The use of whole-genome sequencing in cluster investigation of a multidrug-resistant tuberculosis outbreak

Lalor, MK; Coppola, Nicola; Walker, Timothy M; Anderson, LF; Davidson, J. A. H.; Ratna, Natasha; Mullarkey, Catherine; Gent, Mike; Foster, Kirsty; Brown, Timothy J.; Magee, Jeffrey C.; Barrett, A. M.; Crook, DW; Drobniewski, Francis; Thomas, H Lucy; Abubakar, Ibrahim

doi:10.1183/13993003.02313-2017

Cited by 39 publications

(37 citation statements)

References 29 publications

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“…Major findings from our analysis indicate that (1) estimated recent TB transmission rate using WGS at a SNP threshold of 10 remains high at 24.7%, and (2) there is wide spread of a clone of the Cameroon sub-lineage of lineage 4 with an ongoing transmission at hotspots mostly found within the Ablekuma sub-district of the Accra metropolis. WGS was first used in 2011 to delineate two unrelated transmission events among a cohort of drug users with identical MIRU-VNTR profiles from Vancouver and ever since it has been used in some large studies to understand TB transmission dynamics (34)(35)(36). Despite the continuous progress and decreasing costs of WGS-based typing, there are some important pertaining challenges such as the lack of standardization of WGS analysis pipelines and genomic distances (SNP distance) for defining clusters (37).…”

Section: Discussionmentioning

confidence: 99%

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Whole Genome Sequencing and Spatial Analysis Identifies Recent Tuberculosis Transmission Hotspots in Ghana

et al. 2020

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Whole genome sequencing (WGS) is progressively being used to investigate the transmission dynamics of Mycobacterium tuberculosis complex (MTBC). We used WGS analysis to resolve traditional genotype clusters and explored the spatial distribution of confirmed recent transmission clusters. Bacterial genomes from a total of 452 MTBC isolates belonging to large traditional clusters from a population-based study spanning July 2012 and December 2015 were obtained through short read next-generation sequencing using the illumina HiSeq2500 platform. We performed clustering and spatial analysis using specified R packages and ArcGIS. Of the 452 traditional genotype clustered genomes, 314 (69.5%) were confirmed clusters with a median cluster size of 7.5 genomes and an interquartile range of 4-12. Recent tuberculosis (TB) transmission was estimated as 24.7%. We confirmed the wide spread of a Cameroon sub-lineage clone with a cluster size of 78 genomes predominantly from the Ablekuma sub-district of Accra metropolis. More importantly, we identified a recent transmission cluster associated with isoniazid resistance belonging to the Ghana sub-lineage of lineage 4. WGS was useful in detecting unsuspected outbreaks; hence, we recommend its use not only as a research tool but as a surveillance tool to aid in providing the necessary guided steps to track, monitor, and control TB.

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Section: Discussionmentioning

confidence: 99%

“…One case had no record of residential location. There were 59 males and 17 females with a median age of 34 (IQR, [24][25][26][27][28][29][30][31][32][33][34][35][36][37][38][39][40][41][42][43]. Two participants had no record of gender.…”

Section: Socio-demographic Characteristics Of Individuals Infected Wimentioning

confidence: 99%

Whole Genome Sequencing and Spatial Analysis Identifies Recent Tuberculosis Transmission Hotspots in Ghana

et al. 2020

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“…In recent years, genome-based characterization of MTBC strains became a powerful tool for prospective surveillance and prediction of antimicrobial susceptibilities. In the setting of population displacement, language barriers and fragmented information related to contacts, genotyping has been used to infer the likelihood of transmission between cases [9][10][11]. The advent of extensive genetic DST enables targeted and more individualized treatment regimens [15].…”

Section: Rapid Diagnosis Of Tb and Molecular Typing Of Mtbc Strainsmentioning

confidence: 99%

“…Although genome-based molecular surveillance has significantly improved the assessment of TB transmission dynamics, it is still only irregularly used. Frequent relocation as well as language and cultural barriers pose significant challenges for contact tracing in migrant populations [9][10][11].…”

Section: Introductionmentioning

confidence: 99%

Multidrug-resistant Mycobacterium tuberculosis: a report of cosmopolitan microbial migration and an analysis of best management practices

et al. 2020

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Background Tuberculosis (TB) control is a primary global health priority but the goal to eliminate TB is being threatened by the increase in incidence of multidrug-resistant tuberculosis (MDR-TB). With this series of seven MDR-TB cases in migrant patients with identical Mycobacterium tuberculosis strains we aim to illustrate the challenges encountered during therapy and follow-up: language barriers, access to care for migrant patients, depression due to isolation, adverse reactions to the treatment, management of pediatric TB, further contact tracing. We also discuss best practices for the management of complex MDR-TB cases in settings with low overall TB incidence focusing on modern diagnostic assays and an individualized and an interdisciplinary therapeutic approach. Methods We describe a case series of seven consecutively diagnosed MDR-TB patients, six of them treated at our tertiary care hospital between May 2018 and March 2020. Epidemiologic data was gained by semi-structured patient interviews and reconstruction of the migration route. The origin of the cluster was confirmed by genotyping of the TB-strains. Results Six related patients were diagnosed with pulmonary MDR-TB between May and August 2018. All had a positive Interferon-Gamma-Release Assay (IGRA), in five patients sputum microscopy was positive for acid-fast bacilli (AFB). The genetic and phenotypical drug susceptibility test did not match with MDR-TB strains from an East-African origin. The index patient was identified through genetical fingerprinting. By changing the therapy to a modern MDR-TB regime and using an interdisciplinary and culture-sensitive approach, all patients improved clinically and radiologically. Conclusion Human migration plays an important role for the global spread of MDR-TB in low incidence countries. Early case detection and adequate treatment are key to prevention of outbreaks. Especially language barriers and complex migration routes make genotyping of TB-strains a crucial tool to identify cases clusters, the potential index patient and transmission dynamics. We are fortunate enough to experience times in which new TB-antibiotics were made available and in which molecular assays revolutionized TB-diagnostics. We need to take advantage of that and develop personalized therapies for patients suffering from drug resistant TB.

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“…The utility increases with the proportion of genome obtained; from detection, to speciation and antimicrobial resistance prediction, to phylogenetic and evolutionary insights. This allows whole genome sequencing (WGS) to outperform other rapid molecular methods (such as GeneXpert MTB/RIF, Cepheid, Solna, Sweden) (5)(6)(7)(8).…”

Section: Introductionmentioning

confidence: 99%

DNA Thermo-Protection Facilitates Whole-Genome Sequencing of Mycobacteria Direct from Clinical Samples

George

Rodger

et al. 2020

J Clin Microbiol

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Mycobacterium tuberculosis (MTB) is the leading cause of death from bacterial infection. Improved rapid diagnosis and antimicrobial resistance determination, such as by whole genome sequencing, are required. Our aim was to develop a simple, low-cost method of preparing DNA for sequencing direct from MTB positive clinical samples (without culture). Simultaneous sputum liquefaction, bacteria heat-inactivation (99°C/30min) and enrichment for Mycobacteria DNA was achieved using an equal volume of thermo-protection buffer (4M KCl, 0.05M HEPES buffer pH7.5, 0.1% DTT). The buffer emulated intracellular conditions found in hyperthermophiles, thus protecting DNA from rapid thermo-degradation, which renders it a poor template for sequencing. Initial validation experiments employed Mycobacteria DNA, either extracted or intracellular. Next, mock clinical samples (infection-negative human sputum spiked 0-105 BCG cells/ml) underwent liquefaction in thermo-protection buffer and heat-inactivation. DNA was extracted and sequenced. Human DNA degraded faster than Mycobacteria DNA, resulting in target enrichment. Four replicate experiments achieved MTB detection at 101 BCG cells/ml, with 31-59 MTB complex reads. Maximal genome coverage (>97% at 5x-depth) occurred at 104 BCG cells/ml; >91% coverage (1x depth) at 103 BCG cells/ml. Final validation employed MTB positive clinical samples (n=20), revealing initial sample volumes ≥1ml typically yielded higher mean depth of MTB genome coverage, the overall range 0.55-81.02. A mean depth of 3 gave >96% one-fold TB genome coverage (in 15/20 clinical samples). A mean depth of 15 achieved >99% five-fold genome coverage (in 9/20 clinical samples). In summary, direct-from-sample sequencing of MTB genomes was facilitated by a low cost thermo-protection buffer.

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The use of whole-genome sequencing in cluster investigation of a multidrug-resistant tuberculosis outbreak

Cited by 39 publications

References 29 publications

Whole Genome Sequencing and Spatial Analysis Identifies Recent Tuberculosis Transmission Hotspots in Ghana

Whole Genome Sequencing and Spatial Analysis Identifies Recent Tuberculosis Transmission Hotspots in Ghana

Multidrug-resistant Mycobacterium tuberculosis: a report of cosmopolitan microbial migration and an analysis of best management practices

DNA Thermo-Protection Facilitates Whole-Genome Sequencing of Mycobacteria Direct from Clinical Samples

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