Updated Reference Genome Sequence and Annotation of Mycobacterium bovis AF2122/97

Abstract

We report here an update to the reference genome sequence of the bovine tuberculosis bacillus Mycobacterium bovis AF2122/97, generated using an integrative multiomics approach. The update includes 42 new coding sequences (CDSs), 14 modified annotations, 26 single-nucleotide polymorphism (SNP) corrections, and disclosure that the RD900 locus, previously described as absent from the genome, is in fact present.

A New Phylogenetic Framework for the Animal-adaptedMycobacterium tuberculosisComplex

“…Moreover, bovine TB is responsible for an estimated US$3 billion annual economic loss in livestock production globally (Waters et al 2012) and represents an ongoing threat for zoonotic TB in humans (Olea-Popelka et al 2017). The causative agents of TB in humans and animals are a group of closely related acid-fast bacilli collectively known as the Mycobacterium tuberculosis complex (MTBC) (Brites et al 2017, Malone et al 2017). The human-adapted MTBC comprises five main phylogenetic lineages generally referred to as Mycobacterium tuberculosis sensu stricto (i.e.…”

“…MTBC lineages 5 and 6) (de Jong et al 2010, Brites et al 2017, Yeboah-Manu et al 2017). Among the animal-adapted members of the MTBC, some primarily infect wild mammal species (Malone et al 2017). These include Mycobacterium microti (a pathogen of voles) (Brodin et al 2002), Mycobacterium pinnipedii (seals and sea lions) (Cousins et al 2003), Mycobacterium orygis (antelopes) (van Ingen et al 2012) and the “dassie bacillus” (rock hyrax) (Mostowy et al 2004), which have been known for a long time, as well as the more recently discovered Mycobacterium mungi (mongooses) (Alexander et al 2010), Mycobacterium suricattae (meerkats) (Parsons et al 2013) and the “chimpanzee bacillus” (chimpanzees) (Coscolla et al 2013).…”

“…These include Mycobacterium microti (a pathogen of voles) (Brodin et al 2002), Mycobacterium pinnipedii (seals and sea lions) (Cousins et al 2003), Mycobacterium orygis (antelopes) (van Ingen et al 2012) and the “dassie bacillus” (rock hyrax) (Mostowy et al 2004), which have been known for a long time, as well as the more recently discovered Mycobacterium mungi (mongooses) (Alexander et al 2010), Mycobacterium suricattae (meerkats) (Parsons et al 2013) and the “chimpanzee bacillus” (chimpanzees) (Coscolla et al 2013). Mycobacterium bovis and Mycobacterium caprae on the other hand are mainly found in domesticated cattle and goats, but do also frequently spill over into many different wild animal species (Malone et al 2017). Mycobacterium canettii is also considered part of the MTBC based on nucleotide identity; however M. canettii is likely an environmental microbe only occasionally causing opportunistic infections in humans (Koeck et al 2010, Supply et al 2013).…”

“…For example, M. orygis was first identified in a captive oryx (van Soolingen et al 1994) but has since then been isolated from many different host species including humans (van Ingen et al 2012). Thus, the actual host range of M. orygis remains ill-defined (Malone et al 2017). Similarly, for many of the animal-adapted members of the MTBC, only a few representatives have been isolated so far (e.g.…”

“…only one in the case of the chimpanzee bacillus), limiting inferences with respect to the host range of these microbes. Moreover when studying host tropism, it is important to differentiate between maintenance hosts, in which the corresponding MTBC members traverse their full life cycle, including the transmission to secondary hosts, and spillover hosts, in which the infection leads to a dead end with no onward transmission (Malone et al 2017). For example, M. tuberculosis sensu stricto is well adapted to transmit from human to human (Brites et al 2015) and is occasionally isolated from cattle (Ameni et al 2010).…”