Molecular and microscopy detection of Pneumocystis jirovecii in hospitalized patients during the COVID-19 pandemic

Matouri, Roya; Aboutalebian, Shima; Nasri, Elahe; Sadeghi, Somayeh; Rostami, Soodabeh; Fakhim, Hamed; Ghafel, Safiyeh; Hosseini, Mahnaz Sadat; Mousavi, Seyyed Ali; Rouhi, Faezeh; Pestechian, Nader; Mirhendi, Hossein

doi:10.3389/fmed.2023.1148320

Cited by 4 publications

(2 citation statements)

References 38 publications

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“…Among these cases, A. niger (n=2), A. flavus (n=2), and A. fumigatus (n=1) were isolated in 5 samples, confirmed through direct microscopy, culture, and PCR identification. Also, Among the patients with Candida species colonization, 5 cases had co-existence with Pneumocystis, as documented by specific nested PCR (Matouri et al, 2023). Out of 9 patients with co-occurrence infections with other fungi, one of the patients had a three-fungi isolation of A. fumigatus, Pneumocystis, and C. albicans.…”

Section: Resultsmentioning

confidence: 99%

Yeast species in the respiratory samples of COVID-19 patients; molecular tracking of Candida auris

Rouhi,

Soltani,

Sadeghi

et al. 2024

Front. Cell. Infect. Microbiol.

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IntroductionAlthough the existence of Candida species in the respiratory tract is often considered commensal, it is crucial to recognize the significance of Candida colonization in immunocompromised or COVID-19 patients. The emergence of Candida auris as an emerging pathogen further emphasizes the importance of monitoring yeast infection/colonization, particularly in COVID-19 patients.MethodsIn this study, respiratory samples mainly from COVID-19 patients, primarily those suspected of having a fungal infection, were cultured on Sabouraud dextrose agar plates and the yeast colonies were identified using a two-step multiplex PCR method. The samples suspected of C. auris underwent specific nested PCR followed by sequence analysis.ResultsA total of 199 respiratory samples were collected from 73 women and 126 men, ranging in age from 1.6 to 88 years. Among the patients, 141 had COVID-19, 32 had cancer, 5 were hospitalized in ICU, 2 had chronic obstructive pulmonary disease)COPD(, and others were patients with combination diseases. From these samples, a total of 334 yeast strains were identified. C. albicans (n=132, 39.52%) was the most common species, followed by C. tropicalis (n=67, 20%), C. glabrata (n=56, 16.76%), C. krusei (n=18, 5.4%), C. parapsilosis (n=17, 5.08%), Saccharomyces cerevisiae (n=10, 3%), C. kefyr (n=9, 2.6%), C. dubliniensis (n=7, 2.1%), C. lusitaniae (n=5, 1.5%), C. auris (n=3, 0.9%), C. guilliermondii (n=2, 0.6%), C. rugosa (n=1, 0.3%), C. intermedia (n=1, 0.3%), and Trichosporon spp. (n=1, 0.3%). C. auris was detected in a patient in ICU and two COVID-19 patients. While its presence was confirmed through sequence analysis, our extensive efforts to isolate C. auris were unsuccessful.ConclusionWhile C. albicans colonization remains prevalent, our study found no evidence of Candida lung infection. Since the role of Candida colonization in airway secretions remains ambiguous due to limited research, further studies are imperative to shed light on this matter.

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Section: Resultsmentioning

confidence: 99%

Yeast species in the respiratory samples of COVID-19 patients; molecular tracking of Candida auris

Rouhi,

Soltani,

Sadeghi

et al. 2024

Front. Cell. Infect. Microbiol.

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“…Serum determination of 1,3-β-D-glucan (BDG), a component of the cell wall and considered a panfungal marker, can also be used to support the diagnosis of PCP; it has high sensitivity values of 95-96%, however, its specificity is 84-86% [14]. The development of molecular tools based on conventional or nested PCR for amplification of the coding sequence of the large mitochondrial subunit mtLSU, also called mt26S of ribosomal RNA (rRNA), has considerably increased the sensitivity and specificity of its detection, reaching values of 94-100% [15,16], allowing the analysis of genetic variability through the study of genotypes and coinfections by more than one strain [17]. The introduction of Real-time PCR (RT-PCR) has substantially improved the diagnosis of PCP and has been defined as the most highly sensitive method for P. jirovecii detection with sensitivity and negative predictive values (NPV) of 100% [15].…”

Section: Introductionmentioning

confidence: 99%

Molecular Study of Pneumocystis jirovecii in Respiratory Samples of HIV Patients in Chile

Iturrieta-González,

Chahin,

Cabrera

et al. 2024

JoF

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Pneumocystis is an opportunistic fungus that causes potentially fatal pneumonia (PCP) in immunocompromised patients. The objective of this study was to determine the prevalence of P. jirovecii in HIV patients through phenotypic and molecular study, to investigate the genetic polymorphisms of P. jirovecii at the mitochondrial gene mtLSU and at the nuclear dihydropteroate synthase gene (DHPS), and by analysis of molecular docking to study the effect of DHPS mutations on the enzymatic affinity for sulfamethoxazole. A PCP prevalence of 28.3% was detected, with mtLSU rRNA genotypes 3 (33.3%) and 2 (26.6%) being the most common. A prevalence of 6.7% (1/15) mutations in the DHPS gene was detected, specifically at codon 55 of the amino acid sequence of dihydropteroate synthase. Molecular docking analysis showed that the combination of mutations at 55 and 98 codons is required to significantly reduce the affinity of the enzyme for sulfamethoxazole. We observed a low rate of mutations in the DHPS gene, and molecular docking analysis showed that at least two mutations in the DHPS gene are required to significantly reduce the affinity of dihydropteroate synthase for sulfamethoxazole.

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Molecular assays versus mycological methods for diagnosis of rhino orbital mucormycosis: analysis of 120 fresh clinical specimens from COVID-19 patients

Soltani,

Erami,

Ahmadikia

et al. 2024

Preprint

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Mucormycosis, a fungal emergency, poses a serious threat to both COVID-19 and non-COVID-19 individuals due to its invasive nature, rapid progression, and high rates of morbidity and mortality which highlights the crucial need for its timely detection and management. Here, we investigated the utility of Mucorales-specific real-time PCR (rt-PCR) assays for the detection of mucormycosis from clinical specimens and compared with conventional methods and duplex PCR. Methods: Both SYBR Green and TaqMan rt-PCR methodologies were optimized using Mucorales-specific oligonucleotides to amplify the conserved 18S rDNA targets. DNAs extracted from 120 rhino sinus specimens, which all were collected from COVID-19 patients upon suspicion of invasive fungal infections, were used for molecular diagnosis. The results of both rt PCR assays were compared with the result of direct microscopy, culture, and duplex Mucorales-specific PCR assay. Results: SYBR Green rt-PCR detected Mucorales in 51 out of 120 (91.67% of K0H-positive samples), yielding a unique Tm pattern (80.24 ± 0.70°C), whereas TaqMan-probe PCR and culture methods detected it in 34 (73.84%) and 24 samples, respectively. The SYBR Green-based PCR was also more sensitive/specific than the duplex PCR technique. The lower sensitivity in probe-based PCR can be influenced by various factors such as probe degeneracy, which can lead to false-negative results. Conclusion: SYBR Green-based PCR showed superiority over duplex PCR, culture, and TaqMan-probe PCR in terms of cost-effectiveness, rapidness, and sensitivity for the diagnosis of mucormycosis. As there is no serological test, SYBR Green-based PCR can be used as an affirmatory test to rule in or rule out mucormycosis, particularly in cases with atypical hyphae or septate and non-septate hyphae suggestive of mixed infections in direct examination but negative culture.

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Molecular and microscopy detection of Pneumocystis jirovecii in hospitalized patients during the COVID-19 pandemic

Cited by 4 publications

References 38 publications

Yeast species in the respiratory samples of COVID-19 patients; molecular tracking of Candida auris

Yeast species in the respiratory samples of COVID-19 patients; molecular tracking of Candida auris

Molecular Study of Pneumocystis jirovecii in Respiratory Samples of HIV Patients in Chile

Molecular assays versus mycological methods for diagnosis of rhino orbital mucormycosis: analysis of 120 fresh clinical specimens from COVID-19 patients

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