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Orosz L, Burián K. The "COVID effect" in culture-based clinical microbiology: Changes induced by COVID-19 pandemic in a Hungarian tertiary care center. J Infect Public Health 2024; 17:102453. [PMID: 38820897 DOI: 10.1016/j.jiph.2024.05.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 05/03/2024] [Accepted: 05/14/2024] [Indexed: 06/02/2024] Open
Abstract
BACKGROUND The presence of bacterial and fungal coinfections plays an important role in the mortality of patients with coronavirus 2019 (COVID-19). We compared data from the 3 years before and 3 years after the COVID-19 pandemic outbreak to evaluate its effect on the traits of bacterial and fungal diseases. METHODS We retrospectively collected and analyzed data on positive respiratory tract samples (n = 13,133 samples from 7717 patients) and blood cultures (n = 23,652 from 9653 patients) between 2017 and 2022 from the Clinical Center of the University of Szeged, Hungary. We also evaluated antimicrobial susceptibility test results derived from 169,020 respiratory samples and 549,729 blood cultures to gain insight into changes in antimicrobial resistance. RESULTS The most common respiratory pathogen in the pre-COVID era was Pseudomonas aeruginosa, whereas Candida albicans was the most frequent during the pandemic. The number of respiratory isolates of Acinetobacter baumannii was also markedly increased. In blood cultures, Staphylococcus epidermidis, Escherichia coli, and S. aureus were dominant during the study period, and A. baumannii was widespread in blood cultures during the pandemic years. Resistance to ofloxacin, penicillin, piperacillin-tazobactam, ceftazidime, cefepime, imipenem, ceftolozane-tazobactam, and itraconazole increased significantly in the COVID era. CONCLUSIONS During the COVID-19 pandemic, there were changes in the prevalence of respiratory and blood culture pathogens at the Clinical Center of the University of Szeged. C. albicans became the predominant respiratory pathogen, and the number of A. baumannii isolates increased dramatically. Additionally, antimicrobial resistance notably increased during this period.
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Affiliation(s)
- László Orosz
- Department of Medical Microbiology, University of Szeged, H-6725 Szeged Semmelweis str. 6/b., Hungary.
| | - Katalin Burián
- Department of Medical Microbiology, University of Szeged, H-6725 Szeged Semmelweis str. 6/b., Hungary
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Koupaei M, Asadi A, Mahdizade Ari M, Seyyedi ZS, Mohammadi F, Afifi Rad R, Ghanavati R, Rezaei Khozani N, Darbandi A, Masjedian Jazi F. Secondary Klebsiella pneumoniae infection in patients with COVID-19: A systematic review. Diagn Microbiol Infect Dis 2024; 108:116105. [PMID: 38147789 DOI: 10.1016/j.diagmicrobio.2023.116105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 09/27/2023] [Accepted: 10/09/2023] [Indexed: 12/28/2023]
Abstract
This study aims to investigate the development of secondary bacterial infection and risk factors associated with it in critical COVID-19 patients, and to identify the most common pathogen groups in them. All the cohort studies were retrieved from Scopus, Google Scholar, Web of Science, and MEDLINE from the inception of COVID-19 to 2022 for the following keywords: 'Klebsiella" AND "COVID-19". The most common comorbidities among the patients with COVID-19 were respiratory disease (33.62%), obesity (28.99%), and heart disease or cardiovascular disease (16.31%). We report 42.91% rate of Klebsiella spp co-infection in ICU admission patients, mostly related to K. pneumonia (26.81%), K. aerogenes (9.4%), and K. oxytoca (6.7%). The overall incidence of bacterial infection in hospitalized COVID-19 patients is estimated at 15.5% and in 32.5% of cases of co-infection patients deceased. The threat of carbapenem-resistant K. pneumoniae infections in patients with COVID-19 is imminent, therefore rational antibiotic therapy based on antibiotic sensitivity test should be implemented.
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Affiliation(s)
- Maryam Koupaei
- Department of immunology and microbiology, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Arezoo Asadi
- Endocrine Research Center, Institute of Endocrinology and Metabolism, Iran University of Medica Sciences, Tehran, Iran
| | - Marzie Mahdizade Ari
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Zahra Sadat Seyyedi
- Department of immunology and microbiology, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Fahime Mohammadi
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Roghayeh Afifi Rad
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Nahid Rezaei Khozani
- Department of immunology and microbiology, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Atieh Darbandi
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran; Molecular Microbiology Research Center, Shahed University, Tehran, Iran.
| | - Faramarz Masjedian Jazi
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
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Zhao L, Lv Z, Lin L, Li X, Xu J, Huang S, Chen Y, Fu Y, Peng C, Cao T, Ke Y, Xia X. Impact of COVID-19 pandemic on profiles of antibiotic-resistant genes and bacteria in hospital wastewater. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 334:122133. [PMID: 37399936 DOI: 10.1016/j.envpol.2023.122133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 06/21/2023] [Accepted: 07/01/2023] [Indexed: 07/05/2023]
Abstract
The COVID-19 pandemic has severely affected healthcare worldwide and has led to the excessive use of disinfectants and antimicrobial agents. However, the impact of excessive disinfection measures and specific medication prescriptions on the development and dissemination of bacterial drug resistance during the pandemic remains unclear. This study investigated the influence of the pandemic on the composition of antibiotics, antibiotic resistance genes (ARGs), and pathogenic communities in hospital wastewater using ultra-performance liquid chromatography-tandem mass spectrometry and metagenome sequencing. The overall level of antibiotics decreased after the COVID-19 outbreak, whereas the abundance of various ARGs increased in hospital wastewater. After COVID-19 outbreak, blaOXA, sul2, tetX, and qnrS had higher concentrations in winter than in summer. Seasonal factors and the COVID-19 pandemic have affected the microbial structure in wastewater, especially of Klebsiella, Escherichia, Aeromonas, and Acinetobacter. Further analysis revealed the co-existence of qnrS, blaNDM, and blaKPC during the pandemic. Various ARGs significantly correlated with mobile genetic elements, implying their potential mobility. A network analysis revealed that many pathogenic bacteria (Klebsiella, Escherichia, and Vibrio) were correlated with ARGs, indicating the existence of multi-drug resistant pathogens. Although the calculated resistome risk score did not change significantly, our results suggest that the COVID-19 pandemic shifted the composition of residual antibiotics and ARGs in hospital wastewater and contributed to the dissemination of bacterial drug resistance.
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Affiliation(s)
- Liang Zhao
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Ziquan Lv
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Liangqiang Lin
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Xiaowei Li
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Jian Xu
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Suli Huang
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Yuhua Chen
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Yulin Fu
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Changfeng Peng
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Tingting Cao
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Yuebin Ke
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Xi Xia
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China.
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Sumardi U, Valentino B, Prasetya D, Debora J, Sugianli AK. The Diagnostic Value of Kinetics of NLR to Identify Secondary Pulmonary Bacterial Infection Among COVID-19 Patients at Single Tertiary Hospital in Indonesia. Int J Gen Med 2023; 16:3281-3289. [PMID: 37546238 PMCID: PMC10404039 DOI: 10.2147/ijgm.s417569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 07/25/2023] [Indexed: 08/08/2023] Open
Abstract
Purpose Coronavirus disease 2019 (COVID-19) is a new respiratory tract infection caused by severe acute respiratory syndrome coronavirus-2. The presence of secondary pulmonary bacterial infection (SPBI) made COVID-19 difficult to treat. Neutrophil-lymphocyte count ratio (NLR) is a systemic inflammatory marker used in the diagnosis and prognosis of viral or bacterial infection. At the first 3-5 days after hyperinflammation, it occurs in relation to clinical outcome. Therefore, this study aimed to evaluate the diagnostic value of NLR based on leukocyte kinetics upon admission and after 72 hours among COVID-19 patients with or without SPBI. Patients and Methods This retrospective cross-sectional study analyzed medical records data of admitted patients with COVID-19 according to the International Classification of Disease 10th Revision (ICD-10) between January and December 2021. The list of patients was extracted and followed by a hand search to identify the inclusion or exclusion criteria and stratified into proven and non-proven SPBI based on clinical data. The study distinguished between SPBI by means of a cut-off value (COV) on the first (D1) and third day (D3), assessed using receiver operating characteristics (ROC), as well as determined the magnitude of sensitivity, specificity, and prevalence ratio. Results A screening process was conducted on 2902 COVID-19 patients, of which 236 were included, accounting for 8.1%. Among these patients, 87 (36.9%) were found to have proven SPBI. A considerable difference in NLR value between proven and non-proven SPBI was observed on both D1 (11.1 vs 4.2) and D3 (15.3 vs 5.2), with optimal COV of NLR on D1, D3 was found to be 5.29, 9.47, respectively (p < 0.001). Conclusion NLR on the D1 and D3 distinguished the occurrence of SPBI among COVID-19 patients. The application of NLR assisted in the early determination of bacterial infection and helped in controlling the empirical use of antibiotics.
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Affiliation(s)
- Uun Sumardi
- Department of Internal Medicine, Hasan Sadikin General Hospital, Faculty of Medicine Universitas Padjadjaran, Bandung, Indonesia
| | - Bima Valentino
- Department of Internal Medicine, Hasan Sadikin General Hospital, Faculty of Medicine Universitas Padjadjaran, Bandung, Indonesia
| | - Dimmy Prasetya
- Department of Internal Medicine, Hasan Sadikin General Hospital, Faculty of Medicine Universitas Padjadjaran, Bandung, Indonesia
| | - Josephine Debora
- Department of Internal Medicine, Hasan Sadikin General Hospital, Faculty of Medicine Universitas Padjadjaran, Bandung, Indonesia
| | - Adhi Kristianto Sugianli
- Department of Clinical Pathology, Hasan Sadikin General Hospital, Faculty of Medicine Universitas Padjadjaran, Bandung, Indonesia
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Celik C, Kalin G, Cetinkaya Z, Ildiz N, Ocsoy I. Recent Advances in Colorimetric Tests for the Detection of Infectious Diseases and Antimicrobial Resistance. Diagnostics (Basel) 2023; 13:2427. [PMID: 37510171 PMCID: PMC10377832 DOI: 10.3390/diagnostics13142427] [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: 05/31/2023] [Revised: 06/23/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
Diagnosis of infection-causing microorganisms with sensitive, rapid, selective and economical diagnostic tests is critical to start the right treatment. With these tests, the spread of infections can be prevented. In addition to that, the detection of antimicrobial resistance also makes a significant contribution to public health. In recent years, different types of diagnostic tests have been developed as alternatives to traditional diagnostic tests used in clinics. In particular, colorimetric tests, which minimize the need for an instrument, have advantages owing to their cost effectiveness, rapid response and naked-eye detection and practical use. In this review, we especially focused on pH indicators and nanomaterial-based colorimetric tests in detection of infection-causing microorganisms and antimicrobial resistance.
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Affiliation(s)
- Cagla Celik
- Pharmacy Services Program, Vocational School of Health Services, Hitit University, Corum 19000, Turkey
| | - Gamze Kalin
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Erciyes University, Kayseri 38039, Turkey
| | | | - Nilay Ildiz
- Medical Imaging Department, Vocational School of Health Services, Bandırma Onyedi Eylul University, Bandirma 10200, Turkey
| | - Ismail Ocsoy
- Department of Analytical Chemistry, Faculty of Pharmacy, Erciyes University, Kayseri 38039, Turkey
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Mai HTT, Espinoza JL. The Impact of COVID-19 Pandemic on ESBL-Producing Enterobacterales Infections: A Scoping Review. Antibiotics (Basel) 2023; 12:1064. [PMID: 37370383 DOI: 10.3390/antibiotics12061064] [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: 05/06/2023] [Revised: 06/07/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
Several studies have reported an increased frequency of colonization and/or infection with antibiotic-resistant bacteria (ARB) during the COVID-19 pandemic. Extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-PE) are a group of bacteria with intrinsic resistance to multiple antibiotics, including penicillins, cephalosporins, and monobactams. These pathogens are easy to spread and can cause difficult-to-treat infections. Here, we summarize the available evidence on the impact of the COVID-19 pandemic on infections caused by ESBL-PE. Using specific criteria and keywords, we searched PubMed, MEDLINE, and EMBASE for articles published up to 30 March 2023 on potential changes in the epidemiology of ESBL-E since the beginning of the COVID-19 pandemic. We identified eight studies that documented the impact of COVID-19 on ESBL-E. Five studies were focused on assessing the frequency of ESBL-PE in patient-derived specimens, and three studies investigated the epidemiological aspects of ESBL-PE infections in the context of the COVID-19 pandemic. Some of the studies that were focused on patient specimens reported a decrease in ESBL-PE positivity during the pandemic, whereas the three studies that involved patient data (1829 patients in total) reported a higher incidence of ESBL-PE infections in patients hospitalized for COVID-19 compared with those with other conditions. There are limited data on the real impact of the COVID-19 pandemic on the epidemiology of ESBL-PE infections; however, patient-derived data suggest that the pandemic has exacerbated the spread of these pathogens.
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Affiliation(s)
- Ha Thi Thao Mai
- Department of Biochemistry, Faculty of Medicine, Can Tho University of Medicine and Pharmacy, Can Tho City 900000, Vietnam
| | - J Luis Espinoza
- Faculty of Health Sciences, Kanazawa University, Kanazawa 920-0942, Ishikawa, Japan
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7
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Hartantri Y, Debora J, Widyatmoko L, Giwangkancana G, Suryadinata H, Susandi E, Hutajulu E, Hakiman APA, Pusparini Y, Alisjahbana B. Clinical and treatment factors associated with the mortality of COVID-19 patients admitted to a referral hospital in Indonesia. THE LANCET REGIONAL HEALTH. SOUTHEAST ASIA 2023; 11:100167. [PMID: 36785545 PMCID: PMC9910028 DOI: 10.1016/j.lansea.2023.100167] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 02/11/2023]
Abstract
Background Indonesia had the second-highest number of COVID-19 cases and deaths in South-East Asia. We aimed to determine the factors associated with this mortality and the effect of the recommended COVID-19 treatment regimen during the first 10 months of the epidemic. Methods This was a retrospective cohort study using secondary data from medical records. In total, 689 adult COVID-19 inpatients hospitalized between March and December 2020 were enrolled. Clinical characteristics, laboratory parameters, and treatments were analyzed by survival outcome. Kaplan-Meier statistics were used to estimate survival. Findings Of the 689 patients enrolled, 103 (14.9%) died. Disease severity was highly associated with mortality (hazard ratio [HR]: 7.69, p < 0.001). Other clinical factors associated with mortality were older age and comorbidities. Based on laboratory parameters, higher procalcitonin and C-reactive protein contents and a neutrophil-to-lymphocyte ratio >3.53 were also linked to mortality. Favipiravir was associated with lower mortality, with adjusted HRs of 0.24 (0.11-0.54) and 0.40 (0.17-0.98) among the mild/moderate and severe cases, respectively. Among patients with severe disease, steroids showed some beneficial effects in the early days of hospitalization. Interpretation Older age and comorbidities were associated with disease severity and, consequently, higher mortality. Higher mortality after the second week of hospitalization may be related to secondary bacterial infection. Favipiravir showed significant benefit for COVID-19 survival, while steroids showed benefit only in the early days of admission among patients with severe disease. Funding This research did not receive a specific grant from any funding agency in the public, commercial, or not-for-profit sectors.
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Affiliation(s)
- Yovita Hartantri
- Internal Medicine Department, Hasan Sadikin General Hospital, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Josephine Debora
- Internal Medicine Department, Hasan Sadikin General Hospital, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Leonardus Widyatmoko
- Clinical Pathology Department, Hasan Sadikin General Hospital, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Gezy Giwangkancana
- Anesthesiology and Intensive Care Department, Hasan Sadikin General Hospital, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Hendarsyah Suryadinata
- Internal Medicine Department, Hasan Sadikin General Hospital, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Evan Susandi
- Internal Medicine Department, Hasan Sadikin General Hospital, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Elisabeth Hutajulu
- Internal Medicine Department, Hasan Sadikin General Hospital, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | | | | | - Bachti Alisjahbana
- Internal Medicine Department, Hasan Sadikin General Hospital, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia,Research Center for Care and Control of Infectious Diseases (RC3ID), Universitas Padjadjaran, Bandung, Indonesia,Corresponding author. Jl. Pasteur No. 38, Bandung, 40161, West Java, Indonesia
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de Nies L, Galata V, Martin-Gallausiaux C, Despotovic M, Busi SB, Snoeck CJ, Delacour L, Budagavi DP, Laczny CC, Habier J, Lupu PC, Halder R, Fritz JV, Marques T, Sandt E, O'Sullivan MP, Ghosh S, Satagopam V, Krüger R, Fagherazzi G, Ollert M, Hefeng FQ, May P, Wilmes P. Altered infective competence of the human gut microbiome in COVID-19. MICROBIOME 2023; 11:46. [PMID: 36894986 PMCID: PMC9995755 DOI: 10.1186/s40168-023-01472-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Infections with SARS-CoV-2 have a pronounced impact on the gastrointestinal tract and its resident microbiome. Clear differences between severe cases of infection and healthy individuals have been reported, including the loss of commensal taxa. We aimed to understand if microbiome alterations including functional shifts are unique to severe cases or a common effect of COVID-19. We used high-resolution systematic multi-omic analyses to profile the gut microbiome in asymptomatic-to-moderate COVID-19 individuals compared to a control group. RESULTS We found a striking increase in the overall abundance and expression of both virulence factors and antimicrobial resistance genes in COVID-19. Importantly, these genes are encoded and expressed by commensal taxa from families such as Acidaminococcaceae and Erysipelatoclostridiaceae, which we found to be enriched in COVID-19-positive individuals. We also found an enrichment in the expression of a betaherpesvirus and rotavirus C genes in COVID-19-positive individuals compared to healthy controls. CONCLUSIONS Our analyses identified an altered and increased infective competence of the gut microbiome in COVID-19 patients. Video Abstract.
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Affiliation(s)
- Laura de Nies
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Valentina Galata
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Camille Martin-Gallausiaux
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Milena Despotovic
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Susheel Bhanu Busi
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Chantal J Snoeck
- Clinical and Applied Virology, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Lea Delacour
- Luxembourg Centre for Systems Biomedicine, LCSB Operations, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Deepthi Poornima Budagavi
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Cédric Christian Laczny
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Janine Habier
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Paula-Cristina Lupu
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Rashi Halder
- Scientific Central Services, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Joëlle V Fritz
- Transversal Translation Medicine, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Taina Marques
- Translational Neuroscience Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Estelle Sandt
- Translational Medicine Operations Hub, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Marc Paul O'Sullivan
- Translational Medicine Operations Hub, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Soumyabrata Ghosh
- Bioinformatics Core, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Venkata Satagopam
- Bioinformatics Core, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Rejko Krüger
- Transversal Translation Medicine, Luxembourg Institute of Health, Strassen, Luxembourg
- Translational Neuroscience Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Guy Fagherazzi
- Deep Digital Phenotyping Research Unit, Department of Precision Health, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Markus Ollert
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-Sur-Alzette, Luxembourg
- Department of Dermatology and Allergy Centre, Odense University Hospital, Odense, Denmark
| | - Feng Q Hefeng
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-Sur-Alzette, Luxembourg
| | - Patrick May
- Bioinformatics Core, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Paul Wilmes
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, 6, Avenue du Swing, L-4367, Belvaux, Luxembourg.
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Mai W, Liu Y, Meng Q, Xu J, Wu J. Bacterial Epidemiology and Antimicrobial Resistance Profiles of Respiratory Specimens of Children with Pneumonia in Hainan, China. Infect Drug Resist 2023; 16:249-261. [PMID: 36660346 PMCID: PMC9842527 DOI: 10.2147/idr.s397513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/02/2023] [Indexed: 01/13/2023] Open
Abstract
Purpose To investigate the bacterial species and antimicrobial susceptibility of respiratory specimens of children with pneumonia in Hainan, China. Methods A total of 5017 specimens, including 4986 sputum samples, 19 bronchoalveolar lavage fluid samples and 12 tracheal tube tip samples from hospitalized children with pneumonia from April 1, 2021 to March 31, 2022 were studied. All the bacterial isolates were identified and confirmed with the VITEK 2 system. Antimicrobial susceptibility of all isolates was determined using the Kirby-Bauer method or the VITEK 2 Compact automatic system, following the breakpoints recommended by the Clinical and Laboratory Standards Institute. Results A total of 996 bacterial isolates were collected and classified into 24 species. The top 10 most frequent species were Haemophilus influenzae (356 isolates, 35.7%), Streptococcus pneumoniae (128, 12.9%), Moraxella catarrhalis (114, 11.5%), Escherichia coli (89, 8.9%), Staphylococcus aureus (89, 8.9%), Klebsiella pneumoniae (82, 8.2%), Acinetobacter baumannii (31, 3.1%), Pseudomonas aeruginosa (28, 2.8%), Enterobacter cloacae (18, 1.8%), and Streptococcus agalactiae (13, 1.3%). 70.5% strains had the resistant (R) and/or intermediate (I) phenotypes to at least one of the tested drugs, with a large proportion (54.6%) showing resistance to two or more commonly used antibiotics. In addition, 60.5% (69/114) of M. catarrhalis strains and 42.9% (153/356) of H. influenzae strains produced β-lactamases while 19.1% (17/89) E. coli and 6.1% (5/82) K. pneumoniae strains produced extended-spectrum β-lactamases. Conclusion A diversity of pathogenic bacteria were isolated from the respiratory tract of children with pneumonia in Hainan, China. High-frequency resistance to first-line antimicrobial drugs was observed in Gram-negative and Gram-positive bacteria, including 544 isolates resistant to at least two antibiotics. Rapid identification and susceptibility testing should be implemented for children with bacterial pneumonia in Hainan before drug treatment is recommended.
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Affiliation(s)
- Wenhui Mai
- Center for Science Experiments, Hainan Medical University, Haikou, Hainan Province, People’s Republic of China,Laboratory Department, Haikou Maternal and Child Health Hospital, Haikou, Hainan Province, People’s Republic of China
| | - Yiwei Liu
- Center for Science Experiments, Hainan Medical University, Haikou, Hainan Province, People’s Republic of China,Department of Pathogen Biology, Hainan Medical University, Haikou, Hainan Province, People’s Republic of China
| | - Qiaoyi Meng
- Center for Science Experiments, Hainan Medical University, Haikou, Hainan Province, People’s Republic of China,Department of Pathogen Biology, Hainan Medical University, Haikou, Hainan Province, People’s Republic of China
| | - Jianping Xu
- Center for Science Experiments, Hainan Medical University, Haikou, Hainan Province, People’s Republic of China,Department of Biology, McMaster University, Hamilton, Ontario, Canada,Correspondence: Jianping Xu; Jinyan Wu, Email ;
| | - Jinyan Wu
- Center for Science Experiments, Hainan Medical University, Haikou, Hainan Province, People’s Republic of China,Department of Pathogen Biology, Hainan Medical University, Haikou, Hainan Province, People’s Republic of China,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, Hainan Province, People’s Republic of China
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10
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Hu S, You Y, Zhang S, Tang J, Chen C, Wen W, Wang C, Cheng Y, Zhou M, Feng Z, Tan T, Qi G, Wang M, Liu X. Multidrug-resistant infection in COVID-19 patients: A meta-analysis. J Infect 2023; 86:66-117. [PMID: 36347426 PMCID: PMC9637013 DOI: 10.1016/j.jinf.2022.10.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 10/23/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Siqi Hu
- Hangzhou Institute of Cardiovascular Diseases, Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University,Hangzhou, 310015, China
| | - Yao You
- Hangzhou Institute of Cardiovascular Diseases, Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University,Hangzhou, 310015, China
| | - Shenghui Zhang
- Hangzhou Institute of Cardiovascular Diseases, Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University,Hangzhou, 310015, China
| | - Jiake Tang
- Hangzhou Institute of Cardiovascular Diseases, Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University,Hangzhou, 310015, China
| | - Chen Chen
- Hangzhou Institute of Cardiovascular Diseases, Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University,Hangzhou, 310015, China
| | - Wen Wen
- Hangzhou Institute of Cardiovascular Diseases, Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University,Hangzhou, 310015, China
| | - Chunyi Wang
- Hangzhou Institute of Cardiovascular Diseases, Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University,Hangzhou, 310015, China
| | - Yongran Cheng
- School of Public Health, Hangzhou Medical College, Hangzhou, 311300, China
| | - Mengyun Zhou
- Department of Molecular & Cellular Physiology, Shinshu University School of Medicine, 3900803, Japan
| | - Zhanhui Feng
- Department of Neurology, Affiliated Hospital of Guizhou Medical University, Guiyang, 550000, China
| | - Tao Tan
- Faculty of Applied Science, Macao Polytechnic University, Macao SAR, 999078, China
| | - Guanming Qi
- Division of Pulmonary, Critical Care and Sleep, Tufts Medical Center, Boston, MA, 02111, USA,Corresponding authors
| | - Mingwei Wang
- Hangzhou Institute of Cardiovascular Diseases, Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University,Hangzhou, 310015, China,Corresponding authors
| | - Xiaoyan Liu
- Hangzhou Institute of Cardiovascular Diseases, Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University,Hangzhou, 310015, China,Corresponding authors
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11
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Yahya RO. Problems Associated with Co-Infection by Multidrug-Resistant Klebsiella pneumoniae in COVID-19 Patients: A Review. Healthcare (Basel) 2022; 10:healthcare10122412. [PMID: 36553936 PMCID: PMC9778403 DOI: 10.3390/healthcare10122412] [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: 08/28/2022] [Revised: 11/25/2022] [Accepted: 11/26/2022] [Indexed: 12/02/2022] Open
Abstract
To date, coronavirus disease 2019 (COVID-19) and its variants have been reported as a novel public health concern threatening us worldwide. The presence of Klebsiella pneumoniae in COVID-19-infected patients is a major problem due to its resistance to multiple antibiotics, and it can possibly make the management of COVID-19 in patients more problematic. The impact of co-infection by K. pneumoniae on COVID-19 patients was explored in the current review. The spread of K. pneumoniae as a co-infection among critically ill COVID-19 patients, particularly throughout hospitalization, was identified and recorded via numerous reports. Alarmingly, the extensive application of antibiotics in the initial diagnosis of COVID-19 infection may reduce bacterial co-infection, but it increases the antibiotic resistance of bacteria such as the strains of K. pneumoniae. The correct detection of multidrug-resistant K. pneumoniae can offer a supportive reference for the diagnosis and therapeutic management of COVID-19 patients. Furthermore, the prevention and control of K. pneumoniae are required to minimize the risk of COVID-19. The aim of the present review is, therefore, to report on the virulence factors of the K. pneumonia genotypes, the drug resistance of K. pneumonia, and the impact of K. pneumoniae co-infection with COVID-19 on patients through a study of the published scientific papers, reports, and case studies.
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Affiliation(s)
- Reham Omar Yahya
- Basic Sciences Department, College of Sciences and Health Professions, King Saud Bin Abdulaziz University for Health Sciences, Riyadh 11671, Saudi Arabia;
- King Abduallah International Medical Research Center, Riyadh 11481, Saudi Arabia
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12
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Subagdja MFM, Sugianli AK, Prodjosoewojo S, Hartantri Y, Parwati I. Antibiotic Resistance in COVID-19 with Bacterial Infection: Laboratory-Based Surveillance Study at Single Tertiary Hospital in Indonesia. Infect Drug Resist 2022; 15:5849-5856. [PMID: 36217341 PMCID: PMC9547599 DOI: 10.2147/idr.s379324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/29/2022] [Indexed: 11/05/2022] Open
Abstract
Purpose Coronavirus disease 2019 (COVID-19) is a new pandemic affecting the respiratory system and caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In addition to the increased use of antibiotics, the length of stay of hospitalized patients affects the risk of bacterial infections among the COVID-19 patients. However, this pandemic has interrupted antibiotic surveillance activity and led to an information gap about the prevalence and characteristics of bacterial infection. This study aims to describe the antibiotic resistance in COVID-19 patients with culture-proven bacterial infection using a laboratory-based surveillance approach. Patients and Methods A retrospective study with a cross-sectional design was conducted on adult patients that confirmed positive for COVID-19 according to the International Classification of Diseases 10th Revision (ICD-10). From March 2020 to October 2021, data were obtained from the hospital information system and merged with the culture and antibiotic susceptibility test from laboratory information system at Hasan Sadikin General Hospital. The outcome is the prevalence percentage of resistance to selected antibiotics in patients with COVID-19. The resistance percentage is considered high when equal to or more than 20%. Results There was 2786 adult patient confirmed for COVID-19 according to the ICD-10, and 26.3% (n = 733) of them submitted clinical specimen for culture. The prevalence of bacterial infection among COVID-19 patients was 16.4%, predominating Gram-negative bacteria (GNB). The respiratory specimen dominated the positive growth culture. The GNB were predominantly discovered among the respiratory and non-respiratory specimens. High range resistance to ampicillin-sulbactam (24–100%), ceftriaxone (22–81%), cefotaxime (22–73%) and ciprofloxacin (20–86%) are observed among the GNB. Conclusion There is high resistance to fluoroquinolone and cephalosporins in identified isolate, commonly used as the first-line empirical treatment for respiratory and non-respiratory infection in Indonesia. The continuous antibiotic surveillance is mandatory and crucial to prevent the long-term effects of the COVID-19 pandemic, particularly bacterial infection.
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Affiliation(s)
| | - Adhi Kristianto Sugianli
- Department of Clinical Pathology Faculty of Medicine Universitas Padjadjaran/Dr. Hasan Sadikin General Hospital, Bandung, Indonesia,Correspondence: Adhi Kristianto Sugianli, Pasteur 38, Bandung ZIP 40161, Bandung, Indonesia, Tel +62 22 203 3307, Email
| | - Susantina Prodjosoewojo
- Department of Internal Medicine, Faculty of Medicine Universitas Padjadjaran/Dr. Hasan Sadikin General Hospital, Bandung, Indonesia
| | - Yovita Hartantri
- Department of Internal Medicine, Faculty of Medicine Universitas Padjadjaran/Dr. Hasan Sadikin General Hospital, Bandung, Indonesia
| | - Ida Parwati
- Department of Clinical Pathology Faculty of Medicine Universitas Padjadjaran/Dr. Hasan Sadikin General Hospital, Bandung, Indonesia
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13
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Sokolović D, Drakul D, Joksimović B, Lalović N, Avram N, Milić M, Nogo-Živanović D, Mijović B. Consumption of Antibiotics in Primary Care Setting before and during COVID-19 Pandemic in Republic of Srpska, Bosnia and Herzegovina. Antibiotics (Basel) 2022; 11:antibiotics11101319. [PMID: 36289977 PMCID: PMC9598767 DOI: 10.3390/antibiotics11101319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/17/2022] [Accepted: 09/24/2022] [Indexed: 11/16/2022] Open
Abstract
The pandemic of COVID-19 has brought many changes in health care systems at all levels of health care. The increase in the number of cases of COVID-19 has led to overuse and misuse of antibiotics.The aim of this study was to compare the consumption of antibiotics for systemic use in outpatients in the Republic of Srpska (RS), before and during the first year of the COVID-19 pandemic, as well as the association between antibiotic consumption and the rate of incidence and mortality of COVID-19. The total consumption of the antibiotics for systemic use (J01) in outpatients in the Republic of Srpska during 2019 was 19.40 DDD/TID, with an increase to 30.80 DDD/TID in 2020.Significantly higher use of penicillin (10.58 ± 11.01 DDD/TID in 2019 vs. 17.10 ± 13.63 DDD/TID in 2020), cephalosporins (2.68 ± 1.90 DDD/TID in 2019 vs. 5.93 ± 2.77 DDD/TID in 2020) and macrolides (2.14 ± 2.22 DDD/TID in 2019 vs. 3.40 ± 3.44 DDD/TID in 2020) was observed during the pandemic period. It is necessary to improve the prescribing practice of antibiotics at the primary health care level, public awareness about rational use of antibiotics, as well as the current antibiotic stewardship programs and control their implementation.
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Affiliation(s)
- Dragana Sokolović
- Faculty of Medicine Foča, University of East Sarajevo, Studentska 5, 73300 Foča, Bosnia and Herzegovina
- Correspondence: ; Tel.: +387-6599-4867
| | - Dragana Drakul
- Faculty of Medicine Foča, University of East Sarajevo, Studentska 5, 73300 Foča, Bosnia and Herzegovina
| | - Bojan Joksimović
- Faculty of Medicine Foča, University of East Sarajevo, Studentska 5, 73300 Foča, Bosnia and Herzegovina
| | - Nenad Lalović
- Faculty of Medicine Foča, University of East Sarajevo, Studentska 5, 73300 Foča, Bosnia and Herzegovina
- Department of Surgery, University Hospital Foča, Studentska 5, 73300 Foča, Bosnia and Herzegovina
| | - Nada Avram
- Faculty of Medicine Foča, University of East Sarajevo, Studentska 5, 73300 Foča, Bosnia and Herzegovina
- Department of Ophtalmology, University Hospital Foča, Studentska 5, 73300 Foča, Bosnia and Herzegovina
| | - Marija Milić
- Department of Epidemiology, Faculty of Medicine, University of Pristina Temporarily Seated in Kosovska Mitrovica, Henri Dunant, 38220 Kosovska Mitrovica, Serbia
| | - Dajana Nogo-Živanović
- Faculty of Medicine Foča, University of East Sarajevo, Studentska 5, 73300 Foča, Bosnia and Herzegovina
| | - Biljana Mijović
- Faculty of Medicine Foča, University of East Sarajevo, Studentska 5, 73300 Foča, Bosnia and Herzegovina
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