Skin Metagenomic Sequence Analysis of Early Candida auris Outbreaks in U.S. Nursing Homes

Huang, Xin; Welsh, Rory M.; Deming, Clay; Proctor, Diana M.; Thomas, Pamela J.; Program, Nisc Comparative Sequencing; Gussin, Gabrielle; Huang, Susan S.; Kong, Heidi H.; Bentz, Meghan L.; Vallabhaneni, Snigdha; Chiller, Tom; Jackson, Brendan R; Forsberg, Kaitlin; Conlan, Sean; Litvintseva, Anastasia P.; Segre, Julia A.

doi:10.1128/msphere.00287-21

Cited by 23 publications

(26 citation statements)

References 40 publications

(55 reference statements)

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“…The final US study (submitted to SRA in 2020) was conducted within hospital settings and found a very high number of reads of C. auris sequences on human skin samples (33), in agreement with previous reports from hospital settings (34).…”

Section: Accepted Manuscriptsupporting

confidence: 85%

Finding a Needle in a Haystack – In Silico Search for Environmental Traces of <i>Candida auris </i>

et al. 2022

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Candida auris, first described from an ear infection in Japan, is the most talked about multidrug resistant emerging pathogenic fungal species. Its environmental niche remained a mystery until its first isolation from wetlands of the Andaman Islands, India in 2020. We screened a subset of the world's largest sequence repository, the Sequence Read Archive at NCBI using a DNA metabarcoding approach, based on either the ITS1 or ITS2 region of the official primary fungal DNA barcode, to identify potential environmental sources of C. auris. Our search identified 34 matches with partial C. auris ITS sequences from seven metabarcoding studies, providing wider evidence for the presence of C. auris outside human-maintained facilities.

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Section: Accepted Manuscriptsupporting

confidence: 85%

Finding a Needle in a Haystack – In Silico Search for Environmental Traces of <i>Candida auris </i>

et al. 2022

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“…Briefly, genomic DNA was isolated from stool samples using the Qiagen QIAamp® PowerFecal® Kit, per the manufacturer’s protocol. For skin samples, MasterPure yeast DNA purification kit (Lucigen Corp. Middleton, WI) and Genomic DNA Mini Kit (Invitrogen, Carlsbad, CA), lysis buffer with the addition of 1ul (3500 U) of diluted Ready Lyse solution were used according to the manufacturer’s protocol [ 36 ]. Yield and purity of isolated DNA were confirmed by Qubit analyzer (Invitrogen, Carlsbad, CA) [ 37 ].…”

Section: Methodsmentioning

confidence: 99%

Antibiotic exposure prevents acquisition of beneficial metabolic functions in the preterm infant gut microbiome

Milburn

Beiersdorfer

et al. 2022

Microbiome

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Background Aberrations in the preterm microbiome following antibiotic therapy have been reported in previous studies. The objective of this study was to probe potential underlying mechanisms between this observation and susceptibility to adverse prematurity-related outcomes. Results Metagenomic shotgun sequencing was performed on 133 stool and 253 skin samples collected at 1 and 3 weeks of age from 68 infants born at <36 weeks postmenstrual age and birth weight <2000 g. After accounting for gestational age and maternal antibiotics, the distribution of organisms in all samples and the corresponding metabolic pathway abundance were compared between infants exposed to postnatal antibiotics and antibiotics-naïve infants. In antibiotic-naïve infants, gestational and postnatal age imparted similar trajectories on maturation of the microbial community and associated metabolic functional capacity, with postnatal age exerting greater contribution. Antibiotic exposure was associated with reversal in maturation trajectory from the first week to the third week of age (p< 0.001). Butyrate-producing genera, including Clostridium and Blautia, were significantly more abundant in antibiotic-naïve neonates at 3 weeks postnatal age. Correspondingly, metabolic pathways required for short-chain fatty acid synthesis were significantly increased in antibiotic-naïve infants, but not in antibiotic-exposed neonates, at 3 weeks after birth. Conclusions Early brief antibiotic exposure markedly disrupts developmental trajectory of the neonatal microbiome and its corresponding functional capacity. Our findings may provide a mechanistic explanation for the known associations between antibiotic use and adverse outcomes in preterm infants.

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“…C. auris outbreaks also highlight the need to understand the skin mycobiome in this context. Huang and colleagues utilized metagenomic sequencing to characterize the skin microbiome of skilled nursing facility patients during a C. auris outbreak [9]. They found the patients in the outbreak facility were more likely to harbor a variety of Candida spp., when compared to individual residing in a non-outbreak facility, whose mycobiomes were more likely to be dominated by Malassezia.…”

Section: How Can These Models Be Used For Future Study?mentioning

confidence: 99%

“…This pathogenicity pattern distinguishes C. auris from other Candida species, including Candida albicans, which typically reside as commensals in the gastrointestinal tract prior to the development of disseminated disease.C. auris frequently colonizes the axilla and groin, sites typically sampled in the screening of patients for resistant bacteria, including methicillin-resistant Staphylococcus aureus [9][10][11]. However, a broader investigation of residents in a skilled nursing facility identified C. auris colonization across 10 different body sites, with frequent colonization of 2 or more areas [12].…”

mentioning

confidence: 99%

“…C. auris frequently colonizes the axilla and groin, sites typically sampled in the screening of patients for resistant bacteria, including methicillin-resistant Staphylococcus aureus [9][10][11]. However, a broader investigation of residents in a skilled nursing facility identified C. auris colonization across 10 different body sites, with frequent colonization of 2 or more areas [12].…”

mentioning

confidence: 99%

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Modeling Candida auris skin colonization: Mice, swine, and humans

Eix

Nett

2022

PLoS Pathog

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Skin Metagenomic Sequence Analysis of Early Candida auris Outbreaks in U.S. Nursing Homes

Cited by 23 publications

References 40 publications

Finding a Needle in a Haystack – In Silico Search for Environmental Traces of <i>Candida auris </i>

Finding a Needle in a Haystack – In Silico Search for Environmental Traces of <i>Candida auris </i>

Antibiotic exposure prevents acquisition of beneficial metabolic functions in the preterm infant gut microbiome

Modeling Candida auris skin colonization: Mice, swine, and humans

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