Objectives: This study describes the prevalence and genotype distribution of Pneumocystis jirovecii obtained from nasopharyngeal swabs of immunocompetent Cuban infants with acute respiratory tract infection (RTI).

Methods: One hundred sixty three nasopharyngeal swabs from young children with RTI hospitalized in the respiratory services at the two pediatric centers, Havana-Cuba, were studied. The prevalence was determinate by quantitative PCR (qPCR) assay targeting the P. jirovecii mitochondrial large subunit rRNA gene (mt LSU rRNA). The genotyping was determined by direct sequencing using mt LSU rRNA fragment and restriction fragment–length polymorphism analysis with dihydropteroate synthase gene (DHPS).

Results: qPCR detected P. jirovecii DNA in 48 (29.4%) of the 163 infants samples. The mt LSU rRNA analysis revealed the presence of three different genotypes in the population, with 10% of mixed infections. The predominant type observed was the genotype 2 (48%), followed by genotype 1 (23%), and genotype 3 (19%). When analyzing DHPS genotypes found circulation of the 3 possible genotypes, with 18% of genotypes associated with resistance to sulfa drugs.

Conclusion: The prevalence of P. jirovecii in non-immunosuppressed infants with acute respiratory tract infection and the genotyping results provide evidence that this infant population represents a potential transmission source of this fungi.