New Short Tandem Repeat-Based Molecular Typing Method for Pneumocystis jirovecii Reveals Intrahospital Transmission between Patients from Different Wards.
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.
Laboratoire de Parasitologie-Mycologie, AP-HP, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Paris, France.
Maud
M
Gits-Muselli
Service de transplantation rénale, AP-HP, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Paris, France; Université Paris-Diderot, Sorbonne Cité, Paris, France.
Marie-Noelle
MN
Peraldi
Service de Maladie Infectieuses et tropicales, AP-HP, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Paris, France.
Nathalie
N
de Castro
Service de Médecine interne, AP-HP, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Hôpital Lariboisière, Paris, France.
Véronique
V
Delcey
Laboratoire de Parasitologie-Mycologie, AP-HP, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Paris, France; Université Paris-Diderot, Sorbonne Cité, Paris, France; Institut Pasteur, Unité de Mycologie Moléculaire, Centre National de Référence Mycoses invasives et Antifongiques, Paris, France; CNRS URA3012, Paris, France.
Jean
J
Menotti
Laboratoire de Parasitologie-Mycologie, AP-HP, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Paris, France; Université Paris-Diderot, Sorbonne Cité, Paris, France.
Nicolas
N
Guigue
Laboratoire de Parasitologie-Mycologie, AP-HP, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Paris, France.
Samia
S
Hamane
Service d'Hématologie adulte, AP-HP, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Paris, France.
Emmanuel
E
Raffoux
Université Paris-Diderot, Sorbonne Cité, Paris, France; Service de Pneumologie, AP-HP, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Paris, France.
Anne
A
Bergeron
Service de Réanimation, AP-HP, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Paris, France.
Sandrine
S
Valade
Université Paris-Diderot, Sorbonne Cité, Paris, France; Service de Maladie Infectieuses et tropicales, AP-HP, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Paris, France.
Jean-Michel
JM
Molina
Laboratoire de Parasitologie-Mycologie, AP-HP, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Paris, France; Université Paris-Diderot, Sorbonne Cité, Paris, France; Institut Pasteur, Unité de Mycologie Moléculaire, Centre National de Référence Mycoses invasives et Antifongiques, Paris, France; CNRS URA3012, Paris, France.
Stéphane
S
Bretagne
Laboratoire de Parasitologie-Mycologie, AP-HP, Groupe Hospitalier Saint-Louis-Lariboisière-Fernand-Widal, Paris, France; Université Paris-Diderot, Sorbonne Cité, Paris, France; Institut Pasteur, Unité de Mycologie Moléculaire, Centre National de Référence Mycoses invasives et Antifongiques, Paris, France; CNRS URA3012, Paris, France.
Alexandre
A
Alanio
D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D002648:Child; D002675:Child, Preschool; D004271:DNA, Fungal / Q000235:genetics; D016681:Genome, Fungal; D005838:Genotype; D006801:Humans; D007223:Infant; D018895:Microsatellite Repeats / Q000235:genetics*; D008875:Middle Aged; D009894:Opportunistic Infections / Q000235:genetics* / Q000382:microbiology / Q000503:physiopathology / Q000635:transmission; D058974:Phylogeography; D045363:Pneumocystis carinii / Q000235:genetics* / Q000472:pathogenicity; D011020:Pneumonia, Pneumocystis / Q000235:genetics* / Q000382:microbiology / Q000503:physiopathology / Q000635:transmission; D013183:Sputum / Q000382:microbiology
D004271:DNA, Fungal