Immunogenicity of convalescent and vaccinated sera against clinical isolates of ancestral SARS-CoV-2, Beta, Delta, and Omicron variants.

Background: SARS-CoV-2 Omicron variant of concern (VOC) has evolved multiple mutations within the spike protein, raising concerns of increased antibody evasion. In this study, we assessed the neutralization potential of COVID-19 convalescent sera and sera from vaccinated individuals against ancestral SARS-CoV-2 and VOCs. Methods: The neutralizing activity of sera from 65 coronavirus disease (COVID-19) vaccine recipients and convalescent individuals against clinical isolates of ancestral SARS-CoV-2 and Beta, Delta, and Omicron VOCs was assessed using a micro-neutralization assay. Findings: Convalescent sera from unvaccinated individuals infected by the ancestral virus demonstrated reduced neutralization against Beta and Omicron VOCs. Sera from individuals that received three doses of the Pfizer or Moderna vaccines demonstrated reduced neutralization of the Omicron variant relative to ancestral SARS-CoV-2. Sera from individuals that were naturally infected with ancestral SARS-CoV-2 and subsequently received two doses of the Pfizer vaccine induced significantly higher neutralizing antibody levels against ancestral virus and all VOCs. Infection alone, either with ancestral SARS-CoV-2 or the Delta variant, was not sufficient to induce high neutralizing antibody titers against Omicron. Conclusions: In summary, we demonstrate that convalescent and vaccinated sera display varying levels of SARS-CoV-2 VOC neutralization. Data from this study will inform booster vaccination strategies against SARS-CoV-2 VOCs. Funding: This research was funded by the Canadian Institutes of Health Research (CIHR). VIDO receives operational funding from the Government of Saskatchewan through Innovation Saskatchewan and the Ministry of Agriculture and from the Canada Foundation for Innovation through the Major Science Initiatives for its CL3 facility.

A simple protein-based surrogate neutralization assay for SARS-CoV-2.

Most of the patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mount a humoral immune response to the virus within a few weeks of infection, but the duration of this response and how it correlates with clinical outcomes has not been completely characterized. Of particular importance is the identification of immune correlates of infection that would support public health decision-making on treatment approaches, vaccination strategies, and convalescent plasma therapy. While ELISA-based assays to detect and quantitate antibodies to SARS-CoV-2 in patient samples have been developed, the detection of neutralizing antibodies typically requires more demanding cell-based viral assays. Here, we present a safe and efficient protein-based assay for the detection of serum and plasma antibodies that block the interaction of the SARS-CoV-2 spike protein receptor binding domain (RBD) with its receptor, angiotensin-converting enzyme 2 (ACE2). The assay serves as a surrogate neutralization assay and is performed on the same platform and in parallel with an ELISA for the detection of antibodies against the RBD, enabling a direct comparison. The results obtained with our assay correlate with those of 2 viral-based assays, a plaque reduction neutralization test (PRNT) that uses live SARS-CoV-2 virus and a spike pseudotyped viral vector-based assay.

Influenza Vaccine Effectiveness Among Patients With Cancer: A Population-Based Study Using Health Administrative and Laboratory Testing Data From Ontario, Canada.

PURPOSE: Seasonal influenza vaccination is recommended for patients with cancer despite concerns of disease or treatment-associated immunosuppression. The objective of this study was to evaluate vaccine effectiveness (VE) against laboratory-confirmed influenza for patients with cancer. PATIENTS AND METHODS: We conducted an observational test-negative design study of previously diagnosed patients with cancer 18 years of age and older who underwent influenza testing during the 2010-2011 to 2015-2016 influenza seasons in Ontario, Canada. We linked individual-level cancer registry, respiratory virus testing, and health administrative data to identify the study population and outcomes. Vaccination status was determined from physician and pharmacist billing claims. We used multivariable logistic regression to estimate VE, adjusting for age, sex, rurality, income quintile, cancer characteristics, chemotherapy exposure, comorbidities, previous health care use, influenza season, and calendar time. RESULTS: We identified 26,463 patients with cancer who underwent influenza testing, with 4,320 test-positive cases (16%) and 11,783 (45%) vaccinated. Mean age was 70 years, 52% were male, mean time since diagnosis was 6 years, 69% had solid tumor malignancies, and 23% received active chemotherapy. VE against laboratory-confirmed influenza was 21% (95% CI, 15% to 26%), and VE against laboratory-confirmed influenza hospitalization was 20% (95% CI, 13% to 26%). For patients with solid tumor malignancies, VE was 25% (95% CI, 18% to 31%), compared with 8% (95% CI, -5% to 19%) for patients with hematologic malignancies (P = .015). Active chemotherapy usage did not significantly affect VE, especially among patients with solid tumor cancer. CONCLUSION: Our results support recommendations for influenza vaccination for patients with cancer. VE was decreased for patients with hematologic malignancies, and there was no significant difference in VE among patients with solid tumor cancer receiving active chemotherapy. Strategies to optimize influenza prevention among patients with cancer are warranted.

Efficacy of admission screening for extended-spectrum beta-lactamase producing Enterobacteriaceae.

OBJECTIVE: We hypothesized that admission screening for extended-spectrum ß-lactamase-producing Enterobacteriaceae (ESBL-E) reduces the incidence of hospital-acquired ESBL-E clinical isolates. DESIGN: Retrospective cohort study. SETTING: 12 hospitals (6 screening and 6 non-screening) in Toronto, Canada. PATIENTS: All adult inpatients with an ESBL-E positive culture collected from 2005-2009. METHODS: Cases were defined as hospital-onset (HO) or community-onset (CO) if cultures were positive after or before 72 hours. Efficacy of screening in reducing HO-ESBL-E incidence was assessed with a negative binomial model adjusting for study year and CO-ESBL-E incidence. The accuracy of the HO-ESBL-E definition was assessed by re-classifying HO-ESBL-E cases as confirmed nosocomial (negative admission screen), probable nosocomial (no admission screen) or not nosocomial (positive admission screen) using data from the screening hospitals. RESULTS: There were 2,088 ESBL-E positive patients and incidence of ESBL-E rose from 0.11 to 0.42 per 1,000 inpatient days between 2005 and 2009. CO-ESBL-E incidence was similar at screening and non-screening hospitals but screening hospitals had a lower incidence of HO-ESBL-E in all years. In the negative binomial model, screening was associated with a 49.1% reduction in HO-ESBL-E (p<0.001). A similar reduction was seen in the incidence of HO-ESBL-E bacteremia. When HO-ESBL-E cases were re-classified based on their admission screen result, 46.5% were positive on admission, 32.5% were confirmed as nosocomial and 21.0% were probable nosocomial cases. CONCLUSIONS: Admission screening for ESBL-E is associated with a reduced incidence of HO-ESBL-E. Controlled, prospective studies of admission screening for ESBL-E should be a priority.

The impact of infection on population health: results of the Ontario burden of infectious diseases study.

BACKGROUND: Evidence-based priority setting is increasingly important for rationally distributing scarce health resources and for guiding future health research. We sought to quantify the contribution of a wide range of infectious diseases to the overall infectious disease burden in a high-income setting. METHODOLOGY/PRINCIPAL FINDINGS: We used health-adjusted life years (HALYs), a composite measure comprising premature mortality and reduced functioning due to disease, to estimate the burden of 51 infectious diseases and associated syndromes in Ontario using 2005-2007 data. Deaths were estimated from vital statistics data and disease incidence was estimated from reportable disease, healthcare utilization, and cancer registry data, supplemented by local modeling studies and national and international epidemiologic studies. The 51 infectious agents and associated syndromes accounted for 729 lost HALYs, 44.2 deaths, and 58,987 incident cases per 100,000 population annually. The most burdensome infectious agents were: hepatitis C virus, Streptococcus pneumoniae, Escherichia coli, human papillomavirus, hepatitis B virus, human immunodeficiency virus, Staphylococcus aureus, influenza virus, Clostridium difficile, and rhinovirus. The top five, ten, and 20 pathogens accounted for 46%, 67%, and 75% of the total infectious disease burden, respectively. Marked sex-specific differences in disease burden were observed for some pathogens. The main limitations of this study were the exclusion of certain infectious diseases due to data availability issues, not considering the impact of co-infections and co-morbidity, and the inability to assess the burden of milder infections that do not result in healthcare utilization. CONCLUSIONS/SIGNIFICANCE: Infectious diseases continue to cause a substantial health burden in high-income settings such as Ontario. Most of this burden is attributable to a relatively small number of infectious agents, for which many effective interventions have been previously identified. Therefore, these findings should be used to guide public health policy, planning, and research.

Prevalence and predictors of MRSA, ESBL, and VRE colonization in the ambulatory IBD population.

BACKGROUND AND AIMS: Inflammatory bowel disease (IBD) patients may be at increased risk of acquiring antibiotic-resistant organisms (ARO). We sought to determine the prevalence of colonization of methicillin-resistant Staphylococcus aureus (MRSA), Enterobacteriaceae containing extended spectrum beta-lactamases (ESBL), and vancomycin-resistant enterococi (VRE) among ambulatory IBD patients. METHODS: We recruited consecutive IBD patients from clinics (n=306) and 3 groups of non-IBD controls from our colon cancer screening program (n=67), the family medicine clinic (n=190); and the emergency department (n=428) from the same medical center in Toronto. We obtained nasal and rectal swabs for MRSA, ESBL, and VRE and ascertained risk factors for colonization. RESULTS: Compared to non-IBD controls, IBD patients had similar prevalence of colonization with MRSA (1.5% vs. 1.6%), VRE (0% vs. 0%), and ESBL (9.0 vs. 11.1%). Antibiotic use in the prior 3 months was a risk factor for MRSA (OR, 3.07; 95% CI: 1.10-8.54), particularly metronidazole. Moreover, gastric acid suppression was associated with increased risk of MRSA colonization (adjusted OR, 7.12; 95% CI: 1.07-47.4). Predictive risk factors for ESBL included hospitalization in the past 12 months (OR, 2.04, 95% CI: 1.05-3.95); treatment with antibiotics it the past 3 months (OR, 2.66; 95% CI: 1.37-5.18), particularly prior treatment with vancomycin or cephalosporins. CONCLUSIONS: Ambulatory IBD patients have similar prevalence of MRSA, ESBL and VRE compared to non-IBD controls. This finding suggests that the increased MRSA and VRE prevalence observed in hospitalized IBD patients is acquired in-hospital rather than in the outpatient setting.

Seasonal influenza in adults and children--diagnosis, treatment, chemoprophylaxis, and institutional outbreak management: clinical practice guidelines of the Infectious Diseases Society of America.

Guidelines for the treatment of persons with influenza virus infection were prepared by an Expert Panel of the Infectious Diseases Society of America. The evidence-based guidelines encompass diagnostic issues, treatment and chemoprophylaxis with antiviral medications, and issues related to institutional outbreak management for seasonal (interpandemic) influenza. They are intended for use by physicians in all medical specialties with direct patient care, because influenza virus infection is common in communities during influenza season and may be encountered by practitioners caring for a wide variety of patients.