Validation of β-lactam minimum inhibitory concentration predictions for pneumococcal isolates with newly encountered penicillin binding protein (PBP) sequences

Abstract

BackgroundGenomic sequence-based deduction of antibiotic minimum inhibitory concentration (MIC) has great potential to enhance the speed and sensitivity of antimicrobial susceptibility testing. We previously developed a penicillin-binding protein (PBP) typing system and two methods (Random Forest (RF) and Mode MIC (MM)) that accurately predicted β-lactam MICs for pneumococcal isolates carrying a characterized PBP sequence type (phenotypic β-lactam MICs known for at least one isolate of this PBP type). This study evaluates the prediction performance for previously uncharacterized (new) PBP types and the probability of encountering new PBP types, both of which impact the overall prediction accuracy.ResultsThe MM and RF methods were used to predict MICs of 4309 previously reported pneumococcal isolates in 2 datasets and the results were compared to the known broth microdilution MICs to 6 β-lactams. Based on a method that specifically evaluated predictions for new PBP types, the RF results were more accurate than MM results for new PBP types and showed percent essential agreement (MICs agree within ±1 dilution) >97%, percent category agreement (interpretive results agree) >93%, major discrepancy (sensitive isolate predicted as resistant) rate < 1.2%, and very major discrepancy (resistant isolate predicted as sensitive) rate < 1.4% for all 6 β-lactams. The identification of new PBP types over time was well approximated by a diminishingly increasing curve (Pearson’s r = 0.99) and minimally impacted overall MIC prediction performance.ConclusionsMIC prediction using the RF method could be an accurate alternative of phenotypic susceptibility testing even in the presence of previously uncharacterized PBP types.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-4017-7) contains supplementary material, which is available to authorized users.

Global Distribution of Invasive Serotype 35D Streptococcus pneumoniae Isolates following Introduction of 13-Valent Pneumococcal Conjugate Vaccine

“…Isolates from other locations in the GPS data set were either not randomly selected or consisted of only disease or only carriage isolates and thus could not be used to calculate odds ratios. Susceptibility to chloramphenicol, co-trimoxazole, erythromycin, penicillin, and tetracycline were predicted by the identification of resistant determinants in the assembled genomes using previously described pipelines ( 20 – 22 ). The epidemiological and phylogenetic data can be interactively visualized and analyzed online by using the Microreact tool ( https://microreact.org/project/GPS_serotype_35B_35D ).…”

Pneumococcal lineages associated with serotype replacement and antibiotic resistance in childhood invasive pneumococcal disease in the post-PCV13 era: an international whole-genome sequencing study

“…21 Serotypes were typed in silico, 22,23 and antibiotic susceptibility for penicillin (encoded by the genes pbp1A, pbp2B, and pbp2A), chloramphenicol (cat), erythromycin (ermB, ermTR1, and mefA), cotrimoxazole (folA and folP), and tetracycline (tet[M], tet [O], and tet[S/M]) was predicted using the sequencing reads and the published tools developed by the USA Centers for Disease Control. [24][25][26] The genome sequences were deposited in the European Nucleotide Archive.…”

A Population-Based Descriptive Atlas of Invasive Pneumococcal Strains Recovered Within the U.S. During 2015–2016

“…Genomic DNA preparation, library construction, whole genome sequencing (WGS), and bioinformatics pipeline features have been previously described (Li et al, 2016 , 2017 ; Metcalf et al, 2016a , b ). Streptococcus pneumoniae strains were cultured on Trypticase soy agar supplemented with 5% sheep blood and incubated overnight at 37°C in 5% CO 2 .…”