Whole-genome sequencing of Mycobacterium tuberculosis from Cambodia

Abstract

Cambodia has one of the highest tuberculosis (TB) incidence rates in the WHO Western Pacific region. Remarkably though, the prevalence of multidrug-resistant TB (MDR-TB) remains low. We explored the genetic diversity of Mycobacterium tuberculosis (MTB) circulating in this unique setting using whole-genome sequencing (WGS). From October 2017 until January 2018, we collected one hundred sputum specimens from consenting adults older than 21 years of age, newly diagnosed with bacteriologically confirmed TB in 3 districts of Phnom Penh and Takeo provinces of Cambodia before they commence on their TB treatment, where eighty MTB isolates were successfully cultured and sequenced. Majority of the isolates belonged to Lineage 1 (Indo-Oceanic) (69/80, 86.25%), followed by Lineage 2 (East Asian) (10/80, 12.5%) and Lineage 4 (Euro-American) (1/80, 1.25%). Phenotypic resistance to both streptomycin and isoniazid was found in 3 isolates (3/80, 3.75%), while mono-resistance to streptomycin and isoniazid was identical at 2.5% (N = 2 each). None of the isolates tested was resistant to either rifampicin or ethambutol. The specificities of genotypic prediction for resistance to all drugs tested were 100%, while the sensitivities of genotypic resistance predictions to isoniazid and streptomycin were lower at 40% (2/5) and 80% (4/5) respectively. We identified 8 clusters each comprising of two to five individuals all residing in the Takeo province, making up half (28/56, 50%) of all individuals sampled in the province, indicating the presence of multiple ongoing transmission events. All clustered isolates were of Lineage 1 and none are resistant to any of the drugs tested. This study while demonstrating the relevance and utility of WGS in predicting drug resistance and inference of disease transmission, highlights the need to increase the representation of genotype–phenotype TB data from low and middle income countries in Asia and Africa to improve the accuracies for prediction of drug resistance.

Mycobacterium tuberculosis Lineage Distribution Using Whole-Genome Sequencing and Bedaquiline, Clofazimine, and Linezolid Phenotypic Profiles among Rifampicin-Resistant Isolates from West Java, Indonesia

“…Another possibility could be that these isolates were part of an outbreak, but as this is an archived collection with no epidemiological data, we could not investigate further. In Cambodia, the majority of the lineages are also L1 (Indo-Oceanic), L2 (East Asian), and L4 (Euro-American) [ 52 ]. The high prevalence of the L1 M. tuberculosis strain in Cambodia is perhaps not surprising as it is a common strain in the Southeast Asian countries of India and Bangladesh [ 51 ].…”

Genomic insights into anthropozoonotic tuberculosis in captive sun bears (Helarctos malayanus) and an Asiatic black bear (Ursus thibetanus) in Cambodia

“…Although no human source was identified, detection of the two dominant TB lineages in the human population of Cambodia (Lineage 1 (Indo-Oceanic) and 2 (East Asian/Beijing)) 54 , 55 , as well as drug resistance (no bears had been exposed to anti-TB drugs), support both bear outbreaks being of human origin. Case E1’s history of living within a city household, along with disease onset so soon after arrival, suggests this bear was the index case in the Lineage 1 outbreak, and highlights the risk to bear sanctuaries receiving bears with a history of co-habiting with humans.…”

A description of Lineage 1Mycobacterium tuberculosisfrom Papua, Indonesia

“…Palittapongarnpim, et al ., [6], Edokimov, et al ., [29], and Le Hang, et al ., [36] showed high incidence on L1.1 in Thailand, Cambodia, and Vietnam respectively. While sublineage L1.2.2 can be found across Southeast Asia, the L1.2.2.2 found in the Papua dataset is most commonly found in Thailand [2].…”