Microarray-Based Nucleic Acid Assay and MALDI-TOF MS Analysis for the Detection of Gram-Negative Bacteria in Direct Blood Cultures

Seon Young Kim, MD, PhD; Jeong Su Park, MD, PhD; Yun Ji Hong, MD, PhD; Taek Soo Kim, MD, PhD; Kiho Hong, MD, PhD; Kyoung-Ho Song, MD, PhD; Hyunju Lee, MD, PhD; Eu Suk Kim, MD, PhD; Hong Bin Kim, MD, PhD; Kyoung Un Park, MD, PhD; Junghan Song, MD, PhD; Sun Hoe Koo, MD, PhD; Eui-Chong Kim, MD, PhD


Am J Clin Pathol. 2019;151(2):143-153. 

In This Article

Abstract and Introduction


Objectives: To compare a microarray-based identification and resistance determination system (blood culture gram-negative [BC-GN]; Nanosphere, Northbrook, IL) with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for direct blood cultures (BCs).

Methods: BC-GN and MALDI-TOF MS assay results from direct BCs were compared with conventional test results after pure culture.

Results: Among 124 BCs, 130 gram-negative rods (GNRs), including six cultures with mixed GNRs (117 bacteria were covered by the BC-GN panel), were detected. The BC-GN test presented 116/117 (99.1%) concordance for the identification of targeted GNRs. Among the six polymicrobial BCs, 10 targeted GNRs were correctly identified. Among the 100 BCs tested by MALDI-TOF MS, 88/106 (86.7%) GNRs were correctly identified, and 18 GNRs were not identified. Among the six polymicrobial samples, seven of 12 GNRs (58.3%) were correctly identified.

Conclusions: The BC-GN assay exhibited superior performance compared with MALDI-TOF MS for the identification of targeted GNRs in direct BCs, particularly in polymicrobial samples.


Gram-negative bacteremia is a major concern for public health and causes morbidity and mortality in hospitalized patients.[1,2] The emergence of antibiotic-resistant organisms, including extended-spectrum beta-lactamase (ESBL), carbapenem-resistant Enterobacteriaceae (CRE), and other multidrug-resistant gram-negative bacteria, is strongly associated with hospital mortality.[1] Recent studies have suggested that timely and appropriate antimicrobial treatment can improve patient outcome and reduce the length of hospital stay.[1,3] Novel techniques have been developed for rapid identification directly from blood culture-positive bottles to prevent the time delay of 1 to 2 days after subculture, identification, and susceptibility testing using conventional methods.[4–7] Among these methods, an automated microarray-based assay, the Verigene blood culture gram-negative (BC-GN) test (Nanosphere, Northbrook, IL), can detect 11 clinically important gram-negative bacteria and key resistance determinants. The target genera and species of the BC-GN assay are Acinetobacter species, Citrobacter species, Proteus species, Enterobacter species, Klebsiella pneumoniae, Klebsiella oxytoca, Escherichia coli, Pseudomonas aeruginosa, and Serratia marcescens. The target resistance determinants of BC-GN assay are ESBL CTX-M and the KPC, NDM, VIM, IMP, and OXA group carbapenemases. Several studies have demonstrated that the BN-GN assay provides early identification of important gram-negative bacteria and enables optimal antimicrobial therapy.[3–5,8–12] The length of intensive care unit stay, 30-day mortality, and mortality associated with multidrug-resistant organisms are all significantly decreased by rapid intervention.[3] The other widely investigated assay for the rapid identification of bloodstream infections is matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The introduction of MALDI-TOF MS into clinical microbiology laboratories has allowed more rapid and accurate identification of microorganisms. Because MALDI-TOF MS enables a wide variety of organisms to be accurately detected, efforts to implement MALDI-TOF MS for direct blood culture media are ongoing. Several studies have been conducted to prove the usefulness of MALDI-TOF MS for its accuracy and reduced turnaround time for bacterial identification in direct blood cultures using several different specimen-preparation protocols.[13–27] These studies have shown variable sensitivity, usually between 80% and 90%, and relatively high specificity for the identification of gram-negative bacteria. However, few studies have directly compared these two modalities for the rapid identification of gram-negative bacteria in direct blood cultures and compared their clinical usefulness. Therefore, in this study, we compared the performance and impact of the BC-GN assay and MALDI-TOF MS for the identification of gram-negative bacteria in direct blood cultures compared with those in conventional culture. In addition, we assessed the performance and potential clinical usefulness of the BC-GN assay for the detection of resistance determinants in our study population.