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Rapid antibiotic susceptibility testing method 1. Disk diffusion susceptibility method

TolC mediated resistance

13. Discussion and perspectives

13.2. Rapid antibiotic susceptibility testing method 1. Disk diffusion susceptibility method

Traditional antimicrobial susceptibility (AST) testing for H. influenzae can take 48-72 hours before yielding a result which can be explained by the lack of automation of the test. Unfortunately, the long time needed to perform the AST may lead in infected patients to detrimental outcomes.

13.2.2. Procedure for H. influenzae AST by disk diffusion susceptibility method (traditional procedure)

The inoculum suspension is prepared by selecting several colonies from overnight growth (16-24 hours of incubation) on chocolate agar plates and suspending the colonies in sterile saline to the density of a 0.5 McFarland standard. The inoculum is spread over the entire surface of the Müller-Hinton agar plate supplemented with 5%

defibrinated horse blood and 20 mg/mL β-NAD (MH-F) and the plates are incubated in a humid atmosphere containing 5% CO2 at 35 ± 1°C for 18 ± 2 hours. Thereby, the AST results are only available after 18 hours.

13.2.3. Rapid AST directly from blood culture bottles

Last year, EUCAST came up with a list of recommendations for short incubation (4, 6 and 8 hours) AST directly from positive blood culture bottles for Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus pneumoniae, Enterococcus faecalis and Enterococcus faecium.

However, no recommendations were provided for H. influenzae despite the steady increase of invasive infections caused by NTHi among frail patients.

13.2.4. The EUCAST rapid AST procedure directly from positive blood culture bottles (source: http://www.eucast.org/rapid_ast_in_blood_cultures/)

o Direct inoculation of disk diffusion Müller-Hinton agar plates using 100 - 150 µL directly from a positive blood culture bottle.

o Reduced incubation time from 18 ± 2 hours to 4, 6 and 8 hours. The disk diffusion Müller-Hinton agar plates should be interpreted by using the breakpoints adapted to each incubation time.

o The interpretation of rapid AST results will be done after the identification of

bacteria species.

o The zone diameters will be read only when an obvious zone edge can be

determined. Or else, Müller-Hinton agar plates should be re-incubated and read after 6 or 8 hours.

13.3. H. influenzae rapid AST project 13.3.1. Objectives

This project will be divided into two parts:

1. Development of H. influenzae rapid AST directly from bacterial colonies.

2. Development of H. influenzae rapid AST directly from positive blood culture bottles.

13.3.2. Study design for H. influenzae rapid AST directly from bacterial colonies

I plan to adapt for the H. influenzae rapid AST project the procedures described previously (115).

In order to identify the shortest incubation times for disk diffusion MH-F plates with optimal analytical performances, I will perform time-series image acquisitions on the WASPLab several hours before and up to the traditional incubation duration specific for H. influenzae AST. I plan to compare the results obtained by WASPLab automation (automated inoculation, and automated incubation combined with timely-defined high-resolution digital imaging) against conventional incubation and manual diagnostic, which represents the routine method used in our laboratory. AST analysis for each workflow will be performed by trained clinical microbiologists, blinded of the results obtained by the other method. Results will be compared and optimal imaging times will be defined in the derivation cohort. The assessment between the two methods will be performed on an independent validation cohort using routine clinical H. influenzae strains collected in the bacteriology laboratory at Geneva University Hospitals. In the derivation set, the incubation period of disk diffusion MH-F plates on the WASPLab will be assessed at eight incubation time points (4, 6, 8, 10, 12, 14, 16, and 18h). For each incubation time assessed on the WASPLab, several high-resolution digital images will be taken under different light and exposure conditions according to the manufacturer’s instructions. For the independent validation set, I will perform the same analysis as for the derivation set but only on the incubation time points and imaging conditions that were selected for their optimal analytical performances. The zone diameters will be read only when an obvious zone edge can be determined. I expect to analyse approximatively 300 H. influenzae clinical strains collected in bacteriology laboratory at Geneva University Hospitals.

Figure-1: WASPLab automation (automated inoculation, and automated incubation combined with timely-defined high-resolution digital imaging) and traditional AST testing

13.3.3. Study design for H. influenzae rapid AST directly from positive blood culture The evaluation of the H. influenzae rapid AST directly from positive blood culture will be performed by spiking 200 H. influenzae strains associated with bloodstream infections in 200 negative BD BACTEC Plus Aerobic blood culture bottles, in order to mimic positive blood cultures. The inoculum suspensions will be prepared by selecting several colonies from overnight growth on chocolate agar and suspending the colonies in sterile saline to the density of a 0.5 McFarland standard, corresponding to approximately 3x108 CFU/mL. Five hundred microliters of different inoculum suspensions will be injected in negative BD BACTEC Plus Aerobic blood culture bottles. Inoculated bottles will be immediately placed in the BD BACTEC™ FX system.

Individual blood culture bottles will be removed from the automated blood culture system when growth was detected. One 4mL aliquot were aspirated from each positive bottle with sterile airway needle. The aliquot will be used in WASPLab to perform the

AST according to EUCAST rapid AST procedure directly from positive blood culture bottle. The incubation period of disk diffusion MH-F plates on the WASPLab will be assessed at three incubation time points (4, 6, and 8h). For each incubation time evaluated on the WASPLab, several high-resolution digital images will be taken under different light and exposure conditions according to manufacturer’s instructions. The zone diameters will be read only when an obvious zone edge can be defined.

Figure-2: The workflow of H. influenzae rapid AST directly from positive blood culture 13.3.4. Importance of the H. influenzae rapid AST project

As mentioned previously, in the post-vaccine era, NTHi was recognized as the main cause of increased invasive H. influenzae infection like sepsis and meningitis in elderly persons. This increase is coupled to steadily increase of antibiotic resistance in NTHi.

This project will enable the antimicrobial susceptibility results in hours instead of days and will allow effective antibiotic stewardship interventions. In addition, this project will apply knowledge acquired during my thesis work to techniques and tools that address critical medical needs linked to H. influenzae (translational research).

14. Conclusions

In spite of the many studies showing interesting results, the mechanisms responsible for the heterogeneous expression of resistance have not been fully established. In S. aureus for example the mecA gene, which encodes a low-affinity PBP2a, is involved in methicillin resistance; nonetheless, as reported previously the autolysins and the presence of multiple unrelated regulatory mechanisms influence the resistance level and the heterogeneous resistance phenotype (116). Likewise, mutations in the ftsI gene may be the initial condition for imipenem resistance in H. influenzae, but as documented in this thesis work, additional levels of regulation in the efflux system and the drug influx contribute to the heterogeneous expression of resistance. Finally, NTHi small colony variants (SCVs) were shown to arise under imipenem stress. Thus, the mechanisms of SCVs persistence and resistance, as well as the population dynamics of NTHi, will also need to be thoroughly studied, by adding tools that are currently lacking in routine clinical microbiology laboratories.

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