Anne Torunn Mengshoel

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

BackgroundMycobacterium tuberculosis is characterized by a low mutation rate and a lack of genetic recombination. Yet, the rise of extensively resistant strains paints a picture of a microbe with an impressive adaptive potential. Here we describe the first documented case of extensively drug-resistant tuberculosis evolved from a susceptible ancestor within a single patient.ResultsGenome sequences of nine serial M. tuberculosis isolates from the same patient uncovered a dramatic turnover of competing lineages driven by the emergence, and subsequent fixation or loss of single nucleotide polymorphisms. For most drugs, resistance arose through independent emergence of mutations in more than one clone, of which only one ultimately prevailed as the clone carrying it expanded, displacing the other clones in the process. The vast majority of mutations identified over 3.5 years were either involved in drug resistance or hitchhiking in the genetic background of these. Additionally, RNA-sequencing of isolates grown in the absence of drug challenge revealed that the efflux-associated iniBAC operon was up-regulated over time, whereas down-regulated genes include those involved in mycolic acid synthesis.ConclusionsWe observed both rapid acquisitions of resistance to antimicrobial compounds mediated by individual mutations as well as a gradual increase in fitness in the presence of antibiotics, likely driven by stable gene expression reprogramming. The rapid turnover of resistance mutations and hitchhiking neutral mutations has major implications for inferring tuberculosis transmission events in situations where drug resistance evolves within transmission chains.

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

Significance We used population genomic analyses to reconstruct the recent history and dispersal of a major clade of Mycobacterium tuberculosis in central Asia and beyond. Our results indicate that the fall of the Soviet Union and the ensuing collapse of public health systems led to a rise in M. tuberculosis drug resistance. We also show that armed conflict and population displacement is likely to have aided the export of this clade from central Asia to war-torn Afghanistan and beyond. 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.

A cluster of multidrug-resistant Mycobacterium tuberculosis among patients arriving in Europe from the Horn of Africa: a molecular epidemiological study

Summary Background The risk of tuberculosis outbreaks among people fleeing hardship for refuge in Europe is heightened. We describe the cross-border European response to an outbreak of multidrug-resistant tuberculosis among patients from the Horn of Africa and Sudan. Methods On April 29 and May 30, 2016, the Swiss and German National Mycobacterial Reference Laboratories independently triggered an outbreak investigation after four patients were diagnosed with multidrug-resistant tuberculosis. In this molecular epidemiological study, we prospectively defined outbreak cases with 24-locus mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) profiles; phenotypic resistance to isoniazid, rifampicin, ethambutol, pyrazinamide, and capreomycin; and corresponding drug resistance mutations. We whole-genome sequenced all Mycobacterium tuberculosis isolates and clustered them using a threshold of five single nucleotide polymorphisms (SNPs). We collated epidemiological data from host countries from the European Centre for Disease Prevention and Control. Findings Between Feb 12, 2016, and April 19, 2017, 29 patients were diagnosed with multidrug-resistant tuberculosis in seven European countries. All originated from the Horn of Africa or Sudan, with all isolates two SNPs or fewer apart. 22 (76%) patients reported their travel routes, with clear spatiotemporal overlap between routes. We identified a further 29 MIRU-VNTR-linked cases from the Horn of Africa that predated the outbreak, but all were more than five SNPs from the outbreak. However all 58 isolates shared a capreomycin resistance-associated tlyA mutation. Interpretation Our data suggest that source cases are linked to an M tuberculosis clone circulating in northern Somalia or Djibouti and that transmission probably occurred en route before arrival in Europe. We hypothesise that the shared mutation of tlyA is a drug resistance mutation and phylogenetic marker, the first of its kind in M tuberculosis sensu stricto. Funding The Swiss Federal Office of Public Health, the University of Zurich, the Wellcome Trust, National Institute for Health Research (NIHR) Oxford Biomedical Research Centre (BRC), the Medical Research Council, BELTA-TBnet, the European Union, the German Center for Infection Research, and Leibniz Science Campus Evolutionary Medicine of the Lung (EvoLUNG).

Tuberculosis among children in Oslo, Norway, from 1998 to 2009.

Abstract We investigated all confirmed cases of tuberculosis (TB) among children (age <16 y) in Oslo from 1998 to 2009. The overall incidence rate was 2.6 per 100,000 person-y. All 24 children diagnosed with TB were of non-Western origin, and the overall incidence rate in this group was 8.1 per 100,000 person-y. Among children of Somali origin, the incidence rate was 52.5 per 100,000 person-y. Pulmonary infiltrates (n = 7), hilar lymphadenopathy without infiltrates (n = 7) and lymph node TB in the neck (n = 5) were the most common clinical presentations. However, we also diagnosed TB meningitis, spondylitis, coxitis and pleuritis. None of the children were HIV-infected. Mycobacterium tuberculosis was cultivated in 19 out of 24 cases (79%). Of the 19 culture-positive cases, 13 had been tested with a polymerase chain reaction, of which 7 (54%) were positive. Isolates from 2 patients were resistant to isoniazid, 1 isolate was resistant to streptomycin, and 2 were resistant to both isoniazid and streptomycin. All children were treated according to a directly observed treatment short-course (DOTS) protocol. One child with TB meningitis died. Twenty-one patients finished treatment in Oslo, and all were cured without major sequelae or recurrence. TB among non-Western immigrant children is still a challenge in Norway.

Two Norwegian Patients With Melioidosis Presenting With Bacteraemia and Splenic and Prostatic Abscesses

Infections caused by Burkholderia pseudomallei are rare in nonendemic areas, such as Scandinavia. We report the first two cases of melioidosis in Norway presenting with bacteraemia and splenic and prostatic abscesses, respectively.

Imported toxigenic cutaneous diphtheria in a young male returning from Mozambique to Norway, March 2014

Six outbreaks of infectious syphilis in the United Kingdom, ongoing since 2012, have been investigated among men who have sex with men (MSM) and heterosexual men and women aged under 25 years. Interventions included case finding and raising awareness among healthcare professionals and the public. Targeting at-risk populations was complicated as many sexual encounters involved anonymous partners. Outbreaks among MSM were influenced by the use of geospatial real-time networking applications that allow users to locate other MSM within close proximity.

Diphtheria outbreak in Norway: Lessons learned

Abstract We describe an outbreak of diphtheria in Norway that occurred in 2008 and affected 3 unvaccinated family members. The epidemic caught the public health system off-guard on most levels; the diagnosis was distrusted due to its rarity, no diphtheria anti-toxin was available, and notification procedures were not rigorously followed.

Multidrug-resistant tuberculosis in Norway: a nationwide study, 1995-2014.

SETTING The management of multidrug-resistant tuberculosis (MDR-TB) is strictly regulated in Norway. However, nationwide studies of the epidemic are lacking. OBJECTIVE To describe the MDR-TB epidemic in Norway over two decades. DESIGN Retrospective analysis of data on MDR-TB cases in Norway, 1995-2014, obtained from the national registry, patient records and the reference laboratory, with genotyping and cluster analysis data. Data for non-MDR-TB cases were collected from the national registry. RESULTS Of 4427 TB cases, 89 (2.0%) had MDR-TB, 7% of whom had extensively drug-resistant TB (XDR-TB) and 24% pre-XDR-TB. Of the 89 MDR-TB cases, 96% were immigrants, mainly from the Horn of Africa or the former Soviet Union (FSU); 37% had smear-positive TB; and 4% were human immunodeficiency virus co-infected. Of the 19% infected in Norway, the majority belonged to a Delhi/Central Asian lineage cluster in a local Somali community. Among the MDR-TB cases, smear-positive TB and FSU origin were independent risk factors for XDR/pre-XDR-TB. Treatment was successful in 66%; 17% were lost to follow-up, with illicit drug use and adolescence being independent risk factors. Forty-four per cent of patients treated with linezolid discontinued treatment due to adverse effects. CONCLUSION MDR-TB is rare in Norway and is predominantly seen in immigrants from the Horn of Africa and FSU. Domestic transmission outside immigrant populations is minimal.

Tuberculosis Outbreak in an Educational Institution in Norway

ABSTRACT 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-unit–variable-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.