Clinical Impact of Rapid Identification of Positive Blood Cultures vs. Internal Laboratory Standard

Study Overview
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Brief Summary
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In this before-after study, different new methods for bacterial species identification from positive blood cultures will be compared towards historic controls. All samples are analyzed within the routine workflow for bacterial species identification and antibiotic resistance profiling. Patients with positive blood cultures from 2016 to 2018 receiving a conventional identification methods (controls) will be compared to patients from 2018 and 2019 with a new identification method (cases). The conventional identification method consisted in general of an over-night subculture and subsequent identification of the bacterial pathogen using either biochemical profiling or Matrix-assisted Laser-Desorption/Ionization Time-of-Flight (MALDI-TOF MS). The new identification of positive blood cultures methods include (i) either the newly introduced Biofire FilmArray© Blood Culture Identification (BCID) panel or (ii) in a subset of patients whole genome sequencing (WGS) approaches.

Official Title
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Clinical Impact of Rapid Identification of Positive Blood Cultures vs. Internal Laboratory Standard

Conditions
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Bloodstream Infections

Intervention / Treatment
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* Diagnostic Test: conventional identification method: biochemical profiling or MALDI-TOF MS
* Diagnostic Test: new identification method: Biofire FilmArray© BCID panel
* Diagnostic Test: new identification method: metagenomic WGS


Participation Criteria
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Eligibility Criteria
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Inclusion Criteria: patients with positive blood cultures hospitalized between August 2016 and October 2019 documented refusal of the general consent Exclusion Criteria: outpatients patients hospitalized in other hospitals patients with known bacteremia diagnosed in another hospital
Sexes Eligible for Study
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All

Accepts Healthy Volunteers
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No

Study Plan
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How is the study designed?
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Arms and Interventions

| Participant Group/Arm | Intervention/Treatment |
| --- | --- |
| conventional identification methods (controls)<br>Patients with positive blood cultures from 2016 to 2018 receiving a conventional identification methods (controls). The conventional identification method consisted in general of an over-night subculture and subsequent identification of the bacterial pathogen using either biochemical profiling or MALDI-TOF MS. | Diagnostic Test: conventional identification method: biochemical profiling or MALDI-TOF MS<br>* Identification of bacteria in positive blood cultures with MALDI-TOF MS from a subculture usually one day after the signal for a positive blood culture appears (from 2016 to 2018)<br>|
| new identification method (cases)Biofire FilmArray© BCID panel<br>Patients with positive blood cultures from 2018 and 2019 receiving a new identification method (cases). The new identification method is the Biofire FilmArray© Blood Culture Identification (BCID) panel, a polymerase chain reaction-based method, performed directly from the positive blood culture without the need of subculture to reach single bacterial colonies. The assays allow to identify a panel of 20 most commonly Gram-positive and -negative bacteria and yeast causing blood stream infections. It also allows to determine three resistance genes (mecA, vanA/B and KPC). | Diagnostic Test: new identification method: Biofire FilmArray© BCID panel<br>* The Biofire FilmArray© BCID Panel is performed directly from the positive blood culture without the need of subculture to reach single bacterial colonies (from 2018 and 2019)<br>|
| new identification method (cases) WGS approaches<br>Patients with positive blood cultures from 2018 and 2019 receiving a new identification method (cases). The new identification of positive blood cultures methods in a subset of patients is a whole genome sequencing approach. This so called shotgun metagenomic approach allows to sequence the whole genome (WGS) of pathogens and thereby potentially detect every potential pathogen and also resistance and virulence gene. | Diagnostic Test: new identification method: metagenomic WGS<br>* shotgun metagenomic approach allows to sequence the whole genome (WGS) of pathogens and thereby potentially detect every potential pathogen and also resistance and virulence gene (from 2018 and 2019)<br>|

What is the study measuring?
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Primary Outcome Measures

| Outcome Measure | Measure Description | Time Frame |
| --- | --- | --- |
| Time to optimal antibiotic treatment in hours from positive blood cultures (hours) | Time from blood draw for blood culture testing to start of optimal antibiotic treatment (hours) | 24 hours from collection of blood cultures | 

Secondary Outcome Measures

| Outcome Measure | Measure Description | Time Frame |
| --- | --- | --- |
| Time to effective antibiotic treatment in hours from positive blood cultures (hours) | Time from blood draw for blood culture testing to start of effective antibiotic treatment (hours) | 24 hours from collection of blood cultures | 
| all-cause in hospital mortality (number) | all-cause in hospital mortality (number) | from admission to hospital until release from hospital (approximately 30 days) | 
| duration on ICU in days | duration on ICU in days | from admission to ICU until release from ICU (approximately 20 days) | 
| time to Gram staining and resistance profile from positive blood cultures (hours) | time to Gram staining and resistance profile from positive blood cultures (hours) | 24 hours from collection of blood cultures | 

 Terms related to the study
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Keywords Provided by Centre Hospitalier Valida
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MALDI-TOF MS, Biofire FilmArray© Blood Culture Identification (BCID) panel, shotgun metagenomic approach