Genotypic characterization of drug-resistant Mycobacterium tuberculosis isolates from Peru

Setting : Twenty-nine epidemiologically unrelated and mostly multidrug-resistantMycobacterium tuberculosis (MDR-TB) strains from Peruvian patients.Objective : To investigate the molecular genetics of MDR-TB strains recovered in a Latin American country.Design : Antimicrobial agent susceptibility testing, major genetic group designation, IS 6110 fingerprinting, spoligotyping, and automated deoxyribonucleic acid sequencing of regions of the katG, rpoB, embB, gyrA , and pncA genes with mutations commonly associated with drug resistance.Results : Nineteen isolates were found to be multidrug-resistant by susceptibility testing. IS6110 typing showed that virtually all isolates were unique and therefore had independently acquired drug resistance. Seventy-nine percent of isoniazid-resistant strains had a Ser315Thr amino acid change in KatG. Ninety-five percent of rifampin-resistant isolates had amino acid replacements in the rifampin-resistance determining region of RpoB. Six of 11 ethambutol-resistant strains had EmbB alterations. Eleven pyrazinamide-resistant strains had distinct mutations inpncA .Conclusion : Virtually all organisms evolved drug resistance independently. The types of drug resistance-associated mutations identified were very similar to changes occurring in isolates from other areas of the world. Nucleotide sequence-based strategies for rapid detection of drug resistance-conferring mutants will be applicable to organisms recovered in Peru, and potentially other areas of Latin America.     

Genetic polymorphism in Mycobacterium tuberculosis isolates from patients with chronic multidrug-resistant tuberculosis

Multidrug-resistant tuberculosis (MDR-TB) is a major public health problem because treatment is complicated, cure rates are well below those for drug-susceptible tuberculosis (TB), and patients may remain infectious for months or years, despite receiving the best available therapy. To gain a better understanding of MDR-TB, we characterized serial isolates recovered from 13 human immunodeficiency virus-negative patients with MDR-TB, by use of IS6110 restriction fragment-length polymorphism analysis, spacer oligonucleotide genotyping (i.e., "spoligotyping"), and sequencing of rpoB, katG, mabA-inhA (including promoter), pncA, embB, rpsL, rrs, and gyrA. For all 13 patients, chronic MDR-TB was caused by a single strain of Mycobacterium tuberculosis; 8 (62%) of the 13 strains identified as the cause of MDR-TB belonged to the W-Beijing family. The sputum-derived isolates of 4 (31%) of the 13 patients had acquired additional drug-resistance mutations during the study. In these 4 patients, heterogeneous populations of bacilli with different resistance mutations, as well as mixtures of drug-susceptible and drug-resistant genotypes, were observed. This genetic heterogeneity may require treatment targeted at both drug-resistant and drug-susceptible phenotypes.     

Relationship between the isoniazid-resistant mutation katGS315T and the prevalence of MDR-/XDR-TB in Osaka, Japan

OBJECTIVE: To determine the prevalence of katGS315T mutations in isoniazid (INH) resistant Mycobacterium tuberculosis and to elucidate the association of katGS315T mutations with the prevalence of multidrug-resistant tuberculosis (MDR-TB). DESIGN: From 2001 to 2004, 1655 isolates from all newly registered patients who visited the Osaka Prefectural Medical Centre for Respiratory and Allergic Diseases were tested for drug susceptibility. Genotyping was performed using insertion sequence (IS) 6110-restriction fragment length polymorphism (RFLP) in 1629 of 1655 (98.4%) cases. All 145 isolates of INH-resistant M. tuberculosis, including MDR strains, were tested to detect the katGS315T mutation. RESULTS: Five hundred and sixty isolates (34.4%) shared an RFLP pattern. Of the 145 INH-resistant isolates, 18/48 (37.5%) isolates belonging to the RFLP cluster had katGS315T and 23/97 (23.7%) did not have the mutation. Of the 66 MDR-TB cases, 18/29 (62.1%) isolates belonging to the RFLP cluster had katGS315T and 11/37 (29.7%) did not have the mutation. Of the 29 extensively drug-resistant (XDR) TB cases, 17/21 (80.9%) isolates belonging to the RFLP cluster had katGS315T and 3/8 (37.5%) did not have the mutation. CONCLUSION: The clustering rate by IS6110-RFLP was very high among MDR-/XDR-TB isolates with katGS315T. Our study indicates a strong correlation between the katGS315T mutation and the transmission dynamics of MDR-TB, and especially XDR-TB.     

Frequency and implications of pyrazinamide resistance in managing previously treated tuberculosis patients.

OBJECTIVE: To determine the extent of pyrazinamide (PZA) resistance in isolates from previously treated patients from the Western Cape, South Africa. DESIGN: Drug-resistant isolates, isolates resistant to one or more drugs other than PZA (PZA resistance is not routinely determined) (n = 127), and drug-susceptible (n = 47) clinical isolates of Mycobacterium tuberculosis from previously treated patients from the Western Cape were phenotypically (BACTEC MGIT 960) and genotypically (pncA gene sequencing) analysed for PZA resistance. RESULTS: MGIT analysis found that 68 of the 127 drug-resistant isolates were PZA-resistant. Nearly all (63/68) PZA-resistant isolates had diverse nucleotide changes scattered throughout the pncA gene, and five PZA-resistant isolates had no pncA mutations. Of the 47 phenotypically susceptible isolates, 46 were susceptible to PZA, while one isolate was PZA-monoresistant (OR = 53.0, 95% CI = 7.1-396.5). A pncA polymorphism (Thr114Met) that did not confer PZA resistance was also identified. PZA resistance was strongly associated with multidrug-resistant tuberculosis (MDR-TB). CONCLUSION: An alarmingly high proportion of South African drug-resistant M. tuberculosis isolates are PZA-resistant, indicating that PZA should not be relied upon in managing patients with MDR-TB in the Western Cape. A method for the rapid detection of PZA resistance would be beneficial in managing patients with suspected drug resistance.     

Discrepant results between pyrazinamide susceptibility testing by the reference BACTEC 460TB method and pncA DNA sequencing in patients infected with multidrug-resistant W-Beijing Mycobacterium tuberculosis strains

BACKGROUND: Mycobacterium tuberculosis strains belonging to the W-Beijing family have received broad clinical and public health attention because of their rapid worldwide spread and their frequent association with outbreaks, multidrug resistance, and treatment failures and relapses. METHODS: The present study examined a large number of multidrug-resistant strain-W isolates (isolates of 29 patients) by susceptibility testing for pyrazinamide (PZA) using the reference BACTEC 460TB method (Becton Dickinson Diagnostic Instrument Systems; Sparks, MD) and also by DNA sequencing of the pncA gene. RESULTS: We found that despite of the presence of a strain W-specific Thr47Ala in the pncA gene, all strains showed susceptibility to PZA in the reference BACTEC 460TB system due to their higher minimum inhibitory concentrations (relative to BACTEC 460TB PZA-susceptible strains). CONCLUSIONS: Our results suggest that the current radiometric reference method cannot reproducibly detect PZA resistance in patients infected with W-Beijing strains. Therefore, PZA susceptibility testing should instead be based on analysis of the pncA gene for resistance-associated mutations.     

Characterization of drug-resistant isolates of Mycobacterium tuberculosis derived from Russian inmates.

SETTING: Tuberculosis ward of a prison in Russia. OBJECTIVE: Molecular characterization of drug-resistant isolates. DESIGN: Isolates were collected from all tuberculosis patients occurring in the prison over a 1-year period. RESULTS: Of 130 patients studied, 17 patients produced pan-susceptible isolates and 113 produced isolates resistant to at least one drug, including 85 multidrug-resistant isolates. Mutations at katG315 occurred in 98% of isoniazid-resistant isolates. Mutations in rpoB were found in 89% of rifampicin-resistant isolates. Mutations in pncA occurred in 13% of the 75 isolates tested. By spoligotyping, members of the Beijing (55 isolates) and LAM (31 isolates) families were identified. By IS6110 genotyping, two groups (34 and 55 isolates) of related isolates were found, including three clusters (10, 12, and 16 isolates) with identical patterns. In a study of samples collected 3 months apart from 28 patients, four patients produced isolates containing a mixture of strains and five patients produced specimens containing distinctly different isolates. Isolates of nine patients acquired additional drug resistance. CONCLUSION: Three families of strains accounted for much of the drug-resistant tuberculosis in this population. Multiple resistance, acquisition of resistance, and infection with two or more strains as well as reinfection were observed.     

A population-based study of drug resistance and transmission of tuberculosis in an urban community.

SETTING: A low-income neighborhood of Sao Paulo, Brazil. OBJECTIVE: To determine the incidence, risk factors and transmission patterns of multidrug-resistant tuberculosis (MDR-TB). DESIGN: Prospective longitudinal study of patients with pulmonary TB (PTB). METHODS: Sputum culture-confirmed patients with PTB were recruited between March 2000 and May 2002. Bivariate and multivariate logistic regression analyses were performed to identify factors associated with MDR-TB. Mycobacterium tuberculosis isolates were tested for drug susceptibility and typed by IS6110-RFLP analysis. RESULTS: Of 420 patients, respectively 71% and 27% were new and previously treated; 15.5% of the patients' M. tuberculosis isolates were resistant to at least one drug; of these, 11% and 27% were found among new and previously treated cases, respectively. Respectively 1% and 16.7% of the new and previously treated cases were MDR-TB. RFLP analysis showed that new transmission of MDR strains was uncommon. By multivariate logistic regression analysis, previous TB and hospitalization in the 24 months before TB diagnosis were identified as independent predictors of MDR-TB. CONCLUSIONS: The results showed an intermediate level of MDR-TB incidence in a neighborhood of Sao Paulo and identified predictors that can be targeted for intervention by national and local TB control programs.     

The laboratory as a tool to qualify tuberculosis diagnosis

OBJECTIVES: To evaluate the performance of laboratory diagnosis of tuberculosis, clinical samples underwent culture, species identification and drug susceptibility testing (DST). METHODS: A total of 554 samples from 269 patients were tested for smear microscopy using Kinyoun stain. Culture was performed in Ogawa-Kudoh medium and species identification was performed using the IS6110 amplified region. DST for rifampicin, isoniazid (INH) and streptomycin were carried out using the Resazurin assay. RESULTS: Cultures augmented the number of cases diagnosed by 22.1%, IS6110 amplification identified all Mycobacterium tuberculosis strains thus isolated and DST detected three strains resistant to INH and one multidrug-resistant strain. CONCLUSION: Simultaneous use of different techniques enhanced culture yield, species identification and detection of drug resistance even in a laboratory with limited facilities.     

A clinic-based molecular epidemiologic study of tuberculosis in Monterrey, Mexico.

SETTING: A tuberculosis clinic associated with a university hospital in Monterrey, Mexico, an urban community with high tuberculosis incidence. OBJECTIVE: To determine the diversity of DNA fingerprint patterns and the extent of drug resistance of Mycobacterium tuberculosis isolates from patients who attended the clinic. DESIGN: Isolates of M. tuberculosis obtained from 186 patients during the period from 31 January 1996 to 31 March 1998 were tested for susceptibility to isoniazid, rifampicin, ethambutol and streptomycin. Demographic data and the social history of each patient were obtained prospectively by interview. The IS6110 DNA fingerprints were obtained for 166 of the 186 isolates. Secondary typing was carried out on isolates with fewer than six copies of IS6110. RESULTS: Thirty-two per cent of the tested isolates (60/ 186) were drug-resistant, and 18% (33/186) were multidrug-resistant. Approximately 55% of the resistant isolates (33/60) were attributed to acquired resistance. A total of 106 different IS6110 fingerprint patterns were observed among the 166 fingerprinted isolates. Based on both IS6110 and pTBN12 fingerprinting, 65 (39%) of the 166 isolates were part of 22 DNA fingerprint clusters. Various drug susceptibility patterns were seen in most clusters. CONCLUSION: Fingerprint clustering indicates extensive recent transmission of tuberculosis in patients attending the clinic. The prevalence of drug-resistant tuberculosis is high.     

Surveillance of drug-resistant tuberculosis and molecular evaluation of transmission of resistant strains in refugee and non-refugee populations in North-Eastern Kenya.

SETTING: Three refugee camp complex clinics and an adjacent non-refugee treatment centre in North-Eastern Kenya. OBJECTIVES: To use conventional and molecular epidemiology tools to determine: 1) the prevalence of drug resistance in newly diagnosed patients with smear-positive pulmonary tuberculosis in refugee and non-refugee populations; 2) risk factors for resistance in the two populations; and 3) whether IS6110 restriction fragment length polymorphism (RFLP) and spoligotyping showed similarities in DNA fingerprinting patterns of drug-resistant isolates that could infer transmission within and between the two populations. RESULTS: Of 241 isolates from the camps, 44 (18.3%) were resistant to one or more drugs, seven of which (2.9%) were multidrug-resistant TB (MDR-TB). Of 88 isolates from the non-refugees, five (5.7%) were resistant to one or more drugs without MDR-TB. Drug resistance was higher in the camps than in the non-refugee population (OR = 3.7; 95%CI 1.42-9.68; P < 0.007). Resistance was significantly higher in one camp compared with the other two, despite a comparable ethnic distribution. Unusually, females were more associated with drug resistance than their male counterparts in both populations (OR = 2.3; 95%CI 1.2-4.8; P = 0.008). There was evidence of transmission of streptomycin-resistant strains in the refugee population. DNA fingerprints of resistant strains from the non-refugee population were unique and different from those in the refugee camps. CONCLUSION: The observed high levels of drug resistance and MDR-TB, combined with evidence of transmission of strains resistant to streptomycin in the refugee population, suggest a need for strengthened TB control programmes in settings with a high risk of developing drug-resistant strains.     

Acquisition of drug resistance in multidrug-resistant Mycobacterium tuberculosis during directly observed empiric retreatment with standardized regimens.

The risk of acquiring additional drug resistance in strains of multidrug-resistant tuberculosis (MDR-TB) during failure of empiric standardized retreatment regimens is poorly defined. We sought to estimate this risk by comparing drug susceptibility profiles and RFLP patterns of paired MDR-TB isolates collected from 27 patients before and after retreatment failure. Among 23 patients with paired isolates with concordant RFLP patterns, 19 (83%) had become resistant to at least one additional drug after failed retreatment. In this limited group of MDR-TB patients, acquisition of resistance was common during failure of empiric drug regimens. Further study is needed to confirm these findings.     

Molecular genetics of drug-resistant Mycobacterium tuberculosis isolates in Finland, 1995-2004

SETTING: Modern molecular methods help us to understand the transmission and epidemiology of Mycobacterium tuberculosis. OBJECTIVE: To analyse the molecular epidemiology of drug-resistant tuberculosis (TB), and to characterise isoniazid (INH) and rifampicin (RMP) resistance conferring mutations in Finland during 1995-2004. DESIGN: A total of 3959 new M. tuberculosis isolates underwent drug susceptibility testing; all phenotypically resistant isolates were genotyped by IS6110 restriction fragment length polymorphism and spoligotyping if necessary. INH- and/or RMP-resistant isolates were sequenced for their resistance associated genes, katG locus 315 and rpoB, respectively. RESULT: Of the 3959 isolates tested (92.4% of culture-positive cases), 183 (4.6%) were resistant to at least one first-line anti-tuberculosis drug; 14 (0.4%) isolates were multidrug-resistant. Thirty-seven (20.4%) resistant isolates belonged to 17 clusters, and the largest cluster included four isolates. The Beijing family genotype accounted for 8.8% (16 isolates) of all drug-resistant isolates. A Ser315Thr mutation in katG was found in 46.7% (56 isolates) of the INH-resistant isolates and rpoB was mutated in 85.7% (18 isolates) of the isolates resistant to RMP. CONCLUSION: Transmission of drug-resistant TB is rare in Finland, especially between indigenous and immigrant populations. Screening of mutations that confer INH and RMP resistance seems to be feasible if risk factors for multidrug resistance exist.     

Emergence of multidrug-resistant tuberculosis in a community-based directly observed treatment programme in rural South Africa.

OBJECTIVE: Although little studied in developing countries, multidrug-resistant tuberculosis (MDR-TB) is considered a major threat. We report the molecular epidemiology, clinical features and outcome of an emerging MDR-TB epidemic. METHODS: In 1996 all tuberculosis suspects in the rural Hlabisa district, South Africa, had sputum cultured, and drug susceptibility patterns of mycobacterial isolates were determined. Isolates with MDR-TB (resistant to both isoniazid and rifampicin) were DNA fingerprinted by restriction fragment length polymorphism (RFLP) using IS6110 and polymorphic guanine-cytosine-rich sequence-based (PGRS) probes. Patients with MDR-TB were traced to determine outcome. Data were compared with results from a survey of drug susceptibility done in 1994. RESULTS: The rate of MDR-TB among smear-positive patients increased six-fold from 0.36% (1/275) in 1994 to 2.3% (13/561) in 1996 (P = 0.04). A further eight smear-negative cases were identified in 1996 from culture, six of whom had not been diagnosed with tuberculosis. MDR disease was clinically suspected in only five of the 21 cases (24%). Prevalence of primary and acquired MDR-TB was 1.8% and 4.1%, respectively. Twelve MDR-TB cases (67%) were in five RFLP-defined clusters. Among 20 traced patients, 10 (50%) had died, five had active disease (25%) and five (25%) were apparently cured. CONCLUSIONS: The rate of MDR-TB has risen rapidly in Hlabisa, apparently due to both reactivation disease and recent transmission. Many patients were not diagnosed with tuberculosis and many were not suspected of drug-resistant disease, and outcome was poor.     

The Beijing genotype is emerging among multidrug-resistant Mycobacterium tuberculosis strains from Germany.

SETTING: Germany, 1995 to 2001. OBJECTIVE: To determine the genetic relationship of 451 multidrug-resistant (MDR) Mycobacterium tuberculosis strains from Germany and to identify strains of the Beijing genotype. DESIGN: All strains were analysed using IS6110 fingerprinting and a cluster analysis was performed. Clustering of isolates was used as a measure for recent transmission. RESULTS: Two hundred and fourteen of 433 strains (49.4%) with more than four IS6110 copies formed 46 fingerprint clusters comprising two to 32 patients. Transmission links based on classical epidemiological data could be established for 39 cases (18.2%) and in 14 clusters (30.4%), and included three cases of exogenous reinfection with MDR strains. One hundred and seventy-five strains (38.8%) were of the Beijing genotype with an increasing annual proportion from 19.2% in 1995 to 58.3% in 2001. About 70% of these patients had an indication of foreign birth, mainly the former Soviet Union. CONCLUSION: Transmission of MDR strains seems to be contributing to the spread of MDR-TB in Germany, and exogenous reinfection with MDR strains must be considered as a possible cause of treatment failure. A high proportion of these MDR strains is probably carried over from the former Soviet Union, and strains of the Beijing genotype represent an increasing cause of MDR-TB in Germany.     

重庆市耐多药结核分枝杆菌gyrA与rrs基因突变特征分析

目的分析重庆市耐多药结核分枝杆菌gyrA、rrs基因突变特征及其与氧氟沙星(ofloxacin,Ofx)、卡那霉素耐药(kanamycin,Km)的关系。方法对89株耐多药结核分枝杆菌的Ofx耐药相关基因gyrA和Km耐药相关基因rrs进行序列测定,分析其基因突变特征。结果89株MDR结核分枝杆菌中有50株对Ofx耐药,其中46株(92.00%,46/50)gyrA基因发生突变,突变位点包括74、89、90、91和94位密码子;22株耐Km菌株中,19株(86.36%,19/22)发生rrs基因突变,突变类型均为A1401G。Ofx、Km耐药株的gyrA、rrs基因突变率明显高于相应敏感株的基因突变率,两者之间的差异有统计学意义(χ²=62.937,P<0.001;Fisher双侧P<0.001)。结论gyrA基因90、91、94位密码子突变是重庆市耐多药结核分枝杆菌Ofx耐药的主要机制;rrs基因A1401G突变则是Km耐药的主要原因。     

Genetic diversity and evidence for acquired antimicrobial resistance in Mycobacterium tuberculosis at a large hospital in South India.

OBJECTIVE: To assess genetic diversity and drug resistance of Mycobacterium tuberculosis isolates collected at Christian Medical College Hospital (CMCH), Vellore, India, between July 1995 and May 1996. MATERIALS AND METHODS: Isolates were subjected to IS6110-based restriction fragment length polymorphism (RFLP) analysis and tested for resistance to isoniazid, rifampin, ethambutol, streptomycin, and pyrazinamide, and DNA from selected strains was sequenced in regions associated with drug resistance. RESULTS: One hundred and one M. tuberculosis isolates were collected from 87 patients with pulmonary tuberculosis. Charts of 69 patients were reviewed for history of tuberculosis illness and treatment. DNA from 29 strains was sequenced in katG, rpoB, and gyrA, and sometimes pncA regions. Analysis by RFLP revealed a high degree of genetic diversity, with no identifiable clusters of infection. Of the strains tested, 51% were resistant to at least one antibiotic, and 43% were resistant to more than one drug. There was a high rate of resistance observed in patients whose charts indicated a history of improperly administered tuberculosis treatment, whereas little drug resistance was observed in patients never previously treated for tuberculosis. Sequencing of genes associated with drug resistance revealed several previously unreported mutations in resistant strains. CONCLUSIONS: This analysis suggests that the cases of tuberculosis in the sample are largely reactivation of long-standing infections and that the drug resistance among patients in CMCH is largely acquired or secondary rather than attributable to the spread of drug-resistant strains.     

rpoB mutations as an epidemiologic marker in rifampin-resistant Mycobacterium tuberculosis.

SETTING: Cases of rifampin-resistant Mycobacterium tuberculosis from the prison population in Madrid and from the general population in Spain. OBJECTIVE: To identify the rpoB mutations associated with resistance to rifampin and to investigate rpoB genotyping as an epidemiological marker in rifampin-resistant M. tuberculosis. DESIGN: Twenty-nine rifampin-resistant clinical isolates of M. tuberculosis, 15 obtained from the prison population in Madrid and 14 from the general population in Spain, were characterized by sequence analysis of the 81-bp core region of the rpoB gene and IS6110 DNA fingerprinting. RESULTS: All the isolates had mutations in rpoB, with those in codon 531 accounting for 41% of the total. Twenty-three (79%) isolates were highly resistant to rifampin (minimum inhibitory concentration > or = 64 mg/L). Nineteen different IS6110 fingerprints were observed: one was shared by seven isolates, one by three, two by two, and 15 were unique. Two IS6110 clusters could be divided into subclusters on the basis of rpoB analysis. Epidemiologic links were identified among patients whose isolates had identical IS6110 patterns and rpoB genotypes, but not between those with identical IS6110 patterns and different rpoB genotypes. CONCLUSION: Characterization of rpoB mutations can provide information about susceptibility to rifampin and be a useful epidemiological tool for discrimination of rifampin-resistant strains of M. tuberculosis with identical IS6110 fingerprints.     

Second-line drug resistance in multidrug-resistant tuberculosis cases of various origins in the Netherlands

SETTING: The Netherlands. OBJECTIVE: To investigate the frequency of resistance to second-line drugs among multidrug-resistant tuberculosis (MDR-TB) cases and its correlation with patients' geographic origin. DESIGN: Retrospective laboratory database study of multidrug-resistant Mycobacterium tuberculosis complex strains isolated in the Netherlands between January 1993 and October 2007. RESULTS: We found 153 patients with MDR-TB, of whom 18 (12%) were native Dutch. Complete second-line drug susceptibility testing was performed for 131 MDR-TB patients. Resistance to second-line drugs was noted in primary samples of 28 (21%) MDR-TB patients. Resistance to a single second-line drug was most frequent (24/28 [86%]; 9 to prothionamide [PTH], 6 to para-aminosalicylic acid, 4 to amikacin [AMK], 4 to ciprofloxacin and 1 to cycloserine). Four MDR-TB patients had strains resistant to multiple second-line drugs; two were extensively drug-resistant M. bovis. In MDR-TB patients of European and Central Asian origin, resistance to second-line drugs was most frequent and involved the widest range of drugs. PTH resistance was frequent among African and American MDR-TB patients, while AMK resistance was frequent among South-East Asians. CONCLUSION: Resistance to second-line drugs is infrequent among MDR-TB patients in the Netherlands. Most second-line drug resistance is recorded among immigrants, with substantial differences in second-line drug resistance in MDR-TB patients originating from different geographical areas.