An overview of the evolution of infrared spectroscopy applied to bacterial typing

The sustained emergence of new declared bacterial species makes typing a continuous challenge for microbiologists. Molecular biology techniques have a very significant role in the context of bacterial typing, but they are often very laborious, time consuming and eventually fail when dealing with very closely related species. Spectroscopic-based techniques appear in some situations as a viable alternative to molecular methods with advantages in terms of analysis time and cost. Infrared and mass spectrometry are among the most exploited techniques in this context: particularly, infrared spectroscopy emerged as a very promising method with multiple reported successful applications. This article presents a systematic review on infrared spectroscopy applications for bacterial typing, highlighting fundamental aspects of infrared spectroscopy, a detailed literature review (covering different taxonomic levels and bacterial species), advantages and limitations of the technique over molecular biology methods and a comparison with other competing spectroscopic techniques such as MALDI-TOF MS, Raman and intrinsic fluorescence. Infrared spectroscopy possesses a high potential for bacterial typing at distinct taxonomic levels and worthy of further developments and systematization. The development of databases appears fundamental towards the establishment of infrared spectroscopy as a viable method for bacterial typing.FCT -Fundação para a Ciência e a Tecnologia(PT2020 UID/QUI/50006/2013)info:eu-repo/semantics/publishedVersio

Whole Genome Sequencing and Evolutionary Analysis of Human Respiratory Syncytial Virus A and B from Milwaukee, WI 1998-2010

BACKGROUND: Respiratory Syncytial Virus (RSV) is the leading cause of lower respiratory-tract infections in infants and young children worldwide. Despite this, only six complete genome sequences of original strains have been previously published, the most recent of which dates back 35 and 26 years for RSV group A and group B respectively. METHODOLOGY/PRINCIPAL FINDINGS: We present a semi-automated sequencing method allowing for the sequencing of four RSV whole genomes simultaneously. We were able to sequence the complete coding sequences of 13 RSV A and 4 RSV B strains from Milwaukee collected from 1998-2010. Another 12 RSV A and 5 RSV B strains sequenced in this study cover the majority of the genome. All RSV A and RSV B sequences were analyzed by neighbor-joining, maximum parsimony and Bayesian phylogeny methods. Genetic diversity was high among RSV A viruses in Milwaukee including the circulation of multiple genotypes (GA1, GA2, GA5, GA7) with GA2 persisting throughout the 13 years of the study. However, RSV B genomes showed little variation with all belonging to the BA genotype. For RSV A, the same evolutionary patterns and clades were seen consistently across the whole genome including all intergenic, coding, and non-coding regions sequences. CONCLUSIONS/SIGNIFICANCE: The sequencing strategy presented in this work allows for RSV A and B genomes to be sequenced simultaneously in two working days and with a low cost. We have significantly increased the amount of genomic data that is available for both RSV A and B, providing the basic molecular characteristics of RSV strains circulating in Milwaukee over the last 13 years. This information can be used for comparative analysis with strains circulating in other communities around the world which should also help with the development of new strategies for control of RSV, specifically vaccine development and improvement of RSV diagnostics

Differentiation of Listeria monocytogenes Serovars by Using Artificial Neural Network Analysis of Fourier-Transformed Infrared Spectra

A classification system based on Fourier transform infrared (FTIR) spectroscopy combined with artificial neural network analysis was designed to differentiate 12 serovars of Listeria monocytogenes using a reference database of 106 well-defined strains. External validation was performed using a test set of another 166 L. monocytogenes strains. The O antigens (serogroup) of 164 strains (98.8%) could be identified correctly, and H antigens were correctly determined in 152 (91.6%) of the test strains. Importantly, 40 out of 41 potentially epidemic serovar 4b strains were unambiguously identified. FTIR analysis is superior to PCR-based systems for serovar differentiation and has potential for the rapid, simultaneous identification of both species and serovar of an unknown Listeria isolate by simply measuring a whole-cell infrared spectrum