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Investigation of a Cluster of Sphingomonas koreensis Infections
Ryan C Johnson1, Clay Deming1, Sean Conlan1
1From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program.
Background:
Plumbing systems are an infrequent but known reservoir for opportunistic microbial pathogens that can infect hospitalized patients. In 2016, a cluster of clinical sphingomonas infections prompted an investigation.
Methods:
We performed whole-genome DNA sequencing on clinical isolates of multidrug-resistant Sphingomonas koreensis identified from 2006 through 2016 at the National Institutes of Health (NIH) Clinical Center. We cultured S. koreensis from the sinks in patient rooms and performed both whole-genome and shotgun metagenomic sequencing to identify a reservoir within the infrastructure of the hospital. These isolates were compared with clinical and environmental S. koreensis isolates obtained from other institutions.
Results:
The investigation showed that two isolates of S. koreensis obtained from the six patients identified in the 2016 cluster were unrelated, but four isolates shared more than 99.92% genetic similarity and were resistant to multiple antibiotic agents. Retrospective analysis of banked clinical isolates of sphingomonas from the NIH Clinical Center revealed the intermittent recovery of a clonal strain over the past decade. Unique single-nucleotide variants identified in strains of S. koreensis elucidated the existence of a reservoir in the hospital plumbing. Clinical S. koreensis isolates from other facilities were genetically distinct from the NIH isolates. Hospital remediation strategies were guided by results of microbiologic culturing and fine-scale genomic analyses.
Conclusions:
This genomic and epidemiologic investigation suggests that S. koreensis is an opportunistic human pathogen that both persisted in the NIH Clinical Center infrastructure across time and space and caused health care-associated infections. (Funded by the NIH Intramural Research Programs.).
Insights
Hospital plumbing can harbor opportunistic pathogens like Sphingomonas koreensis, causing healthcare-associated infections. Genomic analysis revealed a persistent reservoir in the NIH Clinical Center
Area of Science:
- Microbiology
- Genomics
- Epidemiology
Background:
- Plumbing systems are a potential reservoir for opportunistic pathogens in hospitals.
- Sphingomonas koreensis can cause infections in hospitalized patients.
- A 2016 cluster of infections prompted an investigation into this pathogen.
Purpose of the Study:
- To investigate the source of multidrug-resistant Sphingomonas koreensis infections.
- To identify a potential reservoir within the hospital infrastructure.
- To compare clinical and environmental isolates.
Main Methods:
- Whole-genome DNA sequencing of clinical and environmental Sphingomonas koreensis isolates.
- Shotgun metagenomic sequencing of hospital sink cultures.
- Comparison of isolates from the National Institutes of Health (NIH) Clinical Center with those from other institutions.
Main Results:
- Four of six clinical isolates from the 2016 cluster were genetically similar and multidrug-resistant.
- A clonal strain of Sphingomonas koreensis was intermittently recovered over a decade.
- Genomic analysis identified the hospital plumbing as a reservoir for S. koreensis.
Conclusions:
- Sphingomonas koreensis is an opportunistic pathogen that can persist in hospital infrastructure.
- The identified reservoir in the NIH Clinical Center plumbing contributed to healthcare-associated infections.
- Genomic and epidemiologic data guided hospital remediation strategies.
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