Mycobacterium tuberculosis whole genome sequencing provides insights into the Manila strain and drug-resistance mutations in the Philippines

Abstract

The Philippines has a high incidence of tuberculosis disease (TB), with an increasing prevalence of multidrug-resistant Mycobacterium tuberculosis (MDR-TB) strains making its control difficult. Although the M . tuberculosis “Manila” ancient lineage 1 strain-type is thought to be prevalent in the country, with evidence of export to others, little is known about the genetic diversity of circulating strains. By whole genome sequencing (WGS) 178 isolates from the Philippines National Drug Resistance Survey, we found the majority (143/178; 80.3%) belonged to the lineage 1 Manila clade, with the minority belonging to lineages 4 (European-American; n = 33) and 2 (East Asian; n = 2). A high proportion were found to be multidrug-resistant (34/178; 19.1%), established through highly concordant laboratory drug susceptibility testing and in silico prediction methods. Some MDR-TB isolates had near identical genomic variation, providing potential evidence of transmission. By placing the Philippine isolates within a phylogeny of global M . tuberculosis (n > 17,000), we established that they are genetically similar to those observed outside the country, including a clade of Manila-like strain-types in Thailand. An analysis of the phylogeny revealed a set of ~200 SNPs that are specific for the Manila strain-type, and a subset can be used within a molecular barcode. Sixty-eight mutations known to be associated with 10 anti-TB drug resistance were identified in the Philippine strains, and all have been observed in other populations. Whilst nine putative streptomycin resistance conferring markers in gid (8) and rrs (1) genes appear to be novel and with functional consequences. Overall, this study provides an important baseline characterisation of M . tuberculosis genetic diversity for the Philippines, and will fill a gap in global datasets and aid the development of a nation-wide database for epidemiological studies and clinical decision making. Further, by establishing a molecular barcode for detecting Manila strains it will assist with the design of diagnostic tools for disease control activities.

Geno-Spatial Distribution of Mycobacterium Tuberculosis and Drug Resistance Profiles in Myanmar–Thai Border Area

“…Table 7 compares the distribution of lineage of MTB from our study with that from other studies [ 9 , 11 , 19 , 27 ]. L1 lineage was the most dominant in our and the Philippines study but in detail, the sublineage pattern was different [ 11 ]. L2 lineage was very prominent in a study from Yangon Region, Myanmar [ 19 ].…”

“…Several studies have described the distribution of lineages of MTB and their associations with geographic and ethnic background of the TB patients in other parts of Southeast Asia [ 9 , 10 , 11 , 12 ]. A few genotyping studies in Myanmar were previously reported [ 7 , 13 , 14 , 15 ].…”

Identification and in silico functional prediction of lineage-specific SNPs distributed in DosR-related proteins and resuscitation-promoting factor proteins of Mycobacterium tuberculosis

“…There were three nsSNPs specific to L1.2.1, which is also known as EAI2 according to spoligotyping. It is a common sublineage of L1 but localized to Southeast Asia, where L1.2.1 was found in approximately 80% of all TB patients in the Philippines ( Phelan et al., 2019 ); L1.2.1.2 is common in Thailand and Myanmar ( Palittapongarnpim et al., 2018 ). The L1.2.1-specific SNPs were located in the coding sequences of narK2 (a proton/nitrate transporter) ( Giffin et al., 2012 ), rpfB and Rv1996 (universal stress protein) ( Table 2 b).…”

New Development of Disaster-Related and Tropical Infectious Diseases Control

“…Independent factors associated with loss to follow-up included patients' higher self-rating of the severity of vomiting as an adverse drug reaction and alcohol abuse [25]. It is known that most prevalent genotype of all MTB (37 cases) belonged to Manila type at 2014 [26] and recent whole genome sequencing clarified that the majority (80.3%) belonged to lineage 1 Manila clade with the minority belonging to lineages 2 and 4 [27]. It is difficult to conclude if new strains have been emerging because the locations of two studies are not the same.…”