Hostname: page-component-745bb68f8f-cphqk Total loading time: 0 Render date: 2025-02-04T15:08:45.295Z Has data issue: false hasContentIssue false
  • English
  • Français

Utilizing whole genome sequencing to characterize central line-associated bloodstream infections due to Staphylococcus epidermidis

Published online by Cambridge University Press:  27 January 2025

Chunyi Zhou Open the ORCID record for Chunyi Zhou [Opens in a new window] ,
Michael Wiley ,
Jessica Wiley Open the ORCID record for Jessica Wiley [Opens in a new window] ,
Kelly Cawcutt Open the ORCID record for Kelly Cawcutt [Opens in a new window] ,
Elizabeth Grashorn ,
Kathie Rogers ,
Emily McCutchen ,
Peter Iwen ,
Paul Fey  and
Mark Rupp Open the ORCID record for Mark Rupp [Opens in a new window]
Chunyi Zhou
Affiliation:
Department of Pathology, Microbiology, and Immunology, University of Nebraska Medical Center, Omaha, NE, USA
Michael Wiley
Affiliation:
Department of Pathology, Microbiology, and Immunology, University of Nebraska Medical Center, Omaha, NE, USA Nebraska Public Health Laboratory, Omaha, NE, USA PraesensBio, LLC, Omaha, NE, USA
Jessica Wiley
Affiliation:
PraesensBio, LLC, Omaha, NE, USA
Kelly Cawcutt
Affiliation:
Division of Infectious Diseases, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, USA Department of Infection Control & Epidemiology, Nebraska Medicine, Omaha, NE, USA
Elizabeth Grashorn
Affiliation:
Department of Infection Control & Epidemiology, Nebraska Medicine, Omaha, NE, USA
Kathie Rogers
Affiliation:
Clinical Microbiology Laboratory, Nebraska Medicine, Omaha, NE, USA
Emily McCutchen
Affiliation:
Nebraska Public Health Laboratory, Omaha, NE, USA
Peter Iwen
Affiliation:
Department of Pathology, Microbiology, and Immunology, University of Nebraska Medical Center, Omaha, NE, USA Nebraska Public Health Laboratory, Omaha, NE, USA
Paul Fey
Affiliation:
Department of Pathology, Microbiology, and Immunology, University of Nebraska Medical Center, Omaha, NE, USA
Mark Rupp*
Affiliation:
Division of Infectious Diseases, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, USA Department of Infection Control & Epidemiology, Nebraska Medicine, Omaha, NE, USA
*
Corresponding author: Mark Rupp; Email: merupp@unmc.edu
Rights & Permissions [Opens in a new window]

Abstract

Whole genome sequencing (WGS) and clinical review were used to characterize 14 cases of central line-associated bloodstream infection (CLABSI) due to Staphylococcus epidermidis. WGS, which demonstrated disparate strains, suggested that 42.9% of S. epidermidis CLABSI cases were due to contamination, while clinical review suggested that 57.1% were contamination events.

Type
Concise Communication
Information
Infection Control & Hospital Epidemiology , First View , pp. 1 - 4
Check for updates
Creative Commons
Creative Common License - CCCreative Common License - BY
This is an Open Access article, distributed under the terms of the Creative Commons Attribution licence (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted re-use, distribution and reproduction, provided the original article is properly cited.
Copyright
© The Author(s), 2025. Published by Cambridge University Press on behalf of The Society for Healthcare Epidemiology of America

Introduction

Central line-associated bloodstream infections (CLABSIs) are linked with morbidity, mortality, and increased healthcare costs.Reference Buetti, Marschall, Drees, Fakih, Hadaway, Maragakis, Monsees, Novosad, O’Grady, Rupp, Wolf, Yokoe and Mermel1 CLABSIs are publicly reported and are often used as a metric for hospital safety, quality, and reputation.Reference Krishnan, Gettler, Campbell, Kalu, Seidelman, Smith and Lewis2 Owing to its ecological niche as a commensal organism of human skin, Staphylococcus epidermidis is a prominent cause of infection of vascular catheters and blood culture contamination. To reconcile these issues, the Center for Disease Control and Prevention (CDC) definition of CLABSI due to commensal skin microbes requires recovery of these organisms from at least 2 blood cultures, the presence of a central venous catheter (CVC), and lack of evidence of an explanatory infection at an alternative site.3 Catheter-related BSI (CRBSI) is a clinical definition that requires additional corroborating evidence such as local signs of infection, cultures of vascular catheter tips revealing the same organism as blood cultures, or a shorter time to positive culture (> 2 h earlier) from blood obtained via the incriminated vascular catheter compared to peripheral blood (differential time-to-positivity, DTP).

A CRBSI is presumed due to a single strain of bacteria, and thus organisms recovered from the peripheral blood, the CVC, and the catheter tip should all be identical.

Whole genome sequencing (WGS) can be used to determine the genetic identity of an organism and allows precise definition of genetic relatedness of one strain of bacteria to another,Reference Schürch, Arredondo-Alonso, Willems and Goering4 helping to differentiate between true cases of CRBSI and blood culture contamination.

Although the overall CLABSI rate decreased at our hospital from 2018 to 2023, the proportion of CLABSI caused by S. epidermidis increased from 27% to 55%. This shift may be attributable to effective CLABSI prevention efforts that decreased CLABSIs caused by other organisms, but we hypothesized that at least some of the CLABSIs were caused by repeated blood culture contamination. We utilized WGS to help characterize S. epidermidis CLABSI and to compare the genetic relationship with a clinical assessment of whether they were likely CRBSI.

Methods

Setting: 680 bed academic medical center

Staphylococcus epidermidis CLABSI: 42 S. epidermidis blood culture isolates from the peripheral blood or CVC from 14 patient’s meeting the CDC-National Healthcare Safety Network (NHSN) criteria for CLABSI during 2023 were prospectively identified and saved for future genetic analysis.

Clinical review of CLABSI: two experienced infectious diseases physicians (MER, KAC) further reviewed S. epidermidis CLABSI cases to assess for likelihood of culture contamination or CRBSI. Clinical signs and symptoms, DTP, and factors potentially related to blood culture contamination (eg difficult phlebotomy, obesity/body mass index, underlying exfoliative dermatitis, etc.) were assessed. Cases were independently graded as likely CRBSI, likely contamination, ambiguous—more likely CRBSI, and ambiguous—more likely contamination. Discrepancies were further discussed, and consensus was established.

WGS and Multi-locus sequence typing (MLST): WGS was performed via Illumina iSeq100 using the Clear Labs sample prep and sequencing platform. MLST typing to determine sequence types (STs) of each isolate was done using the online tools provided by the Center for Genomic Epidemiology (https://cge.food.dtu.dk/services/MLST/). Genome assembly, phylogenetic analysis, and determination of genomic distances were done as previously described.Reference Zhou, Schwee, Matovu, Wiley, Wiley, Berning, Iwen and Fey5 For WGS determination of patients isolates as disparate stains (contamination) or same strain (CRBSI), we used a fifty single-nucleotide variations cutoff, which had been used in prior studies.Reference Shelburne, Dib, Endres, Reitzel, Li, Kalia, Sahasrabhojane, Chaftari, Hachem, Vargas-Cruz, Jiang, Garey, Fowler, Holland, Gu, Miller, Sakurai, Arias, Aitken, Greenberg, Kim, Flores and Raad6

Results

S.epidermidis isolates were obtained only from the peripheral blood in 10 patients, the CVC and peripheral blood in 3 patients, and only the CVC in 1 patient. A summary of WGS results and clinical review is presented in Table 1 and Figure 1. Based on MLST analysis, sequence type 2 (ST2) was the most common among all isolates (N = 31, 70%), followed by ST130 (N = 3, 7%), ST487 (N = 3, 7%), ST7 (N = 2, 5%), ST9 (N = 2, 5%), and ST691 (N = 1, 2%). Genomic distances determined from phylogenetic analysis, favored contamination in 6 patients and favored CRBSI in 8 patients. When clinical review results were compared to WGS determinations, CRBSI determinations agreed in 2 of 2 cases (100%); Contamination determinations agreed in 2 of 4 cases (50%); Ambiguous, less likely CRBSI agreed in 3 of 4 cases (75%); Ambiguous, more likely CRBSI was in agreement in 2 of 3 cases (66%), and Ambiguous, unresolved was determined to be favoring CRBSI by WGS. Overall, clinical review and WGS agreed in 9 of 13 cases (69.2%). Of the 4 cases when clinical review and WGS disagreed, in 3 instances clinical review suggested contamination while WGS determination favored CRBSI; in 1 instance clinical review favored CRBSI, while WGS indicated contamination.

Table 1. Comparison of clinical review of S. epidermidis CLABSI and whole genome sequencing results

WGS, whole genome sequencing; CRBSI, catheter-related bloodstream infection; DTP, differential time-to-positivity > 2 hours.

Figure 1. Phylogenic analysis revealed sequence types and genetic relatedness of the isolates. (A) Phylogenic tree containing all 42 isolates in the study. (B) Phylogenic tree of all 31 ST-2 isolates. (“Patient X-Y” indicates the “Y” th isolate from patient “X”; S. epidermidis GCF 006097375 was used as the reference strain).

Discussion

As the CLABSI definition is widely used for healthcare-associated infection surveillance,Reference O’Grady, Alexander, Burns, Dellinger, Garland, Heard, Lipsett, Masur, Mermel, Pearson, Raad, Randolph, Rupp and Saint7 there is intense interest in improving the precision of the definition. Contamination of blood cultures obtained from CVCs is common and can be difficult to discern from CRBSI. Based on expert clinical review, 57% of CLABSI cases were judged ambiguous and 62.5% favored contamination. Based on WGS, 6 of 14 (43%) were determined to be due to contamination.

WGS of microbes has been extensively applied to clinical diagnostics, research, and epidemiological surveillance.Reference Hilt and Ferrieri8,Reference Boolchandani, D’Souza and Dantas9 This study showed that WGS was useful for the identification of STs of S. epidermidis and defined ST2 as being the most common sequence type in our isolate population. The ST2 sequence type has previously been noted to be responsible for ongoing nosocomial transmission.Reference Shelburne, Dib, Endres, Reitzel, Li, Kalia, Sahasrabhojane, Chaftari, Hachem, Vargas-Cruz, Jiang, Garey, Fowler, Holland, Gu, Miller, Sakurai, Arias, Aitken, Greenberg, Kim, Flores and Raad6 WGS was useful in more precisely defining genetic relatedness and demonstrating intra-patient and inter-patient strain variability. In some instances, identical strains were found from different patients (potentially indicating nosocomial acquisition) while in others, different strains were found in cultures from the same patient (more likely indicating blood culture contamination).

Disparities between the surveillance CLABSI definition, strain relatedness as determined by WGS, and review by clinical experts were noted in this study. Prior studies indicated considerable strain variation in S. epidermidis that made up the human skin microbiome.Reference Severn and Horswill10 Therefore, this study suggested that WGS determination of different strains of S. epidermidis derived from multiple peripheral blood cultures or CVC/peripheral cultures was indicative of culture contamination and excluded CRBSI. Similarly, finding genetically identical strains of S. epidermidis in paired blood cultures favored the diagnosis of CRBSI. In 3 of 14 (21%) cases of CLABSI (patients 1, 7, and 14), clinical review favored the diagnosis of blood culture contamination or less likely CRBSI, which was excluded by WGS. In 1 instance (7%, patient 5), clinical review favored CRBSI diagnosis which was contradicted by finding disparate strains on WGS.

Our study has limitations. First, the criteria chosen to determine strain relatedness in the comparative genomic analysis can be debated. Fifty single-nucleotide variations were used as the cutoff for identical strains, which had been used in prior studies.Reference Shelburne, Dib, Endres, Reitzel, Li, Kalia, Sahasrabhojane, Chaftari, Hachem, Vargas-Cruz, Jiang, Garey, Fowler, Holland, Gu, Miller, Sakurai, Arias, Aitken, Greenberg, Kim, Flores and Raad6 However, this may not be the best measure for defining relatedness among S. epidermidis strains causing CRBSI. Second, being a single-centered study, with a relatively small number of cases and isolates, our results may not be generalizable.

S. epidermidis is a common cause of blood culture contamination and CRBSI, and differentiation between the two on clinical grounds is difficult. This study demonstrated that WGS can be applied to the definition of S. epidermidis CLABSI to better discern true CRBSI from contamination. Further investigation into the utility of WGS in S. epidermidis CLABSI is warranted.

Acknowledgments

The authors would like to thank the molecular technologists at the Nebraska Public Health Laboratory for performing the whole genome sequencing assay and analysis.

Financial support

No financial support was provided relevant to this article.

Competing interests

All authors report no conflicts of interest relevant to this article.

Footnotes

Preliminary results of this study were presented at ASM Microbe 2024 on June 12–17, 2024, in Atlanta, Georgia.

References

Buetti, N, Marschall, J, Drees, M, Fakih, MG, Hadaway, L, Maragakis, LL, Monsees, E., Novosad, S, O’Grady, NP, Rupp, ME, Wolf, J, Yokoe, D, Mermel, LA.. Strategies to prevent central line-associated bloodstream infections in acute-care hospitals: 2022 update. Infect Control Hosp Epidemiol 2022;43: 553–569.CrossRefGoogle ScholarPubMed
Krishnan, J, Gettler, EB, Campbell, M, Kalu, IC, Seidelman, J, Smith, B, Lewis, S. Comparative epidemiology of hospital-onset bloodstream infections (HOBSIs) and central line-associated bloodstream infections (CLABSIs) across a three-hospital health system. Infect Control Hosp Epidemiol 2024;45: 1–7.CrossRefGoogle Scholar
CDC National Healthcare Safety Network (NHSN) Bloodstream Infection Event. NHSN Patient Safety Component Manual. https://www.cdc.gov/nhsn/pdfs/pscmanual/pcsmanual_current.pdf.Google Scholar
Schürch, AC, Arredondo-Alonso, S, Willems, RJL, Goering, RV. Whole genome sequencing options for bacterial strain typing and epidemiologic analysis based on single nucleotide polymorphism versus gene-by-gene-based approaches. Clin Microbiol Infect 2018;24: 350–354.CrossRefGoogle ScholarPubMed
Zhou, C., Schwee, C., Matovu, R.E., Wiley, J.D., Wiley, M.R., Berning, B.J., Iwen, P.C., Fey, P.D.. Eubacterium callanderi bacteremia: a case report. IDCases 2024;36:e01989.CrossRefGoogle ScholarPubMed
Shelburne, SA, Dib, RW, Endres, BT, Reitzel, R, Li, X, Kalia, A, Sahasrabhojane, P, Chaftari, AM, Hachem, R, Vargas-Cruz, NS, Jiang, Y, Garey, K, Fowler, VG Jr., Holland, TL, Gu, J., Miller, W, Sakurai, A., Arias, CA, Aitken, SL, Greenberg, DE, Kim, J, Flores, AR, Raad, I. Whole-genome sequencing of Staphylococcus epidermidis bloodstream isolates from a prospective clinical trial reveals that complicated bacteraemia is caused by a limited number of closely related sequence types. Clin Microbiol Infect 2020;26: 646.e1–646.e8.CrossRefGoogle ScholarPubMed
O’Grady, NP, Alexander, M, Burns, LA, Dellinger, EP, Garland, J, Heard, SO, Lipsett, PA, Masur, H, Mermel, LA, Pearson, ML, Raad, II, Randolph, AG, Rupp, ME, Saint, S. t.H.I.C.P.A. Committee. Summary of recommendations: guidelines for the prevention of intravascular catheter-related infections. Clin Infect Dis 2011;52:1087–1099.CrossRefGoogle ScholarPubMed
Hilt, EE, Ferrieri, P. Next generation and other sequencing technologies in diagnostic microbiology and infectious diseases. Genes (Basel) 2022;1:1566.CrossRefGoogle Scholar
Boolchandani, M, D’Souza, AW, Dantas, G. Sequencing-based methods and resources to study antimicrobial resistance. Nat Rev Genet 2019;20: 356–370.Google ScholarPubMed
Severn, MM, Horswill, AR. Staphylococcus epidermidis and its dual lifestyle in skin health and infection. Nat Rev Microbiol 2023;21: 97–111.CrossRefGoogle ScholarPubMed
Figure 0

Table 1. Comparison of clinical review of S. epidermidis CLABSI and whole genome sequencing results

Figure 1

Figure 1. Phylogenic analysis revealed sequence types and genetic relatedness of the isolates. (A) Phylogenic tree containing all 42 isolates in the study. (B) Phylogenic tree of all 31 ST-2 isolates. (“Patient X-Y” indicates the “Y” th isolate from patient “X”; S. epidermidis GCF 006097375 was used as the reference strain).