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Johnson RC, Deming C, Conlan S, Zellmer CJ, Michelin AV, Lee-Lin S, Thomas PJ, Park M, Weingarten RA, Less J, Dekker JP, Frank KM, Musser KA, McQuiston JR, Henderson DK, Lau AF, Palmore TN, Segre JA. Investigation of a Cluster of Sphingomonas koreensis Infections. N Engl J Med 2018; 379:2529-2539. [PMID: 30586509 PMCID: PMC6322212 DOI: 10.1056/nejmoa1803238] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
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.).
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Affiliation(s)
- Ryan C Johnson
- From 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
| | - Clay Deming
- From 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
| | - Sean Conlan
- From 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
| | - Caroline J Zellmer
- From 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
| | - Angela V Michelin
- From 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
| | - ShihQueen Lee-Lin
- From 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
| | - Pamela J Thomas
- From 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
| | - Morgan Park
- From 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
| | - Rebecca A Weingarten
- From 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
| | - John Less
- From 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
| | - John P Dekker
- From 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
| | - Karen M Frank
- From 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
| | - Kimberlee A Musser
- From 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
| | - John R McQuiston
- From 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
| | - David K Henderson
- From 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
| | - Anna F Lau
- From 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
| | - Tara N Palmore
- From 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
| | - Julia A Segre
- From 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
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