Whole-genome sequencing and Mycobacterium tuberculosis: Challenges in sample preparation and sequencing data analysis

Dohál, Matúš; Porvazník, Igor; Pršo, Kristián; Rasmussen, Erik Michael; Solovič, Ivan; Mokrý, Juraj

doi:10.1016/j.tube.2020.101946

Cited by 16 publications

(12 citation statements)

References 66 publications

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“…Traditionally, MiSeq has been used extensively for eDNA metabarcoding 3 , 9 , 12 , 16 , 23 . Recently, some comparative studies using iSeq and other HTS, particularly MiSeq, have been reported in the medical field 31 , 32 . These studies show that iSeq can be used for whole-genome sequencing and targeted sequencing of pathogenic bacteria with accuracy similar to MiSeq.…”

Section: Discussionmentioning

confidence: 99%

Illumina iSeq 100 and MiSeq exhibit similar performance in freshwater fish environmental DNA metabarcoding

Nakao

Inui

Akamatsu

et al. 2021

Sci Rep

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Environmental DNA (eDNA) analysis is a method of detecting DNA from environmental samples and is used as a biomonitoring tool. In recent studies, Illumina MiSeq has been the most extensively used tool for eDNA metabarcoding. The Illumina iSeq 100 (hereafter, iSeq), one of the high-throughput sequencers (HTS), has a relatively simple workflow and is potentially more affordable than other HTS. However, its utility in eDNA metabarcoding has still not been investigated. In the present study, we applied fish eDNA metabarcoding to 40 water samples from river and lake ecosystems to assess the difference in species detectability and composition between iSeq and MiSeq. To check differences in sequence quality and errors, we also assessed differences in read changes between the two HTS. There were similar sequence qualities between iSeq and MiSeq. Significant difference was observed in the number of species between two HTS, but no difference was observed in species composition between the two HTS. Additionally, the species compositions in common with the conventional method were the same between the two HTS. According to the results, using the same amplicon library for sequencing, two HTS would exhibit a similar performance of fish species detection using eDNA metabarcoding.

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Section: Discussionmentioning

confidence: 99%

Illumina iSeq 100 and MiSeq exhibit similar performance in freshwater fish environmental DNA metabarcoding

Nakao

Inui

Akamatsu

et al. 2021

Sci Rep

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“…Performing systematic whole genome sequencing (WGS) enables rapid, reliable, and complex insight into the Mycobacterium (M.) tuberculosis genome linked to anti-TB drug resistance [2] , and, in phylogenetic analysis, it allows to determine M. tuberculosis complex (MTBC) lineages, analysis of transmission events, and tracing TB outbreaks with a higher discriminatory power compared to traditionally used tools [3] , [4] , [5] , [6] .…”

Section: Introductionmentioning

confidence: 99%

Anti-tuberculosis drug resistance in Slovakia, 2018–2019: The first whole-genome epidemiological study

Dohál

Dvořáková

Šperková

et al. 2022

Journal of Clinical Tuberculosis and Other Mycobacterial Diseas

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Highlights The Euro-American lineage 4.7 was the most represented among the XDR-TB/MDR-TB resistant strains. Seven of 12 isolates (58%) belonged to the same recent transmission chain. Strains originally from Eastern European countries were diagnosed in patients without any epidemiological links with these countries. Incidence of resistant XDR-TB/MDR-TB in Slovakia, while low, still should be taken to monitor.

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“…The whole-genome sequencing (WGS) method allows clinicians to overcome the limitations of the conventional tests used for the diagnosis of mycobacterial infections and better understand the global diversity of NTM species [20]. WGS can identify all single nucleotide polymorphisms (SNPs) associated with resistance, as well as phylogenetic SNPs characteristic for individual NTM species [21].…”

Section: Introductionmentioning

confidence: 99%

Whole Genome Sequencing in the Management of Non-Tuberculous Mycobacterial Infections

et al. 2021

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Infections caused by non-tuberculous mycobacteria (NTM) have been a public health problem in recent decades and contribute significantly to the clinical and economic burden globally. The diagnosis of infections is difficult and time-consuming and, in addition, the conventional diagnostics tests do not have sufficient discrimination power in species identification due to cross-reactions and not fully specific probes. However, technological advances have been made and the whole genome sequencing (WGS) method has been shown to be an essential part of routine diagnostics in clinical mycobacteriology laboratories. The use of this technology has contributed to the characterization of new species of mycobacteria, as well as the identification of gene mutations encoding resistance and virulence factors. Sequencing data also allowed to track global outbreaks of nosocomial NTM infections caused by M. abscessus complex and M. chimaera. To highlight the utility of WGS, we summarize recent scientific studies on WGS as a tool suitable for the management of NTM-induced infections in clinical practice.

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Whole-genome sequencing and Mycobacterium tuberculosis: Challenges in sample preparation and sequencing data analysis

Cited by 16 publications

References 66 publications

Illumina iSeq 100 and MiSeq exhibit similar performance in freshwater fish environmental DNA metabarcoding

Illumina iSeq 100 and MiSeq exhibit similar performance in freshwater fish environmental DNA metabarcoding

Anti-tuberculosis drug resistance in Slovakia, 2018–2019: The first whole-genome epidemiological study

Whole Genome Sequencing in the Management of Non-Tuberculous Mycobacterial Infections

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