Whole genome sequencing confirms Candida albicans and Candida parapsilosis microsatellite sporadic and persistent clones causing outbreaks of candidemia in neonates

Abstract

Whole genome sequencing has been extensively used to describe infection outbreaks, although with limited application on Candida albicans and Candida parapsilosis. We retrospectively studied all patients admitted to the neonatal care unit diagnosed with candidemia caused by C. albicans (n = 46) or C. parapsilosis (n = 31) between 2007 and 2010 (Period 1) and 2011 and 2014 (Period 2). All isolates were genotyped by microsatellite markers. A cluster was defined as a group of ≥ 2 patients infected by strains with identical genotypes. For the validation of microsatellite markers and outbreak investigation, phylogenetic analyses and whole genome pairwise strain comparisons were performed. The number of episodes was significantly higher in Period 1 than in Period 2 (51 vs 32; P = 0.003); the reduction in the number of cases coincided with the educational campaign for catheter care implementation in 2011. Overall, eight genotypes were clusters involving 29 patients. All C. albicans (n = 5) and C. parapsilosis (n = 3) clusters were found during Period 1 before the educational campaign. No statistically significant differences were found between the percentage of C. albicans and C. parapsilosis clusters, but the percentage of patients associated to the clusters was significantly higher for C. parapsilosis clusters in comparison to C. albicans clusters (52% vs 28.2%; P = 0.03). Whole genome sequencing confirmed microsatellite-defined clusters with high bootstrap values. Whole genome sequences confirmed microsatellite-defined clusters, corroborating the presence of outbreaks. Persistent or sporadic Candida clusters causing candidemia in neonates disappeared after the implementation of catheter care educational campaigns. Lay Abstract We retrospectively studied all patients admitted to the neonatal care unit diagnosed with candidemia caused by C. albicans or C. parapsilosis. Reliable whole genome sequences confirmed microsatellite-defined clusters, corroborating the presence of outbreaks before educational campaigns for catheter care.

Amino acid substitutions in specific proteins correlate with farnesol unresponsiveness in Candida albicans

“…To better understand the molecular determinants involved in the response to farnesol in C. albicans , the DNA of the studied strains was sequenced. Assembly and annotation revealed GC content, genome size, and the number of proteins similar to what was previously described for C. albicans and other species of the Candida genus (Table 1 ) [ 27 – 29 ].…”

A pseudo-outbreak of Cyberlindnera fabianii funguria: Implication from whole genome sequencing assay

“…One major issue, as noted in outbreak investigations of all microbes including bacteria and fungi, is lack of consensus for data interpretation. Specifically, setting-up pairwise SNP-based cut-off values for assigning transmission events is still cumbersome, which has limited the wide utility of WGS in epidemiological studies ( Coll et al., 2020 ; Guinea et al., 2021 ). In review of previous reports for outbreaks caused by yeast species that were characterized by WGS, it can be seen that the number of pairwise SNPs described in different studies of diverged species varied significantly, from less than ten to over hundreds.…”

Whole Genome Sequencing, Antibiotic Resistance, and Epidemiology Features of Nontyphoidal Salmonella Isolated From Diarrheic Children: Evidence From North China

“…At the same time, with the decreasing cost of genome sequencing and the continuous advancement of bioinformation analysis technology, WGS is gradually applied to the outbreak investigation and epidemiological analysis at the forefront of disease prevention and control (Guinea et al, 2021 ; Papić et al, 2021 ). WGS-based methods, such as core genome multilocus sequence typing (cgMLST), include all core genes loci present in all given isolates.…”