Short tandem repeat genotyping for P. jirovecii is more sensitive to mixed genotype than MLST

Abstract

Objectives The increasing reports of outbreaks in renal transplant and pediatric units highlight the need for reliable genotyping methods to characterize nosocomial acquisition of Pneumocystis jirovecii . PCR-based methods, mainly MLST, have been widely used in this setting. Recently, short tandem repeat (STR) typing was suggested to be more sensitive to mixed infection and detect minority genotypes. Till now, no comparison between MLST and STR have been performed. Methods Thirty-seven samples (one per patient) from two hospitals were analysed (Paris hospital, n = 18, Nantes hospital, n = 19). Each sample was analysed by both a STR typing assay using 6 nuclear markers as recently developed with a MLST typing scheme relying on 4 loci (2 nuclear: SOD and ITS1; and 2 mitochondrial genes: mtLSU , Cytb ) as recently proposed. Analyses were performed blindly for the other typing method. Results Thirty-two and 35 different genotypes were observed by MLST and STR typing, respectively. Mixtures of genotypes were detected in 6/37 (16.2%) samples and 20/37 (54.1%) in MLST and STR typing, respectively. One mixed infection out of 6 detected using MLST was not observed using STR typing. Overall, one STR marker tends to differentiate samples between Paris and Nantes hospitals (Chi 2 ; P = 0.003). We then analyzed the 18/37 (48.6%) samples with a unique P. jirovecii genotype. Out of the 18/37 (48.6%) samples with no mixture, 18 and 17 different genotypes were delineated using MLST and STR respectively (one STR genotype was recovered from 2 patients). Conclusion This study provides evidence that STR typing markers compared well to MLST for molecular typing of P. jirovecii from clinical samples. The present STRs is less time-consuming and better discriminated the geographical origin and detection of minority genotypes, which can impact on the interpretation of epidemiological data.