Evaluating the economic effects of genomic sequencing of pathogens to prioritise hospital patients competing for isolation beds
Thomas M. Elliott
A F , Nicole Hare A , Krispin Hajkowicz B C , Trish Hurst B , Michelle Doidge B , Patrick N. Harris C and Louisa G. Gordon A D E
A QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Qld 4006, Australia. Email: n.k.hare@hotmail.com; louisa.gordon@qimrberghofer.edu.au
B Infectious Diseases Unit, Royal Brisbane and Women’s Hospital, Butterfield Street, Herston, Qld 4029, Australia. Email: Krispin.Hajkowicz@health.qld.gov.au; Trish.Hurst@health.qld.gov.au; Michelle.Doidge@health.qld.gov.au
C The University of Queensland, Centre for Clinical Research, Building 71/918, Royal Brisbane and Women’s Hospital, Herston, Qld 4006, Australia. Email: p.harris@uq.edu.au
D The University of Queensland, School of Public Health, 266 Herston Road, Herston, Qld 4006, Australia.
E Queensland University of Technology, School of Nursing, QUT N Block, Ring Road, Kelvin Grove, Qld 4059, Australia.
F Corresponding author. Email: thomas.elliott@qimrberghofer.edu.au
Australian Health Review - https://doi.org/10.1071/AH20071
Submitted: 16 April 2020 Accepted: 18 May 2020 Published online: 14 October 2020
Abstract
Objective This study compared the costs and patient movements of a new hospital protocol to discontinue contact precautions for patients with non-multiresistant methicillin-resistant Staphylococcus aureus (nmMRSA), based on whole-genome sequencing (WGS) of pathogens with current practice.
Methods A hybrid simulation model was constructed and analysed over a 12-month time horizon. Six multidrug-resistant organisms and influenza were modelled concurrently where infected patients competed for isolation beds. Model inputs included pathogen incidence, resources for WGS, staff and contact precautions, hospital processes, room allocations and their associated costs. Data were sourced from aggregated records of patient admissions during 2017–18, clinical records and published reports.
Results The WGS protocol resulted in 389 patients isolated (44% of current practice), 5223 ‘isolation bed days’ (56%) and 268 closed-bed days (88%). Over 1 year, the mean (±s.d.) total cost for the WGS protocol was A$749 243 ± 126 667; compared with current practice, the overall cost savings were A$690 864 ± 300 464.
Conclusion Using WGS to inform infection control teams of pathogen transmission averts patients from isolation rooms and reduces significant resources involved in implementing contact precautions.
What is known about the topic? There are an estimated 265 000 hospital-acquired infections (HAI) in Australia each year. WGS can accurately identify the genetic lineage among HAIs and determine transmission clusters that can help infection control staff manage patients. Economic appraisals are lacking to inform whether pathogen genomics services should be adopted within already-stretched hospital budgets.
What does this paper add? An isolation protocol using pathogen genomics to provide additional information on the relatedness of a pathogen between colonised patients showed favourable results for healthcare costs and patient flow. Using WGS, in a confirmatory role, to discontinue certain patients from contact precautions and isolation rooms resulted in cost savings of A$690 864 across 1 year for a single major hospital.
What are the implications for practitioners? Using pathogen WGS services for infection control potentially curbs hospital spending, averts patient isolations and improves patient flow within hospitals.
Keywords: contact precautions, cost consequences, healthcare costs, hospital-acquired infections, infection control, whole-genome sequencing.
References
[1] Mitchell BG, Shaban RZ, MacBeth D, Wood CJ, Russo PL. The burden of healthcare-associated infection in Australian hospitals: a systematic review of the literature. Infect Dis Health 2017; 22 117–28.| The burden of healthcare-associated infection in Australian hospitals: a systematic review of the literature.Crossref | GoogleScholarGoogle Scholar | 31862087PubMed |
[2] Siegel JD, Rhinehart E, Jackson M, Chiarello L. 2007 guideline for isolation precautions: preventing transmission of infectious agents in health care settings. Am J Infect Control 2007; 35 S65–164.
| 2007 guideline for isolation precautions: preventing transmission of infectious agents in health care settings.Crossref | GoogleScholarGoogle Scholar | 18068815PubMed |
[3] Schrank GM, Snyder GM, Davis RB, Branch-Elliman W, Wright SB. The discontinuation of contact precautions for methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus: impact upon patient adverse events and hospital operations. BMJ Qual Saf 2020; 29 1–2.
| The discontinuation of contact precautions for methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus: impact upon patient adverse events and hospital operations.Crossref | GoogleScholarGoogle Scholar | 31320496PubMed |
[4] Harris AD, Pineles L, Belton B, Johnson JK, Shardell M, Loeb M, Newhouse R, Dembry L, Braun B, Perencevich EN, Hall KK, Morgan DJ. Universal glove and gown use and acquisition of antibiotic-resistant bacteria in the ICU: a randomized trial. JAMA 2013; 310 1571–80.
| Universal glove and gown use and acquisition of antibiotic-resistant bacteria in the ICU: a randomized trial.Crossref | GoogleScholarGoogle Scholar | 24097234PubMed |
[5] Balloux F, Brønstad Brynildsrud O, van Dorp L, Shaw LP, Chen H, Harris KA, Wang H, Eldholm V. From theory to practice: translating whole-genome sequencing (WGS) into the clinic. Trends Microbiol 2018; 26 1035–48.
| From theory to practice: translating whole-genome sequencing (WGS) into the clinic.Crossref | GoogleScholarGoogle Scholar | 30193960PubMed |
[6] Smyth ETM, McIlvenny G, Enstone JE, Emmerson AM, Humphreys H, Fitzpatrick F, Davies E, Newcombe RG, Spencer RC. Four country healthcare associated infection prevalence survey 2006: overview of the results. J Hosp Infect 2008; 69 230–48.
| Four country healthcare associated infection prevalence survey 2006: overview of the results.Crossref | GoogleScholarGoogle Scholar |
[7] Agostino JW, Ferguson JK, Eastwood K, Kirk MD. The increasing importance of community-acquired methicillin-resistant Staphylococcus aureus infections. Med J Aust 2017; 207 388–93.
| The increasing importance of community-acquired methicillin-resistant Staphylococcus aureus infections.Crossref | GoogleScholarGoogle Scholar | 29092696PubMed |
[8] Schurch 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; 24 350–4.
| Whole genome sequencing options for bacterial strain typing and epidemiologic analysis based on single nucleotide polymorphism versus gene-by-gene-based approaches.Crossref | GoogleScholarGoogle Scholar | 29309930PubMed |
[9] Humphreys H, Coleman DC. Contribution of whole-genome sequencing to understanding of the epidemiology and control of methicillin-resistant Staphylococcus aureus. J Hosp Infect 2019; 102 189–99.
| Contribution of whole-genome sequencing to understanding of the epidemiology and control of methicillin-resistant Staphylococcus aureus.Crossref | GoogleScholarGoogle Scholar | 30721732PubMed |
[10] Infection Monitoring and Prevention Service. Royal Brisbane and Women’s Hospital: multi resistant organisms, management. Brisbane: Metro North Hospital and Health Service; 2018. Available at: https://www.health.qld.gov.au/__data/assets/pdf_file/0026/444626/multi-resistant-organisms.pdf [verified 21 September 2020].
[11] Queensland Health. Statewide influenza surveillance report. Reporting period: 1 January to 31 December 2018. Brisbane: Queensland Health; 2018. Available at: https://www.health.qld.gov.au/__data/assets/pdf_file/0033/707649/influenza-qld-2018.pdf [verified 11 September 2020].
[12] Bureau of Health Information (BIH). Healthcare quarterly. Admitted patients and elective surgery. Activity and performance, January to March 2017. Sydney: BHI; 2017. Available at: https://www.bhi.nsw.gov.au/__data/assets/pdf_file/0011/364556/report-HQ-APES-jan-march-2017.pdf [verified 11 September 2020].
[13] Lloyd-Smith P, Younger J, Lloyd-Smith E, Green H, Leung V, Romney MG. Economic analysis of vancomycin-resistant enterococci at a Canadian hospital: assessing attributable cost and length of stay. J Hosp Infect 2013; 85 54–9.
| Economic analysis of vancomycin-resistant enterococci at a Canadian hospital: assessing attributable cost and length of stay.Crossref | GoogleScholarGoogle Scholar | 23920443PubMed |
[14] Lee SY, Kotapati S, Kuti JL, Nightingale CH, Nicolau DP. Impact of extended-spectrum beta-lactamase-producing Escherichia coli and Klebsiella species on clinical outcomes and hospital costs: a matched cohort study. Infect Control Hosp Epidemiol 2006; 27 1226–32.
| Impact of extended-spectrum beta-lactamase-producing Escherichia coli and Klebsiella species on clinical outcomes and hospital costs: a matched cohort study.Crossref | GoogleScholarGoogle Scholar | 17080381PubMed |
[15] Thompson WW, Shay DK, Weintraub E, Brammer L, Bridges CB, Cox NJ, Fukuda K. Influenza-associated hospitalizations in the United States. JAMA 2004; 292 1333–40.
| Influenza-associated hospitalizations in the United States.Crossref | GoogleScholarGoogle Scholar | 15367555PubMed |
[16] Kyne L, Hamel MB, Polavaram R, Kelly CP. Health care costs and mortality associated with nosocomial diarrhea due to Clostridium difficile. Clin Infect Dis 2002; 34 346–53.
| Health care costs and mortality associated with nosocomial diarrhea due to Clostridium difficile.Crossref | GoogleScholarGoogle Scholar | 11774082PubMed |
[17] Kirwin E, Varughese M, Waldner D, Simmonds K, Joffe AM, Smith S. Comparing methods to estimate incremental inpatient costs and length of stay due to methicillin-resistant Staphylococcus aureus in Alberta, Canada. BMC Health Serv Res 2019; 19 743
| Comparing methods to estimate incremental inpatient costs and length of stay due to methicillin-resistant Staphylococcus aureus in Alberta, Canada.Crossref | GoogleScholarGoogle Scholar | 31651305PubMed |
[18] Page K, Barnett AG, Graves N. What is a hospital bed day worth? A contingent valuation study of hospital chief executive officers. BMC Health Serv Res 2017; 17 137
| What is a hospital bed day worth? A contingent valuation study of hospital chief executive officers.Crossref | GoogleScholarGoogle Scholar | 28196489PubMed |
[19] Otter JA, Burgess P, Davies F, Mookerjee S, Singleton J, Gilchrist M, Parsons D, Brannigan ET, Robotham J, Holmes AH. Counting the cost of an outbreak of carbapenemase-producing Enterobacteriaceae: an economic evaluation from a hospital perspective. Clin Microbiol Infect 2017; 23 188–96.
| Counting the cost of an outbreak of carbapenemase-producing Enterobacteriaceae: an economic evaluation from a hospital perspective.Crossref | GoogleScholarGoogle Scholar | 27746394PubMed |
[20] Queensland Health. Queensland Health wage rates 2017 Available at: https://www.health.qld.gov.au/hrpolicies/wage-rates/nursing [verified 1 Nov 2019].
[21] Rennert-May E, Conly J, Leal J, Smith S, Manns B. Economic evaluations and their use in infection prevention and control: a narrative review. Antimicrob Resist Infect Control 2018; 7 31
| Economic evaluations and their use in infection prevention and control: a narrative review.Crossref | GoogleScholarGoogle Scholar | 29492261PubMed |
[22] Arefian H, Vogel M, Kwetkat A, Hartmann M.. Economic evaluation of interventions for prevention of hospital acquired infections: a systematic review. PloS One 2016; 11 e0146381
| Economic evaluation of interventions for prevention of hospital acquired infections: a systematic review.Crossref | GoogleScholarGoogle Scholar | 26731736PubMed |
[23] Elliott TM, Lee XJ, Foeglein A, Harris PN, Gordon LG. A hybrid simulation model approach to examine bacterial genome sequencing during a hospital outbreak. BMC Infect Dis 2020; 20 72
| A hybrid simulation model approach to examine bacterial genome sequencing during a hospital outbreak.Crossref | GoogleScholarGoogle Scholar | 31973703PubMed |
[24] Saint S, Higgins LA, Nallamothu BK, Chenoweth C. Do physicians examine patients in contact isolation less frequently? A brief report. Am J Infect Control 2003; 31 354–6.
| Do physicians examine patients in contact isolation less frequently? A brief report.Crossref | GoogleScholarGoogle Scholar | 14608302PubMed |
[25] Guilley-Lerondeau B, Bourigault C, Guille des Buttes AC, Birgand G, Lepelletier D. Adverse effects of isolation: a prospective matched cohort study including 90 direct interviews of hospitalized patients in a French university hospital. Eur J Clin Microbiol Infect Dis 2017; 36 75–80.
| Adverse effects of isolation: a prospective matched cohort study including 90 direct interviews of hospitalized patients in a French university hospital.Crossref | GoogleScholarGoogle Scholar | 27612471PubMed |
[26] Croft LD, Liquori M, Ladd J, Day H, Pineles L, Lamos E, Arnold R, Mehrotra P, Fink JC, Langenberg P, Simoni-Wastila L, Perencevich E, Harris AD, Morgan DJ. The effect of contact precautions on frequency of hospital adverse events. Infect Control Hosp Epidemiol 2015; 36 1268–74.
| The effect of contact precautions on frequency of hospital adverse events.Crossref | GoogleScholarGoogle Scholar | 26278419PubMed |
[27] Sadsad R, Sintchenko V, McDonnell GD, Gilbert GL. Effectiveness of hospital-wide methicillin-resistant Staphylococcus aureus (MRSA) infection control policies differs by ward specialty. PLoS One 2013; 8 e83099
| Effectiveness of hospital-wide methicillin-resistant Staphylococcus aureus (MRSA) infection control policies differs by ward specialty.Crossref | GoogleScholarGoogle Scholar | 24340085PubMed |
