title: 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 9 patients by quantitative polymerase chain reaction. The genomes of all available isolates, originating from patients in the United Kingdom, France, and Tunisia, were sequenced along with the type strain. Genomic data were assembled and annotated, and a high-resolution phylogenetic tree was constructed.
  
  
  RESULTS
  By using high-resolution whole-genome sequencing (WGS) 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 United Kingdom 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 WGS can play in rapidly unraveling the biology of a novel pathogen.
authors.affiliation: School of Medicine, University of St Andrews, United Kingdom.
authors.forename: Stephen H
authors.initials: SH
authors.lastname: Gillespie
authors.affiliation: Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand University College London Centre for Clinical Microbiology, Royal Free Campus, and.
authors.forename: Clare L
authors.initials: CL
authors.lastname: Ling
authors.affiliation: School of Medicine, University of St Andrews, United Kingdom.
authors.forename: Katarina
authors.initials: K
authors.lastname: Oravcova
authors.affiliation: School of Medicine, University of St Andrews, United Kingdom.
authors.forename: Miguel
authors.initials: M
authors.lastname: Pinheiro
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, United Kingdom.
authors.forename: Louise
authors.initials: L
authors.lastname: Wells
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, United Kingdom.
authors.forename: Josephine M
authors.initials: JM
authors.lastname: Bryant
authors.affiliation: University College London Centre for Clinical Microbiology, Royal Free Campus, and.
authors.forename: Timothy D
authors.initials: TD
authors.lastname: McHugh
authors.affiliation: University of Bordeaux, France.
authors.forename: Cecile
authors.initials: C
authors.lastname: Bébéar
authors.affiliation: Department of Immunology, Royal Free Hospital NHS Trust, London, United Kingdom.
authors.forename: David
authors.initials: D
authors.lastname: Webster
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, United Kingdom.
authors.forename: Simon R
authors.initials: SR
authors.lastname: Harris
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, United Kingdom.
authors.forename: Helena M B
authors.initials: HM
authors.lastname: Seth-Smith
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, United Kingdom.
authors.forename: Nicholas R
authors.initials: NR
authors.lastname: Thomson
mesh_terms: D000328:Adult; D058491:Bacterial Load; D018562:Disease Transmission, Infectious; D024881:Drug Resistance, Bacterial / Q000235:genetics; D016680:Genome, Bacterial; D023281:Genomics; D006801:Humans; D007153:Immunologic Deficiency Syndromes / Q000150:complications*; D009154:Mutation; D009174:Mycoplasma / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D009175:Mycoplasma Infections / Q000209:etiology / Q000382:microbiology* / Q000635:transmission; D010802:Phylogeny; D012008:Recurrence; D013183:Sputum / Q000382:microbiology
keywords: Mycoplasma amphoriforme; infection control; primary antibody deficiency; respiratory infection; whole genome sequencing