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Importance: The increased feasibility of whole-genome sequencing has generated significant interest in using such molecular diagnostic approaches to characterize difficult-to-treat, antimicrobial-resistant (AMR) infections. Nevertheless, there are current limitations in the accurate prediction of AMR phenotypes based on existing AMR gene database approaches, which primarily correlate a phenotype with the presence/absence of a single AMR gene. Our study utilized a large cohort of cephalosporin-susceptible Escherichia coli bacteremia samples to determine how increasing the dosage of narrow-spectrum β-lactamase-encoding genes in conjunction with other diverse β-lactam/β-lactamase inhibitor (BL/BLI) genetic determinants contributes to progressively more severe BL/BLI phenotypes. We were able to characterize the complexity of the genetic mechanisms underlying progressive BL/BLI resistance including the critical role of β-lactamase encoding gene amplification. For the diverse array of AMR phenotypes with complex mechanisms involving multiple genomic factors, our study provides an example of how composite risk scores may improve understanding of AMR genotype/phenotype correlations., Competing Interests: The authors declare no conflict of interest.

Extended-spectrum cephalosporin-resistant Escherichia coli (ESC-R- Ec ) is an urgent public health threat with sequence type clonal complex 131 (STc131), phylogroup B2 strains being particularly concerning as the dominant cause of ESC-R- Ec infections. To address the paucity of recent ESC-R- Ec molecular epidemiology data in the United States, we used whole-genome sequencing (WGS) to fully characterize a large cohort of invasive ESC-R- Ec at a tertiary care cancer center in Houston, Texas, collected from 2016 to 2020. During the study time frame, there were 1,154 index E. coli bloodstream infections (BSIs) of which 389 (33.7%) were ESC-R- Ec . Using time series analyses, we identified a temporal dynamic of ESC-R- Ec distinct from ESC-susceptible E. coli (ESC-S- Ec ), with cases peaking in the last 6 months of the calendar year. WGS of 297 ESC-R- Ec strains revealed that while STc131 strains accounted for ~45% of total BSIs, the proportion of STc131 strains remained stable across the study time frame with infection peaks driven by genetically heterogeneous ESC-R- Ec clonal complexes. bla CTX-M variants accounted for most β-lactamases conferring the ESC-R phenotype (89%; 220/248 index ESC-R -Ec ), and amplification of bla CTX-M genes was widely detected in ESC-R- Ec strains, particularly in carbapenem non-susceptible, recurrent BSI strains. Bla CTX-M-55 was significantly enriched within phylogroup A strains, and we identified bla CTX-M-55 plasmid-to-chromosome transmission occurring across non-B2 strains. Our data provide important information regarding the current molecular epidemiology of invasive ESC-R- Ec infections at a large tertiary care cancer center and provide novel insights into the genetic basis of observed temporal variability for these clinically important pathogens. IMPORTANCE Given that E. coli is the leading cause of worldwide ESC-R Enterobacterales infections, we sought to assess the current molecular epidemiology of ESC-R- Ec using a WGS analysis of many BSIs over a 5-year period. We identified fluctuating temporal dynamics of ESC-R- Ec infections, which have also recently been identified in other geographical regions such as Israel. Our WGS data allowed us to visualize the stable nature of STc131 over the study period and demonstrate a limited but genetically diverse group of ESC-R- Ec clonal complexes are detected during infection peaks. Additionally, we provide a widespread assessment of β-lactamase gene copy number in ESC-R- Ec infections and delineate mechanisms by which such amplifications are achieved in a diverse array of ESC-R- Ec strains. These data suggest that serious ESC-R- Ec infections are driven by a diverse array of strains in our cohort and impacted by environmental factors suggesting that community-based monitoring could inform novel preventative measures., Competing Interests: The authors declare no conflict of interest.

Streptococcus pyogenes causes 700 million human infections annually worldwide, yet, despite a century of intensive effort, there is no licensed vaccine against this bacterium. Although a number of large-scale genomic studies of bacterial pathogens have been published, the relationships among the genome, transcriptome, and virulence in large bacterial populations remain poorly understood. We sequenced the genomes of 2,101 emm28 S. pyogenes invasive strains, from which we selected 492 phylogenetically diverse strains for transcriptome analysis and 50 strains for virulence assessment. Data integration provided a novel understanding of the virulence mechanisms of this model organism. Genome-wide association study, expression quantitative trait loci analysis, machine learning, and isogenic mutant strains identified and confirmed a one-nucleotide indel in an intergenic region that significantly alters global transcript profiles and ultimately virulence. The integrative strategy that we used is generally applicable to any microbe and may lead to new therapeutics for many human pathogens.

The genetic defect of coagulation factor V known as factor V Leiden produces a resistance to degradation by activated protein C (APC) and increases the risk of venous thromboembolism. The data on arterial thrombosis associated with APC resistance are still not clearly defined. We conducted a study in patients presenting with acute myocardial infarction (MI) to assess whether factor V Leiden increases the risk of arterial thrombosis. We studied 109 patients who had a diagnosis of acute MI (69 males and 40 females, aged 25-91 years), and 112 controls. The study population was identified by characteristic ECG changes and elevation of serum CK-MB, whereas the control subjects were anonymous healthy blood donors with no known history of coronary artery disease. Blood samples from the patients and controls were analyzed for the factor V Leiden mutation by DNA analysis, using the polymerase chain reaction. Heterozygous factor V Leiden mutation was found in 9 of 109 (8%) MI patients and 5 of 112 (4%) control subjects (P =.42). In conclusion, this study shows no evidence of an association between factor V Leiden and acute MI.

A variable-duration notched-noise experiment was conducted in a noise context. Broadband noise preceded and followed a tone and notched noise of similar duration. Thresholds were measured at four durations (10, 30, 100, and 300 ms), two center frequencies (0.6, 2.0 kHz), and five relative notch widths (0.0, 0.1, 0.2, 0.4, 0.8). At 0.6 kHz, 10-ms thresholds decrease 6 dB across notch widths, while 300-ms thresholds decrease over 35 dB. These trends are similar but less pronounced at 2 kHz. In a second experiment, the short-duration notched noise was replaced with a flat noise which provided an equivalent amount of simultaneous masking and thresholds dropped by as much as 20 dB. A simple combination of simultaneous and nonsimultaneous masking is unable to predict these results. Instead, it appears that the elevated thresholds at short durations are dependent on the spectral shape of the simultaneous masker.

A model for predicting the masked thresholds of the voiceless plosive bursts /k,t,p/ in background noise is proposed. Because plosive bursts are brief, are generated by a noise source, and have different spectral characteristics, the modeling approach accounts for duration, center frequency, and signal bandwidth. Noise-in-noise masking experiments are conducted using a broadband masker and bandpass noise signals of varying bandwidth (100-5483 Hz), duration (10-300 ms), and center frequency (0.4-4 kHz). Data from these experiments are used to parametrize an auditory filter model in which the effective bandwidth and the signal-to-noise ratio at threshold for each filter are duration dependent. The duration-dependent filter model is then used to predict the thresholds of synthetic and naturally spoken plosive bursts in background noise. Finally, results from pilot notched-noise experiments are presented which support duration-dependent frequency selectivity.