The utility of MALDI-TOF MS for outbreak investigation in the neonatal intensive care unit

Abstract

Our aim was to evaluate the performance of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), routinely used in the microbiology laboratory for bacterial identification, for bacterial typing in the setting of extended spectrum beta-lactamase producing Klebsiella pneumoniae (ESBL-KP) outbreak in the neonatal intensive care unit (NICU). Isolates from a 2011 outbreak in the NICU were retrieved from frozen stocks and analyzed by MALDI-TOF. The MALDI typing was compared with core genome multilocus sequence typing (cg-MLST). MALDI typing divided the 33 outbreak isolates into 2 clones: sequence type (ST)-290 and 405. These results were in complete agreement with cg-MLST results. The differentiation of the outbreak isolates into two clones correlated with the patients' location in the NICU, but also with their place of residence. Conclusion: Here, we show that MALDI-TOF MS, which has been integrated into the microbiology laboratory workflow for microbial species identification, can be secondarily used for epidemiological typing at no added cost. What is Known: • Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is now routinely used in the microbiology laboratory for bacterial identification What is New: • MALDI typing was used for outbreak investigation in the NICU and divided the outbreak isolates into two clones • MALDI-TOF MS may be secondarily used for epidemiological typing at no added cost.

Bacterial Sub-Species Typing Using Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry: What Is Promising?

“…Six isolates representing the two clones were chosen for WGS and compared using core genome MLST. The core genome MLST confirmed the MALDI-TOF MS typing results [1].…”

“…Multiple spectra of each isolate recorded either during the same run or different runs were often combined before analysing mass spectral differences for strain distinction [1,3,5,[7][8][9][10]13,14].…”

“…In general, any mass peaks chosen for strain discrimination were below 10,000 m/z [1,2,9,14] or no higher than 15,000 m/z [3,4,10,13]. There was one exception where mass peaks up to 19,293 Daltons were used for strain discrimination, and measures were taken to improve the quality of higher mass peaks.…”

“…Ideally, the same MALDI-TOF MS data used for bacterial identification can also be used for isolate typing, allowing for on-site monitoring of outbreak strains [1]. However, to increase resolution, an extraction step has often been performed for MALDI-TOF MS typing of bacterial isolates [4,7,9,[13][14][15].…”

“…Whole genome sequencing (WGS), in particular, is a very powerful tool for the investigation of phylogenetic relationships and is becoming the gold standard for this purpose. However, in addition to the costs that are still high for data acquisition, considerable bioinformatics expertise is required for data analysis of WGS [1,2].…”