Abstract
Bloodstream infections caused by uncommon or novel fungal species are challenging to identify and treat. We report a series of cases of fungemia due to a rare basidiomycete yeast, Dirkmeia churashimaensis, in neonatal patients in India. Whole-genome sequence typing demonstrated that the patient isolates were genetically indistinguishable, indicating a single-source infection.
Highlights
Bloodstream infections caused by uncommon or novel fungal species are challenging to identify and treat
We report an unusual cluster of 12 cases of fungemia caused by D. churashimaensis among neonatal intensive care units (NICUs) patients in a multispecialty hospital in Delhi, India
Many rare infections occurred among patients admitted to neonatal intensive care units (NICUs)
Summary
Because no multilocus sequence or microsatellite typing were available, we used whole-genome sequencing (WGS) and amplified fragment-length polymorphism typing to understand the genetic relationships among isolates. 25; LSCS thrombocytopenia, CVC, VAN and severe asphyxia, sepsis, MER, 7 d mechanical ventilation. 24; LSCS hypoglycemia, severe VAN and asphyxia, sepsis, CVC, MER, 12 d mechanical ventilation. We searched ITS and D1/D2 region sequences in BLAST (https://blast.ncbi.nlm.nih.gov) and identified isolates from the outbreak as D. churashimaensis. The isolates had >99% identity with D. churashimaensis sequences from GenBank We performed amplified fragment-length polymorphism fingerprint analysis, as described previously [10], which yielded identical banding pattern among all 12 isolates, suggesting clonal origin (Figure 1). We identified average nucleotide identity and SNPs by comparing 6 genomes in MUMmer (http://mummer.sourceforge.net) and compared all the genomes against other publicly available basidiomycete yeast genomes (Table 2) by using progressiveMauve [11]. D. churashimaensis isolates were genotypically indistinguishable and had 99.6% similarity among the genomes (average nucleotide identity >99.6%; Table 2). The average number of SNP differences between isolates was 1,074.5 (range 402–1,621), indicating high clonality
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