allele-specific polymerase chain reaction (MAS-PCR) was developed to simultaneously detect the most frequent mutations associated with isoniazid (INH) and rifampin (RIF) resistance in a single assay. RESULTS: The assay was tested with 53 clinical isolates. Among them, 27 were MDR strains, 17 were mono-resistant to INH, one was mono-resistant to RIF, and eight were susceptible. The MAS-PCR assay showed a specificity of 100% in detecting drug resistance. An equivalent sensitivity of 92.6% in detecting MDR and RIF-resistance was found. The sensitivity for the detection of INH-resistance was 88.6%. CONCLUSIONS: The MAS-PCR assay was a simple and rapid method for detecting the INH and RIF-resistance in Mycobacterium tuberculosis (MT) clinical strains. It is also easy to perform and to interpret. The assay is inexpensive and a less-demanding technique.