Genotypes and drug susceptibility of Mycobacterium tuberculosis Isolates in Shihezi, Xinjiang Province, China

Drug sensitivity of clinical isolates of Mycobacterium tuberculosis and its association with bacterial genotype in the Somali region, Eastern Ethiopia

Background

Drug resistance is becoming a major bottleneck for tuberculosis (TB) control programs in countries with high TB burdens. Although several studies were conducted on the drug sensitivity of Mycobacterium tuberculosis (M. tuberculosis) in central Ethiopia, there is a lack of data on the drug sensitivity of M. tuberculosis in the peripheral regions of the country including in the Somali region. Therefore, the objective of this study was to evaluate the drug sensitivity of M. tuberculosis and its association with bacterial genotype and evaluate the performance of Xpert MTB/RIF (Xpert) in detecting resistance to rifampicin (RIF).

Methods

A total of 302 M. tuberculosis were tested using the BD BACTEC-Mycobacteria Growth Indicator Tube 960 (MGIT 960) system for their drug sensitivity to the first-line anti-TB drugs. Besides, the drug sensitivity of 10 multidrug-resistant (MDR) M. tuberculosis isolates was evaluated for the second-line anti-TB drugs. Additionally, 177 of the 302 isolates were tested for genotypic drug resistance using Xpert. Chi-square and Fisher's exact tests were used for the evaluation of the association between variables and drug sensitivity.

Results

The overall prevalence of resistance to at least one drug was 11.6% (95% CI: 7.9-15.2%), while the prevalence of MDR was 3.3% (95% CI: 1.3-5.3%). Two of the 10 MDR isolates were resistant to capreomycin. The spoligotype Shared International Type (SIT) 149 was significantly associated with either monoresistance or MDR (p < 0.05). Of the 177 isolates tested by Xpert, 6.2% (11/177) were RIF-resistant. Discordant between Xpert and MGIT 960 was observed in one isolate and linked with probe-binding delay (ΔCT max = 5.8). The sensitivity and specificity of the Xpert assay were 100 and 99.4%, respectively, while its positive and negative predictive values were 90.9 and 100%, respectively.

Conclusion

The magnitude of MDR M. tuberculosis in the Somali region of Ethiopia was higher than the national prevalence of MDR-TB warranting the strengthening of the TB control program in the Somali region. Besides, drug resistance was associated with SIT 149 spoligotype (genotype). The Xpert assay was observed to have high sensitivity and specificity in detecting RIF-resistant M. tuberculosis, which is encouraging for its application widely.

Multidrug-Resistant Tuberculosis—Diagnostic Procedures and Treatment of Two Beijing-like TB Cases

The Beijing/W genotype is one of the major molecular families of Mycobacterium tuberculosis complex (MTBC), responsible for approximately 50% of tuberculosis (TB) cases in Far East Asia and at least 25% of TB cases globally. Studies have revealed that the Beijing genotype family is associated with a more severe clinical course of TB, increased ability to spread compared to other genotypes, and an unpredictable response to treatment. Based on the profile of spacers 35–43 in the Direct Repeat (DR) locus of the MTBC genome determined by spoligotyping, classical (typical) and modern (Beijing-like) clones can be identified within the Beijing family. While the modern and ancient Beijing strains appear to be closely related at the genetic level, there are marked differences in their drug resistance, as well as their ability to spread and cause disease. This paper presents two cases of drug-resistant tuberculosis caused by rare mycobacteria from the Beijing family: the Beijing 265 and Beijing 541 subtypes. The genotypes of isolated strains were linked with the clinical course of TB, and an attempt was made to initially assess whether the Beijing subtype can determine treatment outcomes in patients.

Beijing genotype of Mycobacterium tuberculosis is associated with extensively drug-resistant tuberculosis: A global analysis

We found that the frequency of Beijing genotype among XDR-TB strains was high. The data in this study would help guide the TB control program, and we however need further investigation to confirm the reliability of the present findings.

Circulating strains of Mycobacterium tuberculosis: 24 loci MIRU-VNTR analysis in Bangladesh

Bangladesh is among the high burden countries for tuberculosis (TB) and multidrug resistant TB (MDR-TB). As the genetic diversity and distinct phylogeographic distribution of Mycobacterium tuberculosis are responsible for regional differences in drug resistance, this cross sectional study was conducted to identify the circulating M. tuberculosis strains belonging to different lineages among pulmonary tuberculosis and, to investigate the contribution of distinct M. tuberculosis lineages to rifampicin resistant (RR) and rifampicin sensitive (RS) TB. A total of 40 RR and 20 RS isolates were enrolled in this study, all of which confirmed as M. tuberculosis by MPT 64 antigen detection. Furthermore, all isolates were genotyped by 24 loci Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats (MIRU-VNTR), thus comprising the first study to employ this approach in Bangladesh. Beijing was the predominant lineage (26.8%) followed by EAI (23.2%), Delhi/CAS (16.1%), H37Rv (8.9%), Haarlem (7.1%), LAM (5.4%), Cameroon (3.6%) and a NEW-1 (1.8%). Four (7.1%) isolates remained as unidentified. Beijing strains were the significantly predominant (36.8%; p = 0.0135) among the RR isolates in comparison with other strains whereas EAI was the predominant (38.8%) lineage among RS isolates. Also, approximately 13% RR isolates showed genotypic resistance against fluoroquinolones by LPA and, hence, classed as pre-XDR TB albeit no specific lineage was found associated with these latter strains. A low transmission rate (10.5%) and high genetic diversity was detected in this setting with all the clustered strains herein identified belonging to the Beijing lineage. This study highlights 24 loci MIRU-VNTR analysis as a powerful tool for genotyping of Mycobacterium tuberculosis in this setting as it shows a high discriminatory index (0.81).

Circulation of M. tuberculosis Beijing genotype in Latin America and the Caribbean

Lineage 2 (East Asian), which includes the Beijing genotype, is one of the most prevalent lineages of Mycobacterium tuberculosis (Mtb) throughout the world. The Beijing family is associated to hypervirulence and drug-resistant tuberculosis. The study of this genotype's circulation in Latin America is crucial for achieving total control of TB, the goal established by the World Health Organization, for the American sub-continent, before 2035. In this sense, the present work presents an overview of the status of the Beijing genotype for this region, with a bibliographical review, and data analysis of MIRU-VNTRs for available Beijing isolates. Certain countries present a prevalent trend of <5%, suggesting low transmissibility for the region, with the exception of Cuba (17.2%), Perú (16%) and Colombia (5%). Minimum Spanning Tree analysis, obtained from MIRU-VNTR data, shows distribution of specific clonal complex strains in each country. From this data, in most countries, we found that molecular epidemiology has not been a tool used for the control of TB, suggesting that the Beijing genotype may be underestimated in Latin America. It is recommended that countries with the highest incidence of the Beijing genotype use effective control strategies and increased care, as a requirement for public health systems.

Genotypes and genetic characters of Mycobacterium tuberculosis from Myanmar using three typing methods

Knowledge on basic characteristics of Mycobacterium tuberculosis (MTB) is helpful to understand the disease epidemiology and support the prediction of clinical outcome of the disease. The aim of this study was to detect the genotypes and genotypic characters of clinical Mycobacterium tuberculosis (MTB) isolates from new and retreatment rifampicin-resistant patients using three different genotyping methods. Mycobacterial interspersed repetitive units-variable number tandem repeat (MIRU-VNTR) typing was used to determine the diversity of 222 clinical isolates. Spoligotyping and IS6110-restriction fragment length polymorphism (RFLP) typing were also used to investigate the genetic characters of 105 MTB strains. Among the 15 genotypes detected by MIRU-VNTR, Beijing strains were the most prevalent of all strains (54.8%); new cases (40.5%) and retreatment cases (69.4%), followed by EAI strain. Spoligotyping categorized the strains into 11 lineages and 13 orphans whereas 96 different IS6110 patterns were identified using RFLP method. The mode number of IS6110 was 18 and 20. Higher band numbers were found in Beijing genotype (p < 0.001). Clustering rates by spoligotyping, MIRU-VNTR and IS6110-RFLP typing were 0.714, 0.004 and 0.085, respectively. Discriminatory powers of spoligotyping, MIRU-VNTR typing and IS6110-RFLP typing were 0.637, 1.000 and 0.997, respectively. Dominant Beijing genotype in both new and retreatment cases denoting that prevailing tuberculosis in Myanmar changed from EAI to Beijing lineage.

Molecular & genetic characteristics of Mycobacterium tuberculosis strains circulating in the southern part of West Siberia

Background & objectives:

A complicated epidemiological situation characterized by significantly high tuberculosis (TB) morbidity is observed in West Siberia. This study was aimed to investigate the genetic characteristics of Mycobacterium tuberculosis circulating in the southern part of West Siberia (in the Omsk region).

Methods:

From March 2013 to January 2015, 100 isolates of M. tuberculosis were obtained from patients with pulmonary TB living in the Omsk region. Drug susceptibility testing was performed on Lowenstein-Jensen medium (absolute concentration method). Genetic typing of isolates was carried out by variable number tandem repeats of mycobacterial interspersed repetitive units (MIRU-VNTR) typing and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis. The genetic types and characteristics of cluster strains were determined using 15 MIRU-VNTR loci.

Results:

Thirty six VNTR types were found. Twenty six (26.0%) isolates had a unique profile, and the remaining 74 were grouped in 10 clusters containing from 2 to 23 isolates. The Beijing genotype was found in 72 isolates, 61 (85.0%) of which were part of five clusters that included two large clusters containing 23 isolates. Other genetic families, such as Latin-American Mediterranean (LAM, 11.0%), S family (2.0%) and Haarlem (4.0%), were also detected. The genetic family of 11 isolates could not be determined. Six different VNTR profiles were found in these non-classified isolates. Only 16 per cent of isolates were sensitive to anti-TB drugs. The katG315 (94.8%) and rpoB531 (92.2%) mutations were identified in 77 multidrug-resistant M. tuberculosis isolates.

Interpretation & conclusions:

This study showed that the M. tuberculosis population in the Omsk region was heterogeneous. The Beijing genotype predominated and was actively spreading. The findings obtained point to the need for the implementation of more effective preventive measures to stop the spread of drug-resistant M. tuberculosis strains.

Molecular Subtyping of Salmonella enterica Serovar Typhi by Pulsed-Field Gel Electrophoresis and Multiple-Locus Variable-Number Tandem-Repeat Analysis in India: Their Association with Antimicrobial Resistance Profiles

Molecular subtyping and DNA sequencing-based methods, which are commonly used for discriminating Salmonella enterica serovar Typhi (S. Typhi) isolates, lead to improved molecular epidemiological investigations for prevention and control of typhoid fever. We obtained S. Typhi blood isolates (n = 66) from India during 2007-14 for molecular subtyping by pulsed-field gel electrophoresis (PFGE) and multiple-locus variable-number tandem-repeat (VNTR) analysis (MLVA) in association with antibiotic resistance profiles. Genotypic diversity was observed more by MLVA (Simpson's index of diversity, D value = 0.997) than PFGE (D value = 0.864). Two prevalent pulsotypes containing nalidixic acid-resistant (NAL^R) and NAL^R-ciprofloxacin-resistant (CIP^R) S. Typhi isolates circulated in India. Multidrug-resistant (MDR), NAL^R-CIP^R, and most NAL^R isolates were found to be clonal by PFGE. MLVA could differentiate the clonal isolates. Most of the MDR and NAL^R-CIP^R isolates showed variation in single or double VNTR loci, whereas NAL^R isolates varied in more than 2 loci, reflecting higher genetic diversity among the NAL^R isolates. Of the 6 VNTR loci, TR4,699 (D value = 0.838) and Sal02 (D value = 0.890) loci played important roles as MLVA cluster-supporting alleles. The rapid turnaround time and high-level discriminatory power of MLVA may be useful for tracking and controlling the transmission of S. Typhi isolates during epidemiological investigations.

Frequency of rrs and rpsL mutations in streptomycin-resistant Mycobacterium tuberculosis isolates from Iranian patients

OBJECTIVES

Streptomycin (SM) is one of the most effective drugs for the treatment of multidrug-resistant (MDR) tuberculosis. However, resistance to SM is increasingly reported, mainly due to mutations in the rpsL and rrs genes. This study was designed with the aim of determining the nature of SM resistance and the type and frequency of rpsL and rrs mutations among SM-resistant Mycobacterium tuberculosis (MTB) isolates from Iran.

METHODS

A total of 100 clinical monoresistant and MDR MTB isolates were subjected to drug susceptibility testing (DST) for SM. SM-resistant isolates were genotyped by MIRU-VNTR typing. Fragments of the rpsL and rrs genes were amplified to investigate the most common mutations, with subsequent sequence analysis.

RESULTS

By DST, 32 isolates (32%) were identified as SM-resistant, of which 50% (16/32) were MDR. By MIRU-VNTR typing, the SM-resistant isolates were classified into 20 different MIRU types and 8 clusters, with Beijing (22%) being the most prevalent genotype. Mutations in the rrs and rpsL genes were identified in 14 (44%) and 10 (31%) of the 32 SM-resistant isolates, respectively. The most common mutations were at rpsL nucleotide 128 (AAG→AGG, Lys43Arg), found in 7 SM-resistant isolates (22%) and nucleotide 263 (A→G, Lys88Arg) in 3 SM-resistant isolates (9%).

CONCLUSIONS

The results suggest an association between rpsL mutation and SM-resistant strains of Beijing genotype. The existence of SM resistance in 25% of isolates without mutation in rrs and rpsL suggests the occurrence of further mechanisms associated with SM resistance in these isolates.

Immunological Roles of Elevated Plasma Levels of Matricellular Proteins in Japanese Patients with Pulmonary Tuberculosis

Elevated matricellular proteins (MCPs), including osteopontin (OPN) and galectin-9 (Gal-9), were observed in the plasma of patients with Manila-type tuberculosis (TB) previously. Here, we quantified plasma OPN, Gal-9, and soluble CD44 (sCD44) by enzyme-linked immunosorbent assay (ELISA), and another 29 cytokines by Luminex assay in 36 patients with pulmonary TB, six subjects with latent tuberculosis (LTBI), and 19 healthy controls (HCs) from Japan for a better understanding of the roles of MCPs in TB. All TB subjects showed positive results of enzyme-linked immunospot assays (ELISPOTs). Spoligotyping showed that 20 out of 36 Mycobacterium tuberculosis (MTB) strains belong to the Beijing type. The levels of OPN, Gal-9, and sCD44 were higher in TB (positivity of 61.1%, 66.7%, and 63.9%, respectively) than in the HCs. Positive correlations between OPN and Gal-9, between OPN and sCD44, and negative correlation between OPN and ESAT-6-ELISPOT response, between chest X-ray severity score of cavitary TB and ESAT-6-ELISPOT response were observed. Instead of OPN, Gal-9, and sCD44, cytokines G-CSF, GM-CSF, IFN-α, IFN-γ, IL-12p70, and IL-1RA levels were higher in Beijing MTB-infected patients. These findings suggest immunoregulatory, rather than inflammatory, effect of MCPs and can advance the understanding of the roles of MCPs in the context of TB pathology.

Drug-resistant tuberculosis viewed from bacterial and host genomes

The outcome of infection with Mycobacterium tuberculosis (MTB) is largely influenced by the host-pathogen interaction in which both the human host and the MTB genetic backgrounds play an important role. Whether this interaction also influences the selection and expansion of drug-resistant MTB strains is the primary focus of this review. We first outline the main and recent findings regarding MTB determinants implicated in the development of drug resistance. Second, we examine data regarding human genetic factors that may play a role in TB drug resistance. We highlight interesting openings for TB research and therapy.

Molecular Typing Characteristic and Drug Susceptibility Analysis of Mycobacterium tuberculosis Isolates from Zigong, China

China is one of the 22 countries with high TB burden worldwide, and Sichuan contained the second-largest number of TB cases among all of the Chinese provinces. But the characteristics of Mycobacterium tuberculosis circulated in Zigong, Sichuan, were still unknown. To investigate the character and drug resistance profile, 265 clinical isolates were cultured from tuberculosis patient's sputum samples in the year of 2010, of which the genetic profile was determined by using Spoligotyping and MIRU-VNTR typing methods, and the drug sensibility testing to the four first-line and four second-line antituberculosis (anti-TB) drugs was performed by using proportion method on Lowenstein-Jensen (L-J) media. The major Spoligotype was Beijing family (143/265, 53.96%), followed by T (80/265, 30.19%) and H (9/265, 3.40%) genotypes; the total Hunter-Gaston discrimination index (HGDI) of the 24 loci MIRU-VNTR was 0.9995. About 27.17% (72/265) of the isolates were resistant to at least one of the eight tested anti-TB drugs, and for Beijing and non-Beijing family isolates the proportion of drug resistance was 28.47% (41/144) and 25.62% (31/121), respectively. That is, the most prevalent genotype here was Beijing family, and the 24 loci VNTR analysis could supply a high resolution for genotyping, and Beijing and non-Beijing isolates had no difference (p > 0.05) for drug resistance.

The variations of IL-23R are associated with susceptibility and severe clinical forms of pulmonary tuberculosis in Chinese Uygurs

Background

The incidence of tuberculosis (TB) remains high among Chinese Uygurs (a long-dwelling ethnic minority in Xinjiang) in China and the variants in IL-23R likely contribute to individual’s diversity in host response during infection.

Methods

A hospital based one to one matched case–control study was performed to assess the role of single nucleotide polymorphisms (SNPs) and copy number variation (CNV) of IL-23R in susceptibility and clinical features of pulmonary TB in Chinese Uygurs. Thirteen SNPs in IL-23R were genotyped by multiplex SNaPshot and a CNV was analyzed using Taqman real-time PCR in 250 pairs of pulmonary TB patients and controls.

Results

The SNP rs7518660 (OR = 4.78, 95 % CI 3.14–8.52) and the CNV in IL23R (OR = 2.75, 95 % CI 1.51–4.98) were significantly associated with susceptibility to pulmonary TB. The SNP rs11465802 (OR = 3.23, 95 % CI 1.85–5.62) was significantly associated with drug-resistance and the SNP rs1884444 (OR = 3.61, 95 % CI 1.90–6.85) was significantly related to cavitary lesion in Chinese Uygurs.

Conclusions

Our study shows for the first time that SNP and CNV in IL23R were associated with susceptibility, drug resistance and cavity formation of pulmonary TB. Our findings indicate that these IL-23R polymorphisms may be considered as risk factors for active pulmonary TB and its severe clinical forms.

Electronic supplementary material

The online version of this article (doi:10.1186/s12879-015-1284-2) contains supplementary material, which is available to authorized users.

Registration and management of community patients with tuberculosis in north-west China

OBJECTIVES

To describe the registration, management and characteristics of patients with tuberculosis (TB) in north-west China, and investigate whether patients with TB were diagnosed and treated in a timely manner.

STUDY DESIGN

Health-facility-based retrospective data were collected from district patient registers and case reports for all patients with TB registered from January 2009 to December 2011 in Xinjiang Uygur Autonomous Region, north-west China.

METHODS

Patient characteristics and clinical data were collected from the national TB epidemic reporting system using standardized case reporting forms for diagnosis, treatment and outcome. Data were collected and entered by trained health staff in the regional TB clinics.

RESULTS

In total, data for 20,396 patients with TB were collected; of these, 78.5% were farmers. The age peaks were 20-44 years and 60-74 years. Average health-seeking and diagnostic delays were 32 days and two days, respectively. More than half (54.7%) of the patients with smear-negative TB were diagnosed by chest x-ray. Moreover, 94.3% of patients with TB were treated successfully. From 2009 to 2011, the health-seeking delay decreased significantly (P < 0.05), and the diagnostic delay increased significantly (P < 0.05). A significant decreasing trend in smear-positive TB was observed (P < 0.05), along with an increasing trend in treatment success (P < 0.05).

CONCLUSIONS

In north-west China, there is a need to focus on key high-risk populations for prevention and control of TB, such as those aged 20-44 years and 60-74 years, males and farmers. Delays in diagnosis and treatment have a negative effect on cure rates and make it more difficult to control the propagation of TB.

There is no correlation between sublineages and drug resistance of Mycobacterium tuberculosis Beijing/W lineage clinical isolates in Xinjiang, China

The Beijing/W lineage strains are the major prevalent strains in China. The prevalence, mortality and drug-resistant rates of tuberculosis in Xinjiang, Northwestern China are higher than in other parts of the country. Our previous study results showed that the dominant strains of Mycobacterium tuberculosis (MTB) were ‘Beijing/W lineage’ MTB in Xinjiang; those strains had no significant correlation with drug resistance. We investigated whether the prevalence of ‘Beijing/W lineage’ sublineage strains was associated with drug resistance. We collected 478 sputum specimens from patients with pulmonary tuberculosis. Beijing/W strains and their sublineages were identified by distinguishing five specific large sequence polymorphisms, using polymerase chain reaction. All strains were subjected to a drug susceptibility test using the proportion method on Löwenstein–Jensen culture medium. In total, 379 clinical isolates of MTB were isolated and identified, 57·26% of these isolates were identified as Beijing/W strains, of which 11·06% isolates were in sublineage 105, 14·74% isolates in sublineage 207, 69·59% isolates in sublineage 181, and 4·61% isolates in sublineage 150. None of the isolates was in sublineage 142. Our data showed there were four sublineages of Beijing/W isolates in Xinjiang province, China. However, there were no correlations between drug resistance and the sublineages of Beijing/W strains.

Molecular assessment, drug-resistant profile, and spacer oligonucleotide typing (spoligotyping) of Mycobacterium tuberculosis strains from Tamaulipas, México

BACKGROUND

Tuberculosis remains a serious global health problem involving one-third of the world population. A wide diversity of Mycobacterium tuberculosis strains cause about 1.5 million deaths/year worldwide, but in developing countries, the genetic diversity of M. tuberculosis strains remains largely unknown. We conducted a first insight into the population diversity of M. tuberculosis strains from Tamaulipas, Mexico.

METHODS

Seventy-two M. tuberculosis strains were identified and genetic diversity determined by spoligotyping. Drug sensibility testing and punctual mutations in inhA, ahpC, rpoB, and katG genes were assessed.

RESULTS

Spoligotyping analysis showed a higher prevalence of LAM9 > T1 > Haarlem3 subfamilies among 53 spoligotype patterns. Unexpectedly, five Beijing strains conforming four unique spoligopatterns were recovered. The more frequently isolated strains (LAM9 and T1), but none of the Beijing strains, were found resistant to INH or RIF. Also, no drug resistance was found among Haarlem3 isolates. The katG(315) gene mutation was found in 83% of INH-resistant strains, whereas rpoB(526) were associated in only 43% of RIF M. tuberculosis drug-resistant strains.

CONCLUSIONS

This and other studies report a high rate of orphan spoligotypes, which highlights the need for genotyping implementation as a routine technique for better understanding of M. tuberculosis strains in developing countries such as Mexico.