Abstract
While MALDI-TOF mass spectrometry (MS) is widely considered as the reference method for the rapid and inexpensive identification of microorganisms in routine laboratories, less attention has been addressed to its ability for detection of antimicrobial resistance (AMR). Recently, some studies assessed its potential application together with machine learning for the detection of AMR in clinical pathogens. The scope of this study was to investigate MALDI-TOF MS protein mass spectra combined with a prediction approach as an AMR screening tool for relevant foodborne pathogens, such as Campylobacter coli and Campylobacter jejuni. A One-Health panel of 224 C. jejuni and 116 C. coli strains was phenotypically tested for seven antimicrobial resistances, i.e., ciprofloxacin, erythromycin, tetracycline, gentamycin, kanamycin, streptomycin, and ampicillin, independently, and were submitted, after an on- and off-plate protein extraction, to MALDI Biotyper analysis, which yielded one average spectra per isolate and type of extraction. Overall, high performance was observed for classifiers detecting susceptible as well as ciprofloxacin- and tetracycline-resistant isolates. A maximum sensitivity and a precision of 92.3 and 81.2%, respectively, were reached. No significant prediction performance differences were observed between on- and off-plate types of protein extractions. Finally, three putative AMR biomarkers for fluoroquinolones, tetracyclines, and aminoglycosides were identified during the current study. Combination of MALDI-TOF MS and machine learning could be an efficient and inexpensive tool to swiftly screen certain AMR in foodborne pathogens, which may enable a rapid initiation of a precise, targeted antibiotic treatment.
Highlights
Antimicrobial susceptibility testing (AST) is a key technology in diagnostic microbiology and is essential for a targeted treatment and to limit the widespread use of broad-spectrum antibiotics
The latter was transformed into 1,020 Main Spectra Profile (MSP), including 672 and 348 MSPs for C. jejuni and C. coli, respectively
The scope of this study was to consider whether a mass spectrometry technique combined with an machine learning (ML) approach could be utilized for a combined rapid species identification and antimicrobial resistances (AMR) screening for foodborne pathogens
Summary
Antimicrobial susceptibility testing (AST) is a key technology in diagnostic microbiology and is essential for a targeted treatment and to limit the widespread use of broad-spectrum antibiotics. In a concern for harmonization, diskdiffusion and microdilution antibiograms, recommended by the European committee on antimicrobial susceptibility testing (EUCAST, human medicine) or the European food safety authority (EFSA, veterinary medicine), are still the reference methods for determination of antimicrobial resistances (AMR) These tests are based on bacterial growth, requiring between 16 and 24 h for rapid growing pathogens and longer for fastidious pathogens (e.g., mycobacteria and Helicobacter pylori) (Barlam et al, 2016; Arena et al, 2017). Results are usually qualitative and classed into categories, i.e., susceptible or resistant, depending on the breakpoint calibrated by the EUCAST, or expressed as minimum inhibitory concentration (MIC) (Benkova et al, 2020) While these conventional methods are effective, they are cumbersome, time-consuming, and do not enable the rapid choice of an effective targeted anti-infective treatment. Development of “fast microbiology” technologies or rapid diagnostic tests, including Matrix assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS), results in the improvement of the antimicrobial stewardship by decreasing the “patient–physician” workflow before treatment (Bookstaver et al, 2017; Mangioni et al, 2019)
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