Abstract
Rhizopus spp. fungi are ubiquitous in the environment and a rare but substantial cause of infection in immunosuppressed persons and surgery patients. During 2005–2017, an abnormally high number of Rhizopus infections in surgery patients, with no apparent epidemiologic links, were reported in Argentina. To determine the likelihood of a common source of the cluster, we performed whole-genome sequencing on samples collected during 2006–2014. Most isolates were separated by >60 single-nucleotide polymorphisms, and we found no evidence for recombination or nonneutral mutation accumulation; these findings do not support common source or patient-to-patient transmission. Assembled genomes of most isolates were ≈25 Mbp, and multiple isolates had substantially larger assembled genomes (43–51 Mbp), indicative of infections with strain types that underwent genome expansion. Whole-genome sequencing has become an essential tool for studying epidemiology of fungal infections. Less discriminatory techniques may miss true relationships, possibly resulting in inappropriate attribution of point source.
Highlights
Rhizopus spp. fungi are ubiquitous in the environment and a rare but substantial cause of infection in immunosuppressed persons and surgery patients
We analyzed the genomes of R. microsporus var. rhizopodiformis isolates from patients from multiple facilities in Argentina in the context of unrelated controls from outside the geographic area to empirically establish the relationships among them and determine whether infections may have originated from a common source
A total of 21 isolates fell into a single clade that included 3 controls and the publicly available genome of the American Type Culture Collection (ATCC) 11559 strain, first described in 1935 in the USSR [23], with 3,170 single-nucleotide polymorphism (SNP) among them (Figure)
Summary
Rhizopus spp. fungi are ubiquitous in the environment and a rare but substantial cause of infection in immunosuppressed persons and surgery patients. Rhizopus spp. are the Mucorales fungi that most commonly cause mucormycosis [1,2,4] and are the most common non-Aspergillus cause of invasive filamentous fungal infections [5]. Limited molecular analyses of osteomyelitis-associated R. microsporus infections identified commonalities among isolated strains [7]; no genomic epidemiologic analyses have been performed on this nosocomial cluster. Rhizopodiformis isolates from patients from multiple facilities in Argentina in the context of unrelated controls from outside the geographic area to empirically establish the relationships among them and determine whether infections may have originated from a common source We analyzed the genomes of R. microsporus var. rhizopodiformis isolates from patients from multiple facilities in Argentina in the context of unrelated controls from outside the geographic area to empirically establish the relationships among them and determine whether infections may have originated from a common source
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