Integration of sequencing and epidemiological data for surveillance of SARS-CoV-2 infections in a tertiary-care hospital
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ABSTRACT:
PROVIDER: PRJEB50774 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
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| p2645.fasta.gz | Fasta.gz | |||
| p2645_chromosomelist.txt.gz | Txt | |||
| p2646.fasta.gz | Fasta.gz | |||
| p2646_chromosomelist.txt.gz | Txt | |||
| p2648.fasta.gz | Fasta.gz |
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Project description:BackgroundThe ongoing COVID-19 pandemic significantly burdens hospitals and other healthcare facilities. Therefore, understanding the entry and transmission of SARS-CoV-2 is critical for effective prevention and preparedness measures. We performed surveillance and analysis of testing and transmission of SARS-CoV-2 infections in a tertiary-care hospital in Germany during the second and third pandemic waves in fall/winter 2020.MethodsBetween calendar weeks 41/2020 and 1/2021 40% of all positive patient and staff samples (284 total) were subjected to full-length viral genome sequencing. Clusters were defined based on similar genotypes indicating common sources of infection. We integrated phylogenetic, spatial, and temporal metadata to detect nosocomial infections and outbreaks, uncover transmission chains, and evaluate containment measures' effectiveness.ResultsEpidemiologic data and contact tracing readily recognize most healthcare-associated patient infections. However, sequencing data reveal that temporally preceding index cases and transmission routes can be missed using epidemiologic methods, resulting in delayed interventions and serially linked outbreaks being counted as independent events. While hospital-associated transmissions were significantly elevated at a moderate rate of community transmission during the second wave, systematic testing and high vaccination rates among staff have led to a substantial decrease in healthcare-associated infections at the end of the second/beginning of the third wave despite high community transmissions.ConclusionsWhile epidemiologic analysis is critical for immediate containment of healthcare-associated SARS-CoV-2 outbreaks, integration of genomic surveillance revealed weaknesses in identifying staff contacts. Our study underscores the importance of high testing frequency and genomic surveillance to detect, contain and prevent SARS-CoV-2-associated infections in healthcare settings.
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Project description:Real-time molecular survey of Mycobacterium tuberculosis isolates from 2008 to 2018 reveals tuberculosis transmission in a tertiary-care university hospital
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Project description:Whole-genome sequence analysis of Burkholderia pseudomallei clinical isolates from a tertiary care hospital in Bangladesh
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Project description:INTRODUCTION: Larger populations at risk, broader use of antibiotics and longer hospital stays have impacted on the incidence of Candida sp. bloodstream infections (CBSI). OBJECTIVE: To determine clinical and epidemiologic characteristics of patients with CBSI in two tertiary care reference medical institutions in Mexico City. DESIGN: Prospective and observational laboratory-based surveillance study conducted from 07/2008 to 06/2010. METHODS: All patients with CBSI were included. Identification and antifungal susceptibility were performed using CLSI M27-A3 standard procedures. Frequencies, Mann-Whitney U test or T test were used as needed. Risk factors were determined with multivariable analysis and binary logistic regression analysis. RESULTS: CBSI represented 3.8% of nosocomial bloodstream infections. Cumulative incidence was 2.8 per 1000 discharges (incidence rate: 0.38 per 1000 patient-days). C. albicans was the predominant species (46%), followed by C. tropicalis (26%). C. glabrata was isolated from patients with diabetes (50%), and elderly patients. Sixty-four patients (86%) received antifungals. Amphotericin-B deoxycholate (AmBD) was the most commonly used agent (66%). Overall mortality rate reached 46%, and risk factors for death were APACHE II score ≥ 16 (OR = 6.94, CI95% = 2.34-20.58, p<0.0001), and liver disease (OR = 186.11, CI95% = 7.61-4550.20, p = 0.001). Full susceptibility to fluconazole, AmBD and echinocandins among C. albicans, C. tropicalis, and C. parapsilosis was observed. CONCLUSIONS: The cumulative incidence rate in these centers was higher than other reports from tertiary care hospitals from Latin America. Knowledge of local epidemiologic patterns permits the design of more specific strategies for prevention and preemptive therapy of CBSI.
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Project description:IntroductionBecause the risk of health-care associated infections (HAIs) is high in intensive care units, and HAIs are one of the causes of morbidity and mortality and affects the overall quality of health care, the continuous monitoring of HAIs in intensive care patients is essential.Aim and objectivesThis descriptive cross-sectional study was carried out over a period of five years in a tertiary-care teaching hospital. The aim of the study was to investigate the main and specific types of health-care associated Infections and determine the microbiological profile and antimicrobial susceptibility rates of isolates in patients with HAI.Methods: The active surveillance method was used to detect HAIs in patients who spent over 48 hr in a targeted ICU. Patients with blood stream infections (BSI), central line-associated bloodstream infection (CLABSI), catheter-associated urinary tract infections (CAUTI) and ventilator-associated events (VAE) were included in the study. HAI were diagnosed based on the Centre for Disease Control (CDC)'s National Healthcare Safety Network (NHSN) updated definitions of HAIs.ResultsA total of 121,051 patient days, including 7,989 central line days, 64,557 urinary catheter days, and 18,443 ventilator days, were recorded in the study population and 832 HAIs were diagnosed (incidence rate 6.9%). The overall rates of BSI, CLABSI, CAUTI and possible ventilator-associated pneumonia (p-VAP) were 3.7, 10.6, 2.1 and 13.4/1,000 device days, respectively. The most common organism isolated from BSI was Acinetobacter baumanii (n=322, 29%), followed by Klebsiella pneumoniae 225 (n=225, 20.3%). 79.8% of Acinetobacter baumanii strains were resistant to imipenem, 77.1% to ciprofloxacin and 76.4% to ampicillin. The most common organisms isolated from CAUTI were non-albicans Candida species (n=38, 18%), followed by E. coli and Citrobacter spp. (each n=33, each 15.7%).ConclusionsA trend of increasing resistance of Acinetobacter baumannii to carbapenems was observed. Risk factor analysis showed invasive procedures during sepsis and organophosphorous poisoning as significant factors.
| S-EPMC10726722 | biostudies-literature
Project description:Whole genome-based epidemiological surveillance of Listeria monocytogenes in France
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Project description:Whole-genome sequencing revealed independent emergence of vancomycin-resistant Enterococcus faecium causing sequential outbreaks over three years in a tertiary care hospital
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Project description:Of 7,772 laboratory-confirmed cases of respiratory viral infection among hospitalized patients, 22.8% were categorized as having hospital-acquired infection. The overall incidence of hospital-acquired respiratory viral infection was 3.9 (95% confidence interval, 3.7-4.1) cases per 1,000 admitted patients. Rhinovirus was the most common virus (30.3%), followed by influenza virus (17.6%) and parainfluenza virus (15.6%).
| S-EPMC7124227 | biostudies-literature
Project description:Healthcare-associated infections (HAIs) are a major worldwide public-health problem, but less data are available on the long-term trends of HAIs and antimicrobial use in Eastern China. This study describes the prevalence and long-term trends of HAIs and antimicrobial use in a tertiary care teaching hospital in Hefei, Anhui, China from 2010 to 2017 based on annual point-prevalence surveys. A total of 12 505 inpatients were included; 600 HAIs were recorded in 533 patients, with an overall prevalence of 4.26% and a frequency of 4.80%. No evidence was found for an increasing or decreasing trend in prevalence of HAI over 8 years (trend χ2 = 2.15, P = 0.143). However, significant differences in prevalence of HAI were evident between the surveys (χ2 = 21.14, P < 0.001). The intensive care unit had the highest frequency of HAIs (24.36%) and respiratory tract infections accounted for 62.50% of all cases; Escherichia coli was the most common pathogen (16.67%). A 44.13% prevalence of antimicrobial use with a gradually decreasing trend over time was recorded. More attention should be paid to potential high-risk clinical departments and HAI types with further enhancement of rational antimicrobial use.
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Project description:Health care associated infections (HCAIs) add incrementally to the morbidity, mortality, and cost expected of the patient's underlying diseases alone. Approximately, about half all cases of HCAIs are associated with medical devices. As Candida medical device-associated infection is highly drug resistant and can lead to serious life-threatening complications, there is a need of continuous surveillance of these infections to initiate preventive and corrective measures. The present study was conducted at a rural tertiary care hospital of India with an aim to evaluate the rate of medical device-associated Candida infections. Three commonly encountered medical device-associated infections (MDAI), catheter-associated urinary tract infection (CA-UTI), intravascular catheter-related blood stream infections (CR-BSI), and ventilator-associated pneumonia (VAP), were targeted. The overall rate of MDAI in our hospital was 2.1 per 1000 device days. The rate of Candida related CA-UTI and CR-BSI was noted as 1.0 and 0.3, respectively. Untiring efforts taken by team members of Hospital Acquired Infection Control Committee along with maintenance of meticulous hygiene of the hospital and wards may explain the low MDAI rates in our institute. The present surveillance helped us for systematic generation of institutional data regarding MDAI with special reference to role of Candida spp.
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