Multilocus genotyping of Pneumocystis jirovecii from adult HIV-infected patients with Pneumocystis pneumonia

Consensus Multilocus Sequence Typing Scheme for Pneumocystis jirovecii

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.

Polymorphisms involving the Pneumocystis jirovecii-related genes in AIDS patients in eastern China

OBJECTIVE

To investigate the genetic polymorphisms of mitochondrial large ribosomal subunit (mtLSU)-rRNA, dihydrofolate reductase (DHFR), dihydropteroate synthase (DHPS), cytochrome b (CYB), and superoxide dismutase (SOD) genes and its correlation with clinical outcomes of Pneumocystis jirovecii pneumonia in acquired immune deficiency(AIDS) patients.

METHODS

Eighty AIDS patients with P. jirovecii pneumonia that were admitted to our hospital from 2016 to 2018 were included in this study. Their demographic information and clinical data were collected, as well as corresponding saliva specimens for PCR and sequencing of mtLSU-rRNA, DHFR, DHPS, CYB, and SOD genes to analyze genetic polymorphisms, different polymorphic combinations, and clinical outcomes.

RESULTS

Of the 80 saliva specimens, mtLSU-rRNA was successfully amplified and sequenced in 30 cases; CYB was successfully amplified and sequenced in 26 cases; and SOD, DHFR, and DHPS were successfully amplified and sequenced in 18 cases. These results indicate that The mtLSU-rRNA, CYB, and SOD genes were highly polymorphic. mt85T and CYB1 were the variants dominantly detected at the mtLSU-rRNA and CYB loci, respectively. The SOD1 and SOD2 variants (each in 50% of the cases) were detected at the SOD locus. Among the 18 cases that were successfully amplified and sequenced for DHFR and DHPS, three DHFR nonsense mutations and no DHPS mutation were observed. The mt85C, CYB1, SOD1, and DHFR312T genes harbored common polymorphisms (n = 4; 22.22%) and the mt85T, CYB1, SOD1, DHFR312T genes were associated with poor clinical outcomes.

CONCLUSION

The types of genetic polymorphisms and polymorphic combinations of mtLSU-rRNA, DHFR, DHPS, CYB, and SOD in P. jirovecii were related to the clinical outcomes of patients with P. jirovecii pneumonia in Zhejiang Province, China.

Translational Development and Application of (1→3)-β-d-Glucan for Diagnosis and Therapeutic Monitoring of Invasive Mycoses

Early diagnosis and prompt initiation of appropriate antimicrobial therapy are crucial steps in the management of patients with invasive fungal infections. However, the diagnosis of invasive mycoses remains a major challenge in clinical practice, because presenting symptoms may be subtle and non-invasive diagnostic assays often lack sensitivity and specificity. Diagnosis is often expressed on a scale of probability (proven, probable and possible) based on a constellation of imaging findings, microbiological tools and histopathology, as there is no stand-alone assay for diagnosis. Recent data suggest that the carbohydrate biomarker (1→3)-β-d-glucan may be useful in both the diagnosis and therapeutic monitoring of invasive fungal infections due to some yeasts, molds, and dimorphic fungi. In this paper, we review recent advances in the use of (1→3)-β-d-glucan to monitor clinical response to antifungal therapy and explore how this assay may be used in the future.

[Pneumocystis jirovecii: what does this mean?]

Pneumocystis was discovered nearly a century ago. It causes fatal pneumonia in immunocompromised individuals, especially in AIDS patients. Knowledge of the different species remained rudimentary until the mid-eighties when DNA analysis revealed its extensive diversity. In fact, it is no longer considered as a zoonosis. Pneumocystis organisms derived from different hosts have very different DNA sequences, indicating multiple species. Due to the genetic and functional disparities, the organism that causes human PCP is now named Pneumocystis jirovecii/Frenkel, 1999. We continue to call Pneumocystis carinii the species found in rats. This will allow for a single international language and avoid confusion. Changing the organism's name does not preclude the use of the well-known acronym PCP because it can also be read "PneumoCystis Pneumonia." The DNA sequences and genotypage have shown that variations exist among samples of P. jiroveci. Molecular biology is helpful in the study of the mechanisms of transmission, which can only occur in the same host and the different resistances as well as providing a better understanding of the relationship between host and pathogen. P. jirovecii pneumonia in immunosuppressed patients was previously thought to result from the reactivation of a latent infection acquired in early childhood. However, today, it is believed to result from a new infection from an exogenous source.

Pneumocystis jirovecii multilocus gene sequencing: findings and implications

Pneumocystis jirovecii pneumonia (PcP) remains a major cause of respiratory illness among immunocompromised patients, especially patients infected with HIV, but it has also been isolated from immunocompetent persons. This article discusses the application of multilocus genotyping analysis to the study of the genetic diversity of P. jirovecii and its epidemiological and clinical parameters, and the important concepts achieved to date with these approaches. The multilocus typing studies performed until now have shown that there is an important genetic diversity of stable and ubiquitous P. jirovecii genotypes; infection with P. jirovecii is not necessarily clonal, recombination between some P. jirovecii multilocus genotypes has been suggested. P. jirovecii-specific multilocus genotypes can be associated with severity of PcP. Patients infected with P. jirovecii, regardless of the form of infection they present with, are part of a common human reservoir for future infections. The CYB, DHFR, DHPS, mtLSU rRNA, SOD and the ITS loci are suitable genetic targets to be used in further epidemiological studies focused on the identification and characterization of P. jirovecii haplotypes correlated with drug resistance and PcP outcome.

Manganese superoxide dismutase in pathogenic fungi: an issue with pathophysiological and phylogenetic involvements

Manganese-containing superoxide dismutases (MnSODs) are ubiquitous metalloenzymes involved in cell defence against endogenous and exogenous reactive oxygen species. In fungi, using this essential enzyme for phylogenetic analysis of Pneumocystis and Ganoderma genera, and of species selected among Ascomycota, Basidiomycota and Zygomycota, provided interesting results in taxonomy and evolution. The role of mitochondrial and cytosolic MnSODs was explored in some pathogenic Basidiomycota yeasts (Cryptococcus neoformans var. grubii, Cryptococcus neoformans var. gattii, Malassezia sympodialis), Ascomycota filamentous fungi (Aspergillus fumigatus), and Ascomycota yeasts (Candida albicans). MnSOD-based phylogenetic and pathogenic data are confronted in order to evaluate the roles of fungal MnSODs in pathophysiological mechanisms.

Isolates of Pneumocystis jirovecii from Harare show high genotypic similarity to isolates from London at the superoxide dismutase locus

Pneumocystis jirovecii is the cause of Pneumocystis pneumonia (PCP) in humans. Isolates of P. jirovecii obtained from patients in Harare, Zimbabwe were genotyped at the superoxide dismutase locus. High genotypic similarity to isolates of P. jirovecii obtained from patients in London, UK was observed. These data provide additional support for the hypothesis that P. jirovecii is genetically indistinguishable in isolates from geographically diverse locations.