Evolution of extensively drug-resistant Mycobacterium tuberculosisfrom a susceptible ancestor in a single patient

Eldholm, Vegard; Norheim, Gunnstein; Lippe, Bent von der; Kinander, Wibeke; Dahle, Ulf R.; Caugant, Dominique A.; Mannsåker, Turid; Mengshoel, Anne Torunn; Dyrhol‐Riise, Anne Ma; Balloux, François

doi:10.1186/s13059-014-0490-3

Cited by 160 publications

(181 citation statements)

References 46 publications

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“…Briefly, DNA from the strains was extracted using E.Z.N.A. bacterial DNA isolation kits (Omega Bio-tek, Norcross, GA), following three cycles on a Precellys homogenizer (Bertin Corp., MD) at 6,300 rpm for 30 s. DNA sequencing libraries were prepared as previously described (14), and sequencing was performed on the Illumina MiSeq and NextSeq platform (Illumina, San Diego, CA), with all reads performed at 2 ϫ 150 bp at a median depth of 352 (range, 52 to 706). The median pair distance was 221 bp (193 to 245 bp), and median template coverage was 99.14% to 99.21%.…”

Section: Methodsmentioning

confidence: 99%

Tuberculosis Outbreak in an Educational Institution in Norway

et al. 2017

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Within 1 week in April 2013, three cases of pulmonary tuberculosis (TB) were reported among students attending training sessions at an educational institution in Oslo, Norway. By the end of October 2013, a total of nine epidemiologically linked cases had been reported. The outbreak encompassed a total of 24 cases from 2009 to 2014, among which all of the 22 Mycobacterium tuberculosis isolates available had identical mycobacterial interspersed repetitive-unitvariable-number tandem-repeat (MIRU-VNTR) profiles (MtbC15-9 code 10287-189) belonging to the Beijing lineage. Whole-genome sequencing (WGS) of the M. tuberculosis isolates revealed 20 variable nucleotide positions within the cluster, indicating a clonal outbreak. The most likely index case was identified and diagnosed in Norway in 2009 but was born in Asia. WGS analyses verified that all of the cases were indeed part of a single transmission chain. However, even when combining WGS and intensified contact tracing, we were unable to fully reconstruct the TB transmission events.

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Section: Methodsmentioning

confidence: 99%

Tuberculosis Outbreak in an Educational Institution in Norway

et al. 2017

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“…Genomic DNA isolation and preparation of sequencing libraries was performed at the Norwegian Institute of Public Health following a published protocol (34), except using the Kapa HyperPlus Library Preparation Kit (Kapa Biosystems) rather than the Kapa High-Throughput Library Preparation Kit for DNA fragmentation and library preparation. All sequencing reads were paired end (read length 100-250 bp) and had been generated on the Illumina platform (NextSeq 500, HiSeq, or MiSeq).…”

Section: Methodsmentioning

confidence: 99%

Armed conflict and population displacement as drivers of the evolution and dispersal of Mycobacterium tuberculosis

Eldholm

Pettersson

Brynildsrud

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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The "Beijing" Mycobacterium tuberculosis (Mtb) lineage 2 (L2) is spreading globally and has been associated with accelerated disease progression and increased antibiotic resistance. Here we performed a phylodynamic reconstruction of one of the L2 sublineages, the central Asian clade (CAC), which has recently spread to western Europe. We find that recent historical events have contributed to the evolution and dispersal of the CAC. Our timing estimates indicate that the clade was likely introduced to Afghanistan during the 1979-1989 Soviet-Afghan war and spread further after population displacement in the wake of the American invasion in 2001. We also find that drug resistance mutations accumulated on a massive scale in Mtb isolates from former Soviet republics after the fall of the Soviet Union, a pattern that was not observed in CAC isolates from Afghanistan. Our results underscore the detrimental effects of political instability and population displacement on tuberculosis control and demonstrate the power of phylodynamic methods in exploring bacterial evolution in space and time.

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“…BLASTX matches to bacterial and archaeal genes (4bit score 50) were retained to evaluate marker genes of dissimilatory N metabolism: ammonia monooxygenase (amoC), nitrite oxidoreductase (nxrB), hydrazine oxidoreductase (hzo), nitrate reductase (narG), nitrite reductase (nirK+nirS), nitric oxide reductase (norB) and nitrous oxide reductase (nosZ). N gene transcript abundances were normalized based on gene length and expressed as a proportion of the abundance of transcripts matching the gene encoding RNA polymerase subunit B (rpoB), as has been done in studies of diverse bacteria (for example, Schumann et al, 2010;Ceja-Navarro et al, 2014;Dalsgaard et al, 2014;Eldholm et al, 2014). Although rpoB expression can vary (Vandecasteele et al, 2001), rpoB appears to be one of the more stably expressed housekeeping genes (Sue et al, 2004;Sihto et al, 2014).…”

Section: Molecular Analysismentioning

confidence: 99%

Size-fraction partitioning of community gene transcription and nitrogen metabolism in a marine oxygen minimum zone

et al. 2015

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The genetic composition of marine microbial communities varies at the microscale between particleassociated (PA; 41.6 μm) and free-living (FL; 0.2-1.6 μm) niches. It remains unclear, however, how metabolic activities differ between PA and FL fractions. We combined rate measurements with metatranscriptomics to quantify PA and FL microbial activity in the oxygen minimum zone (OMZ) of the Eastern Tropical North Pacific, focusing on dissimilatory processes of the nitrogen (N) cycle. Bacterial gene counts were 8-to 15-fold higher in the FL compared with the PA fraction. However, rates of all measured N cycle processes, excluding ammonia oxidation, declined significantly following particle (41.6 μm) removal. Without particles, rates of nitrate reduction to nitrite (1.5-9.4 nM N d − 1 ) fell to zero and N 2 production by denitrification (0.5-1.7 nM N d − 1 ) and anammox (0.3-1.9 nM N d − 1 ) declined by 53-85%. The proportional representation of major microbial taxa and N cycle gene transcripts in metatranscriptomes followed fraction-specific trends. Transcripts encoding nitrate reductase were uniform among PA and FL fractions, whereas anammox-associated transcripts were proportionately enriched up to 15-fold in the FL fraction. In contrast, transcripts encoding enzymes for N 2 O and N 2 production by denitrification were enriched up to 28-fold in PA samples. These patterns suggest that the majority of N cycle activity, excluding N 2 O and N 2 production by denitrification, is confined to a FL majority that is critically dependent on access to particles, likely as a source of organic carbon and inorganic N. Variable particle distributions may drive heterogeneity in N cycle activity and gene expression in OMZs.

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Evolution of extensively drug-resistant Mycobacterium tuberculosisfrom a susceptible ancestor in a single patient

Cited by 160 publications

References 46 publications

Tuberculosis Outbreak in an Educational Institution in Norway

Tuberculosis Outbreak in an Educational Institution in Norway

Armed conflict and population displacement as drivers of the evolution and dispersal of Mycobacterium tuberculosis

Size-fraction partitioning of community gene transcription and nitrogen metabolism in a marine oxygen minimum zone

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