Genomic cluster formation among invasive group A streptococcal infections in the USA: a whole-genome sequencing and population-based surveillance study.

Background: Clusters of invasive group A streptococcal (iGAS) infection, linked to genomically closely related group A streptococcal (GAS) isolates (referred to as genomic clusters), pose public health threats, and are increasingly identified through whole-genome sequencing (WGS) analysis. In this study, we aimed to assess the risk of genomic cluster formation among iGAS cases not already part of existing genomic clusters.

Methods: In this WGS and population-based surveillance study, we analysed iGAS case isolates from the Active Bacterial Core surveillance (ABCs), which is part of the US Centers for Disease Control and Prevention's Emerging Infections Program, in ten US states from Jan 1, 2015, to Dec 31, 2019.

Photonic-assisted W-band flexible integrated sensing and communication system for fiber-wireless network based on CE-LFM-OFDM.

We have experimentally demonstrated a constant envelope linear frequency modulated orthogonal frequency division multiplexing (CE-LFM-OFDM) signal by employing an orthogonal frequency division multiplexing (OFDM) signal to phase modulate the linear frequency modulation (LFM) carrier. The experimental verification was conducted in the photonic-based integrated sensing and communication (ISAC) system working at 94.5 GHz.

Neural-network-based carrier-less amplitude phase modulated signal generation and end-to-end optimization for fiber-terahertz integrated communication system.

In fiber-terahertz integrated communication systems, nonlinear distortion and inter-symbol interference (ISI) will degrade transmission performance. Pre-compensation is an efficient method to handle the channel distortion as it can avoid noise boosting during channel compensation and reduce receiver side signal processing algorithmic complexity at user-end (UE) considering the asymmetric access scenario. In this paper, we propose and experimentally demonstrate a neural-network (NN)-based carrier-less amplitude phase (CAP) modulated signal generation and end-to-end optimization method for a fiber-terahertz integrated communication system.

A novel invasive Streptococcus pyogenes variant sublineage derived through recombinational replacement of the emm12 genomic region.

Group A streptococcal strains potentially acquire new M protein gene types through genetic recombination (emm switching). To detect such variants, we screened 12,596 invasive GAS genomes for strains of differing emm types that shared the same multilocus sequence type (ST). Through this screening we detected a variant consisting of 16 serum opacity factor (SOF)-positive, emm pattern E, emm82 isolates that were ST36, previously only associated with SOF-negative, emm pattern A, emm12.

Expansion of Invasive Group A Streptococcus M1 Lineage in Active Bacterial Core Surveillance, United States, 2019‒2021.

From 2015-2018 to 2019‒2021, hypertoxigenic M1 lineage among invasive group A Streptococcus increased in the United States (1.7%, 21/1,230 to 11%, 65/603; p<0.001).

Deep-learning-based multi-user framework for end-to-end fiber-MMW communications.

Fiber-wireless integration has been widely studied as a key technology to support radio access networks in sixth-generation wireless communication, empowered by artificial intelligence. In this study, we propose and demonstrate a deep-learning-based end-to-end (E2E) multi-user communication framework for a fiber-mmWave (MMW) integrated system, where artificial neural networks (ANN) are trained and optimized as transmitters, ANN-based channel models (ACM), and receivers. By connecting the computation graphs of multiple transmitters and receivers, we jointly optimize the transmission of multiple users in the E2E framework to support multi-user access in one fiber-MMW channel.

Deep learning based end-to-end visible light communication with an in-band channel modeling strategy.

Aside from ambient light noise, shot noise, and linear/nonlinear effects, strong low-frequency noise (LFN) severely affects the signal quality in LED-based visible light communication (VLC) systems, which hinders the implementation of data-driven end-to-end (E2E) deep learning approaches in real LED-VLC systems. We present a deep learning-based autoencoder to deal with this challenge. A novel modeling strategy is proposed to bypass the influence of the LFN and other low signal-to-noise ratio data when training the channel model of our E2E framework.

Invasive Group A Streptococcal Penicillin Binding Protein 2× Variants Associated with Reduced Susceptibility to β-Lactam Antibiotics in the United States, 2015-2021.

All known group A streptococci [GAS] are susceptible to β-lactam antibiotics. We recently identified an invasive GAS (iGAS) variant (/PBP2x-T553K) with unusually high minimum inhibitory concentrations (MICs) for ampicillin and amoxicillin, although clinically susceptible to β-lactams. We aimed to quantitate PBP2x variants, small changes in β-lactam MICs, and lineages within contemporary population-based iGAS.

Continued Increase of Erythromycin Nonsusceptibility and Clindamycin Nonsusceptibility Among Invasive Group A Streptococci Driven by Genomic Clusters, United States, 2018-2019.

We analyzed 9630 invasive GAS surveillance isolates in the USA. From 2015-2017 to 2018-2019, significant increases in erythromycin-nonsusceptibility (18% vs 25%) and clindamycin-nonsusceptibility (17% vs 24%) occurred, driven by rapid expansions of genomic subclones. Prevention and control of clustered infections appear key to containing antimicrobial resistance.

Invasive Pneumococcal Disease Clusters Disproportionally Impact Persons Experiencing Homelessness, Injecting Drug Users, and the Western United States.

Background: Invasive pneumococcal disease (IPD) isolates forming genomic clusters can reflect rapid disease transmission between vulnerable individuals.

Methods: We performed whole genome sequencing of 2820 IPD isolates recovered during 2019 through Centers for Disease Control and Prevention's Active Bacterial Core surveillance to provide strain information (serotypes, resistance, genotypes), and 2778 of these genomes were analyzed to detect highly related genomic clusters.

Results: Isolates from persons experiencing homelessness (PEH) were more often within genomic clusters than those from persons not experiencing homelessness (PNEH) (105/198 [53.

Genomic Characterization of Group A Streptococci Causing Pharyngitis and Invasive Disease in Colorado, USA, June 2016- April 2017.

Background: The genomic features and transmission link of circulating Group A Streptococcus (GAS) strains causing different disease types, such as pharyngitis and invasive disease, are not well understood.

Methods: We used whole-genome sequencing to characterize GAS isolates recovered from persons with pharyngitis and invasive disease in the Denver metropolitan area from June 2016 to April 2017.

Results: The GAS isolates were cultured from 236 invasive and 417 pharyngitis infections.

Invasive Pneumococcal Strain Distributions and Isolate Clusters Associated With Persons Experiencing Homelessness During 2018.

Background: We aimed to characterize invasive pneumococcal disease (IPD) isolates collected from multistate surveillance in the United States during 2018 and examine within-serotype propensities of isolates to form related clusters.

Methods: We predicted strain features using whole genome sequencing obtained from 2885 IPD isolates obtained through the Center for Disease Control and Prevention's Active Bacterial Core surveillance (ABCs), which has a surveillance population of approximately 34.5 million individuals distributed among 10 states.

Genomic Surveillance of Strains Causing Invasive Disease, United States, 2016-2017.

Background: is a major cause of severe, invasive infections in humans. The bacterial pathogen harbors a wide array of virulence factors and exhibits high genomic diversity. Rapid changes of circulating strains in a community are common.

Upsurge of Conjugate Vaccine Serotype 4 Invasive Pneumococcal Disease Clusters Among Adults Experiencing Homelessness in California, Colorado, and New Mexico.

After 7-valent pneumococcal conjugate vaccine introduction in the United States in 2000, invasive pneumococcal disease (IPD) due to serotype 4 greatly decreased in children and adults. Starting in 2013, serotype 4 IPD incidence increased among adults within 3 of 10 Active Bacterial Core surveillance sites. Of 325 serotype 4 cases among adults in 2010-2018, 36% were persons experiencing homelessness (PEH); incidence of serotype 4 IPD among PEH was 100-300 times higher than in the general population within these 3 areas.

Multistate, Population-Based Distributions of Candidate Vaccine Targets, Clonal Complexes, and Resistance Features of Invasive Group B Streptococci Within the United States, 2015-2017.

Background: Group B Streptococcus (GBS) is a leading cause of neonatal sepsis and meningitis and an important cause of invasive infections in pregnant and nonpregnant adults. Vaccines targeting capsule polysaccharides and common proteins are under development.

Methods: Using whole genome sequencing, a validated bioinformatics pipeline, and targeted antimicrobial susceptibility testing, we characterized 6340 invasive GBS isolates recovered during 2015-2017 through population-based Active Bacterial Core surveillance (ABCs) in 8 states.

Emergent Invasive Group A Streptococcus dysgalactiae subsp. equisimilis, United States, 2015-2018.

The term group A Streptococcus is considered synonymous for the species Streptococcus pyogenes. We describe an emergent invasive S. dysgalactiae subspecies equisimilis lineage that obtained the group A antigen through a single ancestral recombination event between a group C S.

The Role of Wound Care in 2 Group A Streptococcal Outbreaks in a Chicago Skilled Nursing Facility, 2015‒2016.

Two consecutive outbreaks of group A (GAS) infections occurred from 2015-2016 among residents of a Chicago skilled nursing facility. Evaluation of wound care practices proved crucial for identifying transmission factors and implementing prevention measures. We demonstrated shedding of GAS on settle plates during care of a colonized wound.

Genome-wide association analyses of invasive pneumococcal isolates identify a missense bacterial mutation associated with meningitis.

Bacterial mutations predisposing pneumococcus to causing meningitis, a more severe form of invasive pneumococcal disease (IPD), are largely unknown. Knowledge of such mutations may improve our understanding of pathogenesis and inform preventive strategies. Here we report a pneumococcal pbp1b gene mutation (pbp1bA641C causing N214T change in PBP1b transglycosylase domain) that is associated with meningitis in an exploratory cohort of IPD patients (n = 2054, p = 6.

A Population-Based Descriptive Atlas of Invasive Pneumococcal Strains Recovered Within the U.S. During 2015-2016.

Invasive pneumococcal disease (IPD) has greatly decreased since implementation in the U.S. of the 7 valent conjugate vaccine (PCV7) in 2000 and 13 valent conjugate vaccine (PCV13) in 2010.

Population and Whole Genome Sequence Based Characterization of Invasive Group A Streptococci Recovered in the United States during 2015.

Group A streptococci (GAS) are genetically diverse. Determination of strain features can reveal associations with disease and resistance and assist in vaccine formulation. We employed whole-genome sequence (WGS)-based characterization of 1,454 invasive GAS isolates recovered in 2015 by Active Bacterial Core Surveillance and performed conventional antimicrobial susceptibility testing.

Validation of β-lactam minimum inhibitory concentration predictions for pneumococcal isolates with newly encountered penicillin binding protein (PBP) sequences.

Background: Genomic sequence-based deduction of antibiotic minimum inhibitory concentration (MIC) has great potential to enhance the speed and sensitivity of antimicrobial susceptibility testing. We previously developed a penicillin-binding protein (PBP) typing system and two methods (Random Forest (RF) and Mode MIC (MM)) that accurately predicted β-lactam MICs for pneumococcal isolates carrying a characterized PBP sequence type (phenotypic β-lactam MICs known for at least one isolate of this PBP type). This study evaluates the prediction performance for previously uncharacterized (new) PBP types and the probability of encountering new PBP types, both of which impact the overall prediction accuracy.

Invasive Serotype 35B Pneumococci Including an Expanding Serotype Switch Lineage, United States, 2015-2016.

We used whole-genome sequencing to characterize 199 nonvaccine serotype 35B pneumococcal strains that caused invasive pneumococcal disease (IPD) in the United States during 2015-2016 and related these findings to previous serotype 35B IPD data obtained by Active Bacterial Core surveillance. Penicillin-nonsusceptible 35B IPD increased during post-pneumococcal 7-valent conjugate vaccine years (2001-2009) and increased further after implementation of pneumococcal 13-valent conjugate vaccine in 2010. This increase was caused primarily by the 35B/sequence type (ST) 558 lineage.