Human metapneumovirus (HMPV) causes acute respiratory disease worldwide and is the second leading cause of lower respiratory infection and hospitalization in young children in the USA. There is no licensed vaccine or therapeutic. HMPV mutates rapidly; however, the specific genomic features that explain strain dominance remain undefined because there is limited routine genomic surveillance of HMPV. We analyzed prospectively collected nasal specimens and medical data from 8,000 pediatric acute respiratory infection cases and sequenced 219 HMPV whole genomes from Pittsburgh, PA, between 2016 and 2021. Only A2, B1, and B2 subgroups were detected. The dominant subgroup varied between seasons. Variants with an in-frame 111- or 180-nucleotide (nt) insertion that nearly duplicates the preceding flanking region in the 660-nt G gene (encodes the attachment protein) were the predominant A2 viruses detected by 2016-2017. Among B2 viruses, variants with smaller in-frame insertions in the same location of the G gene became dominant by 2017-2018. Each insertion length formed a distinct phylogenetic clade. The insertions are in the ectodomain and contain positively charged residues or predicted O-glycosylation sites. Epidemiological analysis revealed that HMPV infection was independently associated with age, insurance type, and comorbidities. Elevated disease severity was independently associated with age and comorbidities, although not with HMPV subgroup. To our knowledge, in the USA, this is the earliest detection of the A2 insertion variants and the first report of the B2 insertion variants. It is the largest population-based genomic HMPV study that provides a detailed phylodynamics and epidemiological analysis of prospectively collected clinical specimens.IMPORTANCEHuman metapneumovirus (HMPV) is a leading cause of lung infection and pediatric hospitalizations worldwide for which there is no licensed vaccine or therapeutic. Because HMPV mutates rapidly, understanding which mutations enhance its ability to multiply and spread is important for the development of interventions and treatments. We prospectively collected patient data and nasal specimens from children with symptoms of acute respiratory illness. The predominant A2 and B2 HMPV variants circulating in the population contained insertions in the attachment protein, which suggests that these insertions may be advantageous to the virus. Furthermore, our analysis suggests that age, insurance type, and underlying health conditions were associated with HMPV infection. Age and underlying health conditions were associated with elevated HMPV disease severity, whereas HMPV subgroup was not. This large HMPV genomic epidemiological study provides insight into patient factors associated with disease and the emergence of the dominant variants in the USA.

ABSTRACT Klebsiella pneumoniae (KP) isolates belonging to multi-locus sequence type 258 (ST258) are a frequent cause of hospital-associated outbreaks and display extensive multidrug resistance. The KP ST258 lineage consists of two genetically distinct clades, called Clade 1 and Clade 2. These two clades are genetically related to one another, but are historically distinguished by having different capsular polysaccharide types. While bacteria belonging to both clades are isolated from clinical infections, Clade 2 is isolated more frequently compared to Clade 1. To investigate drivers of this difference in clade prevalence, we collected 172 clinical KP ST258 isolates from patients at a single medical center. Clinical review showed that patients infected with Clade 2 isolates were more acutely ill than Clade 1-infected patients, despite having fewer comorbidities. We also found that Clade 2 isolates were more resistant to killing by human serum, despite binding more complement protein C3 than Clade 1 isolates. Additionally, mice infected with a Clade 2 isolate had increased bacterial dissemination from the lungs to the liver and spleen than mice infected with a Clade 1 isolate, and this dissemination required an intact capsule locus. Increased dissemination in mice was not due to differential serum killing, as mouse serum was unable to kill isolates of either clade, but dissemination was associated with decreased macrophage uptake of the Clade 2 isolate. Taken together, these data suggest that KP ST258 Clade 2 is more virulent than Clade 1, although the specific mechanisms at play appear to differ between mice and humans. IMPORTANCE KP ST258 is an epidemic lineage of multidrug-resistant gram-negative bacteria that has caused numerous outbreaks in hospitals around the world. The KP ST258 population is divided into two genetically related but distinct clades, which differ primarily in their capsule type. In this study, we found that patients infected with one of the KP ST258 clades were more acutely ill than patients infected with the other clade. We also observed clade-specific differences both in killing by human serum and in bacterial dissemination in a mouse model of pneumonia. Finally, we identified important limitations in the use of mouse models to study host defenses against multidrug-resistant KP infection. Overall, this work underscores the importance of capsule composition in KP ST258 virulence, identifies differences in the host response to KP infection between mice and humans, and highlights a potential role for complement-targeting immunotherapeutics in the treatment of KP infections.

US data on invasive pneumococcal disease incidence among pregnant and postpartum women are limited. We estimated incidence in those groups using population-based surveillance. Compared with nonpregnant women of childbearing age, incidence was similar for pregnant women but 3.5 times higher for postpartum women. Our findings could inform pneumococcal vaccine recommendations.

Rapid identification of outbreaks in hospitals is essential for controlling pathogens with epidemic potential. Although whole genome sequencing (WGS) remains the gold standard in outbreak investigations, its substantial costs and turnaround times limit its feasibility for routine surveillance, especially in less-equipped facilities. We explore three modalities as rapid alternatives: matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry, antimicrobial resistance (AR) patterns, and electronic health records (EHR). We present a machine learning approach that learns discriminative features from these modalities to support outbreak detection. Multi-species evaluation shows that the integration of these modalities can boost outbreak detection performance. We also propose a tiered surveillance paradigm that can reduce the need for WGS through these alternative modalities. Further analysis of EHR information identifies potentially high-risk contamination routes linked to specific clinical procedures, notably those involving invasive equipment and high-frequency workflows, providing infection prevention teams with actionable targets for proactive risk mitigation

INTRODUCTION:Potential public health effects of adult pneumococcal vaccines are uncertain because of observed changes in pneumococcal serotype epidemiology. Prior analyses favored the 21-valent pneumococcal conjugate vaccine but observed that serotype changes in some populations could decrease its favorability. Value of information analysis could guide further research to clarify uncertainty. METHODS:Analyses evaluated value of information in U.S. cohorts aged 65 years, comparing adult pneumococcal vaccines. Model parameters included vaccine serotype-specific pneumococcal disease and mortality risks from U.S. data, vaccination rates from published literature, and vaccine effectiveness from clinical trials and Delphi panel estimates. Analyses estimated expected value of perfect information and expected value of partial perfect information at willingness-to-pay thresholds from $0 to $200,000 per quality-adjusted life year gained. A secondary analysis examined those aged 50-64 years. Data were collected and analyzed in 2024. RESULTS:In those aged 65 years, value of information estimates were highest at the $100,000/quality-adjusted life year gained threshold and were markedly less at higher thresholds. At $100,000/quality-adjusted life year gained, population expected value of perfect information was $178.1 million; expected value of partial perfect information for pneumococcal disease mortality and disability parameters combined was $89.6 million and for vaccine effectiveness parameters was $73.8 million. The 21-valent pneumococcal conjugate vaccine serotype incidence expected value of partial perfect information was $19 million. In those aged 50-64 years, expected value of partial perfect information for vaccine effectiveness was $2.9 million and for 21-valent pneumococcal conjugate vaccine serotype incidence was $139,080. CONCLUSIONS:Value of information results were more supportive of further research on selected parameters in those aged 65 years than in those aged 50 years. However, expected value of partial perfect information values for 21-valent pneumococcal conjugate vaccine serotype incidence was substantially lower in both age groups, supporting adult 21-valent pneumococcal conjugate vaccine use regardless of serotype uncertainty.

4CMenB vaccine is authorized for protection against serogroup B invasive meningococcal disease (IMD). This study synthesized real-world evidence (RWE) data on effectiveness and impact of 4CMenB vaccine. A systematic search identified RWE on vaccine effectiveness (VE) and vaccine impact of 4CMenB in infants, children and adolescents. A meta-analysis was conducted of 4CMenB VE against serogroup B-IMD in infants and children. The primary meta-analysis used a random-effects model on data from five studies from five countries reporting VE in fully vaccinated infants and children, and estimated pooled VE at 79.7% (95% confidence interval 70.4, 86.1). In sensitivity analyzes, inclusion/exclusion of studies from the primary analysis did not materially change the results. Age-specific data in adolescents were summarized qualitatively. Data identified from Australia reported high effectiveness and impact in adolescents. This meta-analysis provides evidence of high 4CMenB VE against serogroup B-IMD in fully vaccinated infants and children across different geographic regions. Clinical trial registration: N/A.

Introduction:Outbreaks of healthcare-associated infections (HAI) result in substantial patient morbidity and mortality; mitigation efforts by infection prevention teams have the potential to curb outbreaks and prevent transmission to additional patients. The incorporation of whole genome sequencing (WGS) surveillance of suspected high-risk pathogens often identifies outbreaks that are not detected by traditional infection prevention methods and provides evidence for transmission. Our approach to real-time WGS surveillance, the Enhanced Detection System for Healthcare-Associated Transmission (EDS-HAT), has 1) identified serious outbreaks that were otherwise undetected and 2) shown the potential to be cost saving. Methods:We describe our cost-efficient methods to perform WGS surveillance and data analysis of pathogens for institutions that are interested to expand infection prevention surveillance. We provide an overview of the weekly workflow of EDS-HAT during two distinct phases over three years. Results:In an average week at our tertiary healthcare system, we sequenced 60 samples at a cost of less than $100 each during Phase 1, and 80 samples for less than $70 each in Phase 2, inclusive of laboratory reagents and staff salaries. The average turnaround time, from sample collection to reporting data to infection prevention, was ten days. Conclusions:Performing EDS-HAT in real-time can be both feasible and time-efficient. Providing such timely information to aid in outbreak detection could identify transmission events sooner and thus could increase patient safety.

ABSTRACT Background Salmonella Isangi is an under-characterised serovar repeatedly associated with antimicrobial resistant hospital infections. Outbreaks of extensively drug-resistant (XDR) Salmonella Isangi occurred in close succession within hospitals in Malawi and South Africa, prompting us to characterise the serovar using epidemiologic, phenotypic, and genomic perspectives. Methods In Malawi, we integrated hospital blood culture surveillance with environmental sampling from neonatal wards and urban waterways. In South Africa, we analysed isolates from five hospitals involved in a regional outbreak. We used whole genome sequencing (Illumina and MinION) to characterise AMR genes and plasmids, assessed biofilm formation, disinfectant susceptibility, in vivo virulence, and analysed all publicly available Salmonella Isangi genomes. Findings 224 / 345 (65%) of genomes in the global collection belonged to Salmonella Isangi sequence type (ST) 335. Of these, 221 (99%) originated from Malawi and South Africa, including the isolates recovered from both outbreaks. 199 (89%) ST335 genomes carried determinants of resistance to fluoroquinolones and third-generation cephalosporins, consistent with an XDR profile. In Malawi, a single ST335 clade caused the outbreak and was simultaneously present in both the hospital environment and nearby rivers. Inter-hospital transmission of a separate ST335 clade sustained the outbreak in South Africa. Closely related Malawian and South African isolates carried distinct plasmids encoding similar resistance determinants; evidence from our study and public databases suggests gene transfer via a cointegrate intermediate Five non-outbreak South African ST335 isolates harboured additional carbapenem and macrolide resistance genes. Phenotypically, Salmonella Isangi ST335 resembled Salmonella Typhimurium in biofilm formation and disinfectant tolerance but was less virulent in mice. Interpretation Salmonella Isangi ST335 combines a locally untreatable XDR profile with nosocomial transmission and environmental persistence, suggesting a high potential for future outbreaks. A distinct and potentially greater threat lies in the horizontal spread of its resistance determinants to Salmonella Typhimurium and Salmonella Enteritidis, the two dominant invasive serovars in the region. Strengthened surveillance, integrating phenotypic testing with targeted genomics, is urgently needed. Its absence in Malawi, in contrast to South Africa, underscores inequities in preparedness for emerging AMR threats. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This work was supported by the Wellcome Trust through the Core Grant (206545/Z/17/Z) and the COVID-19 Sequencing Grant (220757/Z/20/Z). Additional support was provided by the National Institute for Health Research (NIHR) via Melita Gordon's NIHR Fellowship (NIHR300039). Peter Johnston is funded by the Liverpool Clinical PhD Programme for Health Priorities in the Global South, supported by the Wellcome Trust (223502/Z/21/Z). For open access, the author has applied a CC BY public copyright license to any author-accepted manuscript version arising from this submission. Whole-genome sequencing of Salmonella isolates from South Africa was made possible by support from the SEQAFRICA project which is funded by the Department of Health and Social Care's Fleming Fund using UK aid. The views expressed in this publication are those of the authors and not necessarily those of the UK Department of Health and Social Care or its Management Agent, Mott MacDonald. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Malawian studies were approved by the College of Medicine Research Ethics Committee (COMREC approvals P.10/18/2499 and P.07/20/3089) and sponsored by the Liverpool School of Tropical Medicine. Reuse of sub-cultured bacterial isolates from these studies has been additionally approved (COMREC reference P06/20/3071). Mouse care and housing was carried out in accordance with guidelines established by the Abigail Wexner Research Institute (AWRI) Institutional Animal Care and Use Committee (IACUC) with an approved protocol (AR18-00080). The research activity followed the practices outlined in the Guide for the Care and Use of Laboratory Animals. For South African studies, ethical approval to perform surveillance activities and laboratory analysis on clinical isolates of Salmonella was obtained from the Human Research Ethics Committee of the University of the Witwatersrand, Johannesburg, South Africa (protocol reference numbers: M160667, M1809107, M210752, M230985). I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All the genomes sequenced as part of this study are available from European Nucleotide Archive under the project accession ERP189265, a full list of accessions is available in Supplementary Table 1.

Background:Conjugative plasmids encoding New Delhi metallo-β-lactamase ( bla NDM ) pose a threat for the spread of carbapenem resistance among healthcare-acquired pathogens. Plasmid-associated outbreaks of bla NDM -producing bacteria can involve multiple bacterial species and persist over long time-periods, making their detection and control difficult. We systematically studied the genomic epidemiology of bla NDM -encoding plasmids detected within a single hospital system over a five-year period. Methods:bla NDM -producing isolates were collected from clinical cultures as part of the Enhanced Detection System for Healthcare-Associated Transmission (EDS-HAT) genomic sequencing active surveillance program, or during infection prevention and control (IP&C) investigations. Isolates were identified as bla NDM producers by polymerase chain reaction (PCR); the presence of plasmid-encoded bla NDM genes was confirmed by sequencing on both Illumina and Oxford Nanopore platforms. Plasmids were clustered using Pling and bacterial relatedness of host isolates was evaluated with split kmer analysis. Electronic health record data were used to identify shared unit-level spatiotemporal exposures and epidemiologic links within both plasmid and host clusters. Results:We identified 61 bla NDM -producing isolates collected from 54 patients sampled between November 2020 and July 2025. Isolates belonged to 15 Enterobacterales species; Enterobacter hormaechei was the most frequently sampled species (n=23, 37%), and bla NDM-5 was the most frequently observed bla NDM allele (n=36, 59%). We observed six clusters of genetically similar bla NDM -encoding plasmids each containing 2-28 isolates, and eight singleton plasmids. The two largest plasmid clusters consisted of a highly conserved 46 kb IncX3 family bla NDM-5 -encoding plasmid (n=28 plasmids, 9 species) and a more variable 98-201 kb IncC family bla NDM-1 -encoding plasmid (n=12 plasmids, 6 species). Epidemiologic investigation paired with whole genome sequencing identified spatiotemporal associations between shared patient exposures and putative plasmid and bacterial transmission clusters, suggesting that unit-level exposures contribute to plasmid dissemination. Finally, analysis of publicly available sequences showed that the most prevalent plasmids detected, IncX3( bla NDM-5 ) and IncC( bla NDM-1 ), also demonstrated high global prevalence. Conclusions:This study demonstrates the diversity of bla NDM carrying plasmids within a single hospital system and their capacity to cause prolonged, multispecies outbreaks. Integrating whole genome sequencing with epidemiologic data identified unit-level spatiotemporal overlap as a likely contributor to plasmid dissemination in the hospital.

Accurate and timely identification of hospital outbreak clusters is crucial for preventing the spread of infections that have epidemic potential. While assessing pathogen similarity through whole genome sequencing (WGS) is considered the gold standard for outbreak detection, its high cost and lengthy turnaround time preclude routine implementation in clinical laboratories. We explore the utility of two rapid and cost-effective alternatives to WGS, matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry and antimicrobial resistance (AR) patterns. We develop a machine learning framework that extracts informative representations from MALDI-TOF spectra and AR patterns for outbreak detection and explore their fusion. Through multi-species analyses, we demonstrate that in some cases MALDI-TOF and AR have the potential to reduce reliance on WGS, enabling more accessible and rapid outbreak surveillance.

SARS-CoV-2 transmission was investigated between university students and the surrounding community using whole genome sequencing. Fourteen putative transmission clusters were identified. Proximity assessed using ZIP codes showed clustered cases were more widely dispersed than non-clustered cases, highlighting the need for integrated genomic surveillance, coordinated interventions, and data-driven public health policies.

Abstract Background Trends in Staphylococcus aureus bacteremia (SAB) mortality rates in the United States, including the impact of COVID-19, have not been well described. Methods Active, laboratory- and population-based surveillance data from 20 counties (seven states) were used to examine annual, 30-day mortality rates among U.S. adult patients with methicillin-resistant and methicillin-susceptible Staphylococcus aureus (MRSA and MSSA, respectively) bacteremia during 2005-2022. Medical records and state vital statistics data were linked to ascertain death. Multivariable survival analysis estimated the association between recent SARS-CoV-2 infection (a positive SARS-CoV-2 test ≤30 days before incident culture) and mortality among SAB cases, adjusting for demographics and other risk factors. Analyses were stratified by MRSA/MSSA and epidemiologic class (hospital-onset [HO], healthcare-associated community-onset [HACO], and community-associated [CA]). Results Overall, SAB mortality was 21%. Annual SAB mortality rates were generally stable pre-pandemic before increasing by 33% and 41% among HO MRSA and MSSA cases, respectively, and by 49% among CA MRSA cases, but not among HACO or MSSA CA cases, from 2019 through 2021. Among HO cases with recent SARS-CoV-2 infection, annual mortality rates were as high as 75%. Adjusted hazard ratios for recent SARS-CoV-2 infection ranged from 1.9 (95% confidence interval: 1.5-2.3) (HACO MRSA) to 3.0 (95% confidence interval: 2.4-3.7) (HO MSSA). Conclusions Recent SARS-CoV-2 infection was a significant risk factor for death among patients with SAB during 2020-2022. Strengthening infection prevention efforts in similar respiratory pandemics in the future could help prevent increases in SAB mortality rates.

BACKGROUND:Current methods are insufficient alone for outbreak detection in hospitals. Real-time genomic surveillance offers the potential to detect otherwise unidentified outbreaks. We initiated and evaluated the Enhanced Detection System for Healthcare-associated Transmission (EDS-HAT), a real-time genomic surveillance program for outbreak detection and mitigation. METHODS:This study was conducted at UPMC Presbyterian Hospital from November 2021 to October 2023. Whole genome sequencing (WGS) was performed weekly on healthcare-associated clinical bacterial isolates to identify otherwise undetected outbreaks. IP&C interventions were implemented in real-time based on identified transmission. A clinical and economic impact analysis was conducted to estimate infections avoided and net cost savings. RESULTS:There were 3921 bacterial isolates from patient healthcare-associated infections that underwent WGS, of which 476 (12.1%) clustered into 172 outbreaks (size 2-16 patients). Of the outbreak isolates, 292 (61.3%) had an identified epidemiological link. Among the outbreaks with interventions, 95.6% showed no further transmission on the intervened transmission route. The impact analysis estimated that, over the 2-year period, 62 infections and 4.8 deaths were avoided, with gross cost savings of $1,011,146, and net savings of $695,706, which translates to a 3.2-fold return on investment. Probabilistic sensitivity analysis showed EDS-HAT was cost saving and more effective in 98% of simulations. CONCLUSIONS:Real-time genomic surveillance enabled the rapid detection and control of outbreaks in our hospital and resulted in patient and economic benefits. This study demonstrates the feasibility and effectiveness of integrating genomic surveillance into routine infection prevention practice, offering a paradigm shift in healthcare outbreak detection and control.

BACKGROUND:Group A Streptococcus (GAS) infections are common in children, ranging from mild to life-threatening invasive disease. Large-scale descriptions of changes in pediatric invasive GAS infections in the United States, particularly during the coronavirus disease 2019 (COVID-19) pandemic, are limited. METHODS:We used the Centers for Disease Control and Prevention's (CDC's) Active Bacterial Core surveillance (ABCs), a multistate, population- and laboratory-based surveillance system, to assess changes in pediatric (<18 years old) invasive GAS incidence, clinical presentation, and bacterial strain characteristics from 2004 to 2023. Interrupted time series analysis was used to compare observed versus expected GAS incidence during 2020-2023, informed by trends before the COVID-19 pandemic (2004-2019). RESULTS:During 2004-2023, 2856 invasive GAS cases were identified. Incidence remained stable from 2004 to 2019 (mean incidence 1.9 per 100 000), decreased in 2020 (1.0) and 2021 (0.6), and rebounded in 2022 (1.5) and 2023 (4.4). ICU admission increased from 2011 to 2023; case fatality remained stable. Penicillin resistance was not detected. Clindamycin non-susceptibility doubled from 2011 (3.8%) to 2022 (7.5%), before slightly decreasing in 2023 (6.4%). Infections due to emm1, the most frequently identified emm type in children with severe disease, almost disappeared in 2021 but surged in late 2022. CONCLUSIONS:After remaining stable for more than a decade, pediatric invasive GAS incidence declined during the COVID-19 pandemic and rebounded in 2022, more than doubling 2004-2019 incidence in 2023. Although case fatality remained low, intensive care unit (ICU) admissions increased over time, highlighting the need for effective preventive measures such as vaccines. Increasing clindamycin non-susceptibility bears continued monitoring.

BACKGROUND:Nursing home residents experience a large burden of invasive methicillin-resistant Staphylococcus aureus (MRSA) infections. Data are limited regarding nursing home characteristics associated with differences in facility-level invasive MRSA rates. METHODS:We analyzed 2011-2015 data from CDC's Emerging Infections Program (EIP) active population- and laboratory-based surveillance for invasive MRSA cases within seven states. A nursing home-onset case was defined as MRSA cultured from a normally sterile site in a person living in a nursing home 3 days before culture collection. Facility rates were calculated as nursing home-onset cases per 100,000 resident-days. Nursing home resident-day denominators and facility characteristics were obtained from four Centers for Medicare & Medicaid Services (CMS) datasets. A general estimating equations model with a logit link assessed characteristics of the facilities with highest rates comprising 50% of nursing home MRSA cases ("high rates"). RESULTS:The 626 nursing homes in the surveillance area had 2824 invasive MRSA cases; 82% of facilities had at ≥1 case. The 20% of facilities with highest rates (≥3.84 cases/100,000 resident-days) had 50% of nursing home-onset cases. In multivariable regression, facilities with high rates were more likely to have CMS-derived characteristics of presence of a resident with a multidrug-resistant organism; or greater proportions of residents who were male, were short stay (in the facility <100 days), had a nasogastric or percutaneous gastrostomy tube, or require extensive assistance with bed repositioning; and more likely to be in an EIP area with higher hospital-onset MRSA rates. Higher registered nurses staffing levels (hours/resident/day) and higher proportions of White residents were associated with lower rates. CONCLUSIONS:Facilities with higher invasive MRSA rates served residents with more clinical and functional care needs. Increasing registered nurse staffing in high-risk facilities might assist with reduction of invasive MRSA rates. These findings could help prioritize nursing homes for future MRSA prevention work.

BACKGROUND:Respiratory virus transmission in healthcare settings is not well understood. To investigate the transmission dynamics of common healthcare-associated respiratory virus infections, we performed retrospective whole genome sequencing (WGS) surveillance at three teaching hospitals. METHODS:From January 2, 2018, to January 4, 2020, nasal swab specimens positive for rhinovirus, influenza virus, human metapneumovirus (HMPV), or respiratory syncytial virus (RSV) from patients hospitalized for ≥3 days were sequenced. High-quality genomes were assessed for genetic relatedness using ≤3 single nucleotide polymorphisms (SNPs) as a cutoff, except for rhinovirus (≤10 SNPs). Patient health records were reviewed for genetically related clusters to identify epidemiological connections. RESULTS:We collected 436 viral specimens from 359 patients: rhinovirus (n = 291), influenza virus (n = 50), RSV (n = 48), and HMPV (n = 47). Of these, 42%% (152/359 patients) were from a pediatric hospital, and 58% were from adult hospitals. WGS was performed on 61.2% (178/291) rhinovirus, 78% (39/50) influenza virus, 90% (43/48) RSV, and all HMPV specimens. Among high-quality genomes, we identified 14 genetically related clusters involving 36 patients (range: 2-5 patients per cluster). We identified common epidemiological links for 53% (19/36) of clustered patients; 63% (12/19) of patients had same-unit stays, 26% (5/19) had overlapping hospital stays, and 11% (2/19) shared common providers. On average, genetically related clusters spanned 16 days (range: 0 - 55 days). CONCLUSION:WGS offered new insights into respiratory virus transmission dynamics. These advancements could potentially improve infection prevention and control strategies, leading to enhanced patient safety and healthcare outcomes.

Background:Respiratory virus transmission in healthcare settings is not well understood. To investigate the transmission dynamics of common healthcare-associated respiratory virus infections, we performed retrospective whole genome sequencing (WGS) surveillance at one pediatric and two adult teaching hospitals in Pittsburgh, PA. Methods:From January 2, 2018, to January 4, 2020, nasal swab specimens positive for rhinovirus, influenza, human metapneumovirus (HMPV), or respiratory syncytial virus (RSV) from patients hospitalized for ≥3 days were sequenced on Illumina platform. High-quality genomes were assessed for genetic relatedness using ≤3 single nucleotide polymorphisms (SNPs) cut-off, except for rhinovirus (10 SNPs). Patient health records were reviewed for genetically related clusters to identify epidemiological connections. Results:We collected 436 viral specimens from 359 patients: rhinovirus (n=291), influenza (n=50), HMPV (n=47), and RSV (n=48). Of these, 55% (197/359 patients) were from pediatric hospital and 45% from adult hospitals. Patients ranged in age from 14 days to 93 years, 61% were male, and 74% were white. WGS was performed on 61.2% (178/291) rhinovirus, 78% (39/50) influenza, 92% (44/48) RSV, and all HMPV specimens. Among high-quality genomes, we identified 14 genetically related clusters involving 36 patients, ranging in size from 2-5 patients. We identified common epidemiological links for 53% (19/36) of clustered patients; 63% (12/19) patients had same-unit stay, 26% (5/19) had overlapping hospital stays, and 11% (2/19) shared common provider. On average, genetically related clusters spanned 16 days (range:0-55 days). Conclusion:WGS offered insights into respiratory virus transmission dynamics. These advancements could potentially improve infection prevention and control strategies, leading to enhanced patient safety and healthcare outcomes.

This review outlines recent trends on invasive meningococcal disease (IMD) discussed at the latest meeting of the Global Meningococcal Initiative (GMI). There has been a re-emergence of the Hajj strain sublineage (serogroup W; ST-11 clonal complex), with travel to the Kingdom of Saudi Arabia being a critical factor in transmission. The epidemiology of IMD has also changed following the COVID-19 pandemic, with annual IMD cases increasing in many countries. For example, the highest number of IMD cases since 2014 was reported in the USA in 2023-2024. Atypical presentations of IMD have been prominent irrespective of the pandemic. For instance, an increase in cases of meningococcal epiglottitis has been reported in France in 2022-2023 (serogroups W and Y). When considering vaccination, the GMI has identified a need for broader meningococcal serogroup B (MenB) immunisation owing to the potential impact of the vaccines on reducing IMD incidence caused by other serogroups than MenB. There is also a case for using MenB vaccination to protect against Neisseria gonorrhoeae infection based on initial evidence, albeit further studies will need to be conducted.

Whole-genome sequencing (WGS) is used to establish genetic relatedness of bacteria and track outbreaks in healthcare settings. While WGS provides sufficient discriminatory power to make inferences about genetic relatedness and transmission for most bacterial species, WGS for Clostridioides difficile often fails to do so, even at low single-nucleotide polymorphism (SNP) differences. Multi-locus variable number tandem repeat analysis (MLVA), which analyzes rapidly mutating tandem repeat loci, has previously been shown to be useful for this purpose for C. difficile. We investigated whether in silico MLVA can further elucidate genetic relatedness of C. difficile clusters identified by short-read WGS but lacking epidemiological links. Potential healthcare-associated toxin-positive C. difficile isolates were collected at our hospital from November 2016 to November 2019. Short-read WGS was performed on the Illumina platform to cluster isolates with ≤2 SNPs, and Nanopore long-read sequencing was used to resolve MLVA loci within these clustered isolates. Among 666 isolates, 62 unique patient isolates met the ≤2 SNP criterion and underwent MinION sequencing. Of the 105 pairs with 0-2 SNP differences, 79.0% had a summed tandem-repeat difference (STRD) of 0-5, 10.5% had an STRD of 6-10, and 10.5% had an STRD of 11-20. A significant correlation was found between a lower STRD value and the presence of a unit/procedure-based epidemiological link within low SNP clusters (odds ratio: 0.45; 95% CI: 0.29-0.70). Our findings demonstrate that MLVA provides additional genomic discrimination for closely related C. difficile isolates identified by WGS, enhancing outbreak investigation precision.IMPORTANCEClostridioides difficile is a leading cause of healthcare-associated infections, often spreading undetected within hospitals. To track its transmission, hospitals increasingly rely on bacterial genetic sequencing, but this approach is often not discriminatory enough for identifying the spread of this organism between patients. In this study, we applied an additional genetic method that looks at highly changeable regions of the bacteria's DNA to improve the detection of likely transmission events. By combining two sequencing techniques, we were able to separate seemingly related infections that were not actually linked in the hospital. This enhanced resolution can help infection prevention teams focus their investigations and stop real outbreaks more efficiently, improving patient safety. Our findings support the use of this combined sequencing strategy in routine hospital surveillance and show how it can fill important gaps when standard methods are not sufficient.

Background: Children with hematologic malignancies (HMs) are at increased risk of invasive pneumococcal disease (IPD). Data on long-term IPD trends in U.S. children with HM after 13-valent pneumococcal conjugate vaccine (PCV13) introduction are limited. We assessed IPD trends in children with HM before and after PCV13 introduction and the proportion of IPD cases caused by serotypes contained in new pneumococcal conjugate vaccines (PCV15 and PCV20, introduced after 2019). Methods: During 2005-2019, IPD cases among children <18 years old were identified through the Active Bacterial Core surveillance. We characterized IPD cases by underlying conditions (HM, other IPD risk factors, no IPD risk factors) and time periods [pre-PCV13 (2005-2009), early-PCV13 (2010-2014) and late-PCV13 (2015-2019)]. We estimated incidence rate ratios (IRRs) in children <5 years of age with and without HM and during 2010-2019. Results: We identified 5912 cases of IPD in children <18 years old; 215 (3.6%) were among children with HM. The proportion of IPD cases with PCV13 serotypes decreased over time in all risk groups; however, IRRs among children with vs. without HM were 215.8 [95% confidence interval (CI): 146.1-292.4] and 240.9 (95 CI: 152.3-341.1) in early and late-PCV13 periods, respectively. In late-PCV13 period, PCV15/non-PCV13 serotypes and PCV20/non-PCV15 serotypes caused 19.4% and 4.8% of IPD cases among children with HM. Conclusions: The proportion of PCV13-type IPD decreased in all children after PCV13 introduction. However, children with HM remain at an increased risk of IPD. Continued monitoring of the impact of PCV15 and PCV20 use among children with HM is needed.