Search Results (6)

Recently Candida auris has emerged as a multi-resistant fungal pathogen, with a significant clinical impact, and is able to persist for a long time on human skin and hospital environments. It is a critical issue on the WHO fungal priority list and therefore it is fundamental to reinforce hospital surveillance protocols to limit nosocomial outbreaks. The purpose of this study was to apply Fourier transform infrared spectroscopy (FT-IR) to investigate the phylogenetic relationships among isolated strains from a C. auris outbreak at the University Intensive Care Unit of a Tertiary University hospital in Turin (Italy). To calculate a clustering cut-off, intra- and inter-isolate, distance values were analysed. The data showed the presence of a major Alfa cluster and a minor Beta cluster with a defined C. auris clustering cut-off. The results were validated by an external C. auris strain and Principal Component and Linear Discriminant Analyses. The application of FT-IR technology allowed to obtain important information about the phylogenetic relationships between the analysed strains, defining for the first time a “not WGS-based” clustering cut-off with a statistical–mathematical approach. FT-IR could represent a valid alternative to molecular methods for the rapid and cost-saving typing of C. auris strains with important clinical implications. Full article

Timely and accurate detection and characterization of microbial threats is crucial for effective infection and outbreak management. Additionally, in food production, rapid microbe identification is indispensable for maintaining quality control and hygiene standards. Current methods for typing microbial strains often rely on labor-intensive, time-consuming, and expensive DNA- and sera-serotyping techniques, limiting their applicability in rapid-response scenarios. In this context, the IR Biotyper^®, utilizing Fourier-transform infrared (FTIR) spectroscopy, offers a novel approach, providing specific spectra for fast strain typing within 3 h. This methodology article serves as a comprehensive resource for researchers and technicians aiming to utilize FTIR spectroscopy for microbial strain typing. It encompasses detailed guidelines on sample preparation, data acquisition, and analysis techniques, ensuring the generation of reliable and reproducible results. We highlight the IR Biotyper^®’s rapid and accurate discrimination capabilities, showcasing its potential for real-time pathogen monitoring and source-tracking to enhance public health and food safety. We propose its integration as an early screening method, followed by more detailed analysis with whole-genome sequencing, to optimize detection accuracy and response efficiency in microbial surveillance systems. Full article

Fourier transform infrared spectroscopy (FTIRS) is a diagnostic technique historically used in the microbiological field for the characterization of bacterial strains in relation to the specific composition of their lipid, protein, and polysaccharide components. For each bacterial strain, it is possible to obtain a unique absorption spectrum that represents the fingerprint obtained based on the components of the outer cell membrane. In this study, FTIRS was applied for the first time as an experimental diagnostic tool for the discrimination of two pathogenic species belonging to the Bacillus cereus group, Bacillus anthracis and Bacillus cereus sensu stricto; these are two closely related species that are not so easy to differentiate using classical microbiological methods, representing an innovative technology in the field of animal health. Full article

Several reports have suggested a role for Corynebacterium striatum as an opportunistic pathogen. The authors have conducted a retrospective study at the Clinical Center of the University of Szeged, Hungary, between 2012 and 2021 that revealed significantly increased rifampicin resistance in this species. This work aimed to investigate the reasons behind this phenomenon. The data were collected corresponding to the period between 1 January 2012 and 31 December 2021 at the Department of Medical Microbiology, University of Szeged. To characterize the resistance trends, the antibiotic resistance index was calculated for each antibiotic in use. Fourteen strains with different resistance patterns were further analyzed with Fourier-transform infrared spectroscopy using the IR Biotyper^®. The decline in C. striatum sensitivity to rifampicin seen during the COVID-19 pandemic may have been attributable to the use of Rifadin^® to treat concomitant Staphylococcus aureus infections. The fact that the IR Biotyper^® typing method revealed that the rifampicin-resistant C. striatum strains were closely related supports this hypothesis. The IR Biotyper^® infrared spectroscopy proved to be a modern and fast method to support effective antimicrobial stewardship programs. Full article

Background: Methicillin-resistant S. aureus (MRSA) clonal lineages have been classified based on sequence type (ST) and pulsotype associated with human infection. Providing rapid and accurate epidemiological insight is important to address proper infection control in both community-acquired and nosocomial hospital settings. In this regard, this study was performed to evaluate the IR Biotyper^® (IRBT^®) for strain typing of S. aureus clinical isolates on three media. Methods: A total of 24 S. aureus clinical isolates comprising 15 MRSA isolates (six ST5, three ST72, three ST8, and three ST188 isolates) and nine methicillin-susceptible S. aureus (MSSA) isolates (three ST5, three ST72, and three ST8 isolates) were included for evaluating the IRBT^®. Molecular characterization of all S. aureus isolates was performed by conventional PCR and sequencing methods. The IRBT^® was evaluated according to manufacturer instructions and a modified sample procedure on commonly used BAP, MHA, and TSA media. Subsequently, the spectra obtained by IRBT^® software were compared with dendrograms of PFGE analysis. Results: In this study, the modified sample procedure for reducing the amount of bacteria and bacterial concentration improved the acquisition quality pass rate of the IRBT^®. Each spectrum of S. aureus ST5, ST72, and ST188 isolates on all three media could not be clustered by IRBT^®. However, the dendrogram obtained from the spectra of S. aureus ST8 isolates on TSA medium were in concordance with that obtained by PFGE analysis. In addition, the visual distribution of S. aureus ST8 isolates on TSA medium in a 2D scatter plot appeared as separated point set from those of S. aureus ST5, ST72, and ST188 isolates. Conclusions: The IRBT^® system is a rapid strain typing tool using the FTIR spectroscopic method. This system demonstrated the possibility of discriminating the strain types of S. aureus clinical isolates. Indeed, S. aureus ST8 isolates on TSA medium were successfully differentiated from other strain type isolates. Full article

Typhoidal and para-typhoidal Salmonella are major causes of bacteraemia in resource-limited countries. Diagnostic alternatives to laborious and resource-demanding serotyping are essential. Fourier transform infrared spectroscopy (FTIRS) is a rapidly developing and simple bacterial typing technology. In this study, we assessed the discriminatory power of the FTIRS-based IR Biotyper (Bruker Daltonik GmbH, Bremen, Germany), for the rapid and reliable identification of biochemically confirmed typhoid and paratyphoid fever-associated Salmonella isolates. In total, 359 isolates, comprising 30 S. Typhi, 23 S. Paratyphi A, 23 S. Paratyphi B, and 7 S. Paratyphi C, respectively and other phylogenetically closely related Salmonella serovars belonging to the serogroups O:2, O:4, O:7 and O:9 were tested. The strains were derived from clinical, environmental and food samples collected at different European sites. Applying artificial neural networks, specific automated classifiers were built to discriminate typhoidal serovars from non-typhoidal serovars within each of the four serogroups. The accuracy of the classifiers was 99.9%, 87.0%, 99.5% and 99.0% for Salmonella Typhi, Salmonella Paratyphi A, B and Salmonella Paratyphi C, respectively. The IR Biotyper is a promising tool for fast and reliable detection of typhoidal Salmonella. Hence, IR biotyping may serve as a suitable alternative to conventional approaches for surveillance and diagnostic purposes. Full article