Fungal and bacterial coinfections increase mortality of severely ill COVID-19 patients.

BACKGROUND: SARS-CoV-2 predisposes patients to secondary infections; however, a better understanding of the impact of coinfections on the outcome of hospitalized COVID-19 patients is still necessary. AIM: To analyse death risk due to coinfections in COVID-19 patients. METHODS: The odds of death of 212 severely ill COVID-19 patients were evaluated, with detailed focus on the risks for each pathogen, site of infection, comorbidities and length of hospitalization. FINDINGS: The mortality rate was 50.47%. Fungal and/or bacterial isolation occurred in 89 patients, of whom 83.14% died. Coinfected patients stayed hospitalized longer and had an increased odds of dying (odds ratio (OR): 13.45; R2 = 0.31). The risk of death was increased by bacterial (OR: 11.28) and fungal (OR: 5.97) coinfections, with increased levels of creatinine, leucocytes, urea and C-reactive protein. Coinfections increased the risk of death if patients suffered from cardiovascular disease (OR: 11.53), diabetes (OR: 6.00) or obesity (OR: 5.60) in comparison with patients with these comorbidities but without pathogen isolation. The increased risk of death was detected for coagulase-negative Staphylococcus (OR: 25.39), Candida non-albicans (OR: 11.12), S. aureus (OR: 10.72), Acinetobacter spp. (OR: 6.88), Pseudomonas spp. (OR: 4.77), and C. albicans (OR: 3.97). The high-risk sites of infection were blood, tracheal aspirate, and urine. Patients with coinfection undergoing invasive mechanical ventilation were 3.8 times more likely to die than those without positive cultures. CONCLUSION: Severe COVID-19 patients with secondary coinfections required longer hospitalization and had higher risk of death. The early diagnosis of coinfections is essential to identify high-risk patients and to determine the right interventions to reduce mortality.

Novel PCR primers for improved detection of Mycobacterium leprae and diagnosis of leprosy.

AIMS: Diagnosis of leprosy, a chronic infection caused by Mycobacterium leprae, predominantly depends on clinical manifestations and histopathological analysis, hampering rapid and accurate diagnostics. Our aim was to increase accuracy of leprosy diagnosis by improving M. leprae's DNA detection based on polymerase chain reaction (PCR) technique using new specific primers for the RLEP repetitive sequence. METHODS AND RESULTS: The specific target region, RLEP, of M. leprae's genome was selected based on comparative genomics. After confirming the specificity of this region, using blastn analysis, primers were designed and tested for their in silico specificity. To evaluate the specificity and sensitivity of these primers in vitro, 184 blood samples from patients were used in qPCR. The new primer pair LYON1/LYON2 produced 91% positive samples, whereas the current primer pair LP1/LP2 produced 46%. Specificity and DNA detection limit test were carried out to compare the efficiency of the developed primer pair. The LYON1/LYON2 primer showed 100% specificity, whereas LP1/LP2 showed 64%. The DNA detection limit of LYON1/LYON2 was 10 copies of bacterial genomes per millilitre, whereas LP1/LP2 was 1000 copies of bacterial genomes per millilitre. CONCLUSIONS: In conclusion, the developed LYON1/LYON2 primer pair presented to be a specific and sensitive new molecular marker for the diagnosis of leprosy. SIGNIFICANCE AND IMPACT OF THE STUDY: The development of a specific primer pair for the detection of the M. leprae genome through qPCR technique contributes to a fast, sensitive and specific diagnosis, which is essential to prevent spreading and progression of this disease.

Oral phaeohyphomycosis.

This is the first description of solitary phaeohyphomycosis affecting the mucosal surface. The lesion developed in the inferior lip of a 57-year-old woman. After surgical resection, histopathological examination evidenced characteristic brownish fungal structures within granulomatous-purulent inflammation. Amplification and sequencing of rDNA obtained from paraffin-embedded tissue identified Alternaria species, as the causative agent.

Internal transcribed spacer rRNA gene-based phylogenetic reconstruction using algorithms with local and global sequence alignment for black yeasts and their relatives.

Sequences of rRNA gene internal transcribed spacer (ITS) of a standard set of black yeast-like fungal pathogens were compared using two methods: local and global alignments. The latter is based on DNA-walk divergence analysis. This method has become recently available as an algorithm (DNAWD program) which converts sequences into three-dimensional walks. The walks are compared with, or fit to, each other generating global alignments. The DNA-walk geometry defines a proper metric used to create a distance matrix appropriated for phylogenetic reconstruction. In this work, the analyses were carried out for species currently classified in Capronia, Cladophialophora, Exophiala, Fonsecaea, Phialophora, and Ramichloridium. Main groups were verified by small-subunit rRNA gene data. DNAWD applied to ITS2 alone enabled species recognition as well as phylogenetic reconstruction reflecting clades discriminated in small-subunit rRNA gene phylogeny, which was not possible with any other algorithm using local alignment for the same data set. It is concluded that DNAWD provides rapid insight into broader relationships between groups using genes that otherwise would be hardly usable for this purpose.

Species diversity and polymorphism in the Exophiala spinifera clade containing opportunistic black yeast-like fungi.

A monophyletic group of black yeast-like fungi containing opportunistic pathogens around Exophiala spinifera is analyzed using sequences of the small-subunit (SSU) and internal transcribed spacer (ITS) domains of ribosomal DNA. The group contains yeast-like and annellidic species (anamorph genus Exophiala) in addition to sympodial taxa (anamorph genera Ramichloridium and Rhinocladiella). The new species Exophiala oligosperma, Ramichloridium basitonum, and Rhinocladiella similis are introduced and compared with their morphologically similar counterparts at larger phylogenetic distances outside the E. spinifera clade. Exophiala jeanselmei is redefined. New combinations are proposed in EXOPHIALA: Exophiala exophialae for Phaeococcomyces exophialae and Exophiala heteromorpha for E. jeanselmei var. heteromorpha.

Brain abscess caused by Cladophialophora (Xylohypha) bantiana in a renal transplant patient.

Infectious disease is the most significant cause of morbidity and mortality in allotransplantation because of heavy immunosuppression. Brain abscesses caused by melanized fungi have been found occasionally and are an example of this complication. In this paper, we describe a case in a 61-year-old black man, who received a cadaveric kidney transplantation in December 1993, followed by triple therapy with cyclosporine, azathioprine, and prednisone. The patient developed right hemiparesis at the beginning of April 1998. A computed tomography scan showed a mass in the left parieto-temporal region of the brain. The patient underwent surgery and a brown-colored encapsulated brain abscess was resected. Histology of the tissue revealed a large number of pigmented fungal hyphae. Culture in a Sabouraud dextrose medium with cyclohexamide and chloramphenicol at 25 degrees C resulted in the growth of dark-green colonies. The fungus identified was Cladophialophora bantiana, based on characteristic microscopic features and on growth at 40 degrees C. The abscess recurred in spite of treatment with fluconazole. The patient was submitted to a second brain surgical procedure and was treated with amphotericin B in addition to fluconazole. Ten days later the patient's blood cultures became positive for Escherichia coli. After 3 days the patient died due to septic shock.

Use of RAPD (random amplified polymorphic DNA) to analyse genetic diversity of dematiaceous fungal pathogens.

Thirteen strains of chromoblastomycosis and phaeohyphomycosis etiologic agent fungi were obtained from different geographical origins. These strains were genotypically compared by means of the RAPD (Random Amplified Polymorphic DNA) technique. The data generated showed a high degree of polymorphism between distinct species and a low polymorphism between strains of the same species. The results generated by these tests were subjected to a numerical taxonomy analysis, using the unweighted pair-group method. A phenogram was constructed for the set of strains studied. Based on its structure, we concluded that genotypical data provide enough information to us to use the unweighted pair-group method to cluster the strains in accordance to their respective species. The phenogram grouped in a single branch the strains of Fonsecaea pedrosoi and F. compacta species, indicating a great similarity between these fungi, and suggesting that the classification as distinct species may not be appropriate for these species of the genus Fonsecaea.

In vitro susceptibility of chromoblastomycosis and phaeohyphomycosis agents to antifungal drugs.

The in vitro susceptibility of chromoblastomycosis and phaeohyphomycosis agents to antifungal drugs was appraised using the reference macrodilution method proposed by the National Committee for Clinical Laboratory Standards (NCCLS) for yeasts modified for filamentous fungi. The antifungal drugs amphotericin B, 5-fluorocytosine, itraconazole and fluconazole were tested against one environmental and 18 clinical isolates. This work amended the macrodilution methods proposed by NCCLS and suggests that a conidial suspension free of hyphae leads to a more reliable assay and provides for better reproducibility. The macrodilution method was performed with 10(4) conidia ml-1. The MIC values ranged from 1.0 to 16.0 micrograms ml-1 for amphotericin B and 3.12 to 25.0 micrograms ml-1 for 5-fluorocytosine. A MIC range of 0.06 to 1.95 micrograms ml-1 was determined for itraconazole while 2.0 to 64.0 micrograms ml-1 was detected for fluconazole.

Dematiaceous fungal pathogens: analysis of ribosomal DNA gene polymorphism by polymerase chain reaction-restriction fragment length polymorphism.

Restriction fragment length polymorphisms (RFLP) of ribosomal gene small subunit (SSU rDNA) and internal transcribed spacer (ITS) regions was examined in 12 isolates of dematiaceous agents of chromoblastomycosis and phaeohyphomycosis. The amplicon length of the fragment ITS1-ITS4, comprising the 5.8 rDNA and ITS1-ITS2 spacers, ranged in size from 620 to 690 bp. This result indicated a polymorphism of size in this region. Additionally the RFLP profiles showed a high degree of inter- and intra-specific variability. In contrast, the SSU rDNA amplification, using NS1-NS2 primers, originated a fragment of approximately 570 bp and its restriction profile proved to be well conserved among the species studied and was clustered into only two genetically heterogeneous groups, the first one formed by Fonsecaea pedrosoi and Fonsecaea compacta and the second one formed by Cladophialophora (Cladosporium) carrionii, Cladophialophora (Xylohypha) bantiana, Phialophora verrucosa and Rhinocladiella species.