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

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.We thank the Germans Trias i Pujol Research Institute (IGTP) Translational Genomics Core Facility and staff for their contribution to this publication. We also thank CERCA Programme/Government of Catalonia for their support to the IGTP.S

Transmissibility, hospitalization, and intensive care admissions due to omicron compared to delta variants of SARS-CoV-2 in Catalonia: A cohort study and ecological analysis

The transmissibility of omicron using variant screening data from primary care practices (PCP) and hospital admissions. In addition, we used this data from PCP to establish the two periods when delta and omicron were, respectively, dominant (above 95% of cases). After that, we performed a population-based cohort analysis to calculate the rates of hospital and intensive care unit (ICU) admissions for both periods and to estimate reduction in severity. Rate ratios (RR) and 95% confidence intervals (95% CI) were calculated and stratified by age and vaccination status. In a second analysis, the differential substitution model in primary care vs. hospitals allowed us to obtain a population-level average change in severity.We have included 48,874 cases during the delta period and 560,658 during the omicron period. During the delta period, on average, 3.8% of the detected cases required hospitalization for COVID-19. This percentage dropped to 0.9% with omicron [RR of 0.46 (95% CI: 0.43 to 0.49)]. For ICU admissions, it dropped from 0.8 to 0.1% [RR 0.25 (95% CI: 0.21 to 0.28)]. The proportion of cases hospitalized or admitted to ICU was lower in the vaccinated groups, independently of the variant. Omicron was associated with a reduction in risk of admission to hospital and ICU in all age and vaccination status strata. The differential substitution models showed an average RR between 0.19 and 0.50.Both independent methods consistently show an important decrease in severity for omicron relative to delta. The systematic reduction happens regardless of age. The severity is also reduced for non-vaccinated and vaccinated groups, but it remains always higher in the non-vaccinated population. This suggests an overall reduction in severity, which could be intrinsic to the omicron variant. The fact is that the RR in ICU admission is systematically smaller than in hospitalization points in the same direction.MC received funding from la Caixa Foundation ID 100010434, under agreement LCF/PR/GN17/50300003. MC, CP, and SA received funding from Ministerio de Ciencia, Innovación y Universidades and FEDER, with the project PGC2018-095456- B-I00.Objectius de Desenvolupament Sostenible::3 - Salut i BenestarPostprint (published version

Changes in heart rate variability of flight phobics during a paced breathing task and exposure to fearful stimuli

The aim of this experiment was to explore changes in the vagally mediated heart rate variability (HRV) of flight phobics during exposure to feared stimuli. A paced breathing task was included to control for respiration effects. Sixty-one flight phobics (40 women) with a mean age of 39.07 years (SD = 11.24) participated in the study. The root mean of the squared successive interbeat intervals differences (RMSSD) was taken as the time domain measure of HRV. High frequency (HF: 0.15-0.4 Hz) and low frequency (LF: 0.04-0.15 Hz) band power was calculated on the ECG recordings obtained during free breathing baseline (BL), paced breathing (PB), and exposure (E) to fearful stimuli. Heart rate unexpectedly increased from BL to PB, and decreased from PB to E, while no differences were found between BL and E. No changes in the RMSSD were seen across conditions. HF band power increased, as expected, from BL to PB, and a significant decrease was found from PB to E. LF band power, as well as the LF/HF ratio, increased from BL to E. Discussion focuses on (a) the role of the parasympathetic and the sympathetic nervous systems in fear-related situations, and (b) the effects of paced breathing in preparing the system to cope with threatEn este estudio se analizan los cambios en la variabilidad de la tasa cardíaca (HRV) relacionada con el sistema vagal en sujetos fóbicos durante la exposición a estímulos temidos. Se ha introducido una tarea de respiración pautada para controlar los efectos de la misma en la medida de la HRV. Han participado en el estudio 61 pacientes con fobia a volar (40 mujeres) con una edad media de 39,07 años (SD =11,24). Como medida de la HRV en el dominio del tiempo se ha tomado la RMSSD (media cuadrática de las diferencias de los intervalos RR sucesivos). Se ha calculado la potencia espectral en las bandas de alta (HF: 0.15-0.4 Hz) y de baja frecuencia (LF: 0.04-0.15 Hz) sobre los registros de ECG obtenidos durante una línea base sin respiración controlada (BL), una fase de respiración pautada (PB) y la exposición (E) a estímulos temidos. La tasa cardíaca aumentó de forma inesperada de BL a PB, disminuyó de PB a E, y no se obtuvieron diferencias entre BL y E. No se observaron cambios en RMSSD entre las tres condiciones. La potencia espectral de HF aumentó, como se esperaba, de BL a PB, y disminuyó de forma significativa de PB a E. La potencia espectral de LF, así como la relación LF/HF, aumentó de BL a E. La discusión se centra en (a) el papel de los sistemas simpático y parasimpático en las situaciones de miedo, y (b) los efectos de la respiración pautada en la preparación del sistema para afrontar estímulos temido

Monitoring SARS-CoV-2 variant transitions using differences in diagnostic cycle threshold values of target genes

Monitoring the emergence of new SARS-CoV-2 variants is important to detect potential risks of increased transmission or disease severity. We investigated the identification of SARS-CoV-2 variants from real-time reverse transcriptase polymerase chain reaction (RT-PCR) routine diagnostics data. Cycle threshold (Ct) values of positive samples were collected from April 2021 to January 2022 in the Northern Metropolitan Area of Barcelona (n = 15,254). Viral lineage identification from whole genome sequencing (WGS) was available for 4618 (30.3%) of these samples. Pairwise differences in the Ct values between gene targets (ΔCt) were analyzed for variants of concern or interest circulating in our area. A specific delay in the Ct of the N-gene compared to the RdRp-gene (ΔCt) was observed for Alpha, Delta, Eta and Omicron. Temporal differences in ΔCt correlated with the dynamics of viral replacement of Alpha by Delta and of Delta by Omicron according to WGS results. Using ΔCt, prediction of new variants of concern at early stages of circulation was achieved with high sensitivity and specificity (91.1% and 97.8% for Delta; 98.5% and 90.8% for Omicron). Thus, tracking population-wide trends in ΔCt values obtained from routine diagnostics testing in combination with WGS could be useful for real-time management and response to local epidemics