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

Effectiveness of water system chemical disinfection against Pseudomonas aeruginosa infections, despite a not-so-obvious connection

BACKGROUND

Pseudomonas aeruginosa is a well-recognized opportunistic pathogen frequently responsible for hospital-acquired infections. Acquisition routes of P aeruginosa are both endogenous and exogenous, including transmission from a portion of the hospital water system.

METHODS

The impact of disinfection procedures of the water system and description routes of P aeruginosa transmission in a surgical intensive care unit over a 2-year period were investigated. Two distinct periods A and B were considered, respectively, before and after the disinfection. Fourier transform infrared spectroscopy was used to compare isolates recovered from patients and tap water.

RESULTS

Overall, 21.3% of tap water samples were positive but with a significantly lower rate in period B. Concomitantly, the prevalence of patients positive for P aeruginosa decreased from 2.6% to 1%, suggesting a correlation between the presence of environmental sources and patient contaminations. The results revealed that 18% of patients were involved in cross-transmission events not related to any isolate recovered from water, suggesting transmission through care practices. Conversely, only 1 environmental transmission event was suspected in a patient.

CONCLUSIONS

Although the link between the hospital environment and patients was unclear, HCW-associated care practices could be related to contaminated point-of-use waters and then indirect spreading to patients.

Evaluation of Antimicrobial Resistance Patterns of Pseudomonas aeruginosa Strains Isolated among COVID-19 Patients in Brazil Typed by Fourier-Transform Infrared Spectroscopy

This study aimed to characterize Pseudomonas aeruginosa strains isolated from hospitalized patients during the COVID-19 pandemic. This was achieved using phenotypic and molecular techniques, including their antimicrobial resistance profile and biofilm formation. Eighteen strains were isolated from a hospital in Rio de Janeiro, Brazil, and identified by VITEK®2, MALDI-TOF/MS (VITEK MS® and MALDI Biotyper®), and 16S rRNA sequencing. Fourier-transform infrared (FTIR) spectroscopy, antimicrobial susceptibility testing, and biofilm formation and disinfectant tolerance tests were applied to evaluate the virulence characteristics of the strains. VITEK®2 (≥99%), VITEK MS® (≥82.7%), and MALDI Biotyper® (score ≥ 2.01) accurately identified the P. aeruginosa strains, but 16S rRNA sequencing did not differentiate the species P. aeruginosa from P. paraeruginosa. FTIR typing identified three different clusters, but no correlation between the phenotypical or antimicrobial susceptibility testing patterns was found. Most strains exhibited resistance to various antimicrobials. The exceptions were sensitivity to amikacin and norfloxacin, and consequently, these could be considered potential treatment options. Most strains (n = 15, 83.3%) produced biofilms on polystyrene. Sodium hypochlorite treatment (0.5%/15 min) was shown to be the most effective disinfectant for biofilm elimination. P. aeruginosa biofilm formation and tolerance to disinfectants demonstrate the need for effective cleaning protocols to eliminate contamination by this organism in the hospital environment and medical equipment.

Rapid Classification and Differentiation of Sepsis-Related Pathogens Using FT-IR Spectroscopy

Sepsis is a life-threatening condition arising from a dysregulated host immune response to infection, leading to a substantial global health burden. The accurate identification of bacterial pathogens in sepsis is essential for guiding effective antimicrobial therapy and optimising patient outcomes. Traditional culture-based bacterial typing methods present inherent limitations, necessitating the exploration of alternative diagnostic approaches. This study reports the successful application of Fourier-transform infrared (FT-IR) spectroscopy in combination with chemometrics as a potent tool for the classification and discrimination of microbial species and strains, primarily sourced from individuals with invasive infections. These samples were obtained from various children with suspected sepsis infections with bacteria and fungi originating at different sites. We conducted a comprehensive analysis utilising 212 isolates from 14 distinct genera, comprising 202 bacterial and 10 fungal isolates. With the spectral analysis taking several weeks, we present the incorporation of quality control samples to mitigate potential variations that may arise between different sample plates, especially when dealing with a large sample size. The results demonstrated a remarkable consistency in clustering patterns among 14 genera when subjected to principal component analysis (PCA). Particularly, Candida, a fungal genus, was distinctly recovered away from bacterial samples. Principal component discriminant function analysis (PC-DFA) allowed for distinct discrimination between different bacterial groups, particularly Gram-negative and Gram-positive bacteria. Clear differentiation was also observed between coagulase-negative staphylococci (CNS) and Staphylococcus aureus isolates, while methicillin-resistant S. aureus (MRSA) was also separated from methicillin-susceptible S. aureus (MSSA) isolates. Furthermore, highly accurate discrimination was achieved between Enterococcus and vancomycin-resistant enterococci isolates with 98.4% accuracy using partial least squares-discriminant analysis. The study also demonstrates the specificity of FT-IR, as it effectively discriminates between individual isolates of Streptococcus and Candida at their respective species levels. The findings of this study establish a strong groundwork for the broader implementation of FT-IR and chemometrics in clinical and microbiological applications. The potential of these techniques for enhanced microbial classification holds significant promise in the diagnosis and management of invasive bacterial infections, thereby contributing to improved patient outcomes.

A Comprehensive Methodology for Microbial Strain Typing Using Fourier-Transform Infrared Spectroscopy

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.

Evaluating Fourier-transform infrared spectroscopy with IR Biotyper as a faster and simpler method for investigating the sources of an outbreak of legionellosis

Fourier-transform infrared (FTIR) spectroscopy using the IR Biotyper and core genome single nucleotide polymorphism (cgSNP) analysis were performed on 12 Legionella isolates associated with an outbreak at a spa house in Kanagawa Prefecture, Japan, and 3 non-outbreak isolates. The discriminative power of FTIR spectroscopy for 48-h incubation conditions of L. pneumophila in this outbreak was lower than cgSNP-based typing but higher than serogroup typing. FTIR spectroscopy could screen outbreak isolates from a group of genetically related isolates and may be useful as an initial typing method in Legionella outbreak investigations.

Comparative analysis of IR-Biotyper, MLST, cgMLST, and WGS for clustering of vancomycin-resistant Enterococcus faecium in a neonatal intensive care unit

Healthcare-associated infections caused by vancomycin-resistant Enterococcus faecium (VREFM) pose a significant threat to healthcare. Confirming the relatedness of the bacterial isolates from different patients is challenging. We aimed to assess the efficacy of IR-Biotyper, multilocus sequencing typing (MLST), and core-genome MLST (cgMLST) in comparison with whole-genome sequencing (WGS) for outbreak confirmation in the neonatal intensive care unit (NICU). Twenty VREFM isolates from four neonates and ten control isolates from unrelated patients were analyzed. Genomic DNA extraction, MLST, cgMLST, and WGS were performed. An IR-Biotyper was used with colonies obtained after 24 h of incubation on tryptic soy agar supplemented with 5% sheep blood. The optimal clustering cutoff for the IR-Biotyper was determined by comparing the results with WGS. Clustering concordance was assessed using the adjusted Rand and Wallace indices. MLST and cgMLST identified sequence types (ST) and complex types (CT), revealing suspected outbreak isolates with a predominance of ST17 and CT6553, were confirmed by WGS. For the IR-Biotyper, the proposed optimal clustering cut-off range was 0.106-0.111. Despite lower within-run precision, of the IR-Biotyper, the clustering concordance with WGS was favorable, meeting the criteria for real-time screening. This study confirmed a nosocomial outbreak of VREFM in the NICU using an IR-Biotyper, showing promising results compared to MLST. Although within-run precision requires improvement, the IR-Biotyper demonstrated high discriminatory power and clustering concordance with WGS. These findings suggest its potential as a real-time screening tool for the detection of VREFM-related nosocomial outbreaks.

IMPORTANCE

In this study, we evaluated the performance of the IR-Biotyper in detecting nosocomial outbreaks caused by vancomycin-resistant Enterococcus faecium, comparing it with MLST, cgMLST, and WGS. We proposed a cutoff that showed the highest concordance compared to WGS and assessed the within-run precision of the IR-Biotyper by evaluating the consistency in genetically identical strain when repeated in the same run.

Characterization of an outbreak caused by Elizabethkingia miricola using Fourier-transform infrared (FTIR) spectroscopy

Fourier-transform infrared (FTIR) spectroscopy has the potential to be used for bacterial typing and outbreak characterization. We evaluated FTIR for the characterization of an outbreak caused by Elizabethkingia miricola. During the 2020-2021 period, 26 isolates (23 clinical and 3 environmental) were collected and analyzed by FTIR (IR Biotyper) and core-genome MLST (cgMLST), in addition to antimicrobial susceptibility testing. FTIR spectroscopy and cgMLST showed that 22 of the isolates were related to the outbreak, including the environmental samples, with only one discordance between both methods. Then, FTIR is useful for E. miricola typing and can be easily implemented in the laboratory.

WITHDRAWN: Evaluation of Fourier Transform Infrared spectroscopy (IR Biotyper) as a complement to Whole genome sequencing (WGS) to characterise Enterobacter cloacae , Citrobacter freundii and Klebsiella pneumoniae isolates recovered from hospital sinks

The authors have withdrawn their manuscript due to becoming aware of methodology issues related to the curation of the training set used to determine cut-off values for Biotyper cluster assignation and lack of replicate measurements on different days for the isolates analysed. It is therefore unclear whether the conclusions of the manuscript are founded and no further work is possible to correct these issues as the instrument is no longer available to the authors. If you have any questions, please contact the corresponding author.

Development and validation of a quick, automated, and reproducible ATR FT-IR spectroscopy machine-learning model for Klebsiella pneumoniae typing

The reliability of Fourier-transform infrared (FT-IR) spectroscopy for Klebsiella pneumoniae typing and outbreak control has been previously assessed, but issues remain in standardization and reproducibility. We developed and validated a reproducible FT-IR with attenuated total reflectance (ATR) workflow for the identification of K. pneumoniae lineages. We used 293 isolates representing multidrug-resistant K. pneumoniae lineages causing outbreaks worldwide (2002-2021) to train a random forest classification (RF) model based on capsular (KL)-type discrimination. This model was validated with 280 contemporaneous isolates (2021-2022), using wzi sequencing and whole-genome sequencing as references. Repeatability and reproducibility were tested in different culture media and instruments throughout time. Our RF model allowed the classification of 33 capsular (KL)-types and up to 36 clinically relevant K. pneumoniae lineages based on the discrimination of specific KL- and O-type combinations. We obtained high rates of accuracy (89%), sensitivity (88%), and specificity (92%), including from cultures obtained directly from the clinical sample, allowing to obtain typing information the same day bacteria are identified. The workflow was reproducible in different instruments throughout time (>98% correct predictions). Direct colony application, spectral acquisition, and automated KL prediction through Clover MS Data analysis software allow a short time-to-result (5 min/isolate). We demonstrated that FT-IR ATR spectroscopy provides meaningful, reproducible, and accurate information at a very early stage (as soon as bacterial identification) to support infection control and public health surveillance. The high robustness together with automated and flexible workflows for data analysis provide opportunities to consolidate real-time applications at a global level. IMPORTANCE We created and validated an automated and simple workflow for the identification of clinically relevant Klebsiella pneumoniae lineages by FT-IR spectroscopy and machine-learning, a method that can be extremely useful to provide quick and reliable typing information to support real-time decisions of outbreak management and infection control. This method and workflow is of interest to support clinical microbiology diagnostics and to aid public health surveillance.

Rapid typing of Klebsiella pneumoniae and Pseudomonas aeruginosa by Fourier-transform Infrared spectroscopy informs infection control in veterinary settings

Introduction

The emergence of multi-drug resistant (MDR) pathogens linked to healthcare-associated infections (HCAIs) is an increasing concern in modern veterinary practice. Thus, rapid bacterial typing for real-time tracking of MDR hospital dissemination is still much needed to inform best infection control practices in a clinically relevant timeframe. To this end, the IR Biotyper using Fourier-Transform InfraRed (FTIR) spectroscopy has the potential to provide fast cluster analysis of potentially related organisms with substantial cost and turnaround time benefits.

Materials and methods

A collection of MDR bacterial isolates (n = 199, comprising 92 Klebsiella pneumoniae and 107 Pseudomonas aeruginosa) obtained from companion animal (i.e., dogs, cats and horses) clinical investigations, faecal and environmental screening from four veterinary facilities between 2012 and 2019 was analysed retrospectively by FTIR spectroscopy. Its performance was compared against MLST extracted from whole genomes of a subset of clustering isolates (proportionally to cluster size) for investigation of potential nosocomial transmission between patients and the surrounding hospital environments.

Results

Concordance between the FTIR and MLST types was overall high for K. pneumoniae (Adjusted Rand Index [ARI] of 0.958) and poor for P. aeruginosa (ARI of 0.313). FTIR K. pneumoniae clusters (n = 7) accurately segregated into their respective veterinary facility with evidence of intra-hospital spread of K. pneumoniae between patients and environmental surfaces. Notably, K. pneumoniae ST147 intensely circulated at one Small Animal Hospital ICU. Conversely, Pseudomonas aeruginosa FTIR clusters (n = 18) commonly contained isolates of diversified hospital source and heterogeneous genetic background (as also genetically related isolates spread across different clusters); nonetheless, dissemination of some clones, such as P. aeruginosa ST2644 in the equine hospital, was apparent. Importantly, FTIR clustering of clinical, colonisation and/or environmental isolates sharing genomically similar backgrounds was seen for both MDR organisms, highlighting likely cross-contamination events that led to clonal dissemination within settings.

Conclusion

FTIR spectroscopy has high discriminatory power for hospital epidemiological surveillance of veterinary K. pneumoniae and could provide sufficient information to support early detection of clonal dissemination, facilitating implementation of appropriate infection control measures. Further work and careful optimisation need to be carried out to improve its performance for typing of P. aeruginosa veterinary isolates.

Use of Fourier-transform infrared spectroscopy for real-time outbreak investigation of OXA-48-producing Escherichia coli

BACKGROUND

Efficient infection control during carbapenem-resistant Enterobacterales outbreaks demands rapid and simple techniques for outbreak investigations. WGS, the current gold standard for outbreak identification, is expensive, time-consuming and requires a high level of expertise. Fourier-transform infrared (FTIR) spectroscopy (IR Biotyper) is a rapid typing method based on infrared radiation applied to samples, which provides a highly specific absorption spectrum.

OBJECTIVES

To investigate an outbreak of OXA-48-producing Escherichia coli in real-time using FTIR and subsequently compare the results with WGS.

METHODS

Twenty-one isolates were collected during a nosocomial outbreak, and identification and antibiotic susceptibilities were confirmed by VITEK®2. FTIR was conducted for all isolates, and nine representative isolates were sequenced.

RESULTS

FTIR was able to correctly determine the clonal relatedness of the isolates and to identify the outbreak cluster, as confirmed by WGS. By WGS, isolates in the main FTIR cluster belonged to the same MLST type and core-genome MLST type, and they harboured similar plasmids and resistance genes, whereas the singletons external to the FTIR cluster had different genetic content.

CONCLUSIONS

FTIR can operate as a rapid, efficient and reliable first-line tool for outbreak investigations during a real-time ongoing E. coli outbreak, which can contribute to limiting the spread of pathogens.

Application of Fourier Transform Infrared Spectroscopy to Discriminate Two Closely Related Bacterial Species: Bacillus anthracis and Bacillus cereus Sensu Stricto

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.

Applications of Fourier Transform-Infrared spectroscopy in microbial cell biology and environmental microbiology: advances, challenges, and future perspectives

Microorganisms play pivotal roles in shaping ecosystems and biogeochemical cycles. Their intricate interactions involve complex biochemical processes. Fourier Transform-Infrared (FT-IR) spectroscopy is a powerful tool for monitoring these interactions, revealing microorganism composition and responses to the environment. This review explores the diversity of applications of FT-IR spectroscopy within the field of microbiology, highlighting its specific utility in microbial cell biology and environmental microbiology. It emphasizes key applications such as microbial identification, process monitoring, cell wall analysis, biofilm examination, stress response assessment, and environmental interaction investigation, showcasing the crucial role of FT-IR in advancing our understanding of microbial systems. Furthermore, we address challenges including sample complexity, data interpretation nuances, and the need for integration with complementary techniques. Future prospects for FT-IR in environmental microbiology include a wide range of transformative applications and advancements. These include the development of comprehensive and standardized FT-IR libraries for precise microbial identification, the integration of advanced analytical techniques, the adoption of high-throughput and single-cell analysis, real-time environmental monitoring using portable FT-IR systems and the incorporation of FT-IR data into ecological modeling for predictive insights into microbial responses to environmental changes. These innovative avenues promise to significantly advance our understanding of microorganisms and their complex interactions within various ecosystems.

Fusion data from FT-IR and MALDI-TOF MS result in more accurate classification of specific microbiota

Microbes are usually present as a specific microbiota, and their classification remains a challenge. MALDI-TOF MS is particularly successful in library-based microbial identification at the species level as it analyzes the molecular weight of peptides and ribosomal proteins. FT-IR allows more accurate classification of bacteria at the subspecies level due to the high sensitivity, specificity and repeatability of FT-IR signals from bacteria, which is not achievable with MALDI-TOF MS. Previous studies have shown that more accurate identification results can be obtained by the fusion of FT-IR and MALDI-TOF MS spectral data. Here, we constructed 20 groups of model microbiota samples and used FT-IR, MALDI-TOF MS, and their fusion data to classify them. Hierarchical clustering analysis (HCA) showed that the classification accuracy of FT-IR, MALDI-TOF MS, and the fusion data was 85%, 90%, and 100%, respectively. These results indicate that both FT-IR and MALDI-TOF MS can effectively classify specific microbiota, and the fusion of their spectral data could improve the classification accuracy. The FT-IR and MALDI-TOF MS data fusion strategy may be a promising technology for specific microbiota classification.

Evaluation of Fourier transform-infrared spectroscopy (FT-IR) as a control measure for nosocomial outbreak investigations

Whole-genome sequencing (WGS) provides greater resolution than other molecular epidemiology strategies and is emerging as a new gold standard approach for microbial strain typing. The Bruker IR Biotyper is designed as a screening tool to identify bacterial isolates that require WGS to establish accurate relationships, but its performance and utility in nosocomial outbreak investigations have not been thoroughly investigated. Here, we evaluated the IR Biotyper by retrospectively examining isolates tested by WGS during investigations of potential nosocomial transmission events or outbreaks. Ninety-eight clinical isolates from 14 different outbreak investigations were examined: three collections of Acinetobacter baumannii (n = 2, n = 9, n = 5 isolates in each collection), one of Escherichia coli (n = 16), two of Pseudomonas aeruginosa (n = 2 and n = 5), two of Serratia marcescens (n = 9 and n = 7), five of Staphylococcus aureus (n = 8, n = 4, n = 3, n = 3, n = 17), and one of Stenotrophomonas maltophilia (n = 8). Linear regression demonstrated a weak, positive correlation between the number of pairwise genome-wide single-nucleotide polymorphisms (SNPs) and IR Biotyper spectral distance values for Gram-positive (r = 0.43, P ≤ 0.0001), Gram-negative (r = 0.1554, P = 0.0639), and all organisms combined (r = 0.342, P ≤ 0.0001). Overall, the IR Biotyper had a positive predictive value (PPV) of 55.81% for identifying strains that were closely related by genomic identity, but a negative predictive value (NPV) of 86.79% for identifying unrelated isolates. When experimentally adjusted cut-offs were applied to A. baumannii, P. aeruginosa, and E. coli, the PPV was 62% for identifying strains that were closely related and the NPV was 100% for identifying unrelated isolates. Implementation of the IR Biotyper as a screening tool in this cohort would have reduced the number of Gram-negative isolates requiring further WGS analysis by 50% and would reduce the number of S. aureus isolates needing WGS resolution by 48%.

Fourier-transform infrared spectroscopy for typing of vancomycin-resistant Enterococcus faecium: performance analysis and outbreak investigation

Vancomycin-resistant Enterococci, mainly Enterococcus faecium (VREfm), are causing nosocomial infections and outbreaks. Bacterial typing methods are used to assist in outbreak investigations. Most of them, especially genotypic methods like multi-locus sequence typing (MLST), whole genome sequencing (WGS), or pulsed-field gel electrophoresis, are quite expensive and time-consuming. Fourier-transform infrared (FT-IR) spectroscopy assesses the biochemical composition of bacteria, such as carboxyl groups in polysaccharides. It is an affordable technique and has a faster turnaround time. Thus, the aim of this study was to evaluate FT-IR spectroscopy for VREfm outbreak investigations. Basic performance requirements like reproducibility and the effects of incubation time were assessed in distinct sample sets. After determining a FT-IR spectroscopy cut-off range, the clustering agreement between FT-IR and WGS within a retrospective (n: 92 isolates) and a prospective outbreak (n: 15 isolates) was investigated. For WGS an average nucleotide identity (ANI) cut-off score of 0.999 was used. Basic performance analysis showed reproducible results. Moreover, FT-IR spectroscopy readouts showed a high agreement with WGS-ANI analysis in clinical outbreak investigations (V-measure 0.772 for the retrospective and 1.000 for the prospective outbreak). FT-IR spectroscopy had a higher discriminatory power than MLST in the outbreak investigations. After determining cut-off values to achieve optimal resolution, FT-IR spectroscopy is a promising technique to assist in outbreak investigation as an affordable, easy-to-use tool with a turnaround time of less than one day. IMPORTANCE Vancomycin-resistant Enterococci, mainly Enterococcus faecium (VREfm), are a frequent cause of nosocomial outbreaks. Several bacterial typing methods are used to track transmissions and investigate outbreaks, whereby genome-based techniques are used as a gold standard. Current methods are either expensive, time-consuming, or both. Additionally, often, specifically trained staff needs to be available. This study provides insight into the use of Fourier-transform infrared (FT-IR) spectroscopy, an affordable, easy-to-use tool with a short turnaround time as a typing method for VREfm. By assessing clinical samples, this work demonstrates promising results for species discrimination and reproducibility. FT-IR spectrosopy shows a high level of agreement in the analysis of VREfm outbreaks in comparison with whole genome sequencing-based methods.

Evaluation of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Molecular Typing of Acinetobacter baumannii in Comparison with Orthogonal Methods

Colonization and subsequent health care-associated infection (HCAI) with Acinetobacter baumannii are a concern for vulnerable patient groups within the hospital setting. Outbreaks involving multidrug-resistant strains are associated with increased patient morbidity and mortality and poorer overall outcomes. Reliable molecular typing methods can help to trace transmission routes and manage outbreaks. In addition to methods deployed by reference laboratories, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) may assist by making initial in-house judgments on strain relatedness. However, limited studies on method reproducibility exist for this application. We applied MALDI-TOF MS typing to A. baumannii isolates associated with a nosocomial outbreak and evaluated different methods for data analysis. In addition, we compared MALDI-TOF MS with whole-genome sequencing (WGS) and Fourier transform infrared spectroscopy (FTIR) as orthogonal methods to further explore their resolution for bacterial strain typing. A related subgroup of isolates consistently clustered separately from the main outbreak group by all investigated methods. This finding, combined with epidemiological data from the outbreak, indicates that these methods identified a separate transmission event unrelated to the main outbreak. However, the MALDI-TOF MS upstream approach introduced measurement variability impacting method reproducibility and limiting its reliability as a standalone typing method. Availability of in-house typing methods with well-characterized sources of measurement uncertainty could assist with rapid and dependable confirmation (or denial) of suspected transmission events. This work highlights some of the steps to be improved before such tools can be fully integrated into routine diagnostic service workflows for strain typing. IMPORTANCE Managing the transmission of antimicrobial resistance necessitates reliable methods for tracking outbreaks. We compared the performance of MALDI-TOF MS with orthogonal approaches for strain typing, including WGS and FTIR, for Acinetobacter baumannii isolates correlated with a health care-associated infection (HCAI) event. Combined with epidemiological data, all methods investigated identified a group of isolates that were temporally and spatially linked to the outbreak, yet potentially attributed to a separate transmission event. This may have implications for guiding infection control strategies during an outbreak. However, the technical reproducibility of MALDI-TOF MS needs to be improved for it to be employed as a standalone typing method, as different stages of the experimental workflow introduced bias influencing interpretation of biomarker peak data. Availability of in-house methods for strain typing of bacteria could improve infection control practices following increased reports of outbreaks of antimicrobial-resistant organisms during the COVID-19 pandemic, related to sessional usage of personal protective equipment (PPE).

Use of the quantitative antibiogram method for assessing nosocomial transmission of ESBL-producing Enterobacteriaceae in a French hospital

BACKGROUND

ESBL-producing Enterobacteriaceae (eESBL) have a high prevalence in hospitals but real-time monitoring of nosocomial acquisition through conventional typing methods is challenging. Moreover, patient-to-patient transmission varies between the main species, namely Escherichia coli, and Klebsiella pneumoniae, then questioning the relevance of applying identical preventive measures.

AIM

To detect eESBL cross-transmission events (CTE) using combination of quantitative antibiogram with epidemiological data (combined-QA), and to rule on the effectiveness of standard or contact precautions for eESBL species.

METHODS

First, a validation set was used to confirm the relevance of the combined-QA by comparison to a combination of pulsed-field gel electrophoresis and epidemiological data (combined-PFGE). Secondly, a four-year retrospective analysis was conducted to detect eESBL-CTE in hospitalized patients. Two species were screened i.e. ESBL-E. coli (ESBL-Ec), and ESBL-K. pneumoniae (ESBL-Kp). During the study, only standard precautions were applied to ESBL-Ec patients whereas contact precautions were retained for ESBL-Kp.

FINDINGS

As a proof of concept, results between the two combined methods for the detection of CTE were identical for E. coli, and similar to at least 75% for K. pneumoniae. During the retrospective analysis, 722 patients with ESBL-Ec isolates and 280 with ESBL-Kp isolates were included. Nine CTE were identified for E. coli and 23 for K. pneumoniae, implying 20 (2.7%) and 36 (12.8%) patients, respectively.

CONCLUSION

The QA-combined method constitutes a rapid tool for epidemiological surveillance to detect CTE. In our hospital, standard precautions are sufficient to prevent acquisition of ESBL-Ec whereas contact precautions must be implemented to prevent acquisition of ESBL-Kp.

Evaluation of IR Biotyper for carbapenem-resistant Pseudomonas aeruginosa typing and its application potential for the investigation of nosocomial infection

Pseudomonas aeruginosa is one of the most common opportunistic pathogens causing severe nosocomial infections for its patterns of multidrug resistance, particularly for carbapenems. Timely epidemiological surveillance could greatly facilitate infection control of P. aeruginosa and many deadly pathogens alike. IR Biotyper (IRBT), is a novel real-time typing tool, based on a Fourier-transform infrared (FTIR) spectroscopy system. It is critical to comprehensively establish and evaluate the feasibility of IRBT in P. aeruginosa strain typing. In the current study, we first established standards and schemes for its routine laboratory application, and we found that Mueller-Hinton agar plates give better discriminatory power than blood agar plates. Data showed that the cut-off value of 0.15 with an additional 0.025 range was optimal. Secondly, 27 clinically isolated carbapenem-resistant P. aeruginosa (CRPA) strains collected from October 2010 to September 2011 were evaluated for typing effectiveness by comparing IRBT to the other commonly used typing methods, such as multi-locus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing (WGS)-based typing. When using WGS-based typing as the reference method, the typing method of FTIR spectroscopy (AR = 0.757, SID = 0.749) could better cluster P. aeruginosa strains than MLST and in silico serotyping (AR = 0.544, SID = 0.470). Though PFGE showed the highest discriminatory power, low concordance was observed between PFGE and the other methods. Above all, this study demonstrates the utility of the IRBT as a quick, low-cost, real-time typing tool for the detection of CRPA strains.

Fourier transform infrared spectroscopy; can it be used as a rapid typing method of Neisseria gonorrhoeae?

BACKGROUND

Typing of Neisseria gonorrhoeae is necessary for epidemiologic surveillance, while time consuming and resource intensive. Fourier transform infrared (FTIR) spectroscopy has shown promising results when typing several bacterial species. This study investigates whether FTIR spectroscopy can be used as a rapid method for typing clinical N. gonorrhoeae isolates, comparing FTIR spectroscopy to multi locus sequence typing (MLST), N. gonorrhoeae multi antigen sequence typing (NG-MAST) and whole genome sequencing (WGS).

METHODS

Sixty consecutive isolates from a venereology clinic and three isolates from an outbreak were included. Isolates were analysed with FTIR spectroscopy on the IR Biotyper system (Bruker Daltonik) with the IR Biotyper software (version 2.1) with default analysis settings (spectral range 1300-800 cm^-1). Four technical replicates of each isolate were analysed in three different runs. The output was a hierarchical cluster analysis (HCA) presented as a dendrogram; a tree-like overview of how closely different isolates are related. FTIR spectroscopy was compared to MLST, NG-MAST and WGS to see if the FTIR spectroscopy-dendrogram grouped the isolates in the same clusters.

RESULTS

Fifty-one out of 60 isolates, and the three outbreak isolates, produced at least one spectrum in each run and were included. No agreement between FTIR spectroscopy and MLST or NG-MAST or WGS was shown. The FTIR spectroscopy-dendrogram failed to cluster the outbreak isolates.

CONCLUSION

FTIR spectroscopy (spectral range 1300-800 cm^-1) is not yet suitable for epidemiologic typing of N. gonorrhoeae. Absence of a capsule as well as phase- and antigenic variation of carbohydrate surface structures of the gonococcal cell wall may contribute to our findings. Future studies should include analysis of a wider range of the spectrum recorded (4000-500 cm^-1), and should also explore further mathematical analytic approaches of the similarity between spectra.

A multi-center validation study on the discrimination of Legionella pneumophila sg.1, Legionella pneumophila sg. 2-15 and Legionella non-pneumophila isolates from water by FT-IR spectroscopy

This study developed and validated a method, based on the coupling of Fourier-transform infrared spectroscopy (FT-IR) and machine learning, for the automated serotyping of Legionella pneumophila serogroup 1, Legionella pneumophila serogroups 2-15 as well as their successful discrimination from Legionella non-pneumophila. As Legionella presents significant intra- and inter-species heterogeneities, careful data validation strategies were applied to minimize late-stage performance variations of the method across a large microbial population. A total of 244 isolates were analyzed. In details, the method was validated with a multi-centric approach with isolates from Italian thermal and drinking water (n = 82) as well as with samples from German, Italian, French, and British collections (n = 162). Specifically, robustness of the method was verified over the time-span of 1 year with multiple operators and two different FT-IR instruments located in Italy and Germany. Moreover, different production procedures for the solid culture medium (in-house or commercial) and different culture conditions (with and without 2.5% CO₂) were tested. The method achieved an overall accuracy of 100, 98.5, and 93.9% on the Italian test set of Legionella, an independent batch of Legionella from multiple European culture collections, and an extra set of rare Legionella non-pneumophila, respectively.

Investigating the Origin of Mycobacterium chimaera Contamination in Heater-Cooler Units: Integrated Analysis with Fourier Transform Infrared Spectroscopy and Whole-Genome Sequencing

Mycobacterium chimaera is ubiquitously spread in the environment, including factory and hospital water systems. Invasive cases of M. chimaera infection have been associated with aerosols produced by the use of heater-cooler units (HCU) during cardiac surgery. The aim of this study was to evaluate for the first time the performance of IR-Biotyper system on a large number of M. chimaera isolates collected from longitudinal environmental HCUs samples and water sources from hospitals located in three Italian provinces. In addition, IR-Biotyper results were compared with whole-genome sequencing (WGS) analysis, the reference method for molecular epidemiology, to investigate the origin of M. chimaera contamination of HCUs. From November 2018 to May 2021, 417 water samples from 52 HCUs (Stockert 3T, n = 41 and HCU40, n = 11) and 23 hospital taps (used to fill the HCU tanks) were concentrated, decontaminated, and cultured for M. chimaera. Positive cultures (n = 53) were purified by agar plate subcultures and analyzed by IR-Biotyper platform and Ion Torrent sequencing system. IR-Biotyper spectra results were analyzed using a statistical approach of dimensionality reduction by linear discriminant analysis (LDA), generating three separate clusters of M. chimaera, ascribable to each hospital. Furthermore, the only M. chimaera-positive sample from tap water clustered with the isolates from the HCUs of the same hospital, confirming that the plumbing system could represent the source of HCU contamination and, potentially, of patient infection. According to the genome-based phylogenies and following the classification proposed by van Ingen and collaborators in 2017, three distinct M. chimaera groups appear to have contaminated the HCU water systems: subgroups 1.1, 2.1, and branch 2. Most of the strains isolated from HCUs at the same hospital share a highly similar genetic profile. The nonrandom distribution obtained with WGS and IR-Biotyper leads to the hypothesis that M. chimaera subtypes circulating in the local plumbing colonize HCUs through the absolute filter, in addition with the current hypothesis that contamination occurs at the HCU production site. This opens the possibility that other medical equipment, such as endoscope reprocessing device or hemodialysis systems, could be contaminated by M. chimaera. IMPORTANCE Our manuscript focuses on interventions to reduce waterborne disease transmission, improve sanitation, and control infection. Sanitary water can be contaminated by nontuberculous Mycobacteria, including M. chimaera, a causative agent of invasive infections in immunocompromised patients. We found highly similar genetic and phenotypic profiles of M. chimaera isolated from heater-cooler units (HCU) used during surgery to thermo-regulate patients' body temperature, and from the same hospital tap water. These results lead to the hypothesis that M. chimaera subtypes circulating in the local plumbing colonize HCUs through the absolute filter, adding to the current hypothesis that contamination occurs at the HCU production site. In addition, this opens the possibility that other medical equipment using sanitized water, such as endoscope reprocessing devices or hemodialysis systems, could be contaminated by nontuberculous Mycobacteria, suggesting the need for environmental surveillance and associated control measures.

Optical Methods for Label-Free Detection of Bacteria

Pathogenic bacteria are the leading causes of food-borne and water-borne infections, and one of the most serious public threats. Traditional bacterial detection techniques, including plate culture, polymerase chain reaction, and enzyme-linked immunosorbent assay are time-consuming, while hindering precise therapy initiation. Thus, rapid detection of bacteria is of vital clinical importance in reducing the misuse of antibiotics. Among the most recently developed methods, the label-free optical approach is one of the most promising methods that is able to address this challenge due to its rapidity, simplicity, and relatively low-cost. This paper reviews optical methods such as surface-enhanced Raman scattering spectroscopy, surface plasmon resonance, and dark-field microscopic imaging techniques for the rapid detection of pathogenic bacteria in a label-free manner. The advantages and disadvantages of these label-free technologies for bacterial detection are summarized in order to promote their application for rapid bacterial detection in source-limited environments and for drug resistance assessments.

Plasma versus Serum Analysis by FTIR Spectroscopy to Capture the Human Physiological State

Fourier Transform InfraRed spectroscopy of serum and plasma has been highly explored for medical diagnosis, due to its general simplicity, and high sensitivity and specificity. To evaluate the plasma and serum molecular fingerprint, as obtained by FTIR spectroscopy, to acquire the system metabolic state, serum and plasma spectra were compared to characterize the metabolic state of 30 human volunteers, between 90 days consumption of green tea extract rich in Epigallocatechin-3-gallate (EGCG). Both plasma and serum spectra enabled the high impact of EGCG consumption on the biofluid spectra to be observed, as analyzed by the spectra principal component analysis, hierarchical-cluster analysis, and univariate data analysis. Plasma spectra resulted in the prediction of EGCG consumption with a slightly higher specificity, accuracy, and precision, also pointing to a higher number of significant spectral bands that were different between the 90 days period. Despite this, the lipid regions of the serum spectra were more affected by EGCG consumption than the corresponding plasma spectra. Therefore, in general, if no specific compound analysis is highlighted, plasma is in general the advised biofluid to capture by FTIR spectroscopy the general metabolic state. If the lipid content of the biofluid is relevant, serum spectra could present some advantages over plasma spectra.

In-process real-time probiotic phenotypic strain identity tracking: The use of Fourier transform infrared spectroscopy

Probiotic bacteria, capable of conferring benefits to the host, can present challenges in design, development, scale-up, manufacturing, commercialization, and life cycle management. Strain identification is one of the main quality parameters; nevertheless, this task can be challenging since established methodologies can lack resolution at the strain level for some microorganisms and\or are labor-intensive and time-consuming. Fourier transform infrared spectroscopy (FTIRS) has been largely used for the investigation of pathogenic species in the clinical field, whereas only recently has been proposed for the identification of probiotic strains. Within the probiotic industrial production, bacterial strains can be subjected to stressful conditions that may affect genomic and phenotypic characteristics; therefore, real-time monitoring of all the sequential growth steps is requested. Considering the fast, low-cost, and high-throughput features, FTIRS is an innovative and functional technology for typing probiotic strains from bench-top experiments to large-scale industrial production, allowing the monitoring of stability and identity of probiotic strains. In this study, the discriminatory power of FTIRS was assessed for four Lactiplantibacillus plantarum probiotic strains grown under different conditions, including temperatures (30 and 37°C) and medium (broth and agar), after consecutive sub-culturing steps. A comparison between the generated spectra with pulsed-field gel electrophoresis (PFGE) profiles was also performed. FTIRS was not only able to distinguish the strains of L. plantarum under different growth conditions but also to prove the phenotypic stability of L. plantarum type strain LP-CT after six growing steps. Regardless of the growth conditions, FTIRS spectra related to LP-CT constituted a unique hierarchical cluster, separated from the other L. plantarum strains. These results were confirmed by a PFGE analysis. In addition, based on FTIRS data, broth cultures demonstrated a higher reproducibility and discriminatory power with respect to agar ones. These results support the introduction of FTIRS in the probiotic industry, allowing for the step-by-step monitoring of massive microbial production while also guaranteeing the stability and purity of the probiotic strain. The proposed novel approach can constitute an impressive improvement in the probiotic manufacturing process.

Surveillance of Enterobacter cloacae complex colonization and comparative analysis of different typing methods on a neonatal intensive care unit in Germany

Background

Enterobacter cloacae complex is a group of common opportunistic pathogens on neonatal intensive care units. Active microbiological screening to guide empirical antimicrobial treatment or to detect transmission events is recommended in high-risk preterm neonates. A rise in colonization with E. cloacae complex was observed in a German perinatal centre. The aim of this study was to evaluate the performance of different typing techniques using whole genome sequencing (WGS) as a reference.

Methods

Enterobacter cloacae complex isolates from clinical and screening specimens with an epidemiological link to the neonatal intensive care units were further assessed. Identification and antibiotic susceptibility testing was performed by a combination of VITEK2 (bioMérieux) and MALDI-TOF (Bruker Daltonics), followed by RAPD/rep-PCR and PFGE (XbaI). Retrospectively, all isolates were analyzed by Fourier-transform infrared (FTIR) spectroscopy (IR Biotyper, Bruker Daltonics). Whole genome sequencing with SNP-based clustering was used as the reference method. Furthermore, resistome analysis, sequence type and species identification were derived from the WGS data. Transmission analysis was based on epidemiological and typing data.

Results

Between September 2017 and March 2018 32 mostly preterm neonates were found to be colonized with E. cloacae complex and 32 isolates from 24 patients were available for further typing. RAPD/rep-PCR and PFGE showed good concordance with WGS whereas FTIR displayed mediocre results [adjusted rand index (ARI) = 0.436]. A polyclonal increase and two dominant and overlapping clonal clusters of two different E. hormaechei subspecies were detected. Overall, four different species were identified. Genotyping confirmed third-generation cephalosporin resistance development in isolates of the same patient. During the six-month period several infection prevention interventions were performed and no E. cloacae complex isolates were observed during the following months.

Conclusions

Interpretation of the microbiological results alone to detect transmission events is often challenging and bacterial typing is of utmost importance to implement targeted infection control measures in an epidemic occurrence of E. cloacae complex. WGS is the most discriminatory method. However, traditional methods such as PFGE or RAPD/rep-PCR can provide reliable and quicker results in many settings. Furthermore, research is needed to quickly identify E. cloacae complex to the species level in the microbiological laboratory.

Exploring the identification of multiple bacteria on stainless steel using multi-scale spectral imaging from microscopic to macroscopic

This work investigates non-contact reflectance spectral imaging techniques, i.e. microscopic Fourier transform infrared (FTIR) imaging, macroscopic visible-near infrared (VNIR), and shortwave infrared (SWIR) spectral imaging, for the identification of bacteria on stainless steel. Spectral images of two Gram-positive (GP) bacteria (Bacillus subtilis (BS) and Lactobacillus plantarum (LP)), and three Gram-negative (GN) bacteria (Escherichia coli (EC), Cronobacter sakazakii (CS), and Pseudomonas fluorescens (PF)), were collected from dried suspensions of bacterial cells dropped onto stainless steel surfaces. Through the use of multiple independent biological replicates for model validation and testing, FTIR reflectance spectral imaging was found to provide excellent GP/GN classification accuracy (> 96%), while the fused VNIR-SWIR data yielded classification accuracy exceeding 80% when applied to the independent test sets. However, classification within gram type was far less reliable, with lower accuracies for classification within the GP (< 75%) and GN (≤ 51%) species when calibration models were applied to the independent test sets, underlining the importance of independent model validation when dealing with samples of high biological variability.

Clonal Dissemination of Extended-Spectrum Cephalosporin-Resistant Enterobacterales between Dogs and Humans in Households and Animal Shelters of Romania

Faecal carriage of extended-spectrum cephalosporin-resistant (ESC-R) Enterobacterales in healthy pets is a concerning issue. This study aimed to determine the prevalence, genetic background, and potential for interspecies transmission of these bacteria between dogs and humans within the same household (HH) or shelter environment in Romania. Faecal samples (n = 263) collected from healthy dogs (n = 102), their owners (n = 32), as well as dogs (n = 110) and staff (n = 19) from dog shelters, were screened for ESC-R carriage. Clonal relatedness of canine and human Escherichia coli isolates was established using Fourier Transform Infrared Spectroscopy (FTIR), followed by Illumina WGS of selected isolates. The highest prevalence of ESC-R Enterobacterales faecal carriage was identified in staff working at dog shelters (78.9%), followed by dogs from households (44.11%), dog owners (43.7%), and dogs from shelters (27%). FTIR identified 15 clusters of closely related E. coli isolates, including dog and human isolates from the same environment. Co-carriage of ESC-R isolates in both the dog and owner was identified in 12 HHs (37.5%), with two HHs (6%) having both the owner and dog carrying isolates with identical FTIR spectra, phylogroup, resistance genes, and Inc plasmids. Major ExPEC lineages such as ST127, ST10, ST155, and ST88 were detected in human and dog isolates. Our study revealed a high prevalence of faecal ESC-R E. coli carriage in both dogs and humans from Romanian households and shelters, where bidirectional clonal transmission between humans and dogs is likely. Furthermore, we identified ESC-R Enterobacterales co-carriage in people and dogs sharing the same environment using FTIR, demonstrating its value in AMR surveillance for humans and animals.

Machine learning-based typing of Salmonella enterica O-serogroups by the Fourier-Transform Infrared (FTIR) Spectroscopy-based IR Biotyper system

BACKGROUND

Salmonella enterica is among the major burdens for public health at global level. Typing of salmonellae below the species level is fundamental for different purposes, but traditional methods are expensive, technically demanding, and time-consuming, and therefore limited to reference centers. Fourier transform infrared (FTIR) spectroscopy is an alternative method for bacterial typing, successfully applied for classification at different infra-species levels.

AIM

This study aimed to address the challenge of subtyping Salmonella enterica at O-serogroup level by using FTIR spectroscopy. We applied machine learning to develop a novel approach for S. enterica typing, using the FTIR-based IR Biotyper® system (IRBT; Bruker Daltonics GmbH & Co. KG, Germany). We investigated a multicentric collection of isolates, and we compared the novel approach with classical serotyping-based and molecular methods.

METHODS

A total of 958 well characterized Salmonella isolates (25 serogroups, 138 serovars), collected in 11 different centers (in Europe and Japan), from clinical, environmental and food samples were included in this study and analyzed by IRBT. Infrared absorption spectra were acquired from water-ethanol bacterial suspensions, from culture isolates grown on seven different agar media. In the first part of the study, the discriminatory potential of the IRBT system was evaluated by comparison with reference typing method/s. In the second part of the study, the artificial intelligence capabilities of the IRBT software were applied to develop a classifier for Salmonella isolates at serogroup level. Different machine learning algorithms were investigated (artificial neural networks and support vector machine). A subset of 88 pre-characterized isolates (corresponding to 25 serogroups and 53 serovars) were included in the training set. The remaining 870 samples were used as validation set. The classifiers were evaluated in terms of accuracy, error rate and failed classification rate.

RESULTS

The classifier that provided the highest accuracy in the cross-validation was selected to be tested with four external testing sets. Considering all the testing sites, accuracy ranged from 97.0% to 99.2% for non-selective media, and from 94.7% to 96.4% for selective media.

CONCLUSIONS

The IRBT system proved to be a very promising, user-friendly, and cost-effective tool for Salmonella typing at serogroup level. The application of machine learning algorithms proved to enable a novel approach for typing, which relies on automated analysis and result interpretation, and it is therefore free of potential human biases. The system demonstrated a high robustness and adaptability to routine workflows, without the need of highly trained personnel, and proving to be suitable to be applied with isolates grown on different agar media, both selective and unselective. Further tests with currently circulating clinical, food and environmental isolates would be necessary before implementing it as a potentially stand-alone standard method for routine use.

Comparison of fast Fourier transform infrared spectroscopy biotyping with whole genome sequencing-based genotyping in common nosocomial pathogens

Early detection of bacterial transmission and outbreaks in hospitals is important because nosocomial infections can result in health complications and longer hospitalization. Current practice to detect outbreaks uses genotyping methods amplified fragment length polymorphism (AFLP) and whole genome sequencing (WGS), which are not suitable methods for real-time transmission screening of both susceptible and resistant bacteria. The aim was to assess the typing technique Fourier transform infrared (FTIR) spectroscopy as real-time screening method to discriminate large amounts of susceptible and resistant bacteria at strain level when there is no evident outbreak in comparison with the WGS reference. Isolates of past hospital outbreak strains of Acinetobacter baumannii/calcoaceticus complex (n = 25), Escherichia coli (n = 31), Enterococcus faecium (n = 22), Staphylococcus aureus (n = 37) and Pseudomonas aeruginosa (n = 30) were used for validation of FTIR. Subsequently, Enterococcus faecalis (n = 106) and Enterococcus faecium (n = 104) isolates from weekly routine screening samples when no potential outbreak was present were analysed. FTIR showed reproducibility and congruence of cluster composition with WGS for A. baumannii/calcoaceticus complex and E. faecium outbreak isolates. The FTIR results of E. faecalis and E. faecium isolates from routine samples showed reproducibility, but the congruence of cluster composition with WGS was low. For A. baumannii/calcoaceticus complex and E. faecium outbreak isolates, FTIR appears to be a discriminatory typing tool. However, our study shows the discriminatory power is too low to screen real-time for transmission of E. faecium and E. faecalis at patient wards based on isolates acquired in routine surveillance cultures when there is no clear suspicion of an ongoing outbreak.

Evaluation of Fourier Transform Infrared Spectroscopy as a First-Line Typing Tool for the Identification of Extended-Spectrum β-Lactamase-Producing Klebsiella pneumoniae Outbreaks in the Hospital Setting

Early detection of pathogen cross-transmission events and environmental reservoirs is needed to control derived nosocomial outbreaks. Whole-genome sequencing (WGS) is considered the gold standard for outbreak confirmation, but, in most cases, it is time-consuming and has elevated costs. Consequently, the timely incorporation of WGS results to conventional epidemiology (CE) investigations for rapid outbreak detection is scarce. Fourier transform infrared spectroscopy (FTIR) is a rapid technique that establishes similarity among bacteria based on the comparison of infrared light absorption patterns of bacterial polysaccharides and has been used as a typing tool in recent studies. The aim of the present study was to evaluate the performance of the FTIR as a first-line typing tool for the identification of extended-spectrum β-lactamase-producing Klebsiella pneumoniae (ESBL-Kp) outbreaks in the hospital setting in comparison with CE investigations using WGS as the gold standard method. Sixty-three isolates of ESBL-Kp collected from 2018 to 2021 and classified according to CE were typed by both FTIR and WGS. Concordance was measured using the Adjusted Rand index (AR) and the Adjusted Wallace coefficient (AW) for both CE and FTIR clustering considering WGS as the reference method. Both AR and AW were significantly higher for FTIR clustering than CE clustering (0.475 vs. 0.134, p = 0.01, and 0.521 vs. 0.134, p = 0.009, respectively). Accordingly, FTIR inferred more true clustering relationships than CE (38/42 vs. 24/42, p = 0.001). However, a similar proportion of genomic singletons was detected by both FTIR and CE (13/21 vs. 12/21, p = 1). This study demonstrates the utility of the FTIR method as a quick, low-cost, first-line tool for the detection of ESBL-Kp outbreaks, while WGS analyses are being performed for outbreak confirmation and isolate characterization. Thus, clinical microbiology laboratories would benefit from integrating the FTIR method into CE investigations for infection control measures in the hospital setting.

Validation of Fourier Transform Infrared Spectroscopy for Serotyping of Streptococcus pneumoniae

Fourier transform infrared (FT-IR) spectroscopy (IR Biotyper; Bruker) allows highly discriminatory fingerprinting of closely related bacterial strains. In this study, FT-IR spectroscopy-based capsular typing of Streptococcus pneumoniae was validated as a rapid, cost-effective, and medium-throughput alternative to the classical phenotypic techniques. A training set of 233 strains was defined, comprising 34 different serotypes and including all 24 vaccine types (VTs) and 10 non-vaccine types (NVTs). The acquired spectra were used to (i) create a dendrogram where strains clustered together according to their serotypes and (ii) train an artificial neural network (ANN) model to predict unknown pneumococcal serotypes. During validation using 153 additional strains, we reached 98.0% accuracy for determining serotypes represented in the training set. Next, the performance of the IR Biotyper was assessed using 124 strains representing 59 non-training set serotypes. In this setting, 42 of 59 serotypes (71.1%) could be accurately categorized as being non-training set serotypes. Furthermore, it was observed that comparability of spectra was affected by the source of the Columbia medium used to grow the pneumococci and that this complicated the robustness and standardization potential of FT-IR spectroscopy. A rigorous laboratory workflow in combination with specific ANN models that account for environmental noise parameters can be applied to overcome this issue in the near future. The IR Biotyper has the potential to be used as a fast, cost-effective, and accurate phenotypic serotyping tool for S. pneumoniae.

Using an ATR-FTIR Technique to Detect Pathogens in Patients with Urinary Tract Infections: A Pilot Study

Urinary tract infections (UTIs) are a leading hospital-acquired infection. Although timely detection of causative pathogens of UTIs is important, rapid and accurate measures assisting UTI diagnosis and bacterial determination are poorly developed. By reading infrared spectra of urine samples, Fourier-transform infrared spectroscopy (FTIR) may help detect urine compounds, but its role in UTI diagnosis remains uncertain. In this pilot study, we proposed a characterization method in attenuated total reflection (ATR)-FTIR spectra to evaluate urine samples and assessed the correlation between ATR-FTIR patterns, UTI diagnosis, and causative pathogens. We enrolled patients with a catheter-associated UTI in a subacute-care unit and non-UTI controls (total n = 18), and used urine culture to confirm the causative pathogens of the UTIs. In the ATR-FTIR analysis, the spectral variation between the UTI group and non-UTI, as well as that between various pathogens, was found in a range of 1800-900 cm^-1, referring to the presence of specific constituents of the bacterial cell wall. The results indicated that the relative ratios between different area zones of vibration, as well as multivariate analysis, can be used as a clue to discriminate between UTI and non-UTI, as well as different causative pathogens of UTIs. This warrants a further large-scale study to validate the findings of this pilot research.

Use of Fourier-Transform Infrared Spectroscopy With IR Biotyper® System for Legionella pneumophila Serogroups Identification

Legionella spp. are Gram-negative bacteria that inhabit freshwater environments representing a serious risk for human health. Legionella pneumophila (Lp) is the species most frequently responsible for a severe pneumonia known as Legionnaires' disease. Lp consists of 15 serogroups (Sgs), usually identified by monoclonal or polyclonal antibodies. With regard to Lp serogrouping, it is well known that phenotyping methods do not have a sufficiently high discriminating power, while genotypic methods although very effective, are expensive and laborious. Recently, mass spectrometry and infrared spectroscopy have proved to be rapid and successful approaches for the microbial identification and typing. Different biomolecules (e.g., lipopolysaccharides) adsorb infrared radiation originating from a specific microbial fingerprint. The development of a classification system based on the intra-species identification features allows a rapid and reliable typing of strains for diagnostic and epidemiological purposes. The aim of the study was the evaluation of Fourier Transform Infrared Spectroscopy using the IR Biotyper® system (Bruker Daltonik, Germany) for the identification of Lp at the serogroup (Sg) level for diagnostic purposes as well as in outbreak events. A large dataset of Lp isolates (n = 133) and ATCC reference strains representing the 15 Lp serogroups were included. The discriminatory power of the instrument's classifier, was tested by Principal Component Analysis (PCA) and Linear Discriminant Analysis (LDA). All isolates were classified as follows: 12/133 (9.0%) as Lp Sg1 and 115/133 (86.5%) as Lp Sg 2-15 (including both ATCC and environmental Lp serogroup). Moreover, a mis-classification for 2/133 (1.5%) isolates of Lp Sg 2-15 that returned as Lp Sg1 was observed, and 4/133 (3.0%) isolates were not classified. An accuracy of 95.49% and an error rate of 4.51% were calculated. IR Biotyper® is able provide a quick and cost-effective reliable Lp classification with advantages compared with agglutination tests that show ambiguous and unspecific results. Further studies including a larger number of isolates could be useful to implement the classifier obtaining a robust and reliable tool for the routine Lp serogrouping. IR Biotyper® could be a powerful and easy-to-use tool to identify Lp Sgs, especially during cluster/outbreak investigations, to trace the source of the infection and promptly adopt preventive and control strategies.

Evaluation of IR Biotyper for Lactiplantibacillus plantarum Typing and Its Application Potential in Probiotic Preliminary Screening

IR Biotyper (IRBT), which is a spectroscopic system for microorganism typing based on Fourier transform infrared (FTIR) technology, has been used to detect the spread of clones in clinical microbiology laboratories. However, the use of IRBT to detect probiotics has rarely been reported. Herein, we evaluated the discriminatory power of IRBT to type Lactiplantibacillus plantarum isolates at the strain level and explored its application potential in probiotic preliminary selection. Twenty Lactiplantibacillus isolates collected from pickled radishes during successive fermentation were used to test the robustness of IRBT at the strain level. IRBT was then compared with genotyping methods such as whole-genome sequencing (WGS), pulsed-field gel electrophoresis (PFGE), and multilocus sequence typing (MLST) to evaluate its discrimination power. IRBT distributed the 20 isolates into five clusters, with L. argentoratensis isolate C7-83 being the most distant from the other isolates, which belonged to L. plantarum. IRBT showed good reproducibility, although deviation in the discriminative power of IRBT was found at the strain level across laboratories, probably due to technical variance. All examined methods allowed bacterial identification at the strain level, but IRBT had higher discriminatory power than MLST and was comparable to the WGS and PFGE. In the phenotypic comparison study, we observed that the clustering results of probiotic physiological attributes (e.g., sensitivity to acid and bile salts, hydrophobicity of the cell surface, and resistance to antibiotics) were consistent with the typing results of IRBT. Our results indicated that IRBT is a robust tool for L. plantarum strain typing that could improve the efficiency of probiotic identification and preliminary screening, and can potentially be applied in probiotic traceability and quality control.

Fourier Transform Infrared Spectroscopy for Typing Burkholderia cenocepacia ET12 Isolates

The IR Biotyper and matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) using ClinProTools software (MALDI-TOF MS–ClinProTools) are two novel typing methods that rely on the analysis of carbohydrate and peptide residues in intact bacterial cells. These two methods have shown promising results in the rapid and accurate typing of bacteria. In this study, we evaluated these novel typing methods in comparison with genotypic typing for cluster analysis of Burkholderia cenocepacia epidemic strain ET12, isolated from adult cystic fibrosis patients. Sixty-six isolates of B. cenocepacia were used in this study, 35 of which were identified as the ET12 strain and 31 as non-ET12 strains by repetitive-element PCR (rep-PCR). Twelve isolates were used for the creation of typing models using IR Biotyper and MALDI-TOF MS–ClinProTools, and 54 isolates were used for external validation of the typing models. The IR Biotyper linear discriminant analysis (LDA) model had a diagnostic sensitivity of 84.6% for typing the epidemic strain, ET12. At a cutoff of 70%, MALDI-TOF MS–ClinProTools had 87.5% diagnostic sensitivity in detecting the ET12 strain (P = 1.00). Both methods had a diagnostic specificity of ≥80% for detecting the ET12 strain. In conclusion, IR Biotyper and MALDI-TOF MS–ClinProTools offer rapid typing using proteomics and analysis of small cellular molecules with a low running cost. Our pilot study showed suboptimal accuracy of both methods for typing outbreak strains of B. cenocepacia. Extending the spectral region analyzed by the IR Biotyper can improve the accuracy and has the potential of improving the generalizability of this technique for typing other organisms.

IMPORTANCE Respiratory infections due to Burkholderia cenocepacia, particularly the ET12 epidemic strain, are considered sentinel events for persons with cystic fibrosis, as they are often associated with person-to-person transmission and accelerated decline in lung function and early mortality. Current typing methods are generally only available at reference centers, with long turn-around-times, which can affect the identification of outbreaks and critical patient triage. This pilot study aims to add to the growing literature illustrating the potential utility of Fourier transform infrared spectroscopy (FTIR), a novel rapid method, for the successful typing of clinically significant bacteria. In this study, we evaluated its utility to discriminate between the ET12 clone and non-ET12 isolates of B. cenocepacia and compared it to proteomics cluster analysis using MALDI-TOF MS and ClinProTools software. Both methods had encouraging but suboptimal accuracy (≥85% sensitivity and ≥83% specificity), which will likely be improved by extending the spectral region analyzed by the IR Biotyper with updated software.

Nosocomial outbreak of monoclonal VIM carbapenemase-producing Enterobacter cloacae complex in an intensive care unit during the COVID-19 pandemic: an integrated approach

Background

An outbreak of VIM carbapenemase-expressing Enterobacter cloacae complex occurred between March and October 2020 in an intensive care unit (ICU) of a tertiary care and teaching hospital in France. At the same time, the hospital was facing the COVID-19 first wave.

Aim

To describe the management of an outbreak caused by a VIM-producing Enterobacter cloacae complex strain during the COVID-19 pandemic in an ICU and to show the importance of an integrated approach.

Methods

A multi-focal investigation was conducted including descriptive and molecular epidemiology, environmental screening, and assessment of infection prevention and control measures.

Findings

A total of 14 cases were identified in this outbreak with a high attributable mortality rate (85.7%). The outbreak management was coordinated by a crisis cell, and involved the implementation of multi-disciplinary actions such as: enhanced hygiene measures, microbiological and molecular analysis of patients and environmental E. cloacae complex strains, and simulation-based teaching. All 23 E. cloacae complex strains isolated from patients and environment samples belonged to multi-locus sequence type ST78 and carried bla-_VIM4 gene. Using Fourier transform infrared spectroscopy, all but two isolates were also found to belong to a single cluster. Although the source of this outbreak could not be pinpointed, the spread of the strain was controlled thanks to this multi-focal approach and multi-disciplinary implementation.

Conclusion

This investigation highlighted the usefulness of Fourier transform infra-red spectroscopy in the rapid typing of outbreak strains as well as the importance of an integrated approach to successfully fight against multidrug-resistant micro-organism dissemination and healthcare-associated infections.

Application of Fourier transform infrared spectroscopy for real-time typing of Acinetobacter baumannii outbreak in intensive care unit

Aim: Acinetobacter baumannii is a pathogen of serious concern, often exhibiting multiple antibiotic resistance, frequently associated with hospital outbreaks in intensive care units. A prompt detection and tracking of these isolates is crucial. Reference methods for typing (pulsed-field gel electrophoresis, whole-genome sequencing) are accurate, but expensive and time-consuming, therefore limited to retrospective analysis. Materials & methods: In this study, the application of the FTIR-based IR Biotyper^® (IRBT) to track and monitor in real-time the spread of a multidrug-resistant A. baumannii outbreak was investigated. The index case and the multidrug-resistant A. baumannii isolates collected in the following 3 weeks were investigated. Results: IR Biotyper^® clustering results were fully confirmed by pulsed-field gel electrophoresis results. Conclusions: IR Biotyper represent a promising tool for real-time hospital hygiene, enabling a prompt and reliable typing.

Detecting antimicrobial resistance in Escherichia coli using benchtop attenuated total reflectance-Fourier transform infrared spectroscopy and machine learning

The widespread dissemination of resistance to third-generation cephalosporins in the Enterobacterales through the production of extended-spectrum β-lactamase (ESBL) is considered a critical global crisis requiring urgent attention of clinicians and scientists alike. Rapid diagnostic methods that can identify microbial resistance profiles closer to the point of care are crucial to minimize the overuse of antimicrobial agents and improve patient outcomes. Although Fourier transform infrared (FTIR) microscopy has shown promise in distinguishing between bacterial species, the high cost and technical requirements of the IR microscope may limit broad clinical use. To address the practical needs of a clinical microbiology laboratory, here, we examine the ability of a lower cost portable benchtop attenuated total reflectance (ATR)-FTIR spectrometer to achieve antimicrobial resistance detection, using a simple, clinically aligned sampling protocol. The technical reproducibility was confirmed through multi-day analysis of an Escherichia coli type strain, which serves as quality control. We generated a dataset of 100 E. coli clinical bloodstream isolates with 63 ceftriaxone resistant bla_CTX-M ESBL gene variant strains and developed a classifier for bla_CTX-M genotype detection. After assessing 35 machine learning methods using the training set (n = 71), four methods were further optimised, and the best performing method was evaluated using the held-out testing set (n = 29). A tuned support vector machine model with a polynomial kernel, using the 700-1500 cm^-1 range achieved a sensitivity of 89.2%, and specificity of 66.7% for detecting bla_CTX-M in independent testing, approaching the reported performance of FTIR microscopy. With further algorithm improvement, these data suggest the potential deployment of a portable FTIR spectrometer as a rapid antimicrobial susceptibility prediction platform to enable the efficient use of antimicrobials.

Bifidobacteria Strain Typing by Fourier Transform Infrared Spectroscopy

Fourier transform infrared (FTIR) spectroscopy, a technology traditionally used in chemistry to determine the molecular composition of a wide range of sample types, has gained growing interest in microbial typing. It is based on the different vibrational modes of the covalent bonds between atoms of a given sample, as bacterial cells, induced by the absorption of infrared radiation. This technique has been largely used for the study of pathogenic species, especially in the clinical field, and has been proposed also for the typing at different subspecies levels. The high throughput, speed, low cost, and simplicity make FTIR spectroscopy an attractive technique also for industrial applications, in particular, for probiotics. The aim of this study was to compare FTIR spectroscopy with established genotyping methods, pulsed-field gel electrophoresis (PFGE), whole-genome sequencing (WGS), and multilocus sequence typing (MLST), in order to highlight the FTIR spectroscopy potential discriminatory power at strain level. Our study focused on bifidobacteria, an important group of intestinal commensals generally recognized as probiotics. For their properties in promoting and maintaining health, bifidobacteria are largely marketed by the pharmaceutical, food, and dairy industries. Strains belonging to Bifidobacterium longum subsp. longum and Bifidobacterium animalis subsp. lactis were taken into consideration together with some additional type strains. For B. longum subsp. longum, it was possible to discriminate the strains with all the methods used. Although two isolates were shown to be strictly phylogenetically related, constituting a unique cluster, based on PFGE, WGS, and MLST, no clustering was observed with FTIR. For B. animalis subsp. lactis group, PFGE, WGS, and MLST were non-discriminatory, and only one strain was easily distinguished. On the other hand, FTIR discriminated all the isolates one by one, and no clustering was observed. According to these results, FTIR analysis is not only equivalent to PFGE, WGS, and MLST, but also for some strains, in particular, for B. animalis subsp. lactis group, more informative, being able to differentiate strains not discernible with the other two methods based on phenotypic variations likely deriving from certain genetic changes. Fourier transform infrared spectroscopy has highlighted the possibility of using the cell surface as a kind of barcode making tracing strains possible, representing an important aspect in probiotic applications. Furthermore, this work constitutes the first investigation on bifidobacterial strain typing using FTIR spectroscopy.

Behind Every Great Infection Prevention Program is a Great Microbiology Laboratory: Key Components and Strategies for an Effective Partnership

A great clinical microbiology laboratory supporting a great infection prevention program requires focusing on the following services: rapid and accurate identification of pathogens associated with health care-associated infections; asymptomatic surveillance for health care-acquired pathogens before infections arise; routine use of broad and flexible antimicrobial susceptibility testing to direct optimal therapy; implementation of epidemiologic tracking tools to identify outbreaks; development of clear result communication with interpretative comments for clinicians. These goals are best realized in a collaborative relationship with the infection prevention program so that both can benefit from the shared priorities of providing the best patient care.

Efflux Pump Overexpression Profiling in Acinetobacter baumannii and Study of New 1-(1-Naphthylmethyl)-Piperazine Analogs as Potential Efflux Inhibitors

Overexpression of efflux pumps extruding antibiotics currently used for the treatment of Acinetobacter baumannii infections has been described as an important mechanism causing antibiotic resistance. The first aim of this work was to phenotypically evaluate the overexpression of efflux pumps on a collection of 124 ciprofloxacin-resistant A. baumannii strains. An overexpression of genes encoding one or more efflux pumps was obtained for 19 out of the 34 strains with a positive phenotypic efflux (56%). The most frequent genes overexpressed were those belonging to the RND family, with adeJ being the most prevalent (50%). Interestingly, efflux pump genes coding for MATE and MFS families were also overexpressed quite frequently: abeM (32%) and abaQ (26%). The second aim was to synthesize 1-(1-naphthylmethyl)-piperazine analogs as potential new efflux pump inhibitors and biologically evaluate them against strains with a positive phenotypic efflux. Quinoline and pyridine analogs were found to be more effective than their parent compound, 1-(1-naphthyl methyl)-piperazine. Stereochemistry also played an important part in the inhibitory activity, as quinoline derivative (R)-3a was identified as being the most effective and less cytotoxic. Its inhibitory activity was also correlated with the number of efflux pumps expressed by a strain. The results obtained in this work suggest that quinoline analogs of 1-(1-naphthylmethyl)-piperazine are promising leads in the development of new anti-Acinetobacter baumannii therapeutic alternatives in combination with antibiotics for which an efflux-mediated resistance is suspected.

From farm to fork: Colistin voluntary withdrawal in Portuguese farms reflected in decreasing occurrence of mcr-1-carrying Enterobacteriaceae from chicken meat

Expansion of mcr-carrying Enterobacteriaceae (MCR-E) is a well-recognized problem affecting animals, humans and the environment. Ongoing global control actions involve colistin restrictions among food-animal production, but their impact on poultry-derived products is largely unknown, justifying comprehensive farm-to-fork studies. Occurrence of MCR-E among 53 chicken-meat batches supplied from 29 Portuguese farms shortly after colistin withdrawal was evaluated. Strains (FT-IR/MLST/WGS), mcr plasmids and their adaptive features were characterized by cultural, molecular and genomic approaches. We found high rates of chicken-meat batches (80%-100% - 4 months; 12% - the last month) with multiple MDR + mcr-1-carrying Escherichia coli (Ec-including ST117 and ST648-Cplx) and Klebsiella pneumoniae (Kp-ST147-O5:K35) clones, some of them persisting over time. The mcr-1 was located in the chromosome (Ec-ST297/16-farms) or dispersed IncX4 (Ec-ST602/ST6469/5-farms), IncHI2-ST2/ST4 (Ec-ST533/ST6469/5 farms and Kp-ST147/6-farms) or IncI2 (Ec-ST117/1-farm) plasmids. WGS revealed high load and diversity in virulence, antibiotic resistance and metal tolerance genes. This study supports colistin withdrawal potential efficacy in poultry production and highlights both poultry-production chain as a source of mcr-1 and the risk of foodborne transmission to poultry-meat consumers. Finally, in the antibiotic reduction/replacement context, other potential co-selective pressures (e.g., metals-Cu as feed additives) need to be further understood to guide concerted, effective and durable actions under 'One Health' perspective.

Application and Perspectives of MALDI-TOF Mass Spectrometry in Clinical Microbiology Laboratories

Early diagnosis of severe infections requires of a rapid and reliable diagnosis to initiate appropriate treatment, while avoiding unnecessary antimicrobial use and reducing associated morbidities and healthcare costs. It is a fact that conventional methods usually require more than 24–48 h to culture and profile bacterial species. Mass spectrometry (MS) is an analytical technique that has emerged as a powerful tool in clinical microbiology for identifying peptides and proteins, which makes it a promising tool for microbial identification. Matrix assisted laser desorption ionization–time of flight MS (MALDI–TOF MS) offers a cost- and time-effective alternative to conventional methods, such as bacterial culture and even 16S rRNA gene sequencing, for identifying viruses, bacteria and fungi and detecting virulence factors and mechanisms of resistance. This review provides an overview of the potential applications and perspectives of MS in clinical microbiology laboratories and proposes its use as a first-line method for microbial identification and diagnosis.

Evaluation of the IR Biotyper for Klebsiella pneumoniae typing and its potentials in hospital hygiene management

Klebsiella pneumoniae has emerged as one of the most important pathogens that frequently encounter in community-acquired or hospital-acquired infections. Timely epidemiological surveillance could greatly facilitate infection control of K. pneumoniae and many deadly pathogens alike. In this study, we evaluated the performance of the IR Biotyper, a Fourier transform infrared (FTIR) spectroscopy system for K. pneumoniae isolates typing through (i) optimizing the culture scheme and defining the cutoff value (COV) range and (ii) comparing with commonly used typing tools such as multi-locus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing (WGS). We found that a non-selective and non-chromogenic medium with 24 ± 2 h incubation gives the best discriminatory power for the IR Biotyper (IRBT). COV evaluation indicated that the IRBT is a robust typing method with good reproducibility. Besides, we observed that the modified H2 O-EtOH suspensions preparation method could enhance the quality of the spectrum, especially for those hypermucoviscous strains. For the method comparison study, our data demonstrated that FTIR spectroscopy could accurately cluster K. pneumoniae strains. The typing results of the IRBT were almost entirely in concordance with those from PFGE and WGS. Together with the advantages such as low costs and short turnaround time (less than 3h), the IRBT is a promising tool for strain typing that could make real-time outbreak investigation a reality.

Infrared Spectroscopy of Blood

The magnitude of infectious diseases in the twenty-first century created an urgent need for point-of-care diagnostics. Critical shortages in reagents and testing kits have had a large impact on the ability to test patients with a suspected parasitic, bacteria, fungal, and viral infections. New point-of-care tests need to be highly sensitive, specific, and easy to use and provide results in rapid time. Infrared spectroscopy, coupled to multivariate and machine learning algorithms, has the potential to meet this unmet demand requiring minimal sample preparation to detect both pathogenic infectious agents and chronic disease markers in blood. This focal point article will highlight the application of Fourier transform infrared spectroscopy to detect disease markers in blood focusing principally on parasites, bacteria, viruses, cancer markers, and important analytes indicative of disease. Methodologies and state-of-the-art approaches will be reported and potential confounding variables in blood analysis identified. The article provides an up to date review of the literature on blood diagnosis using infrared spectroscopy highlighting the recent advances in this burgeoning field.

Classification of Salmonella enterica of the (Para-)Typhoid Fever Group by Fourier-Transform Infrared (FTIR) Spectroscopy

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.

Rapid detection and discrimination of food-related bacteria using IR-microspectroscopy in combination with multivariate statistical analysis

Spoilage microorganisms are of great concern for the food industry. While traditional culturing methods for spoilage microorganism detection are laborious and time-consuming, the development of early detection methods has gained a lot of interest in the last decades. In this work a rapid and non-destructive detection and discrimination method of eight important food-related microorganisms (Bacillus subtilis DSM 10, Bacillus coagulans DSM 1, Escherichia coli K12 DSM 498, Escherichia coli TOP10, Micrococcus luteus DSM 20030, Pseudomonas fluorescens DSM 4358, Pseudomonas fluorescens DSM 50090 and Bacillus thuringiensis israelensis DSM 5724) based on IR-microspectroscopy and chemometric evaluation was developed. Sampling was carried out directly from the surface to be tested, without the need for sample preparation such as purification, singulation, centrifugation and washing steps, as an efficient and inexpensive blotting technique using the sample carrier. IR spectra were recorded directly after the blotting from the surface of the sample carrier without any further pretreatments. A combination of data preprocessing, principal component analysis and canonical discriminant analysis was found to be suitable. The spectral range from 400 to 1750 cm^-1 of the IR-microspectrosopic data was determined to be highly sensitive to the time after incubation and sample thickness, resulting in a high standard deviation. Therefore, this area was excluded from the evaluation in favor of the meaningfulness of the chemometric model and, thus, only the spectral range of specific -CH/-NH/-OH excitations (2815-3680 cm^-1) was used for model development. This study showed that the differentiation of food-related microorganisms on genera, species and strain level is feasible. A leave-one-out cross-validation of the training data set showed 100% accuracy. The classification of the ungrouped test data showed with an accuracy of 94.5% that, despite the large biological variance of the analytes such as different times after incubation and the presented sampling (including its variance), a robust and meaningful model for the differentiation of food-related bacteria could be developed by data preprocessing and subsequent chemometric evaluation.