Fourier-Transform InfraRed Spectroscopy Can Quickly Type Gram-Negative Bacilli Responsible for Hospital Outbreaks

Abstract

The typing of epidemic bacterial pathogens in hospitals relies on DNA-based, expensive, and time-consuming techniques, that are often limited to retrospective studies. However, the quick identification of epidemic pathogens in the routine of the microbiology laboratories would expedite infection control procedures that limit the contamination of new patients. IR Biotyper (Bruker Daltonics GmbH) is a new typing machine based on Fourier-transform infrared (FTIR) spectroscopy which generates spectra, aiming at typing the micro-organisms within 3 h. This technique discriminates the isolates by exploring the differences of the surface cell polysaccharides. In this work, we evaluated the ability of the FTIR spectroscopy to recognize Gram-negative bacilli clones responsible for hospital outbreaks. Isolates of Pseudomonas aeruginosa ( n = 100), Klebsiella pneumoniae ( n = 16), Enterobacter cloacae ( n = 23), and Acinetobacter baumannii ( n = 20) were typed by the reference methods Multi-Locus Sequence Typing (defining sequence types – STs) along with or without pulsed field gel electrophoresis (PFGE) (defining pulsotypes), and by FTIR spectroscopy. The congruence of FTIR spectroscopy clustering was compared to those of MLST and PFGE by Adjusted Rand index and Adjusted Wallace coefficient. We found that FTIR spectroscopy accurately clustered P. aeruginosa , K. pneumoniae , and E. cloacae isolates belonging to the same ST. The performance of the FTIR spectroscopy was slightly lower for A. baumannii . Furthermore, FTIR spectroscopy also correctly clustered P. aeruginosa isolates having a similar pulsotype. Overall, the IR Biotyper can quickly (in less than 3 h) detect the spread of clones of P. aeruginosa , K. pneumoniae , E. cloacae , and A. baumannii . The use of this technique by clinical microbiology laboratories may help to tackle the spread of epidemic clones by the quick implementation of infection control measures.

Evaluation of Microsatellite Typing, ITS Sequencing, AFLP Fingerprinting, MALDI-TOF MS, and Fourier-Transform Infrared Spectroscopy Analysis of Candida auris

“…The application of this method to type bacterial species in hospital outbreaks was investigated several times. For instance, typing clinical Klebsiella isolates [ 32 , 36 ] and Gram-negative bacilli clones was successfully performed using FTIR spectroscopy (IR Biotyper) [ 37 ]. A few studies have examined the role of FTIR spectroscopy in the typing of clinical isolates [ 38 ].…”

Vibrational spectroscopic analysis of blood for diagnosis of infections and sepsis: a review of requirements for a rapid diagnostic test

“…Ⅹ Sensitivity of 81% and specificity of 41% for predicting mortality in ED patients with infections 111 . Volume of blood 20-30mL per set 132 <5mL 40 1-5µL 77 1-10µL 72,133 Culture Time 2-7 days 35,87,134 24 hours 45 6-24 hours 77, 135 6-24 hours 72,73,133 Drying Time N/A N/A <30 minutes 78,135 0-60 minutes 73,133 Analysis Time* <2 hours** 35 4-16 hours 40 <20 minutes 136,137 <30minutes 138,139 Positive Predictive Value <55% for 1 culture, <98% for 2 140 30-57% 56…”

A Core Genome Multilocus Sequence Typing Scheme for Pseudomonas aeruginosa

“…PFGE is one of the most useful DNA fingerprinting techniques and a method widely used in hospitals to identify P. aeruginosa outbreaks. However, PFGE is a time-consuming and laborious method, and often not easily reproducible between clinical laboratories (Tenover et al, 1995;Fothergill et al, 2010;Lila et al, 2018;Martak et al, 2019). In contrast, MLST, developed in 2004 for P. aeruginosa, is based on the sequencing and evaluation of the allelic variation of seven housekeeping genes, generating the so-called sequence types (STs) to characterize isolates (Curran et al, 2004).…”