Molecular characterization of drug-resistant Mycobacterium tuberculosis among Filipino patients derived from the national tuberculosis prevalence survey Philippines 2016.

Tuberculosis, caused by Mycobacterium tuberculosis, remains a high burden disease and leading cause of mortality in the Philippines. Understanding the genetic diversity of M. tuberculosis strains in the population, including those that are multi-drug resistant (MDR), will aid in formulating strategies for effective TB control and prevention. By whole genome sequencing of M. tuberculosis isolates (n = 100) from patients of the Philippine 2016 National Tuberculosis Prevalence Survey, we sought to provide a baseline assessment of the genotypic and phylogenetic characteristics of the isolates. The majority (96/100) of the isolates were EAI2-Manila strain-type (lineage 1), with one Lineage 2 (Beijing), one Lineage 3 (CAS1), and two Lineage 4 (LAM9) strains. The EAI2-Manila clade was not significantly associated with patient's phenotypic and in silico drug resistance profile. Five (5/6) MDR-TB isolates predicted by in silico profiling were concordant with phenotypic drug resistance profile. Twenty-one mutations were identified in nine drug resistance-related genes, all of which have been reported in previous studies. Overall, the results from this study contribute to the growing data on the molecular characteristics of Philippine M. tuberculosis isolates, which can help in developing tools for rapid diagnosis of TB in the country, and thereby reducing the high burden of disease.

High TB burden and low notification rates in the Philippines: The 2016 national TB prevalence survey.

SETTING: The 3rd national tuberculosis (TB) survey in the Philippines in 2007 reported a significant decline in the prevalence of TB. Since then, more significant investments for TB control have been made, yet TB burden estimates from routine surveillance data remain relatively stable. OBJECTIVE: To estimate the prevalence of bacteriologically confirmed pulmonary TB in the Philippines amongst individuals aged ≥15 years in 2016. DESIGN: In March-December 2016, we conducted a population-based survey with stratified, multi-stage cluster sampling of residents in 106 clusters aged ≥15 years. Survey participants were screened for TB by symptom-based interview and digital chest X-ray. Those with cough ≥2 weeks and/or haemoptysis and/or chest X-ray suggestive of TB were requested to submit 2 sputum specimens for Xpert MTB/RIF, direct sputum smear microscopy using LED fluorescent microscopy, and mycobacterial solid culture (Ogawa method). Bacteriologically confirmed pulmonary TB was defined as MTB culture positive and/or Xpert positive. RESULTS: There were 46,689 individuals interviewed, and 41,444 (88.8%) consented to a chest X-ray. There were 18,597 (39.8%) eligible for sputum examination and 16,242 (87.3%) submitted at least one specimen. Out of 16,058 sputum-eligible participants, 183 (1.1%) were smear-positive. There were 466 bacteriologically confirmed TB cases: 238 (51.1%) Xpert positive, 69 (14.8%) culture positive, and 159 (34.1%) positive by both Xpert and culture. The estimated TB prevalence per 100,000 population aged ≥15 years was 434 (95% CI: 350-518) for smear-positive TB, and 1,159 (95% CI: 1,016-1,301) for bacteriologically confirmed TB. CONCLUSION: This nationally representative survey found that the TB burden in the Philippines in 2016 was higher than estimated from routine TB surveillance data. There was no evidence of a decline in smear and culture positive TB from the 2007 survey despite significant investments in TB control. New strategies for case-finding and patient-centered care must be intensified and expanded.

Whole-genome sequencing and single nucleotide polymorphisms in multidrug-resistant clinical isolates of Mycobacterium tuberculosis from the Philippines.

OBJECTIVES: Thousands of cases of multidrug-resistant tuberculosis (TB) have been observed in the Philippines, but studies on the Mycobacterium tuberculosis (MTB) genotypes that underlie the observed drug resistance profiles are lacking. This study aimed to analyse the whole genomes of clinical MTB isolates representing various resistance profiles to identify single nucleotide polymorphisms (SNPs) in resistance-associated genes. METHODS: The genomes of ten MTB isolates cultured from banked sputum sources were sequenced. Bioinformatics analysis consisted of assembly, annotation and SNP identification in genes reported to be associated with resistance to isoniazid (INH), rifampicin (RIF), ethambutol (ETH), streptomycin, pyrazinamide (PZA) and fluoroquinolones (FQs). RESULTS: The draft assemblies covered an average of 97.08% of the expected genome size. Seven of the ten isolates belonged to the Indo-Oceanic lineage/EA12-Manila clade. Two isolates were classified into the Euro-American lineage, whilst the pre-XDR (pre-extensively drug-resistant) isolate was classified under the East Asian/Beijing clade. The SNPs katG Ser315Thr, rpoB Ser450Leu and embB Met306Val were found in INH- (4/7), RIF- (3/6) and ETH-resistant (2/6) isolates, respectively, but not in susceptible isolates. Mutations in the inhA promoter and in the pncA and gyrA genes known to be involved in resistance to INH, PZA and FQs, respectively, were also identified. CONCLUSIONS: This study represents the first effort to investigate the whole genomes of Philippine clinical strains of MTB exhibiting various multidrug resistance profiles. Whole-genome data can provide valuable insights to the mechanistic and epidemiological qualities of TB in a high-burden setting such as the Philippines.

Integrated surveillance of pulmonary tuberculosis and paragonimiasis in Zamboanga del Norte, the Philippines.

BACKGROUND: Pulmonary tuberculosis (PTB) and paragonimiasis remain as health problems in certain areas in the Philippines. Both share similar clinical manifestations, which include chronic productive cough, hemoptysis, dyspnea, fever, weight loss, and night sweats. This study aimed to determine the prevalence of PTB, paragonimiasis, and co-infections in Zamboanga del Norte, Philippines. METHODS: This study was conducted in selected villages in two municipalities in Zamboanga del Norte. Patients with chronic cough were interviewed, examined, and requested to submit two sputum samples which were processed using Ziehl-Neelsen method to detect acid-fast bacilli (AFB), and NaOH concentration technique for the detection of Paragonimus ova. RESULTS: A total of 836 patients submitted sputum samples for examination. Prevalence was 6·7% (2·5-12·7%) for paragonimiasis and 1·9% (0·9-6·3%) for PTB. Co-infection rate was 0·3%, with two identified cases. Positivity rates for males and females were 9·6 and 5·8% for paragonimiasis and 3·4 and 1·2% for PTB. CONCLUSION: Pulmonary tuberculosis and paragonimiasis are co-endemic in Zamboanga del Norte, suggesting the need to integrate surveillance and control efforts. Strengthening local health systems through collaboration between different sectors is recommended for effective disease control. Development of more sensitive diagnostic tests is important for more accurate disease surveillance.

A molecular epidemiologic analysis of Mycobacterium tuberculosis among Filipino patients in a suburban community in the Philippines.

BACKGROUND: The Philippines is designated as one of the high tuberculosis (TB) burden countries by WHO. We conducted a molecular epidemiologic analysis of Mycobacterium tuberculosis isolates collected from patients consulting at the health clinics in the city of Santa Rosa, Laguna, a suburban community in the Philippines. METHODS: A total of 116 M. tuberculosis isolates were characterized and genotyped using spoligotyping and 15 loci of variable number of tandem repeats of mycobacterial interspersed repetitive units (15 MIRU-VNTR). The strains were then compared with the international spoligotyping database (SpolDB4). Cluster analyses were done using 15 MIRU-VNTR and spoligotyping. RESULTS: Majority of the patients with pulmonary tuberculosis were young (18-29 year age group at 41.4%) and male (62.1%). 86/116 (74.1%) were sputum-smear positive and 43/116 (37.1%) had severe pulmonary tuberculosis. When the genotyping results were compared to the SpolDB4, there were 10 identified Spoligo-International-Types (SITs) with SIT 19 as the predominant SIT (89/116, 76.7%). 10 out of 116 (8.6%) did not match any SIT in the SpolDB4. The distribution of strains according to major M. tuberculosis clades was as follows: EAI2_Manilla (101/116, 87.1%; U 2/116, 1.7%; LAM2 1/116, 0.9%; EAI3_Ind 1/116, 0.9%; MANU2 1/116, 0.9%. Using univariate and multivariate analysis, there was no significant association shown between the EAI2_Manilla clade and SIT with patient characteristics such as sex and age groups as well as bacillary load based on sputum-smear positivity and severity of pulmonary tuberculosis. Using logistic regression, no patient characteristic, as well as bacillary load or severity of TB, were significant predictors for clade or SIT. Based on the molecular typing method used, spoligotyping identified 4 clusters and 20 genotypes (16 unique strains) with a Hunter-Gaston discrimination index (HGDI) of 0.409. 15 MIRU-VNTR identified 16 clusters and 69 genotypes (53 unique strains) with an HGDI of 0.960. The combination of spoligotyping and 15 MIRU-VNTR identified 11 clusters and 79 genotypes (68 unique strains) with the highest HGDI at 0.970. High case rate of TB among young people in this community suggests the high transmission rate of infection. However, in the absence of significant association between clustering and age, the interpretation of observed high cluster rate warrants caution, and requires further molecular and epidemiological observation. CONCLUSION: This is the first molecular epidemiology study to show the distribution of genotypes of the M. tuberculosis strains, systematically and prospectively sampled, of the patient population in a suburban community in the Philippines. The combination of spoligotyping and 15 MIRU-VNTR identified 11 clusters and 79 genotypes (68 unique strains) with the highest HGDI at 0.970. High case rate of TB among young people in this community suggests the high transmission of infection. However, in the absence of significant association between clustering and age, the interpretation of observed high cluster rate warrants caution, and requires further molecular and epidemiological observation.

Detection and characterization of mutations of multidrug-resistant tuberculosis isolates of the Philippine General Hospital

BACKGROUND: Emergence of multidrug-resistant tuberculosis (MDR-TB) poses a major challenge to prevailing disease management. MDR-TB arises from mutations in several genes comprising the resistance determining regions, including rpoB, katG and gyrA. OBJECTIVE: To detect and characterize mutations in rpoB, katG and gyrA. METHODS: Thirty selected Mycobacterium tuberculosis isolates from the IDS-PGH were subjected to PCR amplification and sequencing. Sequences were compared to the wild type strain H37Rv. RESULTS: Mutations were detected in codons 512, 513, 516, 522, 526, 531 and 533 of rpoB, codons 280, 281, 315 and 333 of katG, and codons 90 and 94 of gyrA sequences. The most frequently mutating codons for rpoB, katG and gyrA were 531, 315 and 94, respectively. A clustering analysis of the sequences showed occurrence of seven, four and three clusters for the genes rpoB, katG and gyrA, respectively. The eight clusters obtained from the concatenated sequences of the three genes represent the eight potential genotypes of local strains. One cluster represents the wild type strain genotype, another cluster represents the XDR strain genotype, and six clusters represent the MDR strain genotypes. CONCLUSION: These findings indicate the utility of multiple RDR sequence analysis in both identifying specific drug resistance mutation and genotyping of various M. tuberculosis isolates.

Detection and characterization of mutations of multidrug-resistant tuberculosis isolates of the Philippine General Hospital

Background. Emergence of multidrug-resistant tuberculosis (MDR-TB) poses a major challenge to prevailing disease management. MDR-TB arises from mutations in several genes comprising the resistance determining regions, including rpoB, katG and gyrA. Objective. To detect and characterize mutations in rpoB, katG and gyrA. Methods. Thirty selected Mycobacterium tuberculosis isolates from the IDS-PGH were subjected to PCR amplification and sequencing. Sequences were compared to the wild type strain H37Rv. Results. Mutations were detected in codons 512, 513, 516, 522, 526, 531 and 533 of rpoB, codons 280, 281, 315 and 333 of katG, and codons 90 and 94 of gyrA sequences. The most frequently mutating codons for rpoB, katG and gyrA were 531, 315 and 94, respectively. A clustering analysis of the sequences showed occurrence of seven, four and three clusters for the genes rpoB, katG and gyrA, respectively. The eight clusters obtained from the concatenated sequences of the three genes represent the eight potential genotypes of local strains. One cluster represents the wild type strain genotype, another cluster represents the XDR strain genotype, and six clusters represent the MDR strain genotypes. Conclusion. These findings indicate the utility of multiple RDR sequence analysis in both identifying specific drug resistance mutation and genotyping of various M. tuberculosis isolates.

A multicentre surveillance study on the characteristics, bacterial aetiologies and in vitro antibiotic susceptibilities in patients with acute exacerbations of chronic bronchitis.

BACKGROUND AND OBJECTIVE: Antimicrobial resistance is a global problem and the prevalence is high in many Asian countries. METHODS: A prospective observational study of the prevalence of bacterial pathogens and their antimicrobial susceptibilities in patients with acute exacerbations of chronic bronchitis (AECB) was conducted in Indonesia, Philippines, Korea, Thailand, Malaysia, Taiwan and Hong Kong from August 2006 to April 2008. The diagnosis of AECB was based on increased cough and worsening of two of following: dyspnoea, increased sputum volume or purulence. Patients who had taken antibiotics within 72 h of presentation were excluded. All bacterial strains were submitted to a central laboratory for re-identification and antimicrobial susceptibility testing to 16 antimicrobial agents according to Clinical and Laboratory Standards Institute. RESULTS: Four hundred and seven isolates were identified among 447 patients of AECB. The most frequent organisms isolated were Klebsiella pneumoniae and associated species (n = 91 + 17), Haemophilus influenzae (n = 71), Pseudomonas aeruginosa (n = 63), Streptococcus pneumoniae (n = 32), Acinetobacter baumannii (n = 22) and Moraxella catarrhalis (n = 21). According to Clinical and Laboratory Standards Institute susceptibility breakpoints, 85.7% and >90% of these pathogens were susceptible to levofloxacin and cefepime respectively. Other options with overall lower susceptibilities include imipenem, ceftazidime, ceftriaxone and amoxicillin/clavulanate. CONCLUSIONS: Gram-negative bacteria including Klebsiella spp., P. aeruginosa and Acinetobacter spp. constitute a large proportion of pathogens identified in patients with AECB in some Asian countries. Surveillance on the local prevalence and antibiotic resistance of these organisms is important in guiding appropriate choice of antimicrobials in the management of AECB.

Pyrosequencing for rapid detection of Mycobacterium tuberculosis resistance to rifampin, isoniazid, and fluoroquinolones.

After isoniazid and rifampin (rifampicin), the next pivotal drug class in Mycobacterium tuberculosis treatment is the fluoroquinolone class. Mutations in resistance-determining regions (RDR) of the rpoB, katG, and gyrA genes occur with frequencies of 97%, 50%, and 85% among M. tuberculosis isolates resistant to rifampin, isoniazid, and fluoroquinolones, respectively. Sequences are highly conserved, and certain mutations correlate well with phenotypic resistance. We developed a pyrosequencing assay to determine M. tuberculosis genotypic resistance to rifampin, isoniazid, and fluoroquinolones. We characterized 102 M. tuberculosis clinical isolates from the Philippines for susceptibility to rifampin, isoniazid, and ofloxacin by using the conventional submerged-disk proportion method and validated our pyrosequencing assay using these isolates. DNA was extracted and amplified by using PCR primers directed toward the RDR of the rpoB, katG, and gyrA genes, and pyrosequencing was performed on the extracts. The M. tuberculosis H37Rv strain (ATCC 25618) was used as the reference strain. The sensitivities and specificities of pyrosequencing were 96.7% and 97.3%, 63.8% and 100%, and 70.0% and 100% for the detection of resistance to rifampin, isoniazid, and ofloxacin, respectively. Pyrosequencing is thus a rapid and accurate method for detecting M. tuberculosis resistance to these three drugs.