Optimizing species identification after antimicrobial pretreatment in Enterobacterales: a prospective cohort study

Initiation of antimicrobial treatment before specimen collection reduces bacterial recovery rate for cultures and alters Gram-stain morphology of the microbe, but very little is known about the effects to the subsequent species identification once the culture becomes positive. This prospective cohort study assessed the impact of antimicrobial pretreatment effect on species identification of the closely related members of Enterobacterales, using conventional and automated phenotypic (Vitek 2) methods, and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) in terms of overall accuracy and cost-effectiveness. A total of 240 Enterobacterales isolates, with visible antimicrobial pretreatment effect (hereafter, the pretreatment effect), were included in the study. On primary culture, the MALDI-TOF MS with a standard cutoff had an inferior success rate (75.0% vs. 97.3%; P < 0.001). Reducing the MALDI-TOF MS cutoff to 1.8 significantly increases its success rate (93.8%) without compromising accuracy (99.6%, vs. benchmark of 100.0%, P = 1). The Vitek 2 automated system maintained high accuracy comparable to the benchmark. Isolates with pretreatment effects had lower prevalence of extended-spectrum β-lactamase-producing Escherichia coli (25.2% vs. 43.4%; P < 0.001) and Klebsiella pneumoniae (9.5% vs. 30.6%; P < 0.001), and carbapenem-resistant E. coli (0.7% vs. 4.3%; P = 0.027) and K. pneumoniae (3.2% vs. 24.5%; P < 0.001) than the general population. Based on a cost-utility analysis, the conventional phenotypic method was the least cost-effective, while the optimized MALDI-TOF MS method was the most cost-effective. MALDI-TOF MS with reduced cutoffs and the automated phenotypic assay are the most cost-effective and accurate methods for isolates with antimicrobial pretreatment effect. Additionally, this effect may serve as an early indicator of lower antimicrobial resistance.