Bacterial discrimination by Fourier transform infrared spectroscopy, MALDI-mass spectrometry and whole-genome sequencing

Aim: Proof-of-concept study, highlighting the clinical diagnostic ability of FT-IR compared with MALDI-TOF MS, combined with WGS. Materials & methods: 104 pathogenic isolates of Neisseria meningitidis, Streptococcus pneumoniae, Streptococcus pyogenes and Staphylococcus aureus were analyzed. Results: Overall prediction accuracy was 99.6% in FT-IR and 95.8% in MALDI-TOF-MS. Analysis of N. meningitidis serogroups was superior in FT-IR compared with MALDI-TOF-MS. Phylogenetic relationship of S. pyogenes was similar by FT-IR and WGS, but not S. aureus or S. pneumoniae. Clinical severity was associated with the zinc ABC transporter and DNA repair genes in S. pneumoniae and cell wall proteins (biofilm formation, antibiotic and complement permeability) in S. aureus via WGS. Conclusion: FT-IR warrants further clinical evaluation as a promising diagnostic tool

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

Accuracy of a Modified qSOFA Score for Predicting Critical Care Admission in Febrile Children

BACKGROUND AND OBJECTIVES: The identification of life-threatening infection in febrile children presenting to the emergency department (ED) remains difficult. The quick Sequential Organ Failure Assessment (qSOFA) was only derived for adult populations, implying an urgent need for pediatric scores. We developed and validated a novel, adapted qSOFA score (Liverpool quick Sequential Organ Failure Assessment [LqSOFA]) and compared its performance with qSOFA, Pediatric Early Warning Score (PEWS), and National Institute for Health and Care Excellence (NICE) high-risk criteria in predicting critical care (CC) admission in febrile children presenting to the ED. METHODS: The LqSOFA (range, 0–4) incorporates age-adjusted heart rate, respiratory rate, capillary refill, and consciousness level on the Alert, Voice, Pain, Unresponsive scale. The primary outcome was CC admission within 48 hours of ED presentation, and the secondary outcome was sepsis-related mortality. LqSOFA, qSOFA, PEWS, and NICE high-risk criteria scores were calculated, and performance characteristics, including area under the receiver operating characteristic curve, were calculated for each score. RESULTS: In the initial (n = 1121) cohort, 47 CC admissions (4.2%) occurred, and in the validation (n = 12 241) cohort, 135 CC admissions (1.1%) occurred, and there were 5 sepsis-related deaths. In the validation cohort, LqSOFA predicted CC admission with an area under the receiver operating characteristic curve of 0.81 (95% confidence interval [CI], 0.76 to 0.86), versus qSOFA (0.66; 95% CI, 0.60 to 0.71), PEWS (0.93; 95% CI, 0.90 to 0.95), and NICE high-risk criteria (0.81; 95% CI, 0.78 to 0.85). For predicting CC admission, the LqSOFA outperformed the qSOFA, with a net reclassification index of 10.4% (95% CI, 1.0% to 19.9%). CONCLUSIONS: In this large study, we demonstrate improved performance of the LqSOFA over qSOFA in identifying febrile children at risk for CC admission and sepsis-related mortality. Further validation is required in other settings

Maternal Vitamin D Status in Type 1 Diabetic Pregnancy: Impact on Neonatal Vitamin D Status and Association with Maternal Glycaemic Control

*<p>Values are expressed as means±SD.</p><p>Continuous variables were compared at baseline using independent student’s <i>t</i> test; categorical variables were compared using Chi squared test.</p

Simultaneous Raman and infrared spectroscopy: a novel combination for studying bacterial infections at the single cell level

Sepsis is a life-threatening clinical condition responsible for approximately 11 million deaths worldwide. Rapid and accurate identification of pathogenic bacteria and its antimicrobial susceptibility play a critical role in reducing the morbidity and mortality rates related to sepsis. Raman and infrared spectroscopies have great potential to be used as diagnostic tools for rapid and culture-free detection of bacterial infections. Despite numerous reports using both methods to analyse bacterial samples, there is to date no study collecting both Raman and infrared signatures from clinical samples simultaneously due to instrument incompatibilities. Here, we report for the first time the use of an emerging technology that provides infrared signatures via optical photothermal infrared (O-PTIR) spectroscopy and Raman spectra simultaneously. We use this approach to analyse 12 bacterial clinical isolates including six isolates of Gram-negative and six Gram-positive bacteria commonly associated with bloodstream infection in humans. To benchmark the single cell spectra obtained by O-PTIR spectroscopy, infrared signatures were also collected from bulk samples via both FTIR and O-PTIR spectroscopies. Our findings showed significant similarity and high reproducibility in the infrared signatures obtained by all three approaches, including similar discrimination patterns when subjected to clustering algorithms. Principal component analysis (PCA) showed that O-PTIR and Raman data acquired simultaneously from bulk bacterial isolates displayed different clustering patterns due to the ability of both methods to probe metabolites produced by bacteria. By contrast, signatures of microbial pigments were identified in Raman spectra, providing complementary and orthogonal information compared to infrared, which may be advantageous as it has been demonstrated that certain pigments play an important role in bacterial virulence. We found that infrared spectroscopy showed higher sensitivity than Raman for the analysis of individual cells. Despite the different patterns obtained by using Raman and infrared spectral data as input for clustering algorithms, our findings showed high data reproducibility in both approaches as the biological replicates from each bacterial strain clustered together. Overall, we show that Raman and infrared spectroscopy offer both advantages and disadvantages and, therefore, having both techniques combined in one single technology is a powerful tool with promising applications in clinical microbiology

Bacterial discrimination by Fourier transform infrared spectroscopy, MALDI-mass spectrometry and whole-genome sequencing.

Aim: Proof-of-concept study, highlighting the clinical diagnostic ability of FT-IR compared with MALDI-TOF MS, combined with WGS. Materials & methods: 104 pathogenic isolates of Neisseria meningitidis, Streptococcus pneumoniae, Streptococcus pyogenes and Staphylococcus aureus were analyzed. Results: Overall prediction accuracy was 99.6% in FT-IR and 95.8% in MALDI-TOF-MS. Analysis of N. meningitidis serogroups was superior in FT-IR compared with MALDI-TOF-MS. Phylogenetic relationship of S. pyogenes was similar by FT-IR and WGS, but not S. aureus or S. pneumoniae. Clinical severity was associated with the zinc ABC transporter and DNA repair genes in S. pneumoniae and cell wall proteins (biofilm formation, antibiotic and complement permeability) in S. aureus via WGS. Conclusion: FT-IR warrants further clinical evaluation as a promising diagnostic tool

Impact of maternal vitamin D status and BMI on neonatal vitamin D levels.

<p><b>(A) Within season comparisons of mean 25OHD levels (nmol/L) in final pregnancy (wk 31–38), post-delivery and cord blood samples from T1DM women and their neonates (n = 29)</b> Error bars indicate S.D. Comparisons were performed using paired samples <i>t</i> test: * = vs. final pregnancy sample; <i>p</i><0.05; ? = vs. post-delivery sample; <i>p</i><0.05. <b>(B) Comparison of mean 25OHD levels (nmol/L) between normal weight (BMI at booking <25 kg/m²; n = 22–24) and obese (BMI at booking >30 kg/m²; n = 16–17) T1DM women in the final pregnancy sample (wk 31–38) and neonatal cord blood.</b> Error bars indicate S.D. Comparisons were performed using independent student’s t-test: *<i>p</i> = 0.026.</p

Vitamin D deficiency and insufficiency of pregnant women and neonates, split by maternal diabetes, using various cut-off levels.

<p>Data are cumulative n and cumulative %.</p