Abstract
Pneumocystis jirovecii is an opportunistic human pathogenic fungus causing severe pneumonia mainly in immunocompromised hosts. Multilocus sequence typing (MLST) remains the gold standard for genotyping of this unculturable fungus. However, the lack of a consensus scheme impedes a global comparison, large scale population studies and the development of a global MLST database. To overcome this problem this study compared all genetic regions (19 loci) currently used in 31 different published Pneumocystis MLST schemes. The most diverse/commonly used eight loci, β-TUB, CYB, DHPS, ITS1, ITS1/2, mt26S and SOD, were further assess for their ability to be successfully amplified and sequenced, and for their discriminatory power. The most successful loci were tested to identify genetically related and unrelated cases. A new consensus MLST scheme consisting of four genetically independent loci: β-TUB, CYB, mt26S and SOD, is herein proposed for standardised P. jirovecii typing, successfully amplifying low and high fungal burden specimens, showing adequate discriminatory power, and correctly identifying suspected related and unrelated isolates. The new consensus MLST scheme, if accepted, will for the first time provide a powerful tool to investigate outbreak settings and undertake global epidemiological studies shedding light on the spread of this important human fungal pathogen.
Highlights
Pneumocystis jirovecii is a major opportunistic pathogen, which can manifest into severe pneumonia, Pneumocystis pneumonia (PCP), in immunocompromised patients
The Fisher exact test statistic value indicated no significant differences between the individual cohort amplification rates for β-TUB, cytochrome b oxidase gene (CYB) and mt26S, and a significant result at p < 0.05 using the Fisher’s exact test [90] for the dihydropteroate synthase (DHPS), superoxide dismutase (SOD) and internal transcribed spacer 1 (ITS1)/2 loci
P. jirovecii is for vital the advancement of understanding of pathogenesis, the biology, epidemiology, prophylaxis and treatment regimen of this human pathogen, but it is pathogenesis, epidemiology, prophylaxis and treatment regimen of this human pathogen, but more vital to help itmanage, preventcontain nosocomial clusters. nosocomial
Summary
Pneumocystis jirovecii is a major opportunistic pathogen, which can manifest into severe pneumonia, Pneumocystis pneumonia (PCP), in immunocompromised patients. PCP can cause interstitial lung disease, along with fever, coughs and dyspnea [1]. The incidence is still relatively high, especially in the developing world, for this underestimated fungus, with reported mortality rates ranging from. J. Fungi 2020, 6, 259; doi:10.3390/jof6040259 www.mdpi.com/journal/jof. P. jirovecii has been linked to nosocomial outbreaks affecting mainly solid organ transplant recipients with devastating consequences. Besides helping to establish epidemiological links among affected patients, allowing for paths of transmission to be mapped and index cases identified within hospital outbreaks, genotyping is an essential tool to achieve knowledge on more general aspects of the epidemiology of microorganisms
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