Whole genome analysis of extensively drug resistant Mycobacterium tuberculosis strains in Peru

Abstract

Peru has the highest burden of multidrug-resistant tuberculosis in the Americas region. Since 1999, the annual number of extensively drug-resistant tuberculosis (XDR-TB) Peruvian cases has been increasing, becoming a public health challenge. The objective of this study was to perform genomic characterization of Mycobacterium tuberculosis strains obtained from Peruvian patients with XDR-TB diagnosed from 2011 to 2015 in Peru. Whole genome sequencing (WGS) was performed on 68 XDR-TB strains from different regions of Peru. 58 (85.3%) strains came from the most populated districts of Lima and Callao. Concerning the lineages, 62 (91.2%) strains belonged to the Euro-American Lineage, while the remaining 6 (8.8%) strains belonged to the East-Asian Lineage. Most strains (90%) had high-confidence resistance mutations according to pre-established WHO-confident grading system. Discordant results between microbiological and molecular methodologies were caused by mutations outside the hotspot regions analysed by commercial molecular assays (rpoB I491F and inhA S94A). Cluster analysis using a cut-off ≤ 10 SNPs revealed that only 23 (34%) strains evidenced recent transmission links. This study highlights the relevance and utility of WGS as a high-resolution approach to predict drug resistance, analyse transmission of strains between groups, and determine evolutionary patterns of circulating XDR-TB strains in the country.

Comparative genomics of drug-resistant strains of Mycobacterium tuberculosis in Ecuador

“…The potential of WGS to provide a quick and comprehensive view of the genotype and reliable prediction of the lineages has been extensively reported [ 5 , 7 , 14 , 40 ]; thus, its application in surveillance programs is necessary. The Euro-American lineage (lineage 4) presents a variable distribution in Argentina with a predominance of M and Ra strains [ 41 ], for Brazil, lineage 4 varies between 25–99% [ 13 , 42 , 43 ], for Colombia, between 85–99% [ 44 – 46 ], for Mexico between 69–98% [ 47 , 48 ] and for Peru around 90% [ 12 , 49 , 50 ]. Ecuador is not an exception, in fact, all the samples analyzed by us belong to the Euro-American lineage.…”

“…This lineage has been described as more transmissible than others [10]. From 10 sub-lineages, including in Lineage 4, LAM (L4.3), Haarlem (L4.1.2), X-type and T families are the most observed members of the Euro-American lineage in South and Central America and the Caribbean, a distribution profile shared with Europe and Middle Africa [11][12][13][14].…”

Type 2 diabetes mellitus and recurrent Tuberculosis: A retrospective cohort in Peruvian military workers

“…The factors associated with recurrent TB are the recurrence time for relapse, HIV coinfection, the strain's genotype, incarceration, and immigration for exogenous reinfection [9] . According to complete genome sequencing analysis, studies carried out in Peru show a TB recurrence of 5.2 % [10] , with 34 % attributed to relapses [11] .…”

In vitro anti-tuberculosis effect of probiotic Lacticaseibacillus rhamnosus PMC203 isolated from vaginal microbiota

“…Tuberculosis (TB), caused by the etiological agent of Mycobacterium tuberculosis that remains the world’s oldest known deadly infectious disease in humans, considering as one of the top ten leading causes of death globally 1 . According to the World Health Organization (WHO) report 2021, 10 million people were infected with tuberculosis bacteria in 2020, with 1.3 million TB deaths among Human immunodeficiency Virus (HIV)-negative people, and an additional 214,000 deaths among people who have HIV 2 .…”