Analysis of potential household transmission events of tuberculosis in the city of Belem, Brazil

Conceição, Emilyn Costa; Guimarães, Arthur Emil Dos Santos; Lopes, Maria Luíza; Furlaneto, Ismari Perini; Rodrigues, Yan Corrêa; Conceição, Marília Lima da; Barros, Wandyra Araújo; Cardoso, Ninarosa Calzavara; Sharma, Abhinav; Lima, Luana Nepomuceno Gondim Costa; Gomes, Harrison Magdinier; Duarte, Rafael Silva; Frota, Cristiane Cunha; Rutaihwa, Liliana K.; Gagneux, Sébastien; Suffys, Philip Noël; Lima, Karla Valéria Batista

doi:10.1016/j.tube.2018.09.011

Cited by 8 publications

(9 citation statements)

References 17 publications

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“…In accordance with previous studies 38 , 39 , using a conservative five-SNP threshold to define genomic transmission clusters enabled the clustering of 43.7% of the isolates included in the study thereby demonstrating that approximately half of the TB cases in metropolitan region between 2014 and 2016 were due to recent transmission. One recent epidemiological transmission study conducted in the Pará State, in North Brazil, across household contacts did find two cases in the same household whose isolates are described as being 9 SNPs apart 40 . In this latter study, the route of transmission is unclear since the temporal distance between these isolates was 7 years and therefore questions if the transmission between these cases was direct and, if missing links are likely to exist.…”

Section: Discussionmentioning

confidence: 99%

Genomic epidemiology of Mycobacterium tuberculosis in Santa Catarina, Southern Brazil

Verza

Scheffer

Salvato

et al. 2020

Sci Rep

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Mycobacterium tuberculosis (M.tb), the pathogen responsible for tuberculosis (TB) poses as the major cause of death among infectious diseases. The knowledge about the molecular diversity of M.tb enables the implementation of more effective surveillance and control measures and, nowadays, Whole Genome Sequencing (WGS) holds the potential to produce high-resolution epidemiological data in a high-throughput manner. Florianópolis, the state capital of Santa Catarina (SC) in south Brazil, shows a high TB incidence (46.0/100,000). Here we carried out a WGS-based evaluation of the M.tb strain diversity, drug-resistance and ongoing transmission in the capital metropolitan region. Resistance to isoniazid, rifampicin, streptomycin was identified respectively in 4.0% (n = 6), 2.0% (n = 3) and 1.3% (n = 2) of the 151 studied strains by WGS. Besides, resistance to pyrazinamide and ethambutol was detected in 0.7% (n = 1) and reistance to ethionamide and fluoroquinolone (FQ) in 1.3% (n = 2), while a single (0.7%) multidrug-resistant (MDR) strain was identified. SNP-based typing classified all isolates into M.tb Lineage 4, with high proportion of sublineages LAM (60.3%), T (16.4%) and Haarlem (7.9%). The average core-genome distance between isolates was 420.3 SNPs, with 43.7% of all isolates grouped across 22 genomic clusters thereby showing the presence of important ongoing TB transmission events. Most clusters were geographically distributed across the study setting which highlights the need for an urgent interruption of these large transmission chains. The data conveyed by this study shows the presence of important and uncontrolled TB transmission in the metropolitan area and provides precise data to support TB control measures in this region.

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Section: Discussionmentioning

confidence: 99%

Genomic epidemiology of Mycobacterium tuberculosis in Santa Catarina, Southern Brazil

Verza

Scheffer

Salvato

et al. 2020

Sci Rep

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“…Currently, two Mtbc-specific pipelines are available, which perform multiple core tasks in single install set-up to produce genetic variant calls from raw Illumina sequence data (MTBseq 34 and 196 UVP-ReSeqTB 35 ). Other pathogen-agnostic pipelines can be used with an Mtbc-specific 197 reference genome and drug resistance database to achieve similar results 33,[36][37][38] . Numerous 198 custom-built pipelines also exist 8,[39][40][41][42][43][44][45][46] , often incorporating similar tools for mapping and variant calling with additional accessory tools and in-house scripts to parse and refine outputs.…”

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confidence: 99%

Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues

et al. 2019

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Whole genome sequencing (WGS) of Mycobacterium tuberculosis has rapidly evolved from a research tool to a clinical application for the diagnosis and management of tuberculosis and in public health surveillance. This evolution has been facilitated by the dramatic drop in costs, advances in technology, and concerted efforts to translate sequencing data into actionable information. There is however a risk that, in the absence of a consensus and international standards, the widespread use of WGS technology may result in data and processes that lack harmonisation, comparability and validation. In this review, we outline the current landscape of WGS pipelines and applications and set out best practices for M. tuberculosis WGS, including standards for bioinformatics pipelines, curated repository of resistance-causing variants, phylogenetic analyses, quality control processes, and standardised reporting. 1. Introduction Mycobacterium tuberculosis complex (Mtbc) pathogens are collectively the top infectious disease killer globally, causing 10 million new tuberculosis (TB) cases annually 1. Increasingly, 95 new TB cases are already resistant to rifampicin and isoniazid (termed multidrug resistance; 96 MDR-TB), the key first line drugs 1. Tackling the spread and drug resistance burden of this pathogen requires concerted global effort in prevention, diagnosis, treatment and surveillance.

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“…The number of notifications is expected to increase even further with the search for contacts and the availability of the PPD or IGRA and radiography service to detect latent cases. Other studies developed in the state capital have already pointed to the need for greater surveillance of TB and the use of strategies to control transmission [24]. In another study, there were oscillations in the number of contaminations by TB, but there was no significant reduction in cases during the years of study [23].…”

Section: Discussionmentioning

confidence: 99%

A Clinical-Epidemiological and Geospatial Study of Tuberculosis in a Neglected Area in the Amazonian Region Highlights the Urgent Need for Control Measures

Mesquita

Conceição

Monteiro

et al. 2021

IJERPH

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Tuberculosis (TB) is an infectious communicable disease, which despite global efforts, still needs special attention in regions with difficult access. This study aims to describe the spatial and epidemiological trends of TB incidences from 2013 to 2018 in Marajó Island, the Amazonian region, Pará, Brazil. We have obtained secondary data from the Brazilian TB databases and performed geospatial and statistical analyses on the data for new TB cases, relapses, and re-admissions. From 2013 to 2018, 749 new cases were reported, in which the diagnostics (culture) was not performed for 652 (87.2%) patient samples, the drug resistance test (DST) was performed for nine (1.2%) samples, and one (0.13%) was multidrug-resistant TB (MDR-TB). The rapid molecular testing (RMT) was performed on 40 (5.3%) patient samples, with results indicating that eight (20%) were susceptible to rifampicin and two (5%) were rifampicin resistant. Overall, the cure rate was 449 (66.7%), while relapses and re-admissions were 41 and 44, respectively. On the geospatial distribution, the municipality of Soure stands out with a high number of incidences, relapses, and re-admissions. Spatially, the eight MDR cases were randomly distributed. Our data highlight the urgent need for TB control measures in this region, by introducing the Xpert-Ultra® MTB/RIF (Cepheid, Sunnyvale, CA, USA) and Ogawa-Kudoh.

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Analysis of potential household transmission events of tuberculosis in the city of Belem, Brazil

Cited by 8 publications

References 17 publications

Genomic epidemiology of Mycobacterium tuberculosis in Santa Catarina, Southern Brazil

Genomic epidemiology of Mycobacterium tuberculosis in Santa Catarina, Southern Brazil

Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues

A Clinical-Epidemiological and Geospatial Study of Tuberculosis in a Neglected Area in the Amazonian Region Highlights the Urgent Need for Control Measures

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