A whole-genome sequencing study of an X-family tuberculosis outbreak focus on transmission chain along 25 years

Monforte

Samper

et al. 2021

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The purpose of this study was to increase our knowledge about Mycobacterium africanum and report the incidence and characteristics of tuberculosis (TB) due to their lineages in Aragon, Spain, over the period 2003–2019. The study includes all the cases in our region, where all the M. tuberculosis complex isolates are systematically characterised. We detected 31 cases of M. africanum among 2598 cases of TB in the period studied. TB caused by M. africanum is rare (1.19%) in our population, and it affects mainly men of economically productive age coming from West African countries. Among the isolates, Lineage (L) 6 was more frequent than L5. The genotyping of these strains identified five clusters and 13 strains with a unique pattern. The isolates’ characterisation identified a copy of IS6110 within the moaX gene, which turned out to be specific for L6. It will allow the differentiation of this lineage from the rest of MTBC with a simple PCR reaction. It remains to be established whether this polymorphism may limit M. africanum transmission. Furthermore, a mutation in the mutT2 promoter was found as specific for L6 strains, which could be related to the high variability found for L6 compared to L5.

Section: Discussionsupporting

confidence: 93%

Analysis of Mycobacterium africanum in the last 17 years in Aragon identifies a specific location of IS6110 in Lineage 6

Monforte

Samper

et al. 2021

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“…(2009) for the first 85 cases. Different from an X-family outbreak which also began in the 1990s among the local population and with a high proportion of HIV + individuals, users of intravenous drugs, and prisoners ( Comín et al., 2021 ), the MtZ outbreak did not show a high percentage of these individuals, just a high proportion of smokers (38%) and a moderate proportion of alcohol dependence (18%). On the other hand, in both outbreaks, young people were the most affected group, with more than 70% of the cases under 45 years old.…”

Section: Discussionmentioning

confidence: 80%

“…As a result of the WGS analysis, a higher number of cases could be included in the transmission chain than just those connected by epidemiological links. However, the direction of the transmission could not be established in the majority of cases, something recurrent in TB outbreak studies ( Casali et al., 2016 ; Hatherell et al., 2016 ; Lalor et al., 2018 ; Comin et al., 2020 ; Comín et al., 2021 ). As an example, cases 51 and 229 from CLS-2.2 had an identical genomic sequence, but case 51 was diagnosed 15 years before, so we think that case 51 would be the first case, as transmission always moves toward SNP accumulation ( Schürch et al., 2010 ).…”

Section: Discussionmentioning

confidence: 99%

The MtZ Strain: Molecular Characteristics and Outbreak Investigation of the Most Successful Mycobacterium tuberculosis Strain in Aragon Using Whole-Genome Sequencing

Front. Cell. Infect. Microbiol.

Madacki

Rabanaque

et al. 2022

Since 2004, a tuberculosis surveillance protocol has been carried out in Aragon, thereby managing to detect all tuberculosis outbreaks that take place in the community. The largest outbreak was caused by a strain named Mycobacterium tuberculosis Zaragoza (MtZ), causing 242 cases as of 2020. The main objective of this work was to analyze this outbreak and the molecular characteristics of this successful strain that could be related to its greater transmission. To do this, we first applied whole-genome sequencing to 57 of the isolates. This revealed two principal transmission clusters and six subclusters arising from them. The MtZ strain belongs to L4.8 and had eight specific single nucleotide polymorphisms (SNPs) in genes considered to be virulence factors [ptpA, mc3D, mc3F, VapB41, pks15 (two SNPs), virS, and VapC50]. Second, a transcriptomic study was carried out to better understand the multiple IS6110 copies present in its genome. This allowed us to observe three effects of IS6110: the disruption of the gene in which the IS6110 is inserted (desA3), the overexpression of a gene (ppe38), and the absence of transcription of genes (cut1:Rv1765c) due to the recombination of two IS6110 copies. Finally, because of the disruption of ppe38 and ppe71 genes by an IS6110, a study of PE_PGRS secretion was carried out, showing that MtZ secretes these factors in higher amounts than the reference strain, thereby differing from the hypervirulent phenotype described for the Beijing strains. In conclusion, MtZ consists of several SNPs in genes related to virulence, pathogenesis, and survival, as well as other genomic polymorphisms, which may be implicated in its success among our population.

“…These included CLS_217, which was independently studied 8 . The rest of the outbreaks were caused by strains from different lineages: one by a L4.1.1.3/X strain, with 21 cases 9 ; one by a L4.7 strain, with 19 cases; one by a L4.4.1.1 strain, with 16 cases; one by a L4.9 strain, producing 13 cases; and one by a L4.6.1.1 strain, with 14 cases.…”

Section: Resultsmentioning

confidence: 99%

Analysis of the twenty-six largest outbreaks of tuberculosis in Aragon using whole-genome sequencing for surveillance purposes

Cebollada

Ibarz

et al. 2022

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The incidence of tuberculosis in Aragon, Spain, is around ten cases per 100,000 inhabitants. Since 2004, a molecular surveillance protocol has been carried out; therefore, all M. tuberculosis strains are genotyped. Recently, whole-genome sequencing has been implemented for relevant isolates. The aim of this work is to characterise at the molecular level the causative strains of the 26 largest outbreaks of the community (including ten or more cases), genotyped by IS6110-RFLP and causing 26% of tuberculosis cases. To achieve this objective, two or three isolates of each IS6110-cluster belonging to different years were selected for sequencing. We found that strains of lineages L4.8, L4.3 and L4.1.2 were the most frequent. The threshold of 12 SNPs as the maximum distance for confirming the belonging to an outbreak was met for 18 of the 26 IS6110-clusters. Four pairs of isolates with more than 90 SNPs were identified as not belonging to the same strain, and four other pairs were kept in doubt as the number of SNPs was close to 12, between 14 and 35. The study of Regions of Difference revealed that they are lineage conserved. Moreover, we could analyse the IS6110 locations for all genome-sequenced isolates, finding some frequent locations in isolates belonging to the same lineage and certain IS6110 movements between the paired isolates. In the vast majority, these movements were not captured by the IS6110-RFLP pattern. After classifying the genes containing SNP by their functional category, we could confirm that the number of SNPs detected in genes considered as virulence factors and the number of cases the strain produced were not related, suggesting that a particular SNP is more relevant than the number. The characteristics found in the most successful strains in our community could be useful for other researchers in epidemiology, virulence and pathogenesis.