Molecular epidemiology and whole genome sequencing analysis of clinical Mycobacterium bovis from Ghana

Otchere, Isaac Darko; Tonder, Andries J. van; Asante-Poku, Adwoa; Sánchez-Busó, Leonor; Coscollá, Mireia; Osei-Wusu, Stephen; Asare, Prince; Aboagye, Samuel Yaw; Ekuban, Samuel Acquah; Yahayah, Abdallah Iddrisu; Forson, Audrey; Laryea, Clement; Parkhill, Julian; Harris, Simon R.; Gagneux, Sébastien; Yeboah-Manu, Dorothy

doi:10.1371/journal.pone.0209395

Cited by 26 publications

(29 citation statements)

References 52 publications

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“…The next split in our phylogeny corresponds to Af1, which has been characterized extensively using the deletion RDAf1 and spoligotyping, and shown to be most prevalent in countries from West- and Central Africa [11]. Here we could only compile nine Af1 genomes, of which five originated in Ghana [54], and the remaining had either a European or an unknown origin. The small diversity of Af1 spoligotyping patterns found in our WGS dataset [11], indicates strong undersampling (Fig.…”

Section: Resultsmentioning

confidence: 99%

An African origin forMycobacterium bovis

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Lay Summary: Mycobacterium bovis and M. caprae are both the most important agents 37 of tuberculosis in livestock and zoonotic tuberculosis in humans. Using phylogenetic and 38 molecular clock inferences based on an extensive collection of whole-genome sequences 39 we provide new insights into the global population structure, phylogeography and 40 evolutionary history of these pathogens. 41 42 Word count abstract: 180 43 Word count main text: 4366 44 Number of Figures: 3 45 46 ABSTRACT 47 48 Background and objectives 49 Mycobacterium bovis and Mycobacterium caprae are the two most important agents of 50 tuberculosis (TB) in livestock and the most important causes of zoonotic TB in humans. 51However, little is known about the global population structure, phylogeography and 52 evolutionary history of these pathogens. 53 Methodology 54We compiled a global collection of 3364 whole-genome sequences from M. bovis and M. 55 caprae originating from 35 countries and inferred their phylogenetic relationships, geographic 56 origins and age. 57 Results 58Our results resolve the phylogenetic relationship among the four previously defined clonal 59 complexes of M. bovis, and another eight newly described here. Our inferences indicate that 60 M. bovis emerged in East Africa likely between the 4 th and 10 th century. While some M. bovis 61 groups remained restricted to East-and West Africa, others have subsequently dispersed to 62 different parts of the world. 63 Conclusions and implications 64Our results allow a better understanding of the global population structure of M. bovis and its 65 evolutionary history. This knowledge can be used to define better molecular markers for 66 epidemiological investigations in settings where whole genome sequencing cannot easily be 67 implemented. 68 69 70 BACKGROUND AND OBJECTIVES 71 Tuberculosis (TB) remains an important burden for global health and the economy [1]. TB is 72 the number one cause of human death due to infection globally, with an estimated 10.0 73 million new cases and 1.6 million deaths occurring every year [1]. TB is caused by members 74 of the Mycobacterium tuberculosis complex (MTBC), which includes seven human-adapted 75 lineages, and several animal-adapted ecotypes including M. bovis and M. caprae. Animal TB 76 complicates the control of human TB due to the zoonotic transfer of TB bacilli from infected 77 animals to exposed human populations through e.g. the consumption of unpasteurized milk or 78 handling of contaminated meat [2]. M. bovis and M. caprae are the most important agents of 79 TB in livestock and the most important agents of zoonotic TB in humans, causing at least 147 80 000 new human cases and 12 500 deaths yearly [1, 3]. Zoonotic TB caused by M. bovis also 81 poses a challenge for patient treatment, due to its natural resistance to pyrazinamide (PZA), 82 one of the four first-line drugs used in the treatment of TB. In addition, TB in livestock 83 accounts for an estimated loss of three billion US dollars per year [4]. In Africa its prevalence 84 is highes...

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Section: Resultsmentioning

confidence: 99%

An African origin forMycobacterium bovis

Loiseau

Menardo

Aseffa

et al. 2019

Preprint

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“…Knowledge of the mutation rate is a critical factor determining the effectiveness of different genotyping methods. The mutation rate describes the frequency at which molecular fingerprint patterns change and is important for appropriate analysis of molecular data for epidemiological or phylogenetic research [ 166 , 167 ]. A higher mutation rate could result inthe high estimation of epidemiologically unrelated MTBC, which occurs at hypervariable loci [ 90 , 168 ].…”

Section: Genotyping Techniques Used In Mtbc Diagnosismentioning

confidence: 99%

Mycobacterium tuberculosis complex in wildlife: Review of current applications of antemortem and postmortem diagnosis

et al. 2020

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Tuberculosis (TB) is a chronic inflammatory and zoonotic disease caused by Mycobacterium tuberculosis complex (MTBC) members, which affects various domestic animals, wildlife, and humans. Some wild animals serve as reservoir hosts in the transmission and epidemiology of the disease. Therefore, the monitoring and surveillance of both wild and domestic hosts are critical for prevention and control strategies. For TB diagnosis, the single intradermal tuberculin test or the single comparative intradermal tuberculin test, and the gamma-interferon test, which is regarded as an ancillary test, are used. Postmortem examination can identify granulomatous lesions compatible with a diagnosis of TB . In contrast, smears of the lesions can be stained for acid-fast bacilli, and samples of the affected organs can be subjected to histopathological analyses. Culture is the gold standard test for isolating mycobacterial bacilli because it has high sensitivity and specificity compared with other methods. Serology for antibody detection allows the testing of many samples simply, rapidly, and inexpensively, and the protocol can be standardized in different laboratories. Molecular biological analyses are also applicable to trace the epidemiology of the disease. In conclusion, reviewing the various techniques used in MTBC diagnosis can help establish guidelines for researchers when choosing a particular diagnostic method depending on the situation at hand, be it disease outbreaks in wildlife or for epidemiological studies. This is because a good understanding of various diagnostic techniques will aid in monitoring and managing emerging pandemic threats of infectious diseases from wildlife and also preventing the potential spread of zoonotic TB to livestock and humans. This review aimed to provide up-to-date information on different techniques used for diagnosing TB at the interfaces between wildlife, livestock, and humans.

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“…In South Africa, African buffaloes (Syncerus caffer) are believed to be a key M. bovis wildlife maintenance host, with reported spill-over to other wildlife species and cattle [2,3]. In addition, cases of bTB have also been reported in people in African countries, especially those in contact with animals [4]. Cases of M. tuberculosis infection also occur in domestic cattle in rural areas of Africa as well as captive wildlife and pets [5][6][7][8].…”

Section: Introductionmentioning

confidence: 99%

The VetMAX™ M. tuberculosis complex PCR kit detects MTBC DNA in antemortem and postmortem samples from white rhinoceros (Ceratotherium simum), African elephants (Loxodonta africana) and African buffaloes (Syncerus caffer)

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Background: Bovine tuberculosis and tuberculosis are chronic infectious diseases caused by the Mycobacterium tuberculosis complex members, Mycobacterium bovis and Mycobacterium tuberculosis, respectively. Infection with M. bovis and M. tuberculosis have significant implications for wildlife species management, public health, veterinary disease control, and conservation endeavours. Results: Here we describe the first use of the VetMAX™ Mycobacterium tuberculosis complex (MTBC) DNA quantitative real-time polymerase chain reaction (qPCR) detection kit for African wildlife samples. DNA was extracted from tissues harvested from 48 African buffaloes and MTBC DNA was detected (test-positive) in all 26 M. bovis culture-confirmed animals with an additional 12 PCR-positive results in culture-negative buffaloes (originating from an exposed population). Of six MTBC-infected African rhinoceros tested, MTBC DNA was detected in antemortem and postmortem samples from five animals. The PCR was also able to detect MTBC DNA in samples from two African elephants confirmed to have M. bovis and M. tuberculosis infections (one each). Culture-confirmed uninfected rhinoceros and elephants' samples tested negative in the PCR assay. Conclusions: These results suggest this new detection kit is a sensitive screening test for the detection of MTBCinfected African buffaloes, African elephants and white rhinoceros.

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Molecular epidemiology and whole genome sequencing analysis of clinical Mycobacterium bovis from Ghana

Cited by 26 publications

References 52 publications

An African origin forMycobacterium bovis

An African origin forMycobacterium bovis

Mycobacterium tuberculosis complex in wildlife: Review of current applications of antemortem and postmortem diagnosis

The VetMAX™ M. tuberculosis complex PCR kit detects MTBC DNA in antemortem and postmortem samples from white rhinoceros (Ceratotherium simum), African elephants (Loxodonta africana) and African buffaloes (Syncerus caffer)

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