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Dos Santos L, Silva LL, Pelloso FC, Maia V, Pujals C, Borghesan DH, Carvalho MD, Pedroso RB, Pelloso SM. Use of machine learning to identify protective factors for death from COVID-19 in the ICU: a retrospective study. PeerJ 2024; 12:e17428. [PMID: 38881861 PMCID: PMC11179634 DOI: 10.7717/peerj.17428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 04/29/2024] [Indexed: 06/18/2024] Open
Abstract
Background Patients in serious condition due to COVID-19 often require special care in intensive care units (ICUs). This disease has affected over 758 million people and resulted in 6.8 million deaths worldwide. Additionally, the progression of the disease may vary from individual to individual, that is, it is essential to identify the clinical parameters that indicate a good prognosis for the patient. Machine learning (ML) algorithms have been used for analyzing complex medical data and identifying prognostic indicators. However, there is still an urgent need for a model to elucidate the predictors related to patient outcomes. Therefore, this research aimed to verify, through ML, the variables involved in the discharge of patients admitted to the ICU due to COVID-19. Methods In this study, 126 variables were collected with information on demography, hospital length stay and outcome, chronic diseases and tumors, comorbidities and risk factors, complications and adverse events, health care, and vital indicators of patients admitted to an ICU in southern Brazil. These variables were filtered and then selected by a ML algorithm known as decision trees to identify the optimal set of variables for predicting patient discharge using logistic regression. Finally, a confusion matrix was performed to evaluate the model's performance for the selected variables. Results Of the 532 patients evaluated, 180 were discharged: female (16.92%), with a central venous catheter (23.68%), with a bladder catheter (26.13%), and with an average of 8.46- and 23.65-days using bladder catheter and submitted to mechanical ventilation, respectively. In addition, the chances of discharge increase by 14% for each additional day in the hospital, by 136% for female patients, 716% when there is no bladder catheter, and 737% when no central venous catheter is used. However, the chances of discharge decrease by 3% for each additional year of age and by 9% for each other day of mechanical ventilation. The performance of the training data presented a balanced accuracy of 0.81, sensitivity of 0.74, specificity of 0.88, and the kappa value was 0.64. The test performance had a balanced accuracy of 0.85, sensitivity 0.75, specificity 0.95, and kappa value of 0.73. The McNemar test found that there were no significant differences in the error rates in the training and test data, suggesting good classification. This work showed that female, the absence of a central venous catheter and bladder catheter, shorter mechanical ventilation, and bladder catheter duration were associated with a greater chance of hospital discharge. These results may help develop measures that lead to a good prognosis for the patient.
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Affiliation(s)
- Lander Dos Santos
- State University of Maringá, Graduate Program in Health Sciences, Maringá, Paraná, Brazil
| | - Lincoln Luis Silva
- Department of Emergency Medicine, Duke University School of Medicine, Durham, NC, United States of America
| | | | | | - Constanza Pujals
- State University of Maringá, Graduate Program in Health Sciences, Maringá, Paraná, Brazil
| | | | - Maria Dalva Carvalho
- State University of Maringá, Graduate Program in Health Sciences, Maringá, Paraná, Brazil
| | - Raíssa Bocchi Pedroso
- State University of Maringá, Graduate Program in Health Sciences, Maringá, Paraná, Brazil
| | - Sandra Marisa Pelloso
- State University of Maringá, Graduate Program in Health Sciences, Maringá, Paraná, Brazil
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Gaudet A, Kreitmann L, Nseir S. ICU-Acquired Colonization and Infection Related to Multidrug-Resistant Bacteria in COVID-19 Patients: A Narrative Review. Antibiotics (Basel) 2023; 12:1464. [PMID: 37760760 PMCID: PMC10525572 DOI: 10.3390/antibiotics12091464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/17/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
A large proportion of ICU-acquired infections are related to multidrug-resistant bacteria (MDR). Infections caused by these bacteria are associated with increased mortality, and prolonged duration of mechanical ventilation and ICU stay. The aim of this narrative review is to report on the association between COVID-19 and ICU-acquired colonization or infection related to MDR bacteria. Although a huge amount of literature is available on COVID-19 and MDR bacteria, only a few clinical trials have properly evaluated the association between them using a non-COVID-19 control group and accurate design and statistical methods. The results of these studies suggest that COVID-19 patients are at a similar risk of ICU-acquired MDR colonization compared to non-COVID-19 controls. However, a higher risk of ICU-acquired infection related to MDR bacteria has been reported in several studies, mainly ventilator-associated pneumonia and bloodstream infection. Several potential explanations could be provided for the high incidence of ICU-acquired infections related to MDR. Immunomodulatory treatments, such as corticosteroids, JAK2 inhibitors, and IL-6 receptor antagonist, might play a role in the pathogenesis of these infections. Additionally, a longer stay in the ICU was reported in COVID-19 patients, resulting in higher exposure to well-known risk factors for ICU-acquired MDR infections, such as invasive procedures and antimicrobial treatment. Another possible explanation is the surge during successive COVID-19 waves, with excessive workload and low compliance with preventive measures. Further studies should evaluate the evolution of the incidence of ICU-acquired infections related to MDR bacteria, given the change in COVID-19 patient profiles. A better understanding of the immune status of critically ill COVID-19 patients is required to move to personalized treatment and reduce the risk of ICU-acquired infections. The role of specific preventive measures, such as targeted immunomodulation, should be investigated.
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Affiliation(s)
- Alexandre Gaudet
- Médecine Intensive Réanimation, CHU de Lille, F-59000 Lille, France;
- CNRS, Inserm U1019-UMR9017-CIIL-Centre d’Infection et d’Immunité de Lille, Institut Pasteur de Lille, CHU Lille, Université de Lille, F-59000 Lille, France
| | - Louis Kreitmann
- Centre for Antimicrobial Optimisation, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London W12 0HS, UK;
- Department of Intensive Care Medicine, Imperial College Healthcare NHS Trust, London NW1 5QH, UK
| | - Saad Nseir
- Médecine Intensive Réanimation, CHU de Lille, F-59000 Lille, France;
- Inserm U1285, Université de Lille, CNRS, UMR 8576-UGSF, F-59000 Lille, France
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Aguirre-Sánchez JR, Quiñones B, Ortiz-Muñoz JA, Prieto-Alvarado R, Vega-López IF, Martínez-Urtaza J, Lee BG, Chaidez C. Comparative Genomic Analyses of Virulence and Antimicrobial Resistance in Citrobacter werkmanii, an Emerging Opportunistic Pathogen. Microorganisms 2023; 11:2114. [PMID: 37630674 PMCID: PMC10457828 DOI: 10.3390/microorganisms11082114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/11/2023] [Accepted: 08/13/2023] [Indexed: 08/27/2023] Open
Abstract
Citrobacter werkmanii is an emerging and opportunistic human pathogen found in developing countries and is a causative agent of wound, urinary tract, and blood infections. The present study conducted comparative genomic analyses of a C. werkmanii strain collection from diverse geographical locations and sources to identify the relevant virulence and antimicrobial resistance genes. Pangenome analyses divided the examined C. werkmanii strains into five distinct clades; the subsequent classification identified genes with functional roles in carbohydrate and general metabolism for the core genome and genes with a role in secretion, adherence, and the mobilome for the shell and cloud genomes. A maximum-likelihood phylogenetic tree with a heatmap, showing the virulence and antimicrobial genes' presence or absence, demonstrated the presence of genes with functional roles in secretion systems, adherence, enterobactin, and siderophore among the strains belonging to the different clades. C. werkmanii strains in clade V, predominantly from clinical sources, harbored genes implicated in type II and type Vb secretion systems as well as multidrug resistance to aminoglycoside, beta-lactamase, fluoroquinolone, phenicol, trimethoprim, macrolides, sulfonamide, and tetracycline. In summary, these comparative genomic analyses have demonstrated highly pathogenic and multidrug-resistant genetic profiles in C. werkmanii strains, indicating a virulence potential for this commensal and opportunistic human pathogen.
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Affiliation(s)
- José R. Aguirre-Sánchez
- Laboratorio Nacional para la Investigación en Inocuidad Alimentaria, Centro de Investigación en Alimentación y Desarrollo A.C. (CIAD), Coordinación Regional Culiacán, Culiacan 80110, Mexico;
| | - Beatriz Quiñones
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, Albany, CA 94710, USA; (B.Q.); (B.G.L.)
| | - José A. Ortiz-Muñoz
- Parque de Innovación Tecnológica de la Universidad Autónoma de Sinaloa, Culiacan 80040, Mexico; (J.A.O.-M.); (R.P.-A.); (I.F.V.-L.)
| | - Rogelio Prieto-Alvarado
- Parque de Innovación Tecnológica de la Universidad Autónoma de Sinaloa, Culiacan 80040, Mexico; (J.A.O.-M.); (R.P.-A.); (I.F.V.-L.)
| | - Inés F. Vega-López
- Parque de Innovación Tecnológica de la Universidad Autónoma de Sinaloa, Culiacan 80040, Mexico; (J.A.O.-M.); (R.P.-A.); (I.F.V.-L.)
| | - Jaime Martínez-Urtaza
- Departament de Genètica i de Microbiologia, Universitat Autờnoma de Barcelona, 08193 Bellaterra, Spain;
| | - Bertram G. Lee
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, Albany, CA 94710, USA; (B.Q.); (B.G.L.)
| | - Cristóbal Chaidez
- Laboratorio Nacional para la Investigación en Inocuidad Alimentaria, Centro de Investigación en Alimentación y Desarrollo A.C. (CIAD), Coordinación Regional Culiacán, Culiacan 80110, Mexico;
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Fakhreddine S, Fawaz M, Hassanein S, Al Khatib A. Prevalence and mortality rate of healthcare-associated infections among COVID-19 patients: a retrospective cohort community-based approach. Front Public Health 2023; 11:1235636. [PMID: 37637822 PMCID: PMC10449454 DOI: 10.3389/fpubh.2023.1235636] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 07/24/2023] [Indexed: 08/29/2023] Open
Abstract
Background The prevalence of HAI among COVID-19 patients ranged between 4.8% and 42.8% with the highest occurrence observed in critically ill patients. The present study aimed to evaluate the clinical features of HAI in severe and critical COVID-19 patients, their microbiological characteristics, and the attributable risk factors. Methods This is an analytical observational, retrospective single-center, cohort study that included 723 patients with severe-critical COVID-19 admitted to Saint George Hospital between September 2020 and February 2021. Data collection included demographic variables (sex, age), comorbidities, laboratory findings, HAI types and agents, COVID-19 treatment modalities, hospitalization settings, length of stay, and mortality rate. Data was analyzed using SPSS version 25. Results The prevalence of patients developing HAI was 7.3% (53 of 723). Five types of nosocomial bacterial infections were tracked noting ventilator-associated pneumonia (41.26%), catheter-associated urinary tract infection (28.6%), hospital-acquired pneumonia (17.44%), catheter-related bloodstream infection (6.35%), and bloodstream infection (6.35%). Binary logistic analysis showed that HAI are statistically affected by four factors noting patients' age (p = 0.039), Length of Stay (p < 0.001), BIPAP (p = 0.019), and mechanical ventilation (p < 0.001). The risk of having HAI increases 3.930 times in case of mechanical ventilation, 2.366 times in case of BIPAP, 1.148 times when the LOS increases 1 day, and 1.029 times when the age is higher with 1 year. Conclusion Since the prevalence of HAI is high among severe and critical COVID-19 patients, it is important to prepare a treatment with diagnostic, preventative, and control measures for this infection.
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Affiliation(s)
- Soha Fakhreddine
- Department of Infectious Diseases, Saint-Georges Hospital, Hadat, Lebanon
- Department of Nursing, Faculty of Health Sciences, Beirut Arab University, Beirut, Lebanon
| | - Mirna Fawaz
- Department of Nursing, Faculty of Health Sciences, Beirut Arab University, Beirut, Lebanon
| | - Salwa Hassanein
- Department of Nursing, Faculty of Health Sciences, Almoosa College, Al Ahsa, Saudi Arabia
- Department of Community Health Nursing, Cairo University, Cairo, Egypt
| | - Alissar Al Khatib
- Department of Nursing, Faculty of Health Sciences, Beirut Arab University, Beirut, Lebanon
- Department of Nursing, Faculty of Health Sciences, Almoosa College, Al Ahsa, Saudi Arabia
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Kwon JH, Nickel KB, Reske KA, Stwalley D, Dubberke ER, Lyons PG, Michelson A, McMullen K, Sahrmann JM, Gandra S, Olsen MA, Burnham JP. Risk factors for hospital-acquired infection during the SARS-CoV-2 pandemic. J Hosp Infect 2023; 133:8-14. [PMID: 36493966 PMCID: PMC9724556 DOI: 10.1016/j.jhin.2022.11.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/08/2022] [Accepted: 11/17/2022] [Indexed: 12/12/2022]
Abstract
OBJECTIVE To evaluate risk factors for hospital-acquired infection (HAI) in patients during the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic, including historical and concurrent cohorts. DESIGN Retrospective cohort. SETTING Three Missouri hospitals, data from 1st January 2017 to 30th September 2020. PARTICIPANTS Patients aged ≥18 years and admitted for ≥48 h. METHODS Univariate and multi-variate Cox proportional hazards models incorporating the competing risk of death were used to determine risk factors for HAI. A-priori sensitivity analyses were performed to assess the robustness of the urine-, blood- and respiratory-culture-based HAI definition. RESULTS The cohort included 254,792 admissions, with 7147 (2.8%) HAIs (1661 blood, 3407 urine, 2626 respiratory). Patients with SARS-CoV-2 had increased risk of HAI (adjusted hazards ratio 1.65, 95% confidence interval 1.38-1.96), and SARS-CoV-2 infection was one of the strongest risk factors for development of HAI. Other risk factors for HAI included certain admitting services, chronic comorbidities, intensive care unit stay during index admission, extremes of body mass index, hospital, and selected medications. Factors associated with lower risk of HAI included year of admission (declined over the course of the study), admitting service and medications. Risk factors for HAI were similar in sensitivity analyses restricted to patients with diagnostic codes for pneumonia/upper respiratory infection and urinary tract infection. CONCLUSIONS SARS-CoV-2 was associated with significantly increased risk of HAI.
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Affiliation(s)
- J H Kwon
- Division of Infectious Diseases, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - K B Nickel
- Division of Infectious Diseases, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - K A Reske
- Division of Infectious Diseases, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - D Stwalley
- Division of Infectious Diseases, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - E R Dubberke
- Division of Infectious Diseases, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - P G Lyons
- Division of Pulmonary and Critical Care Medicine, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - A Michelson
- Division of Pulmonary and Critical Care Medicine, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - K McMullen
- Mercy, Infection Prevention, St Louis, MO, USA
| | - J M Sahrmann
- Division of Infectious Diseases, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - S Gandra
- Division of Infectious Diseases, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - M A Olsen
- Division of Infectious Diseases, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - J P Burnham
- Division of Infectious Diseases, Washington University in St Louis School of Medicine, St Louis, MO, USA.
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Langford BJ, So M, Simeonova M, Leung V, Lo J, Kan T, Raybardhan S, Sapin ME, Mponponsuo K, Farrell A, Leung E, Soucy JPR, Cassini A, MacFadden D, Daneman N, Bertagnolio S. Antimicrobial resistance in patients with COVID-19: a systematic review and meta-analysis. THE LANCET. MICROBE 2023; 4:e179-e191. [PMID: 36736332 PMCID: PMC9889096 DOI: 10.1016/s2666-5247(22)00355-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 10/08/2022] [Accepted: 11/24/2022] [Indexed: 02/03/2023]
Abstract
BACKGROUND Frequent use of antibiotics in patients with COVID-19 threatens to exacerbate antimicrobial resistance. We aimed to establish the prevalence and predictors of bacterial infections and antimicrobial resistance in patients with COVID-19. METHODS We did a systematic review and meta-analysis of studies of bacterial co-infections (identified within ≤48 h of presentation) and secondary infections (>48 h after presentation) in outpatients or hospitalised patients with COVID-19. We searched the WHO COVID-19 Research Database to identify cohort studies, case series, case-control trials, and randomised controlled trials with populations of at least 50 patients published in any language between Jan 1, 2019, and Dec 1, 2021. Reviews, editorials, letters, pre-prints, and conference proceedings were excluded, as were studies in which bacterial infection was not microbiologically confirmed (or confirmed via nasopharyngeal swab only). We screened titles and abstracts of papers identified by our search, and then assessed the full text of potentially relevant articles. We reported the pooled prevalence of bacterial infections and antimicrobial resistance by doing a random-effects meta-analysis and meta-regression. Our primary outcomes were the prevalence of bacterial co-infection and secondary infection, and the prevalence of antibiotic-resistant pathogens among patients with laboratory-confirmed COVID-19 and bacterial infections. The study protocol was registered with PROSPERO (CRD42021297344). FINDINGS We included 148 studies of 362 976 patients, which were done between December, 2019, and May, 2021. The prevalence of bacterial co-infection was 5·3% (95% CI 3·8-7·4), whereas the prevalence of secondary bacterial infection was 18·4% (14·0-23·7). 42 (28%) studies included comprehensive data for the prevalence of antimicrobial resistance among bacterial infections. Among people with bacterial infections, the proportion of infections that were resistant to antimicrobials was 60·8% (95% CI 38·6-79·3), and the proportion of isolates that were resistant was 37·5% (26·9-49·5). Heterogeneity in the reported prevalence of antimicrobial resistance in organisms was substantial (I2=95%). INTERPRETATION Although infrequently assessed, antimicrobial resistance is highly prevalent in patients with COVID-19 and bacterial infections. Future research and surveillance assessing the effect of COVID-19 on antimicrobial resistance at the patient and population level are urgently needed. FUNDING WHO.
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Affiliation(s)
- Bradley J Langford
- Public Health Ontario, Toronto, ON, Canada; Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada.
| | - Miranda So
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada; University Health Network, Toronto, ON, Canada
| | | | - Valerie Leung
- Public Health Ontario, Toronto, ON, Canada; Toronto East Health Network, Toronto, ON, Canada
| | - Jennifer Lo
- Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Tiffany Kan
- North York General Hospital, Toronto, ON, Canada
| | | | - Mia E Sapin
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, ON, Canada
| | - Kwadwo Mponponsuo
- University of Calgary, Calgary, AB, Canada; Alberta Health Services, Calgary, AB, Canada
| | | | - Elizabeth Leung
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada; Unity Health Toronto, Toronto, ON, UK
| | - Jean-Paul R Soucy
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | | | - Derek MacFadden
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, ON, Canada; Ottawa Hospital, Ottawa, ON, Canada
| | - Nick Daneman
- Public Health Ontario, Toronto, ON, Canada; Sunnybrook Health Sciences Centre, Toronto, ON, Canada
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Trends in Pseudomonas aeruginosa ( P. aeruginosa) Bacteremia during the COVID-19 Pandemic: A Systematic Review. Antibiotics (Basel) 2023; 12:antibiotics12020409. [PMID: 36830319 PMCID: PMC9952731 DOI: 10.3390/antibiotics12020409] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/25/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
Pseudomonas aeruginosa (P. aeruginosa) is among the most common pathogens associated with healthcare-acquired infections, and is often antibiotic resistant, causing significant morbidity and mortality in cases of P. aeruginosa bacteremia. It remains unclear how the incidence of P. aeruginosa bacteremia changed during the Coronavirus Disease 2019 (COVID-19) pandemic, with studies showing almost contradictory conclusions despite enhanced infection control practices during the pandemic. This systematic review sought to examine published reports with incidence rates for P. aeruginosa bacteremia during (defined as from March 2020 onwards) and prior to the COVID-19 pandemic. A systematic literature search was conducted in accordance with PRISMA guidelines and performed in Cochrane, Embase, and Medline with combinations of the key words (pseudomonas aeruginosa OR PAE) AND (incidence OR surveillance), from database inception until 1 December 2022. Based on the pre-defined inclusion criteria, a total of eight studies were eligible for review. Prior to the pandemic, the prevalence of P. aeruginosa was on an uptrend. Several international reports found a slight increase in the incidence of P. aeruginosa bacteremia during the COVID-19 pandemic. These findings collectively highlight the continued importance of good infection prevention and control and antimicrobial stewardship during both pandemic and non-pandemic periods. It is important to implement effective infection prevention and control measures, including ensuring hand hygiene, stepping up environmental cleaning and disinfection efforts, and developing timely guidelines on the appropriate prescription of antibiotics.
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Healthcare-associated infections (HAIs) during the coronavirus disease 2019 (COVID-19) pandemic: A time-series analysis. ANTIMICROBIAL STEWARDSHIP & HEALTHCARE EPIDEMIOLOGY : ASHE 2023; 3:e14. [PMID: 36714284 PMCID: PMC9879893 DOI: 10.1017/ash.2022.361] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/10/2022] [Accepted: 11/12/2022] [Indexed: 01/18/2023]
Abstract
Objective To use interrupted time-series analyses to investigate the impact of the coronavirus disease 2019 (COVID-19) pandemic on healthcare-associated infections (HAIs). We hypothesized that the pandemic would be associated with higher rates of HAIs after adjustment for confounders. Design We conducted a cross-sectional study of HAIs in 3 hospitals in Missouri from January 1, 2017, through August 31, 2020, using interrupted time-series analysis with 2 counterfactual scenarios. Setting The study was conducted at 1 large quaternary-care referral hospital and 2 community hospitals. Participants All adults ≥18 years of age hospitalized at a study hospital for ≥48 hours were included in the study. Results In total, 254,792 admissions for ≥48 hours occurred during the study period. The average age of these patients was 57.6 (±19.0) years, and 141,107 (55.6%) were female. At hospital 1, 78 CLABSIs, 33 CAUTIs, and 88 VAEs were documented during the pandemic period. Hospital 2 had 13 CLABSIs, 6 CAUTIs, and 17 VAEs. Hospital 3 recorded 11 CLABSIs, 8 CAUTIs, and 11 VAEs. Point estimates for hypothetical excess HAIs suggested an increase in all infection types across facilities, except for CLABSIs and CAUTIs at hospital 1 under the "no pandemic" scenario. Conclusions The COVID-19 era was associated with increases in CLABSIs, CAUTIs, and VAEs at 3 hospitals in Missouri, with variations in significance by hospital and infection type. Continued vigilance in maintaining optimal infection prevention practices to minimize HAIs is warranted.
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Özbek M, Toy HI, Takan I, Asfa S, Arshinchi Bonab R, Karakülah G, Kontou PI, Geronikolou SA, Pavlopoulou A. A Counterintuitive Neutrophil-Mediated Pattern in COVID-19 Patients Revealed through Transcriptomics Analysis. Viruses 2022; 15:104. [PMID: 36680144 PMCID: PMC9866184 DOI: 10.3390/v15010104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 12/25/2022] [Accepted: 12/27/2022] [Indexed: 01/01/2023] Open
Abstract
The COVID-19 pandemic has persisted for almost three years. However, the mechanisms linked to the SARS-CoV-2 effect on tissues and disease severity have not been fully elucidated. Since the onset of the pandemic, a plethora of high-throughput data related to the host transcriptional response to SARS-CoV-2 infections has been generated. To this end, the aim of this study was to assess the effect of SARS-CoV-2 infections on circulating and organ tissue immune responses. We profited from the publicly accessible gene expression data of the blood and soft tissues by employing an integrated computational methodology, including bioinformatics, machine learning, and natural language processing in the relevant transcriptomics data. COVID-19 pathophysiology and severity have mainly been associated with macrophage-elicited responses and a characteristic "cytokine storm". Our counterintuitive findings suggested that the COVID-19 pathogenesis could also be mediated through neutrophil abundance and an exacerbated suppression of the immune system, leading eventually to uncontrolled viral dissemination and host cytotoxicity. The findings of this study elucidated new physiological functions of neutrophils, as well as tentative pathways to be explored in asymptomatic-, ethnicity- and locality-, or staging-associated studies.
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Affiliation(s)
- Melih Özbek
- Izmir Biomedicine and Genome Center, Balcova, Izmir 35340, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Balcova, Izmir 35220, Turkey
| | - Halil Ibrahim Toy
- Izmir Biomedicine and Genome Center, Balcova, Izmir 35340, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Balcova, Izmir 35220, Turkey
| | - Işil Takan
- Izmir Biomedicine and Genome Center, Balcova, Izmir 35340, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Balcova, Izmir 35220, Turkey
| | - Seyedehsadaf Asfa
- Izmir Biomedicine and Genome Center, Balcova, Izmir 35340, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Balcova, Izmir 35220, Turkey
| | - Reza Arshinchi Bonab
- Izmir Biomedicine and Genome Center, Balcova, Izmir 35340, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Balcova, Izmir 35220, Turkey
| | - Gökhan Karakülah
- Izmir Biomedicine and Genome Center, Balcova, Izmir 35340, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Balcova, Izmir 35220, Turkey
| | | | - Styliani A. Geronikolou
- Clinical, Translational and Experimental Surgery Research Centre, Biomedical Research Foundation Academy of Athens, 11527 Athens, Greece
- University Research Institute of Maternal and Child Health and Precision Medicine, UNESCO on Adolescent Health Care, National and Kapodistrian University of Athens, Aghia Sophia Children’s Hospital, 11527 Athens, Greece
| | - Athanasia Pavlopoulou
- Izmir Biomedicine and Genome Center, Balcova, Izmir 35340, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Balcova, Izmir 35220, Turkey
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Mustafa ZU, Tariq S, Iftikhar Z, Meyer JC, Salman M, Mallhi TH, Khan YH, Godman B, Seaton RA. Predictors and Outcomes of Healthcare-Associated Infections among Patients with COVID-19 Admitted to Intensive Care Units in Punjab, Pakistan; Findings and Implications. Antibiotics (Basel) 2022; 11:antibiotics11121806. [PMID: 36551463 PMCID: PMC9774163 DOI: 10.3390/antibiotics11121806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/21/2022] [Accepted: 12/06/2022] [Indexed: 12/15/2022] Open
Abstract
Healthcare-associated infections (HAIs) have a considerable impact on morbidity, mortality and costs. The COVID-19 pandemic resulted in an appreciable number of hospitalized patients being admitted to intensive care units (ICUs) globally with a greater risk of HAIs. Consequently, there is a need to evaluate predictors and outcomes of HAIs among COVID-19 patients admitted to ICUs. A retrospective study of patients with COVID-19 admitted to ICUs of three tertiary care hospitals in the Punjab province over a five-month period in 2021 was undertaken to ascertain predictors and outcomes of HAIs. Of the 4534 hospitalized COVID-19 patients, 678 were admitted to ICUs, of which 636 patients fulfilled the inclusion criteria. Overall, 67 HAIs were identified among the admitted patients. Ventilator-associated lower respiratory tract infections and catheter-related urinary tract infections were the most frequent HAIs. A significantly higher number of patients who developed HAIs were on anticoagulants (p = 0.003), antithrombotic agents (p < 0.001), antivirals (p < 0.001) and IL-6 inhibiting agents (p < 0.001). Secondary infections were significantly higher in patients who were on invasive mechanical ventilation (p < 0.001), had central venous access (p = 0.023), and urinary catheters (p < 0.001). The mortality rate was significantly higher in those with secondary infections (25.8% vs. 1.2%, p < 0.001). Our study concluded that COVID-19 patients admitted to ICUs have a high prevalence of HAIs associated with greater mortality. Key factors need to be addressed to reduce HAIs.
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Affiliation(s)
- Zia Ul Mustafa
- Discipline of Clinical Pharmacy, School of Pharmaceutical Sciences, Universiti Sains Malaysia, Gelugor 11800, Pinang, Malaysia
- Department of Pharmacy Services, District Headquarter (DHQ) Hospital, Pakpattan 57400, Pakistan
- Correspondence: (Z.U.M.); (B.G.)
| | - Sania Tariq
- Department of Medicine, Faisalabad Medical University, Faisalabad 38000, Pakistan
| | - Zobia Iftikhar
- Department of Medicine, Faisalabad Medical University, Faisalabad 38000, Pakistan
| | - Johanna C. Meyer
- Department of Public Health Pharmacy and Management, School of Pharmacy, Sefako Makgatho Health Sciences University, Ga-Rankuwa, Pretoria 0208, South Africa
| | - Muhammad Salman
- Institute of Pharmacy, Faculty of Pharmaceutical and Allied Health Sciences, Lahore College for Women University, Lahore 54000, Pakistan
| | - Tauqeer Hussain Mallhi
- Department of Clinical Pharmacy, College of Pharmacy, Jouf University, Sakaka 72388, Saudi Arabia
| | - Yusra Habib Khan
- Department of Clinical Pharmacy, College of Pharmacy, Jouf University, Sakaka 72388, Saudi Arabia
| | - Brian Godman
- Department of Public Health Pharmacy and Management, School of Pharmacy, Sefako Makgatho Health Sciences University, Ga-Rankuwa, Pretoria 0208, South Africa
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman P.O. Box 346, United Arab Emirates
- Department of Pharmacoepidemiology, Strathclyde Institute of Pharmacy and Biomedical Science (SIPBS), University of Strathclyde, Glasgow G4 0RE, UK
- Correspondence: (Z.U.M.); (B.G.)
| | - R. Andrew Seaton
- Queen Elizabeth University Hospital, Glasgow G51 4TF, UK
- Scottish Antimicrobial Prescribing Group, Healthcare Improvement Scotland, Glasgow G1 2NP, UK
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Sinto R, Lie KC, Setiati S, Suwarto S, Nelwan EJ, Djumaryo DH, Karyanti MR, Prayitno A, Sumariyono S, Moore CE, Hamers RL, Day NPJ, Limmathurotsakul D. Blood culture utilization and epidemiology of antimicrobial-resistant bloodstream infections before and during the COVID-19 pandemic in the Indonesian national referral hospital. Antimicrob Resist Infect Control 2022; 11:73. [PMID: 35590391 PMCID: PMC9117993 DOI: 10.1186/s13756-022-01114-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 05/11/2022] [Indexed: 11/29/2022] Open
Abstract
Background There is a paucity of data regarding blood culture utilization and antimicrobial-resistant (AMR) infections in low and middle-income countries (LMICs). In addition, there has been a concern for increasing AMR infections among COVID-19 cases in LMICs. Here, we investigated epidemiology of AMR bloodstream infections (BSI) before and during the COVID-19 pandemic in the Indonesian national referral hospital. Methods We evaluated blood culture utilization rate, and proportion and incidence rate of AMR-BSI caused by WHO-defined priority bacteria using routine hospital databases from 2019 to 2020. A patient was classified as a COVID-19 case if their SARS-CoV-2 RT-PCR result was positive. The proportion of resistance was defined as the ratio of the number of patients having a positive blood culture for a WHO global priority resistant pathogen per the total number of patients having a positive blood culture for the given pathogen. Poisson regression models were used to assess changes in rate over time. Results Of 60,228 in-hospital patients, 8,175 had at least one blood culture taken (total 17,819 blood cultures), giving a blood culture utilization rate of 30.6 per 1,000 patient-days. A total of 1,311 patients were COVID-19 cases. Blood culture utilization rate had been increasing before and during the COVID-19 pandemic (both p < 0.001), and was higher among COVID-19 cases than non-COVID-19 cases (43.5 vs. 30.2 per 1,000 patient-days, p < 0.001). The most common pathogens identified were K. pneumoniae (23.3%), Acinetobacter spp. (13.9%) and E. coli (13.1%). The proportion of resistance for each bacterial pathogen was similar between COVID-19 and non-COVID-19 cases (all p > 0.10). Incidence rate of hospital-origin AMR-BSI increased from 130.1 cases per 100,000 patient-days in 2019 to 165.5 in 2020 (incidence rate ratio 1.016 per month, 95%CI:1.016–1.017, p < 0.001), and was not associated with COVID-19 (p = 0.96). Conclusions In our setting, AMR-BSI incidence and etiology were similar between COVID-19 and non-COVID-19 cases. Incidence rates of hospital-origin AMR-BSI increased in 2020, which was likely due to increased blood culture utilization. We recommend increasing blood culture utilization and generating AMR surveillance reports in LMICs to inform local health care providers and policy makers. Supplementary Information The online version contains supplementary material available at 10.1186/s13756-022-01114-x.
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12
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SHEA statement on antibiotic stewardship in hospitals during public health emergencies. Infect Control Hosp Epidemiol 2022; 43:1541-1552. [PMID: 36102000 PMCID: PMC9672827 DOI: 10.1017/ice.2022.194] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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13
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Impact of the COVID-19 Pandemic on the Prevalence of HAIs and the Use of Antibiotics in an Italian University Hospital. Healthcare (Basel) 2022; 10:healthcare10091597. [PMID: 36141209 PMCID: PMC9498585 DOI: 10.3390/healthcare10091597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/19/2022] [Accepted: 08/20/2022] [Indexed: 12/04/2022] Open
Abstract
The COVID-19 pandemic has massively affected healthcare systems globally, causing a possible reduction in attention to traditional infection prevention programs. The objective of this study was to estimate the prevalence of healthcare-associated infections (HAIs) and the use of antimicrobials in an Italian University Hospital and to investigate whether the intensification of hospital infection control measures during the COVID-19 pandemic has affected the prevalence of bacterial HAIs. A point prevalence survey was conducted according to the simplified ECDC protocol. The survey identified a local HAI prevalence of 9.0%, revealing an increase compared to pre-pandemic values (7.3%). The survey also identified an antimicrobial exposure of 40.8%, revealing a decrease in their use compared to the study carried out in the pre-pandemic era (44.6%). Among the organizational challenges experienced during the COVID-19 pandemic, despite the greater attention paid to infection prevention measures aimed at reducing SARS-CoV-2, many healthcare facilities had to contend with the controlled availability of personnel, physical space limitations and a large number of patients. Active surveillance in hospital wards and the consequent reporting by personnel specialized in infection control is fundamental for hospitals to recognize gaps in prevention and report any observed increases in HAIs.
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Bongomin F, Kanyike AM, Musoke P, Sereke SG, Okot J, Kibone W, Semulimi AW, Baluku JB, Nakwagala FN. Prehospital antimicrobial use among people with coronavirus disease 2019 (COVID-19) in Uganda. ANTIMICROBIAL STEWARDSHIP & HEALTHCARE EPIDEMIOLOGY : ASHE 2022; 2:e90. [PMID: 36483441 PMCID: PMC9726531 DOI: 10.1017/ash.2022.238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/23/2022] [Accepted: 04/28/2022] [Indexed: 06/17/2023]
Affiliation(s)
- Felix Bongomin
- Department of Medical Microbiology, Faculty of Medicine, Gulu University, Gulu, Uganda
- School of Medicine, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Andrew Marvin Kanyike
- Department of Internal Medicine, Faculty of Health Sciences, Busitema University, Mbale, Uganda
| | - Phillip Musoke
- School of Medicine, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Senai Goitom Sereke
- School of Medicine, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Jerom Okot
- Department of Medical Microbiology, Faculty of Medicine, Gulu University, Gulu, Uganda
| | - Winnie Kibone
- School of Medicine, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Andrew Weil Semulimi
- Makerere Lung Institute, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Joseph Baruch Baluku
- Makerere Lung Institute, College of Health Sciences, Makerere University, Kampala, Uganda
- Division of Pulmonology, Kiruddu National Referral Hospital, Kampala, Uganda
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Comparing the Occurrence of Healthcare-Associated Infections in Patients with and without COVID-19 Hospitalized during the Pandemic: A 16-Month Retrospective Cohort Study in a Hospital Intensive Care Unit. J Clin Med 2022; 11:jcm11051446. [PMID: 35268538 PMCID: PMC8910983 DOI: 10.3390/jcm11051446] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 03/04/2022] [Accepted: 03/04/2022] [Indexed: 11/17/2022] Open
Abstract
The COVID-19 pandemic has increased the healthcare-associated infection (HAI) risk in intensive care unit (ICU) patients. However, a comparison between patients with and without COVID-19 in terms of HAI incidence has been rarely explored. In this study, we characterized the occurrence of HAI among patients with and without COVID-19 admitted to the ICU of the Umberto I hospital of Rome during the first 16 months of the pandemic and also identified risk factors for HAI acquisition. Patients were divided into four groups according to their ICU admission date. A multivariable conditional risk set regression model for multiple events was constructed for each admission period. Adjusted hazard ratios and 95% confidence intervals were calculated. Overall, 352 COVID-19 and 130 non-COVID-19 patients were included, and a total of 361 HAIs were recorded. We found small differences between patients with and without COVID-19 in the occurrence and type of HAI, but the infections in the two cohorts mostly involved different microorganisms. The results indicate that patient management was likely an important factor influencing the HAI occurrence during the pandemic. Effective prevention and control strategies to reduce HAI rates should be implemented.
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Evaluation of Bi-Lateral Co-Infections and Antibiotic Resistance Rates among COVID-19 Patients. Antibiotics (Basel) 2022; 11:antibiotics11020276. [PMID: 35203877 PMCID: PMC8868529 DOI: 10.3390/antibiotics11020276] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/12/2022] [Accepted: 02/17/2022] [Indexed: 12/20/2022] Open
Abstract
In addition to the pathogenesis of SARS-CoV-2, bacterial co-infection plays an essential role in the incidence and progression of SARS-CoV-2 infections by increasing the severity of infection, as well as increasing disease symptoms, death rate and antimicrobial resistance (AMR). The current study was conducted in a tertiary-care hospital in Lahore, Pakistan, among hospitalized COVID-19 patients to see the prevalence of bacterial co-infections and the AMR rates among different isolated bacteria. Clinical samples for the laboratory diagnosis were collected from 1165 hospitalized COVID-19 patients, of which 423 were found to be positive for various bacterial infections. Most of the isolated bacteria were Gram-negative rods (n = 366), followed by Gram-positive cocci (n = 57). A significant association (p < 0.05) was noted between the hospitalized COVID-19 patients and bacterial co-infections. Staphylococcus aureus (S. aureus) showed high resistance against tetracycline (61.7%), Streptococcus pyogenes against penicillin (100%), E. coli against Amp-clavulanic acid (88.72%), Klebsiella pneumoniae against ampicillin (100%), and Pseudomonas aeruginosa against ciprofloxacin (75.40%). Acinetobacter baumannii was 100% resistant to the majority of tested antibiotics. The prevalence of methicillin-resistant S. aureus (MRSA) was 14.7%. The topmost symptoms of >50% of COVID-19 patients were fever, fatigue, dyspnea and chest pain with a significant association (p < 0.05) in bacterial co-infected patients. The current study results showed a comparatively high prevalence of AMR, which may become a severe health-related issue in the future. Therefore, strict compliance of antibiotic usage and employment of antibiotic stewardship programs at every public or private institutional level are recommended.
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Strelkova DА, Rachina SA, Kuleshov V, Burmistrova E, Sychev IN, Ananicheva N, Vasileva Y, Churkina E. Microbiological monitoring of COVID-19 patients in the ICU: a prospective observational study. CLINICAL MICROBIOLOGY AND ANTIMICROBIAL CHEMOTHERAPY 2022. [DOI: 10.36488/cmac.2022.3.274-282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Objective.
To study spectrum of pathogens and the time to colonization of respiratory samples in patients with severe and critical COVID-19 as well as to analyze incidence of nosocomial infections and structure of prescribed antibacterial drugs.
Materials and Methods.
The prospective observational study included patients aged 18 years and older with confirmed severe and critical COVID-19 from December 2021 to February 2022. During the first 48 hours and then every 2–3 days of hospitalization, a respiratory sample was collected: sputum, tracheal aspirate (if intubated), bronchoalveolar lavage (if bronchoscopy was performed) for microscopy and microbiological examination. Some patients were screened for invasive aspergillosis. Clinical and demographic data, comorbidities, pathogenetic therapy for COVID-19, antibiotic therapy, cases of probable/documented bacterial nosocomial infections, antibiotic-associated diarrhea, and hospital treatment outcomes were recorded.
Results.
A total of 82 patients were included in this study. Patients with lung parenchyma involvement of more than 50% by computer tomography predominated; most of them (77%) required intubation and mechanical ventilation due to progression of respiratory failure, and 76% of patients had a lethal outcome. During the first 48 hours, a respiratory sample was obtained from 47 patients; the rest of the patients presented with non-productive cough. No growth of microorganisms was detected in 31 (36.8%) cases; clinically significant pathogens were detected in 16 (19.5%) patients. A subsequent analysis included data from 63 patients with a sufficient number of samples for dynamic observation were used. During the first 3 days of ICU stay, the most common bacterial pathogens were Klebsiella pneumoniae without acquired antibiotic resistance and methicillin-susceptible Staphylococcus aureus. From 3rd day and afterwards, an increase in the proportion of Acinetobacter baumannii, other non-fermenting bacteria, and carbapenemresistant Enterobacterales was noted. Among the pathogens causing lower respiratory tract infections, A. baumannii and carbapenem-resistant K. pneumoniae were predominant pathogens and accounted for 76% of cases. Positive galactomannan test results were obtained in 4 cases.
Conclusions.
The study confirmed importance of bacterial nosocomial infections in patients with severe and critical COVID-19. In the case of the development of nosocomial lower respiratory tract infections, empirical antimicrobial therapy should take into account the predominance of carbapenem-resistant Enterobacteria and A. baumannii, as well as the possibility of invasive aspergillosis.
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Affiliation(s)
| | | | - V.G. Kuleshov
- City Clinical Hospital named after S.S. Yudin (Moscow, Russia)
| | | | - Igor N. Sychev
- City Clinical Hospital named after S.S. Yudin (Moscow, Russia)
| | - N.A. Ananicheva
- City Clinical Hospital named after S.S. Yudin (Moscow, Russia)
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