New Short Tandem Repeat-Based Molecular Typing Method for Pneumocystis jirovecii Reveals Intrahospital Transmission between Patients from Different Wards

Maud Gits-Muselli (1) , Marie-Noelle Peraldi (2, 3) , Nathalie De Castro (4) , Véronique Delcey (5) , Jean Menotti (1, 3, 6, 7) , Nicolas Guigue (1, 3) , Samia Hamane (1) , Emmanuel Raffoux (8) , Anne Bergeron (9, 3) , Sandrine Valade (10) , Jean-Michel Molina (4, 3) , Stéphane Bretagne (1, 3, 6, 7) , Alexandre Alanio (1, 3, 6, 7)

1 Laboratoire de Parasitologie-Mycologie [CHU Saint Louis, Paris]
2 Service de transplantation rénale
3 UPD7 - Université Paris Diderot - Paris 7
4 Service des Maladies Infectieuses et Tropicales [CHU Saint Louis]
5 Service de Médecine Interne
6 CNRMA - Centre National de Référence Mycologie et Antifongiques-Mycologie Moléculaire
7 Mycologie moléculaire
8 Service d'hématologie biologique
9 Service de pneumologie [Saint-Louis]
10 Service de réanimation médicale

Pneumocystis pneumonia is a severe opportunistic infection in immunocompromised patients caused by the unusual fungus Pneumocystis jirovecii. Transmission is airborne, with both immunocompromised and immunocompetent individuals acting as a reservoir for the fungus. Numerous reports of outbreaks in renal transplant units demonstrate the need for valid genotyping methods to detect transmission of a given genotype. Here, we developed a short tandem repeat (STR)-based molecular typing method for P. jirovecii. We analyzed the P. jirovecii genome and selected six genomic STR markers located on different contigs of the genome. We then tested these markers in 106 P. jirovecii PCR-positive respiratory samples collected between October 2010 and November 2013 from 91 patients with various underlying medical conditions. Unique (one allele per marker) and multiple (more than one allele per marker) genotypes were observed in 34 (32%) and 72 (68%) samples, respectively. A genotype could be assigned to 55 samples (54 patients) and 61 different genotypes were identified in total with a discriminatory power of 0.992. Analysis of the allelic distribution of the six markers and minimum spanning tree analysis of the 61 genotypes identified a specific genotype (Gt21) in our hospital, which may have been transmitted between 10 patients including six renal transplant recipients. Our STR-based molecular typing method is a quick, cheap and reliable approach to genotype Pneumocystis jirovecii in hospital settings and is sensitive enough to detect minor genotypes, thus enabling the study of the transmission and pathophysiology of Pneumocystis pneumonia.

Mots clés: Adolescent; Adult; Aged; 80 and over; Child; Preschool; DNA; Fungal; Genome; Genotype; Humans; Infant; Microsatellite Repeats; Middle Aged; Opportunistic Infections; Phylogeography; Pneumocystis jirovecii; Pneumonia; Pneumocystis; Sputum

Domaines: Sciences du Vivant [q-bio]; Médecine humaine et pathologie

Maud Gits-Muselli, Marie-Noelle Peraldi, Nathalie De Castro, Véronique Delcey, Jean Menotti, et al.. New Short Tandem Repeat-Based Molecular Typing Method for Pneumocystis jirovecii Reveals Intrahospital Transmission between Patients from Different Wards. PLoS ONE, 2015, 10 (5), pp.e0125763. ⟨10.1371/journal.pone.0125763⟩. ⟨pasteur-01405228⟩