Linezolid resistance in Mycobacterium tuberculosis isolates at a tertiary care centre in Mumbai, India.

Background & objectives: Linezolid (LZD) is increasingly being used in tuberculosis (TB) treatment. However, LZD resistance has already been reported, which is highly alarming, given its critical therapeutic role. This study was aimed to phenotypically and genotypically assess LZD resistance in Mycobacterium tuberculosis (MTB) isolates at a laboratory in a tertiary care centre in Mumbai, India. Methods: A sample of 32 consecutive LZD-resistant MTB isolates identified by liquid culture susceptibility testing was subjected to whole-genome sequencing (WGS) on the Illumina NextSeq platform. Sequences were analyzed using BioNumerics software to predict resistance for 12 antibiotics within 15 min. Results: Sixty eight of the 2179 isolates tested for LZD resistance by MGIT-based susceptibility testing (June 2015 to June 2016) were LZD-resistant. Thirty two consecutive LZD-resistant isolates were analyzed by WGS to screen for known mutations conferring LZD resistance. WGS of 32 phenotypically LZD-resistant isolates showed that C154R in the rplC gene and G2814T in the rrl gene were the major resistance determinants. Interpretation & conclusions: LZD resistance poses an important risk to the success of treatment regimens, especially those designed for resistant isolates; such regimens are extensively used in India. As LZD-containing regimens increase in prominence, it is important to support clinical decision-making with an improved understanding of the common mutations conferring LZD resistance and their frequency in different settings.

Targeted next generation sequencing directly from sputum for comprehensive genetic information on drug resistant Mycobacterium tuberculosis.

BACKGROUND: Timely drug resistance detection is essential to global tuberculosis management. Unfortunately, rapid molecular tests assess resistance to only a few drugs, with culture required for comprehensive susceptibility test results. METHODS: We evaluated targeted next generation sequencing (tNGS) for tuberculosis on 40 uncultured sputum samples. Resistance profiles from tNGS were compared with profiles from Xpert MTB/RIF, line probe assay (LPA), pyrosequencing (PSQ), and phenotypic testing. Concordance, sensitivity, specificity, and overall test agreement were compared across assays. RESULTS: tNGS provided results for 39 of 40 samples (97.5%) with faster turnaround than phenotypic testing (median 3 vs. 21 days, p = 0.0068). Most samples were isoniazid and rifampin resistant (N = 31, 79.5%), 21 (53.8%) were fluoroquinolone resistant, and 3 (7.7%) were also resistant to Kanamycin. Half were of the Beijing lineage (N = 20, 51.3%). tNGS from uncultured sputum identified all resistance to isoniazid, rifampin, fluoroquinolones, and second-line injectable drugs that was identified by other methods. Agreement between tNGS and existing assays was excellent for isoniazid, rifampin, and SLDs, very good for levofloxacin, and good for moxifloxacin. CONCLUSION: tNGS can rapidly identify tuberculosis, lineage, and drug resistance with faster turnaround than phenotypic testing. tNGS is a potential alternative to phenotypic testing in high-burden settings.

Evaluation of pyrosequencing for extensive drug resistance-defining anti-tuberculosis drugs for use in public healthcare.

MGIT 960 drug susceptibility testing (DST) for Mycobacterium tuberculosis was compared for performance and speed with pyrosequencing (PSQ). Pulmonary samples (n = 100), from GeneXpert/MTB/Rifampicin-resistant patients receiving second-line treatment for 1-3 months, were subjected to DST and PSQ for seven drugs (isoniazid, rifampicin, kanamycin, amikacin, capreomycin, moxifloxacin, and ofloxacin). The mean time-to-result was 35 and two days for DST and PSQ, respectively. Average concordancy was 92.7%. Theoretically, PSQ showed substantial incremental value over the commercial Genotype MTBDRplus/sl. Mutations not considered in commercial molecular tests were observed by PSQ. Our findings corroborated the association between S315T (katG region) and S531L (rpoB region) and phenotypic resistance. PSQ is more rapid, can be performed from the sample, provides information about all known mutations simultaneously, allows extensive post-processing analyses, and is open to the inclusion of new mutations. It indicates the exact mutation conferring resistance to the particular drug, unlike the qualitative DST.

Correlating rrs and eis promoter mutations in clinical isolates of Mycobacterium tuberculosis with phenotypic susceptibility levels to the second-line injectables.

OBJECTIVE/BACKGROUND: The in vitro drug-susceptibility testing of Mycobacterium tuberculosis reports isolates as resistant or susceptible on the basis of single critical concentrations. It is evident that drug resistance in M. tuberculosis is quite heterogeneous, and involves low level, moderate level, and high level of drug-resistant phenotypes. Thus, the aim of our study was to correlate rrs (X52917) and eis (AF144099) promoter mutations, found in M. tuberculosis isolates, with corresponding minimum inhibitory concentrations of amikacin, kanamycin, and capreomycin. METHODS: Ninety M. tuberculosis clinical isolates were analyzed in this study. The minimum inhibitory concentrations were determined by MGIT 960 for 59 isolates with resistance-associated mutations in the rrs and eis promoter gene regions, and 31 isolates with wild-type sequences, as determined by the GenoType MTBDRsl (version 1) assay. RESULTS: The rrs A1401G mutation was identified in 48 isolates resistant to the second-line injectables. The eis promoter mutations C-14T (n=3), G-10C (n=3), G-10A (n=3), and C-12T (n=2) were found within 11 isolates with various resistance profiles to the second-line injectables. Thirty-one isolates had wild-type sequences for the rrs and eis promoter gene regions of interest, one of which was amikacin, kanamycin, and capreomycin resistant. The isolates with the rrs A1401G mutation had amikacin, kanamycin, and capreomycin minimum inhibitory concentrations of >40mg/L, >20mg/L, and 5-15mg/L, respectively. The isolates with eis promoter mutations had amikacin, kanamycin, and capreomycin minimum inhibitory concentrations of 0.25-1.0mg/L, 0.625-10mg/L, and 0.625-2.5mg/L, respectively. CONCLUSION: This study provides a preliminary basis for the prediction of phenotypic-resistance levels to the second-line injectables based upon the presence of genetic mutations associated with amikacin, kanamycin, and capreomycin resistance. The results suggest that isolates with eis promoter mutations have consistently lower resistance levels to amikacin, kanamycin, and capreomycin than isolates with the rrs A1401G mutation.

Defining multidrug-resistant tuberculosis: correlating GenoType MTBDRplus assay results with minimum inhibitory concentrations.

This study correlates MICs of rifampicin (RIF) and isoniazid (INH) with GenoType MTBDRplus assay results for drug-resistant Mycobacterium tuberculosis (MTB) clinical isolates. MICs of RIF and INH were established for 84 and 90 isolates, respectively, testing 7 concentrations of each drug. Genotypic resistance to each drug was determined by GenoType MTBDRplus assay with 50 representative mutations confirmed by pyrosequencing, with mutations in the rpoB gene associated with RIF resistance and mutations in the katG and/or inhA genes associated with INH resistance. Based upon the correlation of MICs with specific genetic profiles, relative resistance levels were established for each isolate. Results indicate that MTB phenotypic resistance, currently based upon the testing of isolate susceptibility to a single drug concentration, may be more accurately profiled via quantitative MICs, and therefore, the correlation of molecular diagnostic results with specific MICs may allow for more optimal treatment of infections.

Correlating Minimum Inhibitory Concentrations of ofloxacin and moxifloxacin with gyrA mutations using the genotype MTBDRsl assay.

OBJECTIVE: To correlate gyrA mutations found on the Genotype MTBDRsl assay in Mycobacterium tuberculosis (MTB) isolates with Minimum Inhibitory Concentrations (MICs) to the fluoroquinolones compounds ofloxacin (OFX) and moxifloxacin (MXF). METHODS: MICs for OFX and MXF were ascertained for 93 archived clinical MTB isolates that showed gyrA mutations at Ala90Val, Ser91Pro, Asp94Ala, Asn/Tyr, Gly and His. Thirty fluoroquinolones susceptible isolates as determined by presence of all wild-type gyrA bands on the Genotype MTBDRsl assay were also included. RESULTS: gyrA mutations at Ala90Val (n = 25), Ser91Pro (n = 6), Asp94Ala (n = 4), Asp94Asn/Tyr (n = 13), Asp94Gly (n = 42) and Asp94His (n = 3) were observed. Isolates with mutations at Ala90Val or Ser91Pro had MIC90 of 4.0 µg/ml and 1.0 µg/ml for OFX and MXF, respectively, and isolates with mutations at Asp 94Ala, Asn/Tyr, Gly and His had MIC90 of 8.0 µg/ml, and 2.5 µg/ml for OFX and MXF, respectively. CONCLUSIONS: MTB MICs were found to be consistently lower for MXF than for OFX among isolates with the same gyrA mutation (e.g. Ala90Val). The majority of MTB isolates containing mutations at Asp94Ala, Asn/Tyr, Gly and His in gyrA were associated with a moderate level of resistance to MXF (MIC = 2.5 µg/ml), although 3 isolates with the mutations Asp94Asn/Tyr/Gly were associated with a high level of resistance to both fluoroquinolones (MXF MICs = 5.0-8.0 µg/ml, OFX MICs = ≥10.0 µg/ml).

Drug resistance patterns in 111 cases of drug-resistant tuberculosis spine.

PURPOSE: We report the largest study conducted till date of drug resistant tuberculosis in spine analyzing the drug susceptibility patterns in 111 cases of proven drug resistance. METHODS: An observed cross-sectional study was conducted. Six-hundred and eighty-six patients with positive cultures underwent sensitivity testing to 13 commonly used anti-tubercular drugs using BACTEC MGIT-960 system. RESULTS: Females (60.3%) outnumbered males (39.6%). Only three patients (2.7%) were found HIV positive, and none of these had AIDS. Forty-four (39.6%) patients had taken AKT in the past for some form of tuberculosis. Eight (7.2%) patients had history of treatment default. The drug sensitivity testing revealed 87 (78.3%) cases of multi drug resistance (resistance to both isoniazid and rifampicin) and 3 (2.7%) cases of XDR-TB spine. Of the individual drugs, widespread resistance was present to both isoniazid (92.7%) and rifampicin (81.9%), followed by streptomycin (69.3%). Least resistance was found to kanamycin, amikacin and capreomycin. CONCLUSION: It is recommended to do routine biopsy, culture and drug sensitivity testing in all patients of tuberculosis spine to guide selection of appropriate second-line drugs when required. In cases of non availability of drug susceptibility testing despite repeated attempts, it is suggested to use data from large series such as this to plan best empirical chemotherapy protocol.

Immunochromatographic assays for detection of Mycobacterium tuberculosis: what is the perfect time to test?

In this study, we aimed to correlate the analytical performance of SD BIOLINE TB Ag MPT64 Rapid Test kit (MPT64 assay) with the mycobacterial growth unit (GU) reported by the BACTEC MGIT 960 (MGIT 960) instrument. A total of 394 culture isolates reported positive by MGIT 960 were processed daily (until 'day 4') with the MPT64 assay until a positive MPT64 result was obtained and their GU values were noted daily before MPT64 testing. Based on this correlation of MPT64 positivity and corresponding GU values, a GU cut-off was determined. In the validation phase, with the experimentally determined GU cut-off value, 99.1% (576/581) of culture isolates were correctly identified as MTB within 2 days from instrument positivity. All results were available using a single-MPT64 assay strip, making the assay cost-effective. Thus, systematic implementation of the MPT64 assay proved to be cost-effective in a high-throughput laboratory without any delay in patient reporting.

Clonal population of Mycobacterium tuberculosis strains reside within multiple lung cavities.

BACKGROUND: Unsuccessful treatment outcomes among patients with multi-/extensively-drug resistant tuberculosis (TB) have hampered efforts involved in eradicating this disease. In order to better understand the etiology of this disease, we aimed to determine whether single or multiple strains of Mycobacterium tuberculosis (MTB) are localized within lung cavities of patients suffering from chronic progressive TB. METHODOLOGY/FINDINGS: Multiple cavity isolates from lung of 5 patients who had undergone pulmonary resection surgery were analyzed on the basis of their drug susceptibility profile, and genotyped by spoligotyping and 24-loci MIRU-VNTR. The patients past history including treatment was studied. Three of the 5 patients had extensive drug resistant TB. Heteroresistance was also reported within different cavity isolates of the lung. Both genotyping methods reported the presence of clonal population of MTB strain within different cavities of the each patient, even those reporting heteroresistance. Four of the 5 patients were infected with a population of the Beijing genotype. Post-surgery they were prescribed a drug regimen consisting of cycloserine, a fluoroquinolone and an injectable drug. A 6 month post-surgery follow-up reported only 2 patients with positive clinical outcome, showing sputum conversion. CONCLUSION: Identical spoligotype patterns and MIRU-VNTR profiles between multiple cavities of each patient, characterize the presence of clonal population of MTB strains (and absence of multiple MTB infection).

Can cord formation in BACTEC MGIT 960 medium be used as a presumptive method for identification of M. tuberculosis complex?

BACKGROUND: Serpentine cord formation in BACTEC MGIT 960 medium was evaluated as a rapid method for the presumptive identification of M. tuberculosis complex (MTBC). MATERIAL & METHODS: Total 2527 samples were processed for AFB culture using MGIT 960 TB system over a period of three months. AFB smears were prepared from 1000 MGIT tubes flagged positive by the MGIT instrument and stained by ZN method to examine presence or absence of serpentine cording. The cord formation was compared with PNBA [p-nitro benzoic acid] test on MGIT system and all controversial cases were further evaluated by NAP [p-nitro-a-acetylamino-phydroxypropiophenone] test on BACTEC 460 TB system. RESULTS & DISCUSSION: Of the 1000 culture positives, 904 (90.4%) were identified as mycobacteria, of which 869 (96%) showed cording by smear microscopy. One (0.1%) was identified as nocardia. In the remaining 95 (9.5%) cases, primary smear made from MGIT vial was negative. Of 869 cultures showing serpentine cord formation, 842 were confirmed as MTBC and 27 as NTM by PNBA assay on MGIT 960 TB system. The sensitivity, specificity, positive and negative predictive values are found to be 99.6%, 54%, 96% and 91% respectively. An average detection time for PNBA assay was found to be eight days whereas cording results were available on the same day of culture positivity. CONCLUSION: Though highly sensitive it is not very specific and hence cannot be the only test for presumptive diagnosis of MTBC.

Comparison of phenotypic and genotypic methods for pyrazinamide susceptibility testing.

OBJECTIVES: To evaluate Pyrazinamide (PZA) susceptibility results obtained by phenotypic MGIT 960 TB system against enzymatic Pyrazinamidase assay and genotypic pncA gene sequencing. To find the prevalence of infections caused by M. bovis in PZA resistant M. tuberculosis complex isolates. METHODS: 33 consecutive PZA resistant and 30 consecutive PZA susceptible isolates reported for PZA susceptibility testing by MGIT 960 TB system were included in this study. Presence of active pyrazinamidase enzyme was sought by using the Wayne assay. The pncA gene was amplified by PCR and then sequenced to screen mutations. All the PZA resistant isolates were further spoligotyped to identify M. bovis, if present. RESULTS: Of 33 PZA resistant strains by MGIT 960, 31 were Wayne assay negative and two were positive. Of the 30 susceptible PZA strains six were Wayne assay negative reporting false resistance. PncA gene sequencing revealed that 32 of the 33 MGIT PZA resistant isolates had diverse nucleotide changes scattered throughout the pncA gene (one isolate did not show any mutation). Of the 30 phenotypically susceptible isolates, 21 were wild types whilst nine isolates showed the presence of a silent mutation C-T at codon 195. Fifteen mutations found in this study has not been described earlier. Not a single isolate of M. bovis was detected among PZA resistant M. tuberculosis complex isolates. CONCLUSION: MGIT 960 showed better concordance with sequencing results in comparison with Wayne assay. In present study, a high proportion (85%) of MDR-TB isolates from patients receiving anti-TB treatment were found to be resistant to PZA.