Progenitor “Mycobacterium canettii” Clone Responsible for Lymph Node Tuberculosis Epidemic, Djibouti

Yann Blouin, Géraldine Cazajous, Céline Dehan, Charles Soler, Rithy Vong, Mohamed Osman Hassan, Yolande Hauck, Christian Boulais, Dina Andriamanantena, Christophe Martinaud, Émilie Martin, Christine Pourcel, and Gilles Vergnaud

Author affiliations: Université Paris-Sud, Orsay, France (Y. Blouin, Y. Hauck, C. Pourcel, G. Vergnaud); Centre National de la Recherche Scientifique, Orsay (Y. Blouin, Y. Hauck, C. Pourcel, G. Vergnaud); Hôpital Militaire Bouffard, Djibouti, Republic of Djibouti (G. Cazajous, C. Dehan, C. Boulais); Hôpital d'Instruction des Armées Percy, Clamart, France (C. Soler, R. Vong, C. Martinaud);Hôpital Paul Faure, Djibouti (M. Osman Hassan); Hôpital d'Instruction des Armées Bégin, Saint-Mandé, France (D. Andriamanantena); Centre Hospitalier Lyon Sud, Lyon, France (E. Martin); Institut de Recherche Biomédicale des Armées, Brétigny, France (G. Vergnaud)

Abstract

“Mycobacterium canettii,” an opportunistic human pathogen living in an unknown environmental reservoir, is the progenitor species from which Mycobacterium tuberculosisemerged. Since its discovery in 1969, most of the ≈70 known M. canettii strains were isolated in the Republic of Djibouti, frequently from expatriate children and adults. We show here, by whole-genome sequencing, that most strains collected from February 2010 through March 2013, and associated with 2 outbreaks of lymph node tuberculosis in children, belong to a unique epidemic clone within M. canettii. Evolution of this clone, which has been recovered regularly since 1983, may mimic the birth of M. tuberculosis. Thus, recognizing this organism and identifying its reservoir are clinically important.

Most “Mycobacterium canettii” strains have been isolated in the Republic of Djibouti, where 2 hospitals manage tuberculosis (TB) infections among the Djiboutian population and expatriates (1,2). A study of clinical and epidemiologic data linked to M. canettii infections showed that the proportion of TB cases caused by M. canettii was higher among expatriate than among Djiboutian patients and that patients with M. canettii infection were significantly younger than those with M. tuberculosis infection (2). These findings suggested that the Djiboutian population had been immunized against infection by M. canettii. No difference was observed in the frequency of the nonpulmonary form of TB caused by M. tuberculosis or M. canettii.

M. canettii is the progenitor species from which M. tuberculosis emerged (3–5). Genotyping of known M. canettii isolates showed that 70% of them belong to a large cluster called A (1,3). Strains belonging to cluster A were isolated as early as 1983. This observation and the absence of human-to-human transmission support the existence of an environmental reservoir. We report the isolation, since 2010, of 21 new strains of M. canettii in Djibouti, of which 7 were associated with 2 lymph node TB outbreaks in children. We show that 17 of the new strains, including the outbreak strains, belong to cluster A. We use draft whole-genome sequencing to demonstrate that this cluster is remarkable among M. canettii strains and confirm its epidemic status, which suggests an accelerating emergence of a clone, subsequently called clone A. Within clone A, we identify a single horizontal genetic transfer event, presumably resulting from recombination with closely related mycobacteria. We also investigate CRISPRs (clustered regularly interspaced short palindromic repeats) because these structures, which keep a memory of past infections by bacterial viruses, may provide indirect clues about an environmental reservoir. We take advantage of the clone A sequence data, which is, within M. canettii, closest to M. tuberculosis, to better describe the emergence of M. tuberculosis.