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Scheffersomyces spartinae Fungemia among Pediatric Patients, Pakistan, 2020-2024
Abstract:
Prevalence of emerging fungal infections is increasing, particularly among immunocompromised persons, children, and older persons. We report 108 cases of Scheffersomyces spartinae infection in pediatric patients from Karachi and other cities in Pakistan, of which 107 were identified from blood cultures. Cultures were initially misidentified as Clavispora lusitaniae by a biochemical assay before speciation as S. spartinae by whole-genome sequencing. All isolates were from children <12 years of age, and >69% were from children <1 month of age. Isolates were genetically distinct across regions of Pakistan; however, genetic diversity was low in isolates from patients in Karachi and nearby Nawabshah and had median differences of just 9 pairwise nucleotide variants. This study demonstrates S. spartinae is a potentially emerging pathogen in neonates and young infants in Pakistan. The findings highlight the limitations of phenotypic identification for detecting emerging fungal infections and underscore the value of molecular identification approaches.
Insights
Emerging fungal infections are rising. Scheffersomyces spartinae was identified in 108 pediatric cases in Pakistan, primarily in neonates, highlighting the need for accurate molecular diagnostics.
Area of Science:
- Mycology
- Infectious Diseases
- Genomics
Background:
- Emerging fungal infections pose a growing threat, especially to vulnerable populations like children.
- Scheffersomyces spartinae (S. spartinae) is increasingly recognized as a potential pathogen.
Purpose of the Study:
- To report a significant number of S. spartinae infections in pediatric patients in Pakistan.
- To highlight the challenges in identifying emerging fungal pathogens using traditional methods.
Main Methods:
- Whole-genome sequencing was employed for accurate fungal speciation.
- Biochemical assays were used for initial identification, revealing misclassifications.
- Analysis of genetic diversity among S. spartinae isolates from different regions.
Main Results:
- 108 cases of S. spartinae infection were identified in pediatric patients in Pakistan.
- 107 cases were detected from blood cultures, predominantly in infants under one month old.
- Molecular sequencing confirmed S. spartinae, distinguishing it from misidentified Clavispora lusitaniae.
Conclusions:
- S. spartinae is identified as a potentially emerging fungal pathogen in neonates and infants in Pakistan.
- Phenotypic identification methods have limitations in detecting novel or emerging fungal infections.
- Molecular identification techniques are crucial for accurate diagnosis and surveillance of fungal pathogens.
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