Investigation of a Cluster of Sphingomonas koreensis Infections

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.).

Figure 1.. Sphingomonas Infections at the National Institutes of Health (NIH) Clinical Center, According to Year.

A new NIH Clinical Center building was constructed in 2004 and opened in 2005.

Figure 2.. Genome Comparisons of the Sphingomonas Isolates Obtained from Patients at the NIH Clinical Center.

Panel A shows antibiotic susceptibility patterns for the sphingomonas isolates obtained from patients. Panel B shows the genetic relatedness of the isolates on the basis of average nucleotide identity, with purple squares indicating the greatest similarity. Isolates are named according to species (Sphingomonas koreensis [SK] or other sphingomonas species [S]), location (NIH), patient number (Pt), and date (month [MM] and year [YY]). Sphingomonas isolates from 2016 are highlighted in red.

Figure 3.. Phylogenetic Tree of the S. koreensis Isolates from the NIH Clinical Center.

The phylogenetic tree was constructed on the basis of single-nucleotide variants (SNVs) across the core genome. Circles of the same color at the end of the nodes indicate environmental isolates (Env) from the same sink. Black circles indicate that no other isolates were cultured from a given sink. The circles at the end of the nodes for isolates obtained from patients are colored to match the isolates from the sink in the room in which the patient was staying. The labels of isolates obtained from patients are highlighted in red, and isolates obtained from sinks are labeled in black.

Figure 4.. Metagenomic Sequencing of Multiple S. koreensis Strains Cultured from Sinks in Patient Rooms at the NIH Clinical Center.

Panels A and B show the relative abundance of three S. koreensis strains (SK-NIH.Env5_1116, SK-NIH.Env10_0317, and SK-NIH. Env11_0417) collected from the same sink in one patient room in November 2016, March 2017, and April 2017. The relative abundance of each isolate is represented by the colored bars in Panel A. Relative abundance was estimated by calculation of the mean allele frequency of SNVs that were unique to each isolate (dots). The sink was replaced after the first positive sample was obtained in November 2016 (indicated by the gray sink in Panel B), but S. koreensis was cultured again from this sink in March 2017 and in April 2017. The colored rods in Panel B correspond to the three isolates in Panel A. Panels C and D show the relative abundance of two other S. koreensis strains (SK-NIH.Env9_0217 and SK-NIH.Env18_0517) that were detected in the sinks of two adjoining patient rooms. The colored rods in Panel D correspond to the two isolates in Panel C. The rods that appear outside the circle indicate individually cultured isolates. The gray rods in Panels B and D represent isolates with unknown SNV profiles. The water in the two rooms in Panel D was supplied by the same pipes (blue bars).