Genomic investigations unmask Mycoplasma amphoriforme, a new respiratory pathogen

Abstract

Background. Mycoplasma amphoriforme has been associated with infection in patients with Primary Antibody Deficiency (PAD). Little is known about the natural history of infection with this organism and its ability to be transmitted in the community. Methods. The bacterial load was estimated in sequential sputum samples from nine patients by qPCR. The genomes of all available isolates, originating from patients in the UK, France and Tunisia, were sequenced along with the type strain. Genomic data was assembled, annotated and a high-resolution phylogenetic tree constructed. Results. By using high-resolution whole genome sequence data we show that patients can be chronically infected with M. amphoriforme manifesting as a relapsing remitting bacterial load interspersed by periods when the organism is undetectable. Importantly we demonstrate transmission of strains within a clinical environment. Antibiotic resistance mutations accumulate in isolates taken from patients who received multiple courses of antibiotics. Conclusions. Mycoplasma amphoriforme isolates form a closely related species responsible for a chronic relapsing and remitting infection in PAD patients in the UK and from immunocompetent patients in other countries. We provide strong evidence of transmission between patients attending the same clinic suggesting that screening and isolation may be necessary for susceptible patients. This work demonstrates the critical role that whole genome sequencing can play in unravelling the biology of a novel pathogen rapidly.