1
|
Williams A, Repetto E, Lebbie I, Khalife M, Jensen TO. Are C-reactive protein and procalcitonin safe and useful for antimicrobial stewardship purposes in patients with COVID-19? A scoping review. ANTIMICROBIAL STEWARDSHIP & HEALTHCARE EPIDEMIOLOGY : ASHE 2024; 4:e129. [PMID: 39290622 PMCID: PMC11406566 DOI: 10.1017/ash.2024.372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 07/04/2024] [Accepted: 07/05/2024] [Indexed: 09/19/2024]
Abstract
Objective The primary objectives of this study were to assess the usefulness of C-reactive protein (CRP) and procalcitonin (PCT) in the diagnosis of bacterial co-infections in coronavirus disease 2019 (COVID-19) and if their incorporation in antimicrobial stewardship (AMS) programs is safe and useful, stratified by severity of disease as level of care, intensive care unit (ICU) or non-ICU. Our secondary objectives were to identify cut-off values for antibiotic decision-making and identify reported results from low- and middle-income countries (LMICs). Design A scoping review of published literature, adhering to the PRISMA statement for Systematic Reviews and Meta-analyses Extension for Scoping Reviews guidelines. The last search was performed in January 2024. Results Fifty-nine studies were included in this scoping review: 20 studies reporting predictive values and/or sensitivity/specificity results for PCT, 8 reporting clear objectives on AMS, and 3 studies from LMICs. Conclusion In the context of non-ICU hospitalized COVID-19 patients in high-income countries, a PCT value below 0.25 mg/L can be a useful tool to rule out bacterial co-infection. The wide range of reported negative predictive values suggests that PCT should be interpreted in the context of other clinical findings. Our results do not support the use of CRP in the same manner as PCT. There is a clear need for more studies in LMICs.
Collapse
Affiliation(s)
- Anita Williams
- Wesfarmers Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, Australia
- Middle East Medical Unit, Médecins Sans Frontières, Beirut, Lebanon
- Luxembourg Operational Research (LuxOR) Unit, Médecins Sans Frontières, Luxembourg City, Luxembourg
| | - Ernestina Repetto
- Infectious Diseases Department, Université Libre de Bruxelles (ULB), CHU Saint-Pierre, Brussels, Belgium
| | - Ishmael Lebbie
- Kenema Project, Médecins Sans Frontières, Operational Centre Brussels, Kenema City, Sierra Leone
| | - Mohamad Khalife
- Middle East Medical Unit, Médecins Sans Frontières, Beirut, Lebanon
| | - Tomas Oestergaard Jensen
- Medical Department, Médecins Sans Frontières, Operational Center Paris, Paris, France
- Center of Excellence for Health, Immunity, and Infections, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
2
|
Hilvers E, Matizanadzo J, McClure V, Butterick P, Morgan M. Clostridioides difficile infection following COVID-19: A nationwide analysis using routine surveillance data in Wales. J Hosp Infect 2024:S0195-6701(24)00264-0. [PMID: 39094737 DOI: 10.1016/j.jhin.2024.07.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 07/17/2024] [Accepted: 07/19/2024] [Indexed: 08/04/2024]
Abstract
BACKGROUND CDI incidence has increased in Wales from summer 2020 and has remained elevated. There is evidence of poorer outcomes from concurrent CDI and COVID-19 infections, but it is not clear if infection with COVID-19 directly impacts likelihood of CDI infection. AIM We investigated the relationship between CDI and COVID-19 and the impact of secondary infections. METHODS We conducted two analytical studies using routine surveillance data: i) population level ecological case control study comparing CDI cases in the Welsh population by SARS-COV-2 exposure in the previous 90 days, ii) cohort study of COVID-19 cases by secondary infection presence, investigating CDI development within 90 days. FINDINGS Case control: 12% (196/1645) of CDI cases had prior COVID-19 and were twice as likely to have had COVID-19 compared to general population controls, when controlling for other infection history (OR 2.1, CI 1.8-2.5, p<0.0001). CDI cases were 8 times more likely to have had other infections, independent of COVID-19 history (OR 8.0, CI 7.0-9.0, p<0.001). COHORT STUDY 2% (2,255/137,620)) of the COVID-19 cohort developed >1 secondary infection, and <1% (185/137620) developed CDI within 90 days. CDI risk was four times higher in those with secondary infections, after age and sex adjustment (RR 4.6, CI 3.1 - 6.1, p<0.001). CDI risk increased with age and did not differ by sex. CONCLUSIONS Findings suggest a relationship between COVID-19 and CDI. However, incidence of CDI following COVID-19 was a rare outcome generally, suggesting other factors are likely contributing to the increased rates of CDI observed since 2020.
Collapse
Affiliation(s)
- Ember Hilvers
- Welsh Healthcare Epidemiologist Network (WHEN), Public Health Wales, Cardiff, Wales.
| | - Joshua Matizanadzo
- Communicable Disease Surveillance Centre (CDSC) Field Epidemiology Team, Public Health Wales, Cardiff, Wales
| | - Victoria McClure
- Healthcare Associated Infections and Antimicrobial Resistance Team (HARP), Public Health Wales, Cardiff, Wales
| | - Philip Butterick
- Welsh Healthcare Epidemiologist Network (WHEN), Public Health Wales, Cardiff, Wales
| | - Mari Morgan
- Healthcare Associated Infections and Antimicrobial Resistance Team (HARP), Public Health Wales, Cardiff, Wales
| |
Collapse
|
3
|
Sanikhani R, Akbari M, Hosseinzadeh M, Siavash M, Badmasti F, Solgi H. Outbreak of colistin and carbapenem-resistant Klebsiella pneumoniae ST16 co-producing NDM-1 and OXA-48 isolates in an Iranian hospital. BMC Microbiol 2024; 24:59. [PMID: 38368365 PMCID: PMC10874040 DOI: 10.1186/s12866-024-03207-6] [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: 08/10/2023] [Accepted: 01/28/2024] [Indexed: 02/19/2024] Open
Abstract
BACKGROUND Colistin and carbapenem-resistant Klebsiella pneumoniae (Col-CRKP) represent a significant and constantly growing threat to global public health. We report here an outbreak of Col-CRKP infections during the fifth wave of COVID-19 pandemic. METHODS The outbreak occurred in an intensive care unit with 22 beds at a teaching university hospital, Isfahan, Iran. We collected eight Col-CRKP strains from seven patients and characterized these strains for their antimicrobial susceptibility, determination of hypermucoviscous phenotype, capsular serotyping, molecular detection of virulence and resistance genes. Clonal relatedness of the isolates was performed using MLST. RESULTS The COVID-19 patients were aged 24-75 years with at least 50% pulmonary involvement and were admitted to the intensive care unit. They all had superinfection caused by Col-CRKP, and poor responses to antibiotic treatment and died. With the exception of one isolate that belonged to the ST11, all seven representative Col-CRKP strains belonged to the ST16. Of these eight isolates, one ST16 isolate carried the iucA and ybtS genes was identified as serotype K20 hypervirulent Col-CRKP. The blaSHV and blaNDM-1 genes were the most prevalent resistance genes, followed by blaOXA-48 and blaCTX-M-15 and blaTEM genes. Mobilized colistin-resistance genes were not detected in the isolates. CONCLUSIONS The continual emergence of ST16 Col-CRKP strains is a major threat to public health worldwide due to multidrug-resistant and highly transmissible characteristics. It seems that the potential dissemination of these clones highlights the importance of appropriate monitoring and strict infection control measures to prevent the spread of resistant bacteria in hospitals.
Collapse
Affiliation(s)
| | - Mojtaba Akbari
- Isfahan Endocrine and Metabolism Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Majid Hosseinzadeh
- Department of Genetics and Molecular Biology, School of Medicine Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mansour Siavash
- Isfahan Endocrine and Metabolism Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Farzad Badmasti
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran.
| | - Hamid Solgi
- Isfahan Endocrine and Metabolism Research Center, Isfahan University of Medical Sciences, Isfahan, Iran.
- Department of Laboratory Medicine, Amin Hospital, Isfahan University of Medical Sciences, Isfahan, Iran.
| |
Collapse
|
4
|
Mutua JM, Njeru JM, Musyoki AM. Extended-spectrum β-lactamase- producing gram-negative bacterial infections in severely ill COVID-19 patients admitted in a national referral hospital, Kenya. Ann Clin Microbiol Antimicrob 2023; 22:91. [PMID: 37838665 PMCID: PMC10576885 DOI: 10.1186/s12941-023-00641-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 09/26/2023] [Indexed: 10/16/2023] Open
Abstract
BACKGROUND Bacterial infections in COVID-19 patients, especially those caused by multidrug-resistant gram-negative strains, are associated with increased morbidity, hospital stay and mortality. However, there is limited data on the epidemiology of extended-spectrum β-lactamase (ESBL)-producing bacteria in COVID-19 patients. Here, we assessed the prevalence and the factors associated with ESBL-producing gram-negative bacterial (GNB) infections among severely ill COVID-19 patients admitted in Kenyatta National Hospital (KNH), Kenya. METHODS We adopted a descriptive cross-sectional study design for patients admitted between October 2021 and February 2022, purposively recruiting 120 SARS-CoV- 2 infected participants based on clinical presentation. Demographics and clinical characteristics data were collected using structured questionnaires and case report forms. Clinical samples were collected and analyzed by standard microbiological methods in the KNH Microbiology laboratory and the Centre for Microbiology Research, Kenya Medical Research Institute. RESULTS GNB infections prevalence was 40.8%, majorly caused by ESBL-producers (67.3%) predominated by Klebsiella pneumoniae (45.5%). Generally, 73% of the ESBL producers harboured our target ESBL genes, mainly CTX-M-type (59%, 17/29) in K. pneumoniae (76.9%, 20/26). GNB harbouring TEM-type (83%, 10/12) and SHV-type (100%, 7/7) genes showed ESBLs phenotypes and inhibitor resistance, mainly involving clavulanate, but most of them remained susceptible to tazobactam (60%, 6/10). SHV-type genes carrying ESBL producers showed resistance to both cefotaxime (CTX) and ceftazidime (CAZ) (K. pneumoniae), CAZ (E. coli) or CTX (E. cloacae complex and K. pneumoniae). About 87% (20/23) of isolates encoding CTX-M-type β-lactamases displayed CTX/ceftriaxone (CRO) resistance phenotype. About 42% of isolates with CTX-M-type β-lactamases only hydrolyzed ceftazidime (CAZ). Isolates with OXA-type β-lactamases were resistant to CTX, CAZ, CRO, cefepime and aztreonam. Patients with comorbidities were 10 times more likely to have an ESBL-producing GNB infection (aOR = 9.86, 95%CI 1.30 - 74.63, p = 0.003). CONCLUSION We report a high prevalence of ESBL-GNB infections in severely ill COVID-19 patients, predominantly due to Klebsiella pneumoniae harbouring CTX-M type ESBL genes. The patient's underlying comorbidities increased the risk of ESBL-producing GNB infection. In COVID-19 pandemic, enhanced systematic and continuous surveillance of ESBL-producing GNB, strict adherence to infection control measures and antimicrobial stewardship policies are warranted in the current study setting.
Collapse
Affiliation(s)
- Jeniffer Munyiva Mutua
- Department of Laboratory Medicine, Kenyatta National Hospital, 20723-00202, Nairobi, Kenya.
- Department of Medical Laboratory Sciences, Kenyatta University, 43844-00100, Nairobi, Kenya.
| | - John Mwaniki Njeru
- Centre for Microbiology Research, Kenya Medical Research Institute, 19464-00200, Nairobi, Kenya
| | - Abednego Moki Musyoki
- Department of Medical Laboratory Sciences, Kenyatta University, 43844-00100, Nairobi, Kenya
| |
Collapse
|
5
|
Gentges J, El-Kouri N, Rahman T, Mushtaq N, Hudson E, Scheck D. Use of nares swab to de-escalate vancomycin for patients with suspected methicillin-resistant Staphylococcus aureus. ANTIMICROBIAL STEWARDSHIP & HEALTHCARE EPIDEMIOLOGY : ASHE 2023; 3:e167. [PMID: 38028911 PMCID: PMC10644157 DOI: 10.1017/ash.2023.444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/02/2023] [Accepted: 08/07/2023] [Indexed: 12/01/2023]
Abstract
Introduction According to the US Center for Disease Control and Prevention, 30%-50% of antibiotic use in hospitals is unnecessary or inappropriate. The coronavirus disease 2019 pandemic further complicates antibiotic use leading to greater initiation of empiric antibiotics. The result is antibiotic overuse and increased duration of unnecessary therapy. Vancomycin is a drug of last resort, primarily relegated to the treatment of Methicillin-Resistant Staphylococcus aureus (MRSA). De-escalating vancomycin can mean waiting on MRSA culture results, which may take up to 96 h. Nares screening for MRSA is shown to possess high negative predictive value for ruling out suspected MRSA pneumonia, intra-abdominal infections, and bacteremia. Methods This before-and-after study examines the impact of vancomycin therapy de-escalation due to absence of MRSA colonization detected via PCR assay of nares swabs. An intervention with providers using SMART goals was designed to increase nasal swabbing for MRSA and ultimately decrease vancomycin use at a large, tertiary-care urban hospital. Results There was a significant increase in use of vancomycin nares swabs (28/150 vs 48/100, p = 0.040) in the immediate pre/postintervention period, and significant decreases in vancomycin usage days/1,000 patient days of 2.34% per month (p = 0.039) over a two year period after the intervention. Conclusion An intervention using PCR nares swabs to detect MRSA led to significant, lasting decreases in vancomycin usage at this hospital. Similar interventions should be planned at hospitals experiencing overuse of this antibiotic.
Collapse
Affiliation(s)
- Joshua Gentges
- Department of Emergency Medicine, The University of Oklahoma School of Community Medicine (OUSCM), Tulsa, OK, USA
| | - Nadeem El-Kouri
- Department of Emergency Medicine, The University of Oklahoma School of Community Medicine (OUSCM), Tulsa, OK, USA
| | | | | | | | - David Scheck
- Infectious Disease/Hospital Epidemiologist Hillcrest Medical Center, Tulsa, OK, USA
| |
Collapse
|
6
|
Mobarak-Qamsari M, Jenaghi B, Sahebi L, Norouzi-Shadehi M, Salehi MR, Shakoori-Farahani A, Khoshnevis H, Abdollahi A, Feizabadi MM. Evaluation of Acinetobacter baumannii, Klebsiella pneumoniae, and Staphylococcus aureus respiratory tract superinfections among patients with COVID-19 at a tertiary-care hospital in Tehran, Iran. Eur J Med Res 2023; 28:314. [PMID: 37660109 PMCID: PMC10474718 DOI: 10.1186/s40001-023-01303-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 08/19/2023] [Indexed: 09/04/2023] Open
Abstract
BACKGROUND The emergence of healthcare-associated infections (HAIs) or superinfections in COVID-19 patients has resulted in poor prognosis and increased mortality. METHODS In a cross-sectional study, 101 respiratory samples were collected from ICU-admitted COVID-19 patients. The HAI rate, demographics, and antibiotic resistance were assessed. RESULTS The HAI rate was 83.16% (76.62% bacterial and 6.54% fungal). The prevalence of 3 major HAI-causing organisms included Klebsiella pneumoniae (41.5%), Acinetobacter baumannii (20.8%), and Staphylococcus aureus (4.9%). Mortality and intubation ventilation proportions of 90% (p = 0.027) and 92.2% (p = 0.02) were significant among patients with superinfection, respectively. Multiple logistic regression analysis showed SpO2 pressure (odds ratio 0.842; 95% CI 0.750-0.945; p = 0.004) as a predictive factor in the association between antibiotic usage and mortality. More than 50% of patients received carbapenems. The resistance rates to at least one antibiotic of third-generation cephalosporins, aminoglycosides, quinolones/fluoroquinolones, tetracyclines, and β-lactam inhibitors were 95.2%, 95.2%, 90%, 57.1%, and 100% among A. baumannii isolates and 71.4%, 55%, 69%, 61.9%, and 59.5% among K. pneumoniae isolates, respectively. A proportion of 60% was recorded for methicillin-resistant S. aureus isolates. CONCLUSION As a result, antibiotic treatment should be administered following the microbial resistance profile. Contact isolation and infection control measures should be implemented as needed.
Collapse
Affiliation(s)
- Maryam Mobarak-Qamsari
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Bita Jenaghi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Leyla Sahebi
- Family Health Research Institute. Maternal, Fetal, and Neonatal Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahsa Norouzi-Shadehi
- Department of Infectious Disease, School of Medicine, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad-Reza Salehi
- Department of Infectious Diseases, School of Medicine, Imam Khomeini Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Abbas Shakoori-Farahani
- Department of Medical Genetics, School of Medicine, Imam Khomeini Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Hoda Khoshnevis
- Imam Khomeini Hospital Complex, School of Medicine, Imam Khomeini Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Alireza Abdollahi
- Department of Pathology, School of Medicine, Imam Khomeini Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad-Mehdi Feizabadi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
- Thorax Research Center, Imam Khomeini Hospital Complex., Tehran University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
7
|
Alhoufie ST, Mumena WA, Alsharif N, Makhdoom HM, Almutawif YA, Alfarouk KO, Alharbi MZ, Aljabri K, Aljifri A. Epidemiological Characteristics and Outcomes Predictors for Intensive Care Unit COVID-19 Patients in Al-Madinah, Saudi Arabia. Retrospective Cohort Study. Infect Drug Resist 2023; 16:5573-5586. [PMID: 37645558 PMCID: PMC10461755 DOI: 10.2147/idr.s419724] [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: 05/03/2023] [Accepted: 08/17/2023] [Indexed: 08/31/2023] Open
Abstract
Introduction The global pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, COVID-19) increased the demand for intensive care unit (ICU) services. Mortality and morbidity rates among ICU COVID-19 patients are affected by several factors, such as severity, comorbidities, and coinfections. In this study, we describe the demographic characteristics of COVID-19 patients admitted to an ICU in Saudi Arabia, and we determined the predictors for mortality and prolonged ICU length of stay. Additionally, we determined the prevalence of bacterial coinfection and its effect on the outcomes for ICU COVID-19 patients. Methods We retrospectively studied the medical records of 142 COVID-19 patients admitted to the ICU at a tertiary hospital in Madinah, Saudi Arabia. Data on demographics, medical history, mortality, length of stay, and presence of coinfection were collected for each patient. Results Neutrophil-to-Lymphocyte ratio (NLR) and intubation were reliable predictors of mortality and ICU length of stay among these ICU COVID-19 patients. Moreover, bacterial coinfections were detected in 23.2% of the patients and significantly (p < 0.001) prolonged their ICU length of stay, explaining the 10% increase in the length of stay for these patients. Furthermore, mortality reached 70% among the coinfected patients, and 60.8% of the isolated coinfecting pathogens were multidrug-resistant (MDR) strains of Klebsiella pneumoniae, Acinetobacter baumannii, and Staphylococcus aureus. Conclusion Increased NLR and intubation are predictors of mortality and prolonged length of stay in COVID-19 patients admitted to the ICU. Coinfection with MDR bacterial strains potentially results in complications and is a high-risk factor for prolonged ICU length of stay.
Collapse
Affiliation(s)
- Sari T Alhoufie
- Medical Laboratories Technology Department, College of Applied Medical Sciences, Taibah University, Al-Madinah Al-Munwarah, Saudi Arabia
| | - Walaa A Mumena
- Department of Clinical Nutrition, College of Applied Medical Sciences, Taibah University, Al-Madinah Al-Munwarah, Saudi Arabia
| | - Naif Alsharif
- King Salman Medical City, Al-Madinah General Hospital, Al-Madinah Al-Munwarah, Saudi Arabia
| | - Hatim M Makhdoom
- Medical Laboratories Technology Department, College of Applied Medical Sciences, Taibah University, Al-Madinah Al-Munwarah, Saudi Arabia
| | - Yahya A Almutawif
- Medical Laboratories Technology Department, College of Applied Medical Sciences, Taibah University, Al-Madinah Al-Munwarah, Saudi Arabia
| | | | - Mohammed Z Alharbi
- King Salman Medical City, Al-Madinah General Hospital, Al-Madinah Al-Munwarah, Saudi Arabia
| | - Khaled Aljabri
- King Salman Medical City, Al-Madinah General Hospital, Al-Madinah Al-Munwarah, Saudi Arabia
| | - Alanoud Aljifri
- Al-Madinah Health Cluster, Ministry of Health, Al-Madinah Al-Munwarah, Saudi Arabia
| |
Collapse
|
8
|
Satjawattanavimol S, Teerapuncharoen K, Kaewlai R, Disayabutr S. Prevalence of early bacterial co-infection in hospitalized patients with COVID-19 pneumonia: a retrospective study. J Thorac Dis 2023; 15:3568-3579. [PMID: 37559639 PMCID: PMC10407494 DOI: 10.21037/jtd-22-1681] [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: 11/23/2022] [Accepted: 05/26/2023] [Indexed: 08/11/2023]
Abstract
BACKGROUND Identification of bacterial co-infection is crucial in determining outcomes of patients with coronavirus disease 2019 (COVID-19) pneumonia. The present study aims to evaluate the prevalence and associated factors of early bacterial co-infection in patients with COVID-19 pneumonia. METHODS The present study is a retrospective study. Patients with COVID-19 pneumonia, who were admitted to Siriraj Hospital between April 1 and August 31, 2021, were randomly enrolled and classified as the "Early bacterial co-infection" group, defined by an infection occurring within the first 48 hours after admission, and the "Unlikely early bacterial co-infection" group. RESULTS A total of 245 patients were enrolled. The prevalence of early bacterial co-infection was 15.5%. Chest X-rays showed characteristic findings for COVID-19 pneumonia in 37.6%. The median Brixia chest X-ray scores and C-reactive protein levels were significantly higher in the Early bacterial co-infection group. The most common causative pathogens included Staphylococcus aureus, Pseudomonas aeruginosa, and Stenotrophomonas maltophilia. Patients with early bacterial co-infection had a significantly higher all-cause mortality compared to the Unlikely early bacterial co-infection group (P=0.012). The Charlson Comorbidity Index ≥4, high level of respiratory support, and mass-liked or diffuse opacities on chest X-rays were independent factors associated with the early bacterial co-infection. CONCLUSIONS The prevalence of early bacterial co-infection in patients with COVID-19 pneumonia was low but it was associated with mortality. There is insufficient evidence to support the empirical use of antibiotics in these patients. A further prospective study is required to confirm the results of the present study.
Collapse
Affiliation(s)
- Silp Satjawattanavimol
- Division of Respiratory Disease and Tuberculosis, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Krittika Teerapuncharoen
- Division of Respiratory Disease and Tuberculosis, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Rathachai Kaewlai
- Department of Radiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Supparerk Disayabutr
- Division of Respiratory Disease and Tuberculosis, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| |
Collapse
|
9
|
Gurukkalot K, Rajendran V. Repurposing Polyether Ionophores as a New-Class of Anti-SARS-Cov-2 Agents as Adjunct Therapy. Curr Microbiol 2023; 80:273. [PMID: 37414909 DOI: 10.1007/s00284-023-03366-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 06/05/2023] [Indexed: 07/08/2023]
Abstract
The emergence of SARS-CoV-2 and its variants have posed a significant threat to humankind in tackling the viral spread. Furthermore, currently repurposed drugs and frontline antiviral agents have failed to cure severe ongoing infections effectively. This insufficiency has fuelled research for potent and safe therapeutic agents to treat COVID-19. Nonetheless, various vaccine candidates have displayed a differential efficacy and need for repetitive dosing. The FDA-approved polyether ionophore veterinary antibiotic for treating coccidiosis has been repurposed for treating SARS-CoV-2 infection (as shown by both in vitro and in vivo studies) and other deadly human viruses. Based on selectivity index values, ionophores display therapeutic effects at sub-nanomolar concentrations and exhibit selective killing ability. They act on different viral targets (structural and non-structural proteins), host-cell components leading to SARS-CoV-2 inhibition, and their activity is further enhanced by Zn2+ supplementation. This review summarizes the anti-SARS-CoV-2 potential and molecular viral targets of selective ionophores like monensin, salinomycin, maduramicin, CP-80,219, nanchangmycin, narasin, X-206 and valinomycin. Ionophore combinations with Zn2+ are a new therapeutic strategy that warrants further investigation for possible human benefits.
Collapse
Affiliation(s)
- Keerthana Gurukkalot
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India
| | - Vinoth Rajendran
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India.
| |
Collapse
|
10
|
Pădureanu V, Caragea DC, Florescu MM, Vladu IM, Rădulescu PM, Florescu DN, Rădulescu D, Pădureanu R, Efrem IC. Role of the SARS‑COV2 infection in the evolution of acute pancreatitis (Review). Biomed Rep 2023; 19:49. [PMID: 37383680 PMCID: PMC10293881 DOI: 10.3892/br.2023.1632] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 05/10/2023] [Indexed: 06/30/2023] Open
Abstract
Acute pancreatitis is characterized as an inflammatory illness that is life-threatening and causes necrosis as well as simple edema when pancreatic enzymes are activated intraglandularly. It is not known whether severe acute respiratory syndrome coronavirus 2 causes acute pancreatitis. Patients with acute pancreatitis who test positive for coronavirus disease 2019 (COVID-19) frequently have biliary or alcoholic causes. It is unclear how common acute pancreatitis is in patients with COVID-19. By contrast with patients without COVID-19, however, COVID-19-positive patients with acute pancreatitis have a higher mortality as well as a higher risk of necrosis and admission to an intensive care unit. The most common cause of mortality in COVID-19-positive individuals with concurrent severe pancreatitis is acute respiratory distress syndrome. The present study discussed research on the link between COVID-19 infection and acute pancreatitis.
Collapse
Affiliation(s)
- Vlad Pădureanu
- Department of Internal Medicine, University of Medicine and Pharmacy of Craiova, Craiova 200349, Romania
| | - Daniel Cosmin Caragea
- Department of Nephrology, University of Medicine and Pharmacy of Craiova, Craiova 200349, Romania
| | - Mirela Marinela Florescu
- Department of Morphology, University of Medicine and Pharmacy of Craiova, Craiova 200349, Romania
| | - Ionela Mihaela Vladu
- Department of Diabetes, Nutrition and Metabolic Diseases, University of Medicine and Pharmacy of Craiova, Craiova 200349, Romania
| | - Patricia Mihaela Rădulescu
- University of Medicine and Pharmacy of Craiova Doctoral School, University of Medicine and Pharmacy of Craiova, Craiova 200349, Romania
| | - Dan Nicolae Florescu
- Department of Gastroenterology, University of Medicine and Pharmacy of Craiova, Craiova 200349, Romania
| | - Dumitru Rădulescu
- Department of Surgery, University of Medicine and Pharmacy of Craiova, Craiova 200349, Romania
| | - Rodica Pădureanu
- Department of Internal Medicine, University of Medicine and Pharmacy of Craiova, Craiova 200349, Romania
| | - Ion Cristian Efrem
- Department of Internal Medicine, University of Medicine and Pharmacy of Craiova, Craiova 200349, Romania
| |
Collapse
|
11
|
Choi Y, Kang M, Shin DH, Jung J, Choi SJ, Kim NH, Moon SM, Song KH, Kim ES, Jung J, Kim HB. Antibiotic Prescription in Patients With Coronavirus Disease 2019: Analysis of National Health Insurance System Data in the Republic of Korea. J Korean Med Sci 2023; 38:e189. [PMID: 37365725 DOI: 10.3346/jkms.2023.38.e189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/10/2023] [Indexed: 06/28/2023] Open
Abstract
BACKGROUND Although coronavirus disease 2019 (COVID-19) is a viral infection, antibiotics are often prescribed due to concerns about accompanying bacterial infection. Therefore, we aimed to analyze the number of patients with COVID-19 who received antibiotic prescriptions, as well as factors that influenced antibiotics prescription, using the National Health Insurance System database. METHODS We retrospectively reviewed claims data for adults aged ≥ 19 years hospitalized for COVID-19 from December 1, 2019 to December 31, 2020. According to the National Institutes of Health guidelines for severity classification, we calculated the proportion of patients who received antibiotics and the number of days of therapy per 1,000 patient-days. Factors contributing to antibiotic use were determined using linear regression analysis. In addition, antibiotic prescription data for patients with influenza hospitalized from 2018 to 2021 were compared with those for patients with COVID-19, using an integrated database from Korea Disease Control and Prevention Agency-COVID19-National Health Insurance Service cohort (K-COV-N cohort), which was partially adjusted and obtained from October 2020 to December 2021. RESULTS Of the 55,228 patients, 46.6% were males, 55.9% were aged ≥ 50 years, and most patients (88.7%) had no underlying diseases. The majority (84.3%; n = 46,576) were classified as having mild-to-moderate illness, with 11.2% (n = 6,168) and 4.5% (n = 2,484) having severe and critical illness, respectively. Antibiotics were prescribed to 27.3% (n = 15,081) of the total study population, and to 73.8%, 87.6%, and 17.9% of patients with severe, critical, and mild-to-moderate illness, respectively. Fluoroquinolones were the most commonly prescribed antibiotics (15.1%; n = 8,348), followed by third-generation cephalosporins (10.4%; n = 5,729) and beta-lactam/beta-lactamase inhibitors (6.9%; n = 3,822). Older age, COVID-19 severity, and underlying medical conditions contributed significantly to antibiotic prescription requirement. The antibiotic use rate was higher in the influenza group (57.1%) than in the total COVID-19 patient group (21.2%), and higher in severe-to-critical COVID-19 cases (66.6%) than in influenza cases. CONCLUSION Although most patients with COVID-19 had mild to moderate illness, more than a quarter were prescribed antibiotics. Judicious use of antibiotics is necessary for patients with COVID-19, considering the severity of disease and risk of bacterial co-infection.
Collapse
Affiliation(s)
- Yunsang Choi
- Division of Infectious Diseases, Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Minsun Kang
- Artificial Intelligence and Big-Data Convergence Centre, Gil Medical Centre, Gachon University College of Medicine, Incheon, Korea
- Department of Preventive Medicine, Gachon University College of Medicine, Incheon, Korea
| | - Dong Hoon Shin
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Jongtak Jung
- Division of Infectious Diseases, Department of Internal Medicine, Soonchunhyang University Seoul Hospital, Soonchunhyang University College of Medicine, Seoul, Korea
| | - Seong Jin Choi
- Division of Infectious Diseases, Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Nak-Hyun Kim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Song Mi Moon
- Division of Infectious Diseases, Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Kyoung-Ho Song
- Division of Infectious Diseases, Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Eu Suk Kim
- Division of Infectious Diseases, Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Jaehun Jung
- Artificial Intelligence and Big-Data Convergence Centre, Gil Medical Centre, Gachon University College of Medicine, Incheon, Korea
- Department of Preventive Medicine, Gachon University College of Medicine, Incheon, Korea
| | - Hong Bin Kim
- Division of Infectious Diseases, Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea.
| |
Collapse
|
12
|
Harte E, Kumarasamysarma S, Phillips B, Mackay O, Rashid Z, Malikova N, Mukit A, Ramachandran S, Biju A, Brown K, Watts R, Hodges C, Tuckwell W, Wetherall N, Breen H, Price S, Szakmany T. Procalcitonin Values Fail to Track the Presence of Secondary Bacterial Infections in COVID-19 ICU Patients. Antibiotics (Basel) 2023; 12:antibiotics12040709. [PMID: 37107071 PMCID: PMC10135291 DOI: 10.3390/antibiotics12040709] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 03/29/2023] [Accepted: 04/03/2023] [Indexed: 04/08/2023] Open
Abstract
The development of secondary bacterial infections in COVID-19 patients has been associated with increased mortality and worse clinical outcomes. Consequently, many patients have received empirical antibiotic therapies with the potential to further exacerbate an ongoing antimicrobial resistance crisis. The pandemic has seen a rise in the use of procalcitonin testing to guide antimicrobial prescribing, although its value remains elusive. This single-centre retrospective study sought to analyse the efficacy of procalcitonin in identifying secondary infections in COVID-19 patients and evaluate the proportion of patients prescribed antibiotics to those with confirmed secondary infection. Inclusion criteria comprised patients admitted to the Grange University Hospital intensive care unit with SARS-CoV-2 infection throughout the second and third waves of the pandemic. Data collected included daily inflammatory biomarkers, antimicrobial prescriptions, and microbiologically proven secondary infections. There was no statistically significant difference between PCT, WBC, or CRP values in those with an infection versus those without. A total of 57.02% of patients had a confirmed secondary infection, with 80.2% prescribed antibiotics in Wave 2, compared to 44.07% with confirmed infection and 52.1% prescribed antibiotics in Wave 3. In conclusion, procalcitonin values failed to indicate the emergence of critical care-acquired infection in COVID-19 patients.
Collapse
Affiliation(s)
- Elsa Harte
- School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | | | | | - Olivia Mackay
- School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Zohra Rashid
- School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | | | - Abdullah Mukit
- School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | | | - Anna Biju
- School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Kate Brown
- School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Rosie Watts
- School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Charlie Hodges
- School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | | | - Nick Wetherall
- School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Henry Breen
- School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Shannon Price
- School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Tamas Szakmany
- Department of Anaesthesia, Intensive Care and Pain Medicine, Cardiff University, Cardiff CF14 4XN, UK
- Critical Care Directorate, Grange University Hospital, Aneurin Bevan University Health Board, Cwmbran NP44 2XJ, UK
| |
Collapse
|
13
|
Recommendations and guidelines for the diagnosis and management of Coronavirus Disease-19 (COVID-19) associated bacterial and fungal infections in Taiwan. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2023; 56:207-235. [PMID: 36586743 PMCID: PMC9767873 DOI: 10.1016/j.jmii.2022.12.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/30/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022]
Abstract
Coronavirus disease-19 (COVID-19) is an emerging infectious disease caused by SARS-CoV-2 that has rapidly evolved into a pandemic to cause over 600 million infections and more than 6.6 million deaths up to Nov 25, 2022. COVID-19 carries a high mortality rate in severe cases. Co-infections and secondary infections with other micro-organisms, such as bacterial and fungus, further increases the mortality and complicates the diagnosis and management of COVID-19. The current guideline provides guidance to physicians for the management and treatment of patients with COVID-19 associated bacterial and fungal infections, including COVID-19 associated bacterial infections (CABI), pulmonary aspergillosis (CAPA), candidiasis (CAC) and mucormycosis (CAM). Recommendations were drafted by the 7th Guidelines Recommendations for Evidence-based Antimicrobial agents use Taiwan (GREAT) working group after review of the current evidence, using the grading of recommendations assessment, development, and evaluation (GRADE) methodology. A nationwide expert panel reviewed the recommendations in March 2022, and the guideline was endorsed by the Infectious Diseases Society of Taiwan (IDST). This guideline includes the epidemiology, diagnostic methods and treatment recommendations for COVID-19 associated infections. The aim of this guideline is to provide guidance to physicians who are involved in the medical care for patients with COVID-19 during the ongoing COVID-19 pandemic.
Collapse
|
14
|
Muflih SM, Al-Azzam S, Karasneh RA, Bleidt BA, Conway BR, Bond SE, Aldeyab MA. Public knowledge of antibiotics, self-medication, and household disposal practices in Jordan. Expert Rev Anti Infect Ther 2023; 21:477-487. [PMID: 36843495 DOI: 10.1080/14787210.2023.2182770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
BACKGROUND This study aimed to assess public understanding of antibiotics, self-medication, and drug disposal practices. METHODS A cross-sectional self-administered online survey was undertaken in Jordan. RESULTS The study was completed by 1,105 participants. When asked about their knowledge of antibiotics, rational antibiotic use, and disposal practices, 16% percent believed they should discontinue antibiotics once they felt better, and 12% agreed to take the same antibiotics prescribed to others for the same illness. Self-medication with antibiotics was practiced by 44% of the participants. Prior experience, healthcare costs, and pharmacy location were all major determinants of self-medication. Only 6.4% of unneeded antibiotics were returned to the pharmacy, 60% were kept at home, and 26.6% were disposed of at home. Almost half of those who kept the antibiotics said they would use them again, and one-third said they would give them to friends and family. Respondents who had used antibiotics within the previous 6 months (p = 0.052) and relied on medication leaflets (p = 0.031) and physician recommendations (p = 0.001) were less likely to self-medicate with antibiotics. CONCLUSIONS The study highlighted areas of inappropriate use of antibiotics, self-medication and the improper antibiotic disposal that can inform antimicrobial stewardship.
Collapse
Affiliation(s)
- Suhaib M Muflih
- Department of Clinical Pharmacy, Faculty of Pharmacy, Jordan University of Science and Technology, Irbid, Jordan
| | - Sayer Al-Azzam
- Department of Clinical Pharmacy, Faculty of Pharmacy, Jordan University of Science and Technology, Irbid, Jordan
| | - Reema A Karasneh
- Department of Basic Medical Sciences, Faculty of Medicine, Yarmouk University, Irbid, Jordan
| | - Barry A Bleidt
- Department of Socio behavioral and Administrative Pharmacy, College of Pharmacy, Nova Southeastern University, Davie-Fl, USA
| | - Barbara R Conway
- Department of Pharmacy, School of Applied Sciences, University of Huddersfield, Huddersfield, UK.,Institute of Skin Integrity and Infection Prevention, University of Huddersfield, Huddersfield, UK
| | - Stuart E Bond
- Pharmacy Department, Mid Yorkshire Hospitals NHS Trust, Wakefield, UK
| | - Mamoon A Aldeyab
- Department of Pharmacy, School of Applied Sciences, University of Huddersfield, Huddersfield, UK
| |
Collapse
|
15
|
Gong X, Khan A, Wani MY, Ahmad A, Duse A. COVID-19: A state of art on immunological responses, mutations, and treatment modalities in riposte. J Infect Public Health 2023; 16:233-249. [PMID: 36603376 PMCID: PMC9798670 DOI: 10.1016/j.jiph.2022.12.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 12/25/2022] [Accepted: 12/26/2022] [Indexed: 12/31/2022] Open
Abstract
Over the last few years, the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) unleashed a global public health catastrophe that had a substantial influence on human physical and mental health, the global economy, and socio-political dynamics. SARS-CoV-2 is a respiratory pathogen and the cause of ongoing COVID-19 pandemic, which testified how unprepared humans are for pandemics. Scientists and policymakers continue to face challenges in developing ideal therapeutic agents and vaccines, while at the same time deciphering the pathology and immunology of SARS-CoV-2. Challenges in the early part of the pandemic included the rapid development of diagnostic assays, vaccines, and therapeutic agents. The ongoing transmission of COVID-19 is coupled with the emergence of viral variants that differ in their transmission efficiency, virulence, and vaccine susceptibility, thus complicating the spread of the pandemic. Our understanding of how the human immune system responds to these viruses as well as the patient groups (such as the elderly and immunocompromised individuals) who are often more susceptible to serious illness have both been aided by this epidemic. COVID-19 causes different symptoms to occur at different stages of infection, making it difficult to determine distinct treatment regimens employed for the various clinical phases of the disease. Unsurprisingly, determining the efficacy of currently available medications and developing novel therapeutic strategies have been a process of trial and error. The global scientific community collaborated to research and develop vaccines at a neck-breaking speed. This review summarises the overall picture of the COVID-19 pandemic, different mutations in SARS-CoV-2, immune response, and the treatment modalities against SARS-CoV-2.
Collapse
Affiliation(s)
- Xiaolong Gong
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Amber Khan
- Department of Clinical Haematology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mohmmad Younus Wani
- Department of Chemistry, College of Science, University of Jeddah, P.O. Box 80327, Jeddah 21589, Kingdom of Saudi Arabia
| | - Aijaz Ahmad
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa,Division of Infection Control, Charlotte Maxeke Johannesburg Academic Hospital, National Health Laboratory Service, Johannesburg, South Africa,Corresponding author at: Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Adriano Duse
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa,Division of Infection Control, Charlotte Maxeke Johannesburg Academic Hospital, National Health Laboratory Service, Johannesburg, South Africa
| |
Collapse
|
16
|
Lane S, Hilliam Y, Bomberger JM. Microbial and Immune Regulation of the Gut-Lung Axis during Viral-Bacterial Coinfection. J Bacteriol 2023; 205:e0029522. [PMID: 36409130 PMCID: PMC9879096 DOI: 10.1128/jb.00295-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Viral-bacterial coinfections of the respiratory tract have long been associated with worsened disease outcomes. Clinical and basic research studies demonstrate that these infections are driven via complex interactions between the infecting pathogens, microbiome, and host immune response, although how these interactions contribute to disease progression is still not fully understood. Research over the last decade shows that the gut has a significant role in mediating respiratory outcomes, in a phenomenon known as the "gut-lung axis." Emerging literature demonstrates that acute respiratory viruses can modulate the gut-lung axis, suggesting that dysregulation of gut-lung cross talk may be a contributing factor during respiratory coinfection. This review will summarize the current literature regarding modulation of the gut-lung axis during acute respiratory infection, with a focus on the role of the microbiome, secondary infections, and the host immune response.
Collapse
Affiliation(s)
- Sidney Lane
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Yasmin Hilliam
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Jennifer M. Bomberger
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| |
Collapse
|
17
|
Zsichla L, Müller V. Risk Factors of Severe COVID-19: A Review of Host, Viral and Environmental Factors. Viruses 2023; 15:175. [PMID: 36680215 PMCID: PMC9863423 DOI: 10.3390/v15010175] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/04/2023] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
The clinical course and outcome of COVID-19 are highly variable, ranging from asymptomatic infections to severe disease and death. Understanding the risk factors of severe COVID-19 is relevant both in the clinical setting and at the epidemiological level. Here, we provide an overview of host, viral and environmental factors that have been shown or (in some cases) hypothesized to be associated with severe clinical outcomes. The factors considered in detail include the age and frailty, genetic polymorphisms, biological sex (and pregnancy), co- and superinfections, non-communicable comorbidities, immunological history, microbiota, and lifestyle of the patient; viral genetic variation and infecting dose; socioeconomic factors; and air pollution. For each category, we compile (sometimes conflicting) evidence for the association of the factor with COVID-19 outcomes (including the strength of the effect) and outline possible action mechanisms. We also discuss the complex interactions between the various risk factors.
Collapse
Affiliation(s)
- Levente Zsichla
- Institute of Biology, Eötvös Loránd University, 1117 Budapest, Hungary
- National Laboratory for Health Security, Eötvös Loránd University, 1117 Budapest, Hungary
| | - Viktor Müller
- Institute of Biology, Eötvös Loránd University, 1117 Budapest, Hungary
- National Laboratory for Health Security, Eötvös Loránd University, 1117 Budapest, Hungary
| |
Collapse
|
18
|
Akrami S, Montazeri EA, Saki M, Neisi N, Khedri R, Dini SA, Motlagh AA, Ahmadi F. Bacterial profiles and their antibiotic resistance background in superinfections caused by multidrug-resistant bacteria among COVID-19 ICU patients from southwest Iran. J Med Virol 2023; 95:e28403. [PMID: 36515422 PMCID: PMC9877791 DOI: 10.1002/jmv.28403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 11/12/2022] [Accepted: 12/10/2022] [Indexed: 12/15/2022]
Abstract
This study investigated the bacterial causes of superinfections and their antibiotic resistance pattern in severe coronavirus disease 2019 (COVID-19) patients admitted to the intensive care unit (ICU) of Razi Hospital in Ahvaz, southwest Iran. In this cross-sectional study, endotracheal tube (ETT) secretion samples of 77 intubated COVID-19 patients, confirmed by reverse transcription-quantitative polymerase chain reaction, were investigated by standard microbiology test and analytical profile index kit. Antibiotic susceptibility testing was performed by disc diffusion. The presence of Haemophilus influenzae and Mycoplasma pneumoniae was investigated by the polymerase chain reaction (PCR). Using culture and PCR methods, 56 (72.7%) of the 77 COVID-19 patients (mean age of 55 years, 29 male and 27 female) had superinfections. Using culture, 67 isolates including 29 (43.2%) Gram-positive and 38 (56.7%) Gram-negative bacteria (GNB) were identified from 49 COVID-19 patients. The GNB were more predominant than the Gram-positive pathogens. Klebsiella pneumoniae (28.4%, n = 19/67) was the most common isolate followed by Staphylococcus aureus (22.4%, n = 15/67). Using PCR, 10.4% (8/77) and 11.7% (9/77) of ETT secretion specimens had H. influenzae and M. pneumoniae amplicons, respectively. Gram-positive and Gram-negative isolates showed high resistance rates (>70.0%) to majority of the tested antibiotics including fluoroquinolone, carbapenems, and cephalosporins and 68.7% (46/67) of isolates were multidrug-resistant (MDR). This study showed a high frequency rate of superinfections by MDR bacteria among COVID-19 patients in southwest Iran. The prevention of long-term consequences caused by COVID-19, demands continuous antibiotic surveillance particularly in management of bacterial superinfections.
Collapse
Affiliation(s)
- Sousan Akrami
- Infectious and Tropical Diseases Research Center, Health Research InstituteAhvaz Jundishapur University of Medical SciencesAhvazIran
- Department of Microbiology, School of MedicineTehran University of Medical SciencesTehranIran
- Students’ Scientific Research Center (SSRC)Tehran University of Medical SciencesTehranIran
| | - Effat Abbasi Montazeri
- Infectious and Tropical Diseases Research Center, Health Research InstituteAhvaz Jundishapur University of Medical SciencesAhvazIran
- Department of Microbiology, Faculty of MedicineAhvaz Jundishapur University of Medical SciencesAhvazIran
| | - Morteza Saki
- Infectious and Tropical Diseases Research Center, Health Research InstituteAhvaz Jundishapur University of Medical SciencesAhvazIran
- Department of Microbiology, Faculty of MedicineAhvaz Jundishapur University of Medical SciencesAhvazIran
| | - Niloofar Neisi
- Infectious and Tropical Diseases Research Center, Health Research InstituteAhvaz Jundishapur University of Medical SciencesAhvazIran
- Department of Medical Virology, School of MedicineAhvaz Jundishapur University of Medical SciencesAhvazIran
| | - Reza Khedri
- Student Research CommitteeAhvaz Jundishapur University of Medical SciencesAhvazIran
| | - Sahar Allah Dini
- Infectious and Tropical Diseases Research Center, Health Research InstituteAhvaz Jundishapur University of Medical SciencesAhvazIran
- Department of Infectious Diseases and Tropical Medicine, Razi Teaching Hospital, School of MedicineAhvaz Jundishapur University of Medical SciencesAhvazIran
| | - Atefeh Akbari Motlagh
- Infectious and Tropical Diseases Research Center, Health Research InstituteAhvaz Jundishapur University of Medical SciencesAhvazIran
- Department of Infectious Diseases and Tropical Medicine, Razi Teaching Hospital, School of MedicineAhvaz Jundishapur University of Medical SciencesAhvazIran
| | - Fatemeh Ahmadi
- Infectious and Tropical Diseases Research Center, Health Research InstituteAhvaz Jundishapur University of Medical SciencesAhvazIran
- Department of Infectious Diseases and Tropical Medicine, Razi Teaching Hospital, School of MedicineAhvaz Jundishapur University of Medical SciencesAhvazIran
| |
Collapse
|
19
|
Evaluation of co-circulating pathogens and microbiome from COVID-19 infections. PLoS One 2022; 17:e0278543. [PMID: 36455065 PMCID: PMC9714956 DOI: 10.1371/journal.pone.0278543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 11/18/2022] [Indexed: 12/05/2022] Open
Abstract
Co-infections or secondary infections with SARS-CoV-2 have the potential to affect disease severity and morbidity. Additionally, the potential influence of the nasal microbiome on COVID-19 illness is not well understood. In this study, we analyzed 203 residual samples, originally submitted for SARS-CoV-2 testing, for the presence of viral, bacterial, and fungal pathogens and non-pathogens using a comprehensive microarray technology, the Lawrence Livermore Microbial Detection Array (LLMDA). Eighty-seven percent of the samples were nasopharyngeal samples, and 23% of the samples were oral, nasal and oral pharyngeal swabs. We conducted bioinformatics analyses to examine differences in microbial populations of these samples, as a proxy for the nasal and oral microbiome, from SARS-CoV-2 positive and negative specimens. We found 91% concordance with the LLMDA relative to a diagnostic RT-qPCR assay for detection of SARS-CoV-2. Sixteen percent of all the samples (32/203) revealed the presence of an opportunistic bacterial or frank viral pathogen with the potential to cause co-infections. The two most detected bacteria, Streptococcus pyogenes and Streptococcus pneumoniae, were present in both SARS-CoV-2 positive and negative samples. Human metapneumovirus was the most prevalent viral pathogen in the SARS-CoV-2 negative samples. Sequence analysis of 16S rRNA was also conducted to evaluate bacterial diversity and confirm LLMDA results.
Collapse
|
20
|
Omer I, Abuthiyab N, Al Zaid N, Alkanani R, Abualnaja R, Khan G. Procalcitonin as a Tool to Antimicrobial Stewardship in COVID-19 Patients with Superimposed Bacterial Infections: A Systematic Review. J Inflamm Res 2022; 15:6055-6064. [PMID: 36353123 PMCID: PMC9639592 DOI: 10.2147/jir.s377644] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/20/2022] [Indexed: 07/30/2023] Open
Abstract
ABSTRACT Procalcitonin is an inflammatory marker that had shown marked potential as an antimicrobial stewardship tool for administering antibiotics when needed in patients with pneumonia as it raises concurrently with other inflammatory markers, yet no systematic review has assessed its potential in COVID-19 patients. This systematic review aimed to assess the potential appropriateness of procalcitonin as an antimicrobial stewardship tool in COVID-19 patients with superimposed bacterial and non-bacterial infections. All study designs published after 2019 were included in this systematic review. We included all studies that had reported procalcitonin levels in COVID-19 patients with suspected superimposed secondary infection(s). We searched MEDLINE, Scopus, and the Directory for Open Access Journal from April 2022 to May 2022 and retrieved all related articles for screening with no restrictions on language. We conducted risk of bias assessment according to the Critical Appraisal Skills Programme (CASP) criteria for cohort and case-control studies. Results were presented according to procalcitonin cut-off values, gold standard test used to confirm infection, and overall study conclusion(s), among other variables. This systematic review included 18 articles with 7196 patients in 8 countries. Despite different cut-off values of procalcitonin used, thirteen studies had indicated the appropriateness of using procalcitonin as antimicrobial stewardship tool in COVID-19 patients. We urge physicians to take this into account when treating COVID-19 patients suspected of superimposed infections and we look forward to further studies with standardized procalcitonin cut-off values that may provide appropriate quantitative data that can contribute to clinical guidelines. REGISTRATION PROSPERO CRD42022315013.
Collapse
Affiliation(s)
- Ibrahim Omer
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
- King Abdullah International Medical Research Center, Jeddah, Saudi Arabia
| | - Noorah Abuthiyab
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
- King Abdullah International Medical Research Center, Jeddah, Saudi Arabia
| | - Nura Al Zaid
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
- King Abdullah International Medical Research Center, Jeddah, Saudi Arabia
| | - Raghad Alkanani
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
- King Abdullah International Medical Research Center, Jeddah, Saudi Arabia
| | - Reema Abualnaja
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
- King Abdullah International Medical Research Center, Jeddah, Saudi Arabia
| | - Ghadeer Khan
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
- King Abdullah International Medical Research Center, Jeddah, Saudi Arabia
| |
Collapse
|
21
|
He D, Fu C, Ning M, Hu X, Li S, Chen Y. Biofilms possibly harbor occult SARS-CoV-2 may explain lung cavity, re-positive and long-term positive results. Front Cell Infect Microbiol 2022; 12:971933. [PMID: 36250053 PMCID: PMC9554432 DOI: 10.3389/fcimb.2022.971933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 09/14/2022] [Indexed: 01/08/2023] Open
Abstract
During the COVID-19 pandemic, there have been an increasing number of COVID-19 patients with cavitary or cystic lung lesions, re-positive or long-term positive nucleic acid tests, but the mechanism is still unclear. Lung cavities may appear at long time interval from initial onset of coronavirus infection, generally during the absorption phase of the disease. The main histopathological characteristic is diffuse alveolar damage and may have more severe symptoms after initial recovery from COVID-19 and an increased mortality rate. There are many possible etiologies of pulmonary cavities in COVID-19 patients and we hypothesize that occult SARS-CoV-2, in the form of biofilm, is harbored in the airway lacuna with other pathogenic microorganisms, which may be the cause of pulmonary cavities and repeated and long-term positive nucleic acid tests.
Collapse
Affiliation(s)
- Daqian He
- Department of Thoracic Surgery I, The Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Hospital, Yunnan Cancer Center), Kunming, China
| | - Chaojiang Fu
- Emergency Department (Outpatient Chemotherapy Center), The Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Hospital, Yunnan Cancer Center), Kunming, China
| | - Mingjie Ning
- Department of Thoracic Surgery I, The Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Hospital, Yunnan Cancer Center), Kunming, China
| | - Xianglin Hu
- Department of Thoracic Surgery I, The Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Hospital, Yunnan Cancer Center), Kunming, China
| | - Shanshan Li
- Department of Anesthesiology, The Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Hospital, Yunnan Cancer Center), Kunming, China
- *Correspondence: Ying Chen, ; Shanshan Li,
| | - Ying Chen
- Department of Thoracic Surgery I, The Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Hospital, Yunnan Cancer Center), Kunming, China
- *Correspondence: Ying Chen, ; Shanshan Li,
| |
Collapse
|
22
|
Abad CL, Sandejas JCM, Poblete JB, Malundo AFG, Salamat MSS, Alejandria MM. Bacterial coinfection and antimicrobial use among patients with COVID-19 infection in a referral center in the Philippines: A retrospective cohort study. IJID REGIONS 2022; 4:123-130. [PMID: 35822190 PMCID: PMC9263707 DOI: 10.1016/j.ijregi.2022.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/28/2022] [Accepted: 07/01/2022] [Indexed: 12/15/2022]
Abstract
The rate of COVID-19 and community-acquired coinfections was low. Those who are coinfected have higher mortality, and need to be identified early. Antibiotic use was disproportionately high and varied little over time. Blood cultures are low yield, and should not be performed routinely.
Objective This study aimed to describe community-acquired bacterial coinfection (CAI) and antimicrobial use among COVID-19 patients. Methods Electronic records were retrospectively reviewed, and clinical data, laboratory data, antibiotic use, and outcomes of patients with and without CAI were compared. Results Of 1116 patients, 55.1% received antibiotics within 48 hours, but only 66 (5.9%) had documented CAI, mainly respiratory (40/66, 60.6%). Patients with CAI were more likely to present with myalgia (p = 0.02), nausea/vomiting (p = 0.014), altered sensorium (p = 0.007), have a qSOFA ≥ 2 (p = 0.016), or require vasopressor support (p < 0.0001). Patients with CAI also had higher median WBC count (10 vs 7.6 cells/mm3), and higher levels of procalcitonin (0.55 vs 0.13, p = 0.0003) and ferritin (872 vs 550, p = 0.028). Blood cultures were drawn for almost half of the patients (519, 46.5%) but were positive in only a few cases (30/519, 5.8%). Prescribing frequency was highest at the start and declined only slightly over time. The mortality of those with CAI (48.5%) was higher compared with those without CAI (14.3%). Conclusion Overall CAI rate was low (5.9%) and antimicrobial use disproportionately high (55.0%), varying little over time. The mortality rate of coinfected patients was high. Certain parameters can be used to better identify those with CAI and those who need blood cultures.
Collapse
|
23
|
Ćurčić M, Tarle M, Almahariq H, Hleb S, Havaš J, Pražetina M, Lasić H, Dolenc E, Kukoč A, Mihelčić A, Miko I, Romić A, Tipura D, Drmić Ž, Čučković M, Blagaj V, Lukšić I, Peršec J, Šribar A. Distribution of Pathogens and Predictive Values of Biomarkers of Inflammatory Response at ICU Admission on Outcomes of Critically Ill COVID-19 Patients with Bacterial Superinfections-Observations from National COVID-19 Hospital in Croatia. Diagnostics (Basel) 2022; 12:2069. [PMID: 36140471 PMCID: PMC9497731 DOI: 10.3390/diagnostics12092069] [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: 08/04/2022] [Revised: 08/18/2022] [Accepted: 08/22/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Superinfections contribute to mortality and length of stay in critically ill COVID-19 patients. The aim of this study was to determine the incidence and pathogen distribution of bacterial and fungal superinfections of the lower respiratory tract (LRTI), urinary tract (UTI) and bloodstream (BSI) and to determine the predictive value of biomarkers of inflammatory response on their ICU survival rates. METHODS A retrospective observational study that included critically ill COVID-19 patients treated during an 11-month period in a Croatian national COVID-19 hospital was performed. Clinical and diagnostic data were analyzed according to the origin of superinfection, and multivariate regression analysis was performed to determine the predictive values of biomarkers of inflammation on their survival rates. RESULTS 55.3% critically ill COVID-19 patients developed bacterial or fungal superinfections, and LRTI were most common, followed by BSI and UTI. Multidrug-resistant pathogens were the most common causes of LRTI and BSI, while Enterococcus faecalis was the most common pathogen causing UTI. Serum ferritin and neutrophil count were associated with decreased chances of survival in patients with LRTI, and patients with multidrug-resistant isolates had significantly higher mortality rates, coupled with longer ICU stays. CONCLUSION The incidence of superinfections in critically ill COVID-19 patients was 55.3%, and multidrug-resistant pathogens were dominant. Elevated ferritin levels and neutrophilia at ICU admission were associated with increased ICU mortality in patients with positive LRTI.
Collapse
Affiliation(s)
- Maja Ćurčić
- Clinical Department for Anesthesiology, Reanimatology and Intensive Care Medicine, University Hospital Dubrava, 10000 Zagreb, Croatia
| | - Marko Tarle
- School of Dental Medicine, University of Zagreb, 10000 Zagreb, Croatia
- Department of Maxillofacial Surgery, University Hospital Dubrava, 10000 Zagreb, Croatia
| | - Hani Almahariq
- Clinical Department for Anesthesiology, Reanimatology and Intensive Care Medicine, University Hospital Dubrava, 10000 Zagreb, Croatia
| | - Sonja Hleb
- Clinical Department for Anesthesiology, Reanimatology and Intensive Care Medicine, University Hospital Dubrava, 10000 Zagreb, Croatia
| | - Juraj Havaš
- Clinical Department for Anesthesiology, Reanimatology and Intensive Care Medicine, University Hospital Dubrava, 10000 Zagreb, Croatia
| | - Marko Pražetina
- Clinical Department for Anesthesiology, Reanimatology and Intensive Care Medicine, University Hospital Dubrava, 10000 Zagreb, Croatia
| | - Hrvoje Lasić
- Clinical Department for Anesthesiology, Reanimatology and Intensive Care Medicine, University Hospital Dubrava, 10000 Zagreb, Croatia
| | - Emil Dolenc
- Clinical Department for Anesthesiology, Reanimatology and Intensive Care Medicine, University Hospital Dubrava, 10000 Zagreb, Croatia
| | - Andrea Kukoč
- Clinical Department for Anesthesiology, Reanimatology and Intensive Care Medicine, University Hospital Dubrava, 10000 Zagreb, Croatia
| | - Antonija Mihelčić
- Clinical Department for Anesthesiology, Reanimatology and Intensive Care Medicine, University Hospital Dubrava, 10000 Zagreb, Croatia
| | - Ivan Miko
- Clinical Department for Anesthesiology, Reanimatology and Intensive Care Medicine, University Hospital Dubrava, 10000 Zagreb, Croatia
| | - Andrea Romić
- Clinical Department for Anesthesiology, Reanimatology and Intensive Care Medicine, University Hospital Dubrava, 10000 Zagreb, Croatia
| | - Danijela Tipura
- Clinical Department for Anesthesiology, Reanimatology and Intensive Care Medicine, University Hospital Dubrava, 10000 Zagreb, Croatia
| | - Željka Drmić
- Clinical Department for Anesthesiology, Reanimatology and Intensive Care Medicine, University Hospital Dubrava, 10000 Zagreb, Croatia
| | - Marcela Čučković
- Clinical Department for Anesthesiology, Reanimatology and Intensive Care Medicine, University Hospital Dubrava, 10000 Zagreb, Croatia
| | - Vanja Blagaj
- Clinical Department for Anesthesiology, Reanimatology and Intensive Care Medicine, University Hospital Dubrava, 10000 Zagreb, Croatia
| | - Ivica Lukšić
- Department of Maxillofacial Surgery, University Hospital Dubrava, 10000 Zagreb, Croatia
- School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
| | - Jasminka Peršec
- Clinical Department for Anesthesiology, Reanimatology and Intensive Care Medicine, University Hospital Dubrava, 10000 Zagreb, Croatia
- School of Dental Medicine, University of Zagreb, 10000 Zagreb, Croatia
| | - Andrej Šribar
- Clinical Department for Anesthesiology, Reanimatology and Intensive Care Medicine, University Hospital Dubrava, 10000 Zagreb, Croatia
- School of Dental Medicine, University of Zagreb, 10000 Zagreb, Croatia
| |
Collapse
|
24
|
Pathophysiology of Methicillin-Resistant Staphylococcus aureus Superinfection in COVID-19 Patients. PATHOPHYSIOLOGY 2022; 29:405-413. [PMID: 35997388 PMCID: PMC9397082 DOI: 10.3390/pathophysiology29030032] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/19/2022] [Accepted: 07/23/2022] [Indexed: 11/25/2022] Open
Abstract
The global spread of the coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has infected humans in all age groups, deteriorated host immune responses, and caused millions of deaths. The reasons for individuals succumbing to COVID-19 were not only the SARS-CoV-2 infection but also associated bacterial infections. Antibiotics were largely used to prevent bacterial infections during COVID-19 illness, and many bacteria became resistant to conventional antibiotics. Although COVID-19 was considered the main culprit behind the millions of deaths, bacterial coinfections and superinfections were the major factors that increased the mortality rate in hospitalized patients. In the present study, we assessed the pathophysiology of methicillin-resistant Staphylococcus aureus (MRSA) superinfection in COVID-19 patients in Pakistan. A total of 3492 COVID-19 hospitalized patients were screened among which 224 strain were resistant to methicillin; 110 strains were tazobactam-resistant; 53 strains were ciprofloxacin-resistant; 23 strains were gentamicin-resistant; 11 strains were azithromycin-resistant; 3 strains were vancomycin-resistant. A high frequency of MRSA was detected in patients aged ≥50 with a prevalence of 7.33%, followed by patients aged >65 with a prevalence of 5.48% and a 5.10% prevalence in patients aged <50. In addition, pneumonia was detected in the COVID-19-associated MRSA (COVID-MRSA) that showed decreased levels of lymphocytes and albumin and increased the mortality rate from 2.3% to 25.23%. Collectively, an MRSA superinfection was associated with increased mortality in COVID-19 after 12 to 18 days of hospitalization. The study assessed the prevalence of MRSA, mortality rate, pneumonia, and the emergence of antibiotic resistance as the main outcomes. The study summarized that COVID-MRSA aggravated the treatment and recovery of patients and suggested testing MRSA as critical for hospitalized patients.
Collapse
|
25
|
Mzava O, Cheng AP, Chang A, Smalling S, Djomnang LAK, Lenz JS, Longman R, Steadman A, Gómez-Escobar LG, Schenck EJ, Salvatore M, Satlin MJ, Suthanthiran M, Lee JR, Mason CE, Dadhania D, De Vlaminck I. A metagenomic DNA sequencing assay that is robust against environmental DNA contamination. Nat Commun 2022; 13:4197. [PMID: 35864089 PMCID: PMC9304412 DOI: 10.1038/s41467-022-31654-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 06/28/2022] [Indexed: 11/30/2022] Open
Abstract
Metagenomic DNA sequencing is a powerful tool to characterize microbial communities but is sensitive to environmental DNA contamination, in particular when applied to samples with low microbial biomass. Here, we present Sample-Intrinsic microbial DNA Found by Tagging and sequencing (SIFT-seq) a metagenomic sequencing assay that is robust against environmental DNA contamination introduced during sample preparation. The core idea of SIFT-seq is to tag the DNA in the sample prior to DNA isolation and library preparation with a label that can be recorded by DNA sequencing. Any contaminating DNA that is introduced in the sample after tagging can then be bioinformatically identified and removed. We applied SIFT-seq to screen for infections from microorganisms with low burden in blood and urine, to identify COVID-19 co-infection, to characterize the urinary microbiome, and to identify microbial DNA signatures of sepsis and inflammatory bowel disease in blood.
Collapse
Affiliation(s)
- Omary Mzava
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Alexandre Pellan Cheng
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Adrienne Chang
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Sami Smalling
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | | | - Joan Sesing Lenz
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Randy Longman
- Division of Gastroenterology and Hepatology, Weill Cornell Medicine, Jill Roberts Center for IBD, New York, NY, USA
| | | | - Luis G Gómez-Escobar
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Edward J Schenck
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Mirella Salvatore
- Divisionof Public Health Programs, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Michael J Satlin
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Manikkam Suthanthiran
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
- Department of Transplantation Medicine, New York Presbyterian Hospital-Weill Cornell Medical Center, New York, NY, 10065, USA
| | - John R Lee
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York City, NY, USA
- WorldQuant Initiative for Quantitative Prediction, New York, NY, 11238, USA
| | - Darshana Dadhania
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
- Department of Transplantation Medicine, New York Presbyterian Hospital-Weill Cornell Medical Center, New York, NY, 10065, USA
| | - Iwijn De Vlaminck
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA.
| |
Collapse
|
26
|
Ngouanom Kuate MP, Bongomin F, Ndip RN. SARS-CoV-2, HIV, and Mycobacterium tuberculosis triple co-infection. Clin Case Rep 2022; 10:e6018. [PMID: 35846931 PMCID: PMC9280753 DOI: 10.1002/ccr3.6018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 05/07/2022] [Accepted: 05/16/2022] [Indexed: 11/10/2022] Open
Abstract
Tuberculosis (TB)-related death has increased for the first time in a decade due to the coronavirus disease 2019 (COVID-19), globally. People living with HIV (PLWHIV) might be at a higher risk of developing COVID-19-related complications. Herein, we describe the first case of a patient surviving from SARS-CoV-2-TB-HIV triple co-infection in Cameroon. A 36-year-old Cameroonian woman presented at the emergency unit of the Jamot Hospital, Yaoundé with symptoms of anorexia, productive cough, weight loss, and fever. The SARS-CoV-2 rapid antigen test on nasopharyngeal sample was positive. Chest X-ray showed bilateral parenchymal and tracheal calcifications most consistent with prior pulmonary histoplasmosis, varicella, or TB. She was tested HIV positive, and the sputum sample tested positive for TB on auramine staining. TB therapy (rifampicin, isoniazid, pyrazinamide, and ethambutol) and COVID-19 treatment were initiated, and the symptoms improved after 2 weeks of treatment. The SARS-CoV-2 rapid antigen and real-time polymerase chain reaction tests were negative after 2 weeks. She was discharged home on antiretroviral therapy and TB therapy. Coinfection with both TB, HIV, and SARS-CoV-2 may be common in Cameroon but not reported. The similar clinical features of COVID-19 and TB usually lead to misdiagnosis. Early diagnosis and initiation of appropriate treatment improve outcome.
Collapse
Affiliation(s)
| | - Felix Bongomin
- Department of Medical Microbiology and Immunology, Faculty of MedicineGulu UniversityGuluUganda
| | - Roland Ndip Ndip
- Department of Microbiology and Parasitology, Faculty of ScienceUniversity of BueaBueaCameroon
| |
Collapse
|
27
|
Lingas EC. Empiric Antibiotics in COVID 19: A Narrative Review. Cureus 2022; 14:e25596. [PMID: 35795519 PMCID: PMC9250242 DOI: 10.7759/cureus.25596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/31/2022] [Indexed: 11/05/2022] Open
|
28
|
Chiu NC, Lo KH, Chen CC, Huang SY, Weng SL, Wang CJ, Kuo HH, Chi H, Lien CH, Tai YL, Lin CY. The impact of COVID-19 on routine vaccinations in Taiwan and an unexpected surge of pneumococcal vaccination. Hum Vaccin Immunother 2022; 18:2071079. [PMID: 35561305 PMCID: PMC9359358 DOI: 10.1080/21645515.2022.2071079] [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] [Indexed: 11/05/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has had substantial impacts, including disruptions in routine vaccinations. In Taiwan, COVID-19 was relatively controllable, and the reduction in routine vaccinations was not profound. The impact of the pandemic on vaccination remained unclear. We collected vaccination uptake data at our hospital and analyzed the weekly trends of different vaccines. We calculated the monthly number of vaccinations and compared consumption before and during the COVID-19 pandemic (year 2019 vs years 2020 and 2021). Except for self-paid pneumococcal conjugate vaccines (PCV13), a mild (14.6%, p < .001) monthly decrease in government-funded routine vaccination and a moderate (28.2%, p = .018) monthly decrease in self-paid vaccination were observed during the COVID-19 pandemic. Interestingly, an unexpected surge of PCV13 vaccination occurred with a 355.8% increase. The shortage of COVID-19 vaccines and the potential benefits of PCV13 against COVID-19 may have contributed to this surge. In conclusion, our study found an obvious disruption of vaccination rates in Taiwan during the COVID-19 epidemic. However, an increase in PCV13 vaccination was also observed, and the important role of the infodemic was emphasized.
Collapse
Affiliation(s)
- Nan-Chang Chiu
- Department of Pediatrics, MacKay Children's Hospital, Taipei city, Taiwan.,Department of Medicine, MacKay Medical College, New Taipei city, Taiwan
| | - Kai-Hsun Lo
- Department of Pharmacy, Hsinchu MacKay Memorial Hospital, Hsinchu, Taiwan
| | - Chung-Chu Chen
- Department of Internal Medicine, Hsinchu MacKay Memorial Hospital, Hsinchu, Taiwan.,Teaching Center of Natural Science, Minghsin University of Science and Technology, Hsinchu, Taiwan
| | - Shih-Yu Huang
- Department of Internal Medicine, Hsinchu MacKay Memorial Hospital, Hsinchu, Taiwan.,Teaching Center of Natural Science, Minghsin University of Science and Technology, Hsinchu, Taiwan
| | - Shun-Long Weng
- Department of Medicine, MacKay Medical College, New Taipei city, Taiwan.,Department of Obstetrics and Gynecology, Hsinchu MacKay Memorial Hospital, Hsinchu, Taiwan
| | - Chung-Jen Wang
- Department of Pharmacy, Hsinchu MacKay Memorial Hospital, Hsinchu, Taiwan
| | - Hsiao-Huai Kuo
- Department of Pharmacy, Hsinchu MacKay Memorial Hospital, Hsinchu, Taiwan
| | - Hsin Chi
- Department of Pediatrics, MacKay Children's Hospital, Taipei city, Taiwan.,Department of Medicine, MacKay Medical College, New Taipei city, Taiwan
| | - Chi-Hone Lien
- Department of Pediatrics, Hsinchu MacKay Memorial Hospital, Hsinchu, Taiwan
| | - Yu-Lin Tai
- Department of Pediatrics, Hsinchu MacKay Memorial Hospital, Hsinchu, Taiwan
| | - Chien-Yu Lin
- Department of Medicine, MacKay Medical College, New Taipei city, Taiwan.,Department of Pediatrics, Hsinchu MacKay Memorial Hospital, Hsinchu, Taiwan
| |
Collapse
|
29
|
Marino A, Campanella E, Stracquadanio S, Ceccarelli M, Zagami A, Nunnari G, Cacopardo B. Corynebacterium striatum Bacteremia during SARS-CoV2 Infection: Case Report, Literature Review, and Clinical Considerations. Infect Dis Rep 2022; 14:383-390. [PMID: 35645221 PMCID: PMC9149851 DOI: 10.3390/idr14030042] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 02/01/2023] Open
Abstract
Bacterial infections, especially those in hospital settings, represent a major complication of COVID-19 patients, complicating management and worsening clinical outcomes. Corynebacterium striatum is a non-diphtheric actinobacterium that has been reported as being the causative agent of several different infections, affecting both immunocompetent and immunocompromised patients. Recently, C. striatum has been recognized as a nosocomial pathogen that is responsible for severe infection in critical patients, as well as in fragile and immunocompromised subjects. C. striatum has been described as the etiological agent of bacteremia, central line infections, and endocarditis. We report a case of a 91-year-old woman who was hospitalized due to SARS-CoV-2 infection, who developed C. striatum bacteremia and died despite antimicrobial therapy and clinical efforts. Furthermore, we discuss C. striatum diagnosis and treatment based on evidence from the scientific literature.
Collapse
Affiliation(s)
- Andrea Marino
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy;
- Department of Clinical and Experimental Medicine, Unit of Infectious Diseases, ARNAS Garibaldi Hospital, University of Catania, 95122 Catani, Italy; (M.C.); (A.Z.); (B.C.)
| | - Edoardo Campanella
- Department of Clinical and Experimental Medicine, Unit of Infectious Diseases, University of Messina, 98124 Messina, Italy; (E.C.); (G.N.)
| | - Stefano Stracquadanio
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy;
| | - Manuela Ceccarelli
- Department of Clinical and Experimental Medicine, Unit of Infectious Diseases, ARNAS Garibaldi Hospital, University of Catania, 95122 Catani, Italy; (M.C.); (A.Z.); (B.C.)
| | - Aldo Zagami
- Department of Clinical and Experimental Medicine, Unit of Infectious Diseases, ARNAS Garibaldi Hospital, University of Catania, 95122 Catani, Italy; (M.C.); (A.Z.); (B.C.)
| | - Giuseppe Nunnari
- Department of Clinical and Experimental Medicine, Unit of Infectious Diseases, University of Messina, 98124 Messina, Italy; (E.C.); (G.N.)
| | - Bruno Cacopardo
- Department of Clinical and Experimental Medicine, Unit of Infectious Diseases, ARNAS Garibaldi Hospital, University of Catania, 95122 Catani, Italy; (M.C.); (A.Z.); (B.C.)
| |
Collapse
|
30
|
Predictive model for bacterial co-infection in patients hospitalized for COVID-19: a multicenter observational cohort study. Infection 2022; 50:1243-1253. [PMID: 35488112 PMCID: PMC9053127 DOI: 10.1007/s15010-022-01801-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 03/05/2022] [Indexed: 11/05/2022]
Abstract
Objective The aim of our study was to build a predictive model able to stratify the risk of bacterial co-infection at hospitalization in patients with COVID-19. Methods Multicenter observational study of adult patients hospitalized from February to December 2020 with confirmed COVID-19 diagnosis. Endpoint was microbiologically documented bacterial co-infection diagnosed within 72 h from hospitalization. The cohort was randomly split into derivation and validation cohort. To investigate risk factors for co-infection univariable and multivariable logistic regression analyses were performed. Predictive risk score was obtained assigning a point value corresponding to β-coefficients to the variables in the multivariable model. ROC analysis in the validation cohort was used to estimate prediction accuracy. Results Overall, 1733 patients were analyzed: 61.4% males, median age 69 years (IQR 57–80), median Charlson 3 (IQR 2–6). Co-infection was diagnosed in 110 (6.3%) patients. Empirical antibiotics were started in 64.2 and 59.5% of patients with and without co-infection (p = 0.35). At multivariable analysis in the derivation cohort: WBC ≥ 7.7/mm3, PCT ≥ 0.2 ng/mL, and Charlson index ≥ 5 were risk factors for bacterial co-infection. A point was assigned to each variable obtaining a predictive score ranging from 0 to 5. In the validation cohort, ROC analysis showed AUC of 0.83 (95%CI 0.75–0.90). The optimal cut-point was ≥2 with sensitivity 70.0%, specificity 75.9%, positive predictive value 16.0% and negative predictive value 97.5%. According to individual risk score, patients were classified at low (point 0), intermediate (point 1), and high risk (point ≥ 2). CURB-65 ≥ 2 was further proposed to identify patients at intermediate risk who would benefit from early antibiotic coverage. Conclusions Our score may be useful in stratifying bacterial co-infection risk in COVID-19 hospitalized patients, optimizing diagnostic testing and antibiotic use. Supplementary Information The online version contains supplementary material available at 10.1007/s15010-022-01801-2.
Collapse
|
31
|
Ali YM, Lynch NJ, Khatri P, Bamigbola IE, Chan ACY, Yabuki M, Demopulos GA, Heeney JL, Pai S, Baxendale H, Schwaeble WJ. Secondary Complement Deficiency Impairs Anti-Microbial Immunity to Klebsiella pneumoniae and Staphylococcus aureus During Severe Acute COVID-19. Front Immunol 2022; 13:841759. [PMID: 35572551 PMCID: PMC9094484 DOI: 10.3389/fimmu.2022.841759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 03/21/2022] [Indexed: 01/08/2023] Open
Abstract
A high incidence of secondary Klebsiella pneumoniae and Staphylococcus aureus infection were observed in patients with severe COVID-19. The cause of this predisposition to infection is unclear. Our data demonstrate consumption of complement in acute COVID-19 patients reflected by low levels of C3, C4, and loss of haemolytic activity. Given that the elimination of Gram-negative bacteria depends in part on complement-mediated lysis, we hypothesised that secondary hypocomplementaemia is rendering the antibody-dependent classical pathway activation inactive and compromises serum bactericidal activity (SBA). 217 patients with severe COVID-19 were studied. 142 patients suffered secondary bacterial infections. Klebsiella species were the most common Gram-negative organism, found in 58 patients, while S. aureus was the dominant Gram-positive organism found in 22 patients. Hypocomplementaemia was observed in patients with acute severe COVID-19 but not in convalescent survivors three months after discharge. Sera from patients with acute COVID-19 were unable to opsonise either K. pneumoniae or S. aureus and had impaired complement-mediated killing of Klebsiella. We conclude that hyperactivation of complement during acute COVID-19 leads to secondary hypocomplementaemia and predisposes to opportunistic infections.
Collapse
Affiliation(s)
- Youssif M. Ali
- Department of Veterinary Medicine, School of Biological Sciences, University of Cambridge, Cambridge, United Kingdom
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Nicholas J. Lynch
- Department of Veterinary Medicine, School of Biological Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Priyanka Khatri
- Department of Veterinary Medicine, School of Biological Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Ifeoluwa E. Bamigbola
- Department of Veterinary Medicine, School of Biological Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Andrew C. Y. Chan
- Department of Veterinary Medicine, School of Biological Sciences, University of Cambridge, Cambridge, United Kingdom
| | | | | | - Jonathan L. Heeney
- Department of Veterinary Medicine, School of Biological Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Sumita Pai
- Royal Papworth Hospital NHS Foundation Trust, Cambridge, United Kingdom
| | - Helen Baxendale
- Royal Papworth Hospital NHS Foundation Trust, Cambridge, United Kingdom
| | - Wilhelm J. Schwaeble
- Department of Veterinary Medicine, School of Biological Sciences, University of Cambridge, Cambridge, United Kingdom
| |
Collapse
|
32
|
Said KB, Alsolami A, Moussa S, Alfouzan F, Bashir AI, Rashidi M, Aborans R, Taha TE, Almansour H, Alazmi M, Al-Otaibi A, Aljaloud L, Al-Anazi B, Mohialdin A, Aljadani A. COVID-19 Clinical Profiles and Fatality Rates in Hospitalized Patients Reveal Case Aggravation and Selective Co-Infection by Limited Gram-Negative Bacteria. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19095270. [PMID: 35564665 PMCID: PMC9101447 DOI: 10.3390/ijerph19095270] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 04/19/2022] [Accepted: 04/22/2022] [Indexed: 01/08/2023]
Abstract
Bacterial co-infections may aggravate COVID-19 disease, and therefore being cognizant of other pathogens is imperative. We studied the types, frequency, antibiogram, case fatality rates (CFR), and clinical profiles of co-infecting-pathogens in 301 COVID-19 patients. Co-infection was 36% (n = 109), while CFR was 31.2% compared to 9.9% in non-co-infected patients (z-value = 3.1). Four bacterial species dominated, namely, multidrug-resistant Klebsiella pneumoniae (37%, n = 48), extremely drug-resistant Acinetobacter baumannii (26%, n = 34), multidrug-resistant Eschericia. coli (18.6%, n = 24), and extremely drug-resistant Pseudomonas aeruginosa (8.5%, n = 11), in addition to other bacterial species (9.3%, n = 12). Increased co-infection of K. pneumoniae and A. baumannii was associated with increased death rates of 29% (n = 14) and 32% (n = 11), respectively. Klebsiella pneumoniae was equally frequent in respiratory and urinary tract infections (UTI), while E. coli mostly caused UTI (67%), and A. baumannii and P. aeruginosa dominated respiratory infections (38% and 45%, respectively). Co-infections correlated with advance in age: seniors ≥ 50 years (71%), young adults 21–49 years (25.6%), and children 0–20 years (3%). These findings have significant clinical implications in the successful COVID-19 therapies, particularly in geriatric management. Future studies would reveal insights into the potential selective mechanism(s) of Gram-negative bacterial co-infection in COVID-19 patients.
Collapse
Affiliation(s)
- Kamaleldin B. Said
- Department of Pathology, College of Medicine, University of Ha’il, Ha’il 55476, Saudi Arabia; (A.A.-O.); (L.A.); (B.A.-A.)
- Genomics, Bioinformatics and Systems Biology, Carleton University, 1125 Colonel-By Dr, Ottawa, ON K1S 5B6, Canada
- ASC, McGill University, 21111 Lakeshore Rd, Montreal, QC H9X 3L9, Canada
- Correspondence: Correspondence: ; Tel.: +966-500771459
| | - Ahmed Alsolami
- Department of Internal Medicine, College of Medicine, University of Ha’il, Ha’il 55476, Saudi Arabia; (A.A.); (A.A.)
| | - Safia Moussa
- Department of Microbiology, King Salman Specialist Hospital, Ha’il 55476, Saudi Arabia; (S.M.); (F.A.)
| | - Fayez Alfouzan
- Department of Microbiology, King Salman Specialist Hospital, Ha’il 55476, Saudi Arabia; (S.M.); (F.A.)
| | - Abdelhafiz I. Bashir
- Department of Physiology, College of Medicine, University of Ha’il, Ha’il 55476, Saudi Arabia;
| | - Musleh Rashidi
- Ministry of Health, Hail Region, Ha’il 55476, Saudi Arabia;
| | - Rana Aborans
- Department of Community Medicine, Faculty of Medicine, University of Ha’il, Ha’il 55476, Saudi Arabia;
| | - Taha E. Taha
- Department of Epidemiology, John Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA;
| | - Husam Almansour
- Health Management Department, College of Public Health and Health Informatics, University of Ha’il, Ha’il 81481, Saudi Arabia;
| | - Mashari Alazmi
- College of Computer Science and Engineering, University of Ha’il, Ha’il 81481, Saudi Arabia;
| | - Amal Al-Otaibi
- Department of Pathology, College of Medicine, University of Ha’il, Ha’il 55476, Saudi Arabia; (A.A.-O.); (L.A.); (B.A.-A.)
| | - Luluh Aljaloud
- Department of Pathology, College of Medicine, University of Ha’il, Ha’il 55476, Saudi Arabia; (A.A.-O.); (L.A.); (B.A.-A.)
| | - Basmah Al-Anazi
- Department of Pathology, College of Medicine, University of Ha’il, Ha’il 55476, Saudi Arabia; (A.A.-O.); (L.A.); (B.A.-A.)
| | - Ahmed Mohialdin
- Department of Surgery, College of Medicine, University of Ha’il, Ha’il 55476, Saudi Arabia;
| | - Ahmed Aljadani
- Department of Internal Medicine, College of Medicine, University of Ha’il, Ha’il 55476, Saudi Arabia; (A.A.); (A.A.)
| |
Collapse
|
33
|
Karuna T, Garg R, Kumar S, Singh G, Prasad L, Krishen Pandita K, Pakhare A, Saigal S, Khurana AK, Joshi R, Walia K, Khadanga S. Clinico–Epidemio-Microbiological Exploratory Review Among COVID-19 Patients with Secondary Infection in Central India. Infect Drug Resist 2022; 15:1667-1676. [PMID: 35422635 PMCID: PMC9005231 DOI: 10.2147/idr.s355742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 03/16/2022] [Indexed: 12/19/2022] Open
Abstract
Purpose Secondary infections (SI) in COVID-19 have been documented from 3.6% to 72% in various studies with mortality ranging from 8.1% to 57.6%. There is a gap in knowledge for clinico–epidemio-microbilogical association among COVID-19 patients with concomitant SI. Patients and Methods This is a retrospective chart review, in central India. The study was undertaken for hospitalized adult patients during 1st June 2020 to 30th November 2020, with laboratory proven COVID-19 infection and secondary infection. Results Out of the total 2338 number of patients, only 265 (11.3%) patients were investigated for microbiological identification of SI. Male gender was predominant (76.8%) and the mean age was 53.7 ± 17.8 years. Only 3.5% (82/2338) of patients were having microbiologically confirmed (bacterial or fungal) SI. The overall mortality was 50.9% (54/82) with a differential mortality of 88.8% (48/54) in high-priority areas and 21.4% (6/28) in low-priority areas. Blood was the most commonly investigated sample (56%) followed by urine (20.7%) and respiratory secretion (15.8%). A. baumanii complex (20/82, 24.3%) was the most common bacteria isolated followed by K. pneumonia (12/82, 14.6%) and E. coli (11/82, 13.4%). Candida spp. (20/82, 24.3%) was the most common fungal pathogen isolated. Sixty percent (12/20) of Acinetobacter spp. were carbapenam-resistant and 70.3% of Enterobacterales were carbapenam-resistant. Fluconazole resistant Candida spp. was isolated only in 10% (2/20) of cases. Diabetes was the most common co-morbidity 54.8% (45/82) followed by hypertension (41.4%) and chronic heart disease (13.4%). The negative predictors of secondary infections are urinary catheterization, placement of central line and mechanical ventilation (invasive and non-invasive). Conclusion There is an urgent need of better anti-microbial stewardship practices in India (institutional and extra institutional) for curtailment of secondary infection rates particularly among COVID-19 patients.
Collapse
Affiliation(s)
- T Karuna
- Department of Microbiology, AIIMS, Bhopal, Madhya Pradesh, India
| | - Rahul Garg
- Department of General Medicine, AIIMS, Bhopal, Madhya Pradesh, India
| | - Shweta Kumar
- Department of General Medicine, AIIMS, Bhopal, Madhya Pradesh, India
| | - Gyanendra Singh
- Department of Community and Family Medicine, AIIMS, Bhopal, Madhya Pradesh, India
| | - Lakshmi Prasad
- Department of Hospital Administration, AIIMS, Bhopal, Madhya Pradesh, India
| | | | - Abhijit Pakhare
- Department of Community and Family Medicine, AIIMS, Bhopal, Madhya Pradesh, India
| | - Saurabh Saigal
- Department of Critical Care, AIIMS, Bhopal, Madhya Pradesh, India
| | | | - Rajnish Joshi
- Department of General Medicine, AIIMS, Bhopal, Madhya Pradesh, India
| | - Kamini Walia
- Indian Council of Medical Research, New Delhi, India
| | - Sagar Khadanga
- Department of General Medicine, AIIMS, Bhopal, Madhya Pradesh, India
- Correspondence: Sagar Khadanga, Department of General Medicine, AIIMS, Bhopal, Madhya Pradesh, India, Email
| |
Collapse
|
34
|
SeyedAlinaghi S, Karimi A, Barzegary A, Pashaei Z, Afsahi AM, Alilou S, Janfaza N, Shojaei A, Afroughi F, Mohammadi P, Soleimani Y, Nazarian N, Amiri A, Tantuoyir MM, Oliaei S, Mehraeen E, Dadras O. Mucormycosis infection in patients with COVID-19: A systematic review. Health Sci Rep 2022; 5:e529. [PMID: 35252593 PMCID: PMC8885749 DOI: 10.1002/hsr2.529] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 01/23/2022] [Accepted: 01/25/2022] [Indexed: 02/05/2023] Open
Abstract
INTRODUCTION Several reports previously described mucormycosis co-infection in patients with COVID-19. As mucormycosis and COVID-19 co-infection might adversely affect patients' outcomes, we aimed to systematically review the related evidence and the subsequent outcomes. METHODS We conducted a systematic review of relevant articles searching the keywords in the online databases of PubMed, Scopus, Embase, Cochrane, and Web of Science. All the records from the start of the pandemic until June 12th, 2021 underwent title/abstract and then full-text screening process, and the eligible studies were included. We did not include any language or time restrictions for the included studies. RESULTS We found 31 eligible studies reporting 144 total cases of COVID-19 and mucormycosis co-infection. The nose, cranial sinuses, and orbital cavity were the most commonly involved organs, although the cerebrum, lungs, and heart were also involved in the studies. Pre-existing diabetes mellitus (DM), as well as corticosteroid use, were the most commonly identified risk factors, but other underlying conditions and immunomodulatory drug use were also present in several cases. Aspergillus was the most commonly reported micro-organism that caused further co-infections in patients with concurrent COVID-19 and mucormycosis. As most of the studies were case reports, no reliable estimate of the mortality rate could be made, but overall, 33.6% of the studied cases died. CONCLUSION Early diagnosis of mucormycosis co-infection in COVID-19 patients and selecting the right treatment plan could be a challenge for physicians. Patients with underlying co-morbidities, immunocompromised patients, and those receiving corticosteroids are at higher risk of developing mucormycosis co-infection and it is crucial to have an eye examination for early signs and symptoms suggesting a fungal infection in these patients.
Collapse
Affiliation(s)
- SeyedAhmad SeyedAlinaghi
- Iranian Research Center for HIV/AIDSIranian Institute for Reduction of High‐Risk Behaviors, Tehran University of Medical SciencesTehranIran
| | - Amirali Karimi
- School of MedicineTehran University of Medical SciencesTehranIran
| | | | - Zahra Pashaei
- Iranian Research Center for HIV/AIDSIranian Institute for Reduction of High‐Risk Behaviors, Tehran University of Medical SciencesTehranIran
| | - Amir Masoud Afsahi
- Department of RadiologySchool of Medicine, University of California, San Diego (UCSD)San DiegoCaliforniaUSA
| | - Sanam Alilou
- School of MedicineTehran University of Medical SciencesTehranIran
| | - Nazanin Janfaza
- Internal Medicine DepartmentImam Khomeini Hospital Complex, School of Medicine, Tehran University of Medical SciencesTehranIran
| | - Alireza Shojaei
- Iranian Research Center for HIV/AIDSIranian Institute for Reduction of High‐Risk Behaviors, Tehran University of Medical SciencesTehranIran
| | - Fatemeh Afroughi
- School of MedicineIslamic Azad UniversityTehranIran
- Pars HospitalIran University of Medical SciencesTehranIran
| | - Parsa Mohammadi
- School of MedicineTehran University of Medical SciencesTehranIran
| | | | | | - Ava Amiri
- Iranian Research Center for HIV/AIDSIranian Institute for Reduction of High‐Risk Behaviors, Tehran University of Medical SciencesTehranIran
| | - Marcarious M. Tantuoyir
- School of MedicineTehran University of Medical SciencesTehranIran
- Biomedical Engineering UnitUniversity of Ghana Medical Center (UGMC)AccraGhana
| | - Shahram Oliaei
- HBOT Research CenterGolestan Hospital, Islamic Republic of Iran, Navy and AJA Medical UniversityTehranIran
| | - Esmaeil Mehraeen
- Department of Health Information TechnologyArdebil University of Medical SciencesArdebilIran
| | - Omid Dadras
- Department of Global Health and SocioepidemiologyGraduate School of Medicine, Kyoto UniversityKyotoJapan
| |
Collapse
|
35
|
Bacterial Coinfections Increase Mortality of Severely Ill COVID-19 Patients in Saudi Arabia. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19042424. [PMID: 35206609 PMCID: PMC8871991 DOI: 10.3390/ijerph19042424] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 02/15/2022] [Accepted: 02/16/2022] [Indexed: 02/01/2023]
Abstract
Coronavirus disease 19 (COVID-19) is an ongoing global pandemic that is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The severity and mortality rates of COVID-19 are affected by several factors, such as respiratory diseases, diabetes, and hypertension. Bacterial coinfections are another factor that could contribute to the severity of COVID-19. Limited studies have investigated morbidity and mortality due to microbial coinfections in COVID-19 patients. Here, we retrospectively studied the effects of bacterial coinfections on intensive care unit (ICU)-admitted patients with COVID-19 in Asir province, Saudi Arabia. We analyzed electronic medical records of hospitalized patients with COVID-19 at Asir Central Hospital. A total of 34 patients were included, and the clinical data of 16 patients infected with SARS-CoV-2 only and 18 patients coinfected with SARS-CoV-2 and bacterial infections were analyzed in our study. Our data showed that the length of stay at the hospital for patients infected with both SARS-CoV-2 and bacterial infection was 35.2 days, compared to 16.2 days for patients infected with only SARS-CoV-2 (p = 0.0001). In addition, higher mortality rates were associated with patients in the coinfection group compared to the SARS-CoV-2-only infected group (50% vs. 18.7%, respectively). The study also showed that gram-negative bacteria are the most commonly isolated bacteria in COVID-19 patients. To conclude, this study found that individuals with COVID-19 who presented with bacterial infections are at higher risk for a longer stay at the hospital and potentially death. Further studies with a larger population are warranted to better understand the clinical outcomes of COVID-19 with bacterial infections.
Collapse
|
36
|
Moya‐Salazar J, Sauñe SS, Valer R, Salazar‐Hernandez R, Loza W, Suxe E, Chicoma‐Flores K, Contreras‐Pulache H. Fungal, parasitological, and bacterial coinfection in a severely ill COVID-19 patient in Peru. Clin Case Rep 2022; 10:e05395. [PMID: 35223005 PMCID: PMC8855487 DOI: 10.1002/ccr3.5395] [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: 06/23/2021] [Revised: 01/17/2022] [Accepted: 01/24/2022] [Indexed: 11/10/2022] Open
Abstract
COVID-19 patients are prone to coinfections during their hospitalization. These coinfections are challenging as they involve longer hospital stays, high costs, and higher risk of mortality. Here, we present a case of a patient with multi-infection by resistant parasites, fungi, and bacteria during his hospitalization in a hospital in Lima, Peru.
Collapse
Affiliation(s)
- Jeel Moya‐Salazar
- Hospital Nacional Docente Madre Niño San BartoloméLimaPeru
- South America Center for Education and Research in Public HealthUniversidad Norbert WienerLimaPeru
- Infectious UnitNesh HubbsLimaPeru
| | - Sharon S. Sauñe
- Department of PathologyHospital Carlos Lanfranco La HozLimaPeru
| | - Roxana Valer
- Department of PathologyHospital Carlos Lanfranco La HozLimaPeru
| | | | - Wilfredo Loza
- Department of PathologyHospital Carlos Lanfranco La HozLimaPeru
| | - Evelyn Suxe
- Department of PathologyHospital Carlos Lanfranco La HozLimaPeru
| | | | - Hans Contreras‐Pulache
- South America Center for Education and Research in Public HealthUniversidad Norbert WienerLimaPeru
| |
Collapse
|
37
|
Subbaram K, Ali PSS, Ali S. Enhanced endocytosis elevated virulence and severity of SARS-CoV-2 due to hyperglycemia in type 2 diabetic patients. GENE REPORTS 2022; 26:101495. [PMID: 35043090 PMCID: PMC8758565 DOI: 10.1016/j.genrep.2022.101495] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 01/10/2022] [Indexed: 12/15/2022]
Abstract
Diabetes mellitus is a metabolic disease that causes hyperglycemia. In COVID-19 patients the severity of the disease depends on myriad factors but diabetes mellitus is the most important comorbidity. The current review was conducted to investigate the virulence of SARS-CoV-2 and disease severity of COVID-19 in type 2 diabetes mellitus patients and relevant treatment. The literature published in PubMed, Scopus, Web of Science, and Google Scholar was reviewed up to September 2021. The keywords including SARS-CoV-2, type 2 diabetes mellitus in COVID-19, hyperglycemia in COVID-19, opportunistic infections in type 2 diabetes mellitus and COVID-19 were used in different combinations. Hyperglycemic individuals over-express ACE-2 receptors in the lungs thus increasing the SARS-CoV-2 susceptibility and replication. Although dipeptidyl peptidase-4 plays an important role in glucose homeostasis, additionally it also stimulates the production of proinflammatory cytokines such as IL-6 and TNF-α creating a cytokine storm. Cytokine storm might be responsible for respiratory insufficiency in severe COVID-19 patients. Type 2 diabetes mellitus is associated with immunosuppression and the patients are prone to get many opportunistic infections. Type 2 diabetes mellitus patients with severe COVID-19 have lymphopenia. Moreover, in type 2 diabetes mellitus patients the neutrophils exhibit decreased chemotaxis, hydrogen peroxide production, and phagocytosis. Reduction in lymphocyte count and defective neutrophil capacity renders them with COVID-19 susceptible to opportunistic bacterial and fungal infections increasing the mortality rate. The opportunistic bacterial infections in COVID-19 patients were due to Staphylococcus aureus, Streptococcus pneumonia, and coagulase-negative Staphylococci, E. coli, Pseudomonas aeruginosa, and Klebsiella sp. In COVID-19 patients with type 2 diabetes mellitus, mucormycosis was found to be the most common fungal infection with a higher predilection to males. Hyperglycemia in COVID-19 patients with type 2 diabetes mellitus enhances the SARS-CoV-2 replication with an adverse outcome. A strong correlation exists between the poor prognosis of COVID-19 and type 2 diabetes mellitus. Proper glycemic control in COVID-19 patients with diabetes mellitus might lessen the severity of the disease.
Collapse
Key Words
- ACE-2, Angiotensin-converting enzyme 2
- ARDS, Acute respiratory distress syndrome
- ATP, Adenosine tri phosphate
- CLR, C-lectin type receptors
- COVID-19
- COVID-19, Coronavirus disease 2019
- Endocytosis
- GRP78, non-immune receptor glucose regulated protein 78
- Hyperglycemia
- IFN-1, Interferon-1
- MERS, Middle East respiratory syndrome
- NRP1, neuropilin-1
- Opportunistic infections
- SARS, Severe acute respiratory syndrome
- SARS-CoV-2
- SARS-CoV-2, Severe acute respiratory syndrome coronavirus-2
- T2DM, Type 2 diabetes mellitus
- TLR, toll-like receptors
- TMPRSS2, Transmembrane Serine Protease 2
- Type 2 diabetes mellitus
- WHO, World Health Organization
Collapse
Affiliation(s)
- Kannan Subbaram
- School of Medicine, The Maldives National University, Male', Maldives
| | - P Shaik Syed Ali
- School of Medicine, The Maldives National University, Male', Maldives
| | - Sheeza Ali
- School of Medicine, The Maldives National University, Male', Maldives
| |
Collapse
|
38
|
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.
Collapse
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)
| | | | | |
Collapse
|
39
|
Mzava O, Cheng AP, Chang A, Smalling S, Djomnang Kounatse LA, Lenz J, Longman R, Steadman A, Salvatore M, Suthanthiran M, Lee JR, Mason CE, Dadhania D, De Vlaminck I. A metagenomic DNA sequencing assay that is robust against environmental DNA contamination. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 34845444 DOI: 10.1101/2021.12.02.470912v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
Metagenomic DNA sequencing is a powerful tool to characterize microbial communities but is sensitive to environmental DNA contamination, in particular when applied to samples with low microbial biomass. Here, we present contamination-free metagenomic DNA sequencing (Coffee-seq), a metagenomic sequencing assay that is robust against environmental contamination. The core idea of Coffee-seq is to tag the DNA in the sample prior to DNA isolation and library preparation with a label that can be recorded by DNA sequencing. Any contaminating DNA that is introduced in the sample after tagging can then be bioinformatically identified and removed. We applied Coffee-seq to screen for infections from microorganisms with low burden in blood and urine, to identify COVID-19 co-infection, to characterize the urinary microbiome, and to identify microbial DNA signatures of inflammatory bowel disease in blood.
Collapse
Affiliation(s)
- Omary Mzava
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA
| | - Alexandre Pellan Cheng
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA
| | - Adrienne Chang
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA
| | - Sami Smalling
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA
| | | | - Joan Lenz
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA
| | - Randy Longman
- Jill Roberts Center for IBD, Weill Cornell Medicine, Division of Gastroenterology and Hepatology, New York, NY, USA
| | | | - Mirella Salvatore
- Division of Public Health Programs, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Manikkam Suthanthiran
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine, New York, NY, 10065, USA.,Department of Transplantation Medicine, New York Presbyterian Hospital-Weill Cornell Medical Center, New York, NY, 10065, USA
| | - John R Lee
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine, New York, NY, 10065, USA.,Department of Transplantation Medicine, New York Presbyterian Hospital-Weill Cornell Medical Center, New York, NY, 10065, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York City, NY, USA
| | - Darshana Dadhania
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine, New York, NY, 10065, USA.,Department of Transplantation Medicine, New York Presbyterian Hospital-Weill Cornell Medical Center, New York, NY, 10065, USA
| | - Iwijn De Vlaminck
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA
| |
Collapse
|
40
|
Mzava O, Cheng AP, Chang A, Smalling S, Djomnang Kounatse LA, Lenz J, Longman R, Steadman A, Salvatore M, Suthanthiran M, Lee JR, Mason CE, Dadhania D, De Vlaminck I. A metagenomic DNA sequencing assay that is robust against environmental DNA contamination. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.11.22.469599. [PMID: 34845444 PMCID: PMC8629186 DOI: 10.1101/2021.11.22.469599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Metagenomic DNA sequencing is a powerful tool to characterize microbial communities but is sensitive to environmental DNA contamination, in particular when applied to samples with low microbial biomass. Here, we present contamination-free metagenomic DNA sequencing (Coffee-seq), a metagenomic sequencing assay that is robust against environmental contamination. The core idea of Coffee-seq is to tag the DNA in the sample prior to DNA isolation and library preparation with a label that can be recorded by DNA sequencing. Any contaminating DNA that is introduced in the sample after tagging can then be bioinformatically identified and removed. We applied Coffee-seq to screen for infections from microorganisms with low burden in blood and urine, to identify COVID-19 co-infection, to characterize the urinary microbiome, and to identify microbial DNA signatures of inflammatory bowel disease in blood.
Collapse
Affiliation(s)
- Omary Mzava
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA
| | - Alexandre Pellan Cheng
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA
| | - Adrienne Chang
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA
| | - Sami Smalling
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA
| | | | - Joan Lenz
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA
| | - Randy Longman
- Jill Roberts Center for IBD, Weill Cornell Medicine, Division of Gastroenterology and Hepatology, New York, NY, USA
| | | | - Mirella Salvatore
- Division of Public Health Programs, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Manikkam Suthanthiran
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
- Department of Transplantation Medicine, New York Presbyterian Hospital–Weill Cornell Medical Center, New York, NY, 10065, USA
| | - John R. Lee
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
- Department of Transplantation Medicine, New York Presbyterian Hospital–Weill Cornell Medical Center, New York, NY, 10065, USA
| | - Christopher E. Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York City, NY, USA
| | - Darshana Dadhania
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
- Department of Transplantation Medicine, New York Presbyterian Hospital–Weill Cornell Medical Center, New York, NY, 10065, USA
| | - Iwijn De Vlaminck
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA
| |
Collapse
|
41
|
Antibiotic Prescriptions Targeting Bacterial Respiratory Infections in Admitted Patients with COVID-19: A Prospective Observational Study. Infect Dis Ther 2021; 10:2575-2591. [PMID: 34529255 PMCID: PMC8444524 DOI: 10.1007/s40121-021-00535-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 09/03/2021] [Indexed: 12/29/2022] Open
Abstract
Introduction Although bacterial co- and superinfections are rarely present in patients with COVID-19, overall antibiotic prescribing in admitted patients is high. In order to counter antibiotic overprescribing, antibiotic stewardship teams need reliable data concerning antibiotic prescribing in admitted patients with COVID-19. Methods In this prospective observational cohort study, we performed a quantitative and qualitative evaluation of antibiotic prescriptions in patients admitted to the COVID-19 ward of a 721-bed Belgian university hospital between 1 May and 2 November 2020. Data on demographics, clinical and microbiological parameters and antibiotic consumption were collected. Defined daily doses (DDD) were calculated for antibiotics prescribed in the context of a (presumed) bacterial respiratory tract infection and converted into two indicators: DDD/admission and DDD/100 hospital bed days. A team of infectious disease specialists performed an appropriateness evaluation for every prescription. A driver analysis was performed to identify factors increasing the odds of an antibiotic prescription in patients with a confirmed COVID-19 diagnosis. Results Of 403 eligible participants with a suspected COVID-19 infection, 281 were included. In 13.8% of the 203 admissions with a COVID-19 confirmed diagnosis, antibiotics were initiated for a (presumed) bacterial respiratory tract co-/superinfection (0.86 DDD/admission; 8.92 DDD/100 bed days; 39.4% were scored as ‘appropriate’). Five drivers of antibiotic prescribing were identified: history of cerebrovascular disease, high neutrophil/lymphocyte ratio in male patients, age, elevated ferritin levels and the collection of respiratory samples for bacteriological analysis. Conclusion In the studied population, the antibiotic consumption for a (presumed) bacterial respiratory tract co-/superinfection was low. In particular, the small total number of DDDs in patients with confirmed COVID-19 diagnosis suggests thoughtful antibiotic use. However, antibiotic stewardship programmes remain crucial to counter unnecessary and inappropriate antibiotic use in hospitalized patients with COVID-19. Trial Registration The study is registered at ClinicalTrials.gov (NCT04544072). Supplementary Information The online version contains supplementary material available at 10.1007/s40121-021-00535-2.
Collapse
|
42
|
Soltani S, Faramarzi S, Zandi M, Shahbahrami R, Jafarpour A, Akhavan Rezayat S, Pakzad I, Abdi F, Malekifar P, Pakzad R. Bacterial coinfection among coronavirus disease 2019 patient groups: an updated systematic review and meta-analysis. New Microbes New Infect 2021; 43:100910. [PMID: 34226847 PMCID: PMC8245302 DOI: 10.1016/j.nmni.2021.100910] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/01/2021] [Accepted: 06/23/2021] [Indexed: 12/17/2022] Open
Abstract
The pandemic of severe acute respiratory syndrome coronavirus 2 raised the attention towards bacterial coinfection and its role in coronavirus disease 2019 (COVID-19) disease. This study aims to systematically review and identify the pooled prevalence of bacterial coinfection in the related articles. A comprehensive search was conducted in international databases, including MEDLINE, Scopus, Web of Science, and Embase, to identify the articles on the prevalence of bacterial coinfections in COIVD-19 patients from 1 December 2019 until 30 December 2020. All observational epidemiological studies that evaluated the prevalence of bacterial coinfections in patients with COVID-19 were included without any restriction. Forty-two studies including a total sample size of 54,695 were included in the analysis. The pooled estimate for the prevalence of bacterial coinfections was 20.97% (95% CI: 15.95-26.46), and the pooled prevalence of bacterial coinfections was 5.20% (95% CI: 2.39-8.91) for respiratory subtype and 4.79% (95% CI: 0.11-14.61) for the gastrointestinal subtype. The pooled prevalence for Eastern Mediterranean Regional Office and South-East Asia Regional Office was 100% (95% CI: 82.35-100.00) and 2.61% (95% CI: 1.74-3.62). This rate of coinfection poses a great danger towards patients, especially those in critical condition. Although there are multiple complications and adverse effects related to extensive use of antibiotics to treat patients with COVID-19, it seems there is no other option except applying them, and it needs to be done carefully.
Collapse
Affiliation(s)
- S. Soltani
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
| | - S. Faramarzi
- Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - M. Zandi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
| | - R. Shahbahrami
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
| | - A. Jafarpour
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
- Gerash Amir-al-Momenin Medical and Educational Center, Gerash University of Medical Sciences, Gerash, Iran
| | - S. Akhavan Rezayat
- Department of Management & Health Economics, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - I. Pakzad
- Medical Microbiology, Department of Microbiology, School of Medicine, Ilam University Medical Sciences, Ilam, Iran
| | - F. Abdi
- School of Nursing and Midwifery, Alborz University of Medical Sciences, Karaj, Iran
| | - P. Malekifar
- Epidemiology, Department of Epidemiology, School of Public Health, Tehran University Medical Sciences, Tehran, Iran
| | - R. Pakzad
- Epidemiology, Department of Epidemiology, Faculty of Health, Ilam University Medical Sciences, Ilam, Iran
- Student Research Committee, Ilam University Medical Sciences, Ilam, Iran
| |
Collapse
|
43
|
Contamination of Hospital Surfaces with Bacterial Pathogens under the Current COVID-19 Outbreak. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18179042. [PMID: 34501634 PMCID: PMC8431522 DOI: 10.3390/ijerph18179042] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/18/2021] [Accepted: 08/23/2021] [Indexed: 12/23/2022]
Abstract
The SARS-CoV-2 pandemic remains a global health issue for several reasons, such as the low vaccination rates and a lack of developed herd immunity to the evolution of SARS-CoV-2, as well as its potential inclination to elude neutralizing antibodies. It should be noted that the severity of the COVID-19 disease is significantly affected by the presence of co-infections. Comorbid conditions are caused not only by pathogenic and opportunistic microorganisms but also by some representatives of the environmental microbiome. The presence of patients with moderate and severe forms of the disease in hospitals indicates the need for epidemiological monitoring of (1) bacterial pathogens circulating in hospitals, especially the ESKAPE group pathogens, and (2) the microbiome of various surfaces in hospitals. In our study, we used combined methods based on PCR and NGS sequencing, which are widely used for epidemiological monitoring. Through this approach, we identified the DNA of pathogenic bacteria (Klebsiella pneumoniae, Pseudomonas aeruginosa, Staphylococcus aureus, CoNS, and Achromobacter spp.) on various surfaces. We also estimated the microbiome diversity of surfaces and identified the potential reservoirs of infections using 16S rRNA profiling. Although we did not assess the viability of identified microorganisms, our results indicate the possible risks of insufficient regular disinfection of surfaces, regardless of department, at the Infectious Diseases Hospital. Controlling the transmission of nosocomial diseases is critical to the successful treatment of COVID-19 patients, the rational use of antimicrobial drugs, and timely decontamination measures.
Collapse
|
44
|
Copaja-Corzo C, Hueda-Zavaleta M, Benites-Zapata VA, Rodriguez-Morales AJ. Antibiotic Use and Fatal Outcomes among Critically Ill Patients with COVID-19 in Tacna, Peru. Antibiotics (Basel) 2021; 10:959. [PMID: 34439009 PMCID: PMC8388967 DOI: 10.3390/antibiotics10080959] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 07/31/2021] [Accepted: 08/07/2021] [Indexed: 01/08/2023] Open
Abstract
Overuse of antibiotics during the Coronavirus Disease 2019 (COVID-19) pandemic could increase the selection of extensively resistant bacteria (XDR). However, it is unknown what impact they could have on the evolution of patients, particularly critically ill patients. This study aimed to evaluate the characteristics and impact of ICU-acquired infections in patients with COVID-19. A retrospective cohort study was conducted, evaluating all patients with critical COVID-19 admitted to the intensive care unit (ICU) of a hospital in Southern Peru from 28 March 2020 to 1 March 2021. Of the 124 patients evaluated, 50 (40.32%) developed a healthcare-associated infection (HAI), which occurred at a median of 8 days (IQR 6-17) after ICU admission. The proportion of patients with HAI that required ceftriaxone was significantly higher; the same was true for the use of dexamethasone. Forty bacteria isolations (80%) were classified as XDR to antibiotics, with the most common organisms being Acinetobacter baumannii (54%) and Pseudomonas aeruginosa (22%); 33% (41/124) died at the ICU during the follow-up. In the adjusted analysis, healthcare-associated infection was associated with an increased risk of mortality (aHR= 2.7; 95% CI: 1.33-5.60) and of developing acute renal failure (aRR = 3.1; 95% CI: 1.42-6.72). The incidence of healthcare infection mainly by XDR pathogens is high in critically ill patients with COVID-19 and is associated with an increased risk of complications or death.
Collapse
Affiliation(s)
- Cesar Copaja-Corzo
- Faculty of Health Sciences, Universidad Privada de Tacna, Tacna 23003, Peru;
| | - Miguel Hueda-Zavaleta
- Faculty of Health Sciences, Universidad Privada de Tacna, Tacna 23003, Peru;
- Hospital III Daniel Alcides Carrión EsSalud, Tacna 23000, Peru
| | - Vicente A. Benites-Zapata
- Unidad de Investigación para la Generación y Síntesis de Evidencias en Salud, Universidad San Ignacio de Loyola, Lima 15024, Peru;
| | - Alfonso J. Rodriguez-Morales
- Master Program on Clinical Epidemiology and Biostatistics, Universidad Cientifica del Sur, Lima 15046, Peru
- Grupo de Investigación Biomedicina, Faculty of Medicine, Fundación Universitaria Autónoma de las Américas, Belmonte, Pereira, Risaralda 660003, Colombia
| |
Collapse
|
45
|
Le NPK, Herz C, Gomes JVD, Förster N, Antoniadou K, Mittermeier-Kleßinger VK, Mewis I, Dawid C, Ulrichs C, Lamy E. Comparative Anti-Inflammatory Effects of Salix Cortex Extracts and Acetylsalicylic Acid in SARS-CoV-2 Peptide and LPS-Activated Human In Vitro Systems. Int J Mol Sci 2021; 22:ijms22136766. [PMID: 34201817 PMCID: PMC8268791 DOI: 10.3390/ijms22136766] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/15/2021] [Accepted: 06/20/2021] [Indexed: 12/21/2022] Open
Abstract
The usefulness of anti-inflammatory drugs as an adjunct therapy to improve outcomes in COVID-19 patients is intensely discussed in this paper. Willow bark (Salix cortex) has been used for centuries to relieve pain, inflammation, and fever. Its main active ingredient, salicin, is metabolized in the human body into salicylic acid, the precursor of the commonly used pain drug acetylsalicylic acid (ASA). Here, we report on the in vitro anti-inflammatory efficacy of two methanolic Salix extracts, standardized to phenolic compounds, in comparison to ASA in the context of a SARS-CoV-2 peptide challenge. Using SARS-CoV-2 peptide/IL-1β- or LPS-activated human PBMCs and an inflammatory intestinal Caco-2/HT29-MTX co-culture, Salix extracts, and ASA concentration-dependently suppressed prostaglandin E2 (PGE2), a principal mediator of inflammation. The inhibition of COX-2 enzyme activity, but not protein expression was observed for ASA and one Salix extract. In activated PBMCs, the suppression of relevant cytokines (i.e., IL-6, IL-1β, and IL-10) was seen for both Salix extracts. The anti-inflammatory capacity of Salix extracts was still retained after transepithelial passage and liver cell metabolism in an advanced co-culture model system consisting of intestinal Caco-2/HT29-MTX cells and differentiated hepatocyte-like HepaRG cells. Taken together, our in vitro data suggest that Salix extracts might present an additional anti-inflammatory treatment option in the context of SARS-CoV-2 peptides challenge; however, more confirmatory data are needed.
Collapse
Affiliation(s)
- Nguyen Phan Khoi Le
- Molecular Preventive Medicine, University Medical Center and Faculty of Medicine, University of Freiburg, 79108 Freiburg, Germany; (N.P.K.L.); (C.H.); (J.V.D.G.)
| | - Corinna Herz
- Molecular Preventive Medicine, University Medical Center and Faculty of Medicine, University of Freiburg, 79108 Freiburg, Germany; (N.P.K.L.); (C.H.); (J.V.D.G.)
| | - João Victor Dutra Gomes
- Molecular Preventive Medicine, University Medical Center and Faculty of Medicine, University of Freiburg, 79108 Freiburg, Germany; (N.P.K.L.); (C.H.); (J.V.D.G.)
| | - Nadja Förster
- Division Urban Plant Ecophysiology, Humboldt-Universität zu Berlin, 14195 Berlin, Germany; (N.F.); (I.M.); (C.U.)
| | - Kyriaki Antoniadou
- Food Chemistry and Molecular Sensory Science, Technical University of Munich, Lise-Meitner-Str. 34, 85354 Freising, Germany; (K.A.); (V.K.M.-K.); (C.D.)
| | - Verena Karolin Mittermeier-Kleßinger
- Food Chemistry and Molecular Sensory Science, Technical University of Munich, Lise-Meitner-Str. 34, 85354 Freising, Germany; (K.A.); (V.K.M.-K.); (C.D.)
| | - Inga Mewis
- Division Urban Plant Ecophysiology, Humboldt-Universität zu Berlin, 14195 Berlin, Germany; (N.F.); (I.M.); (C.U.)
| | - Corinna Dawid
- Food Chemistry and Molecular Sensory Science, Technical University of Munich, Lise-Meitner-Str. 34, 85354 Freising, Germany; (K.A.); (V.K.M.-K.); (C.D.)
| | - Christian Ulrichs
- Division Urban Plant Ecophysiology, Humboldt-Universität zu Berlin, 14195 Berlin, Germany; (N.F.); (I.M.); (C.U.)
| | - Evelyn Lamy
- Molecular Preventive Medicine, University Medical Center and Faculty of Medicine, University of Freiburg, 79108 Freiburg, Germany; (N.P.K.L.); (C.H.); (J.V.D.G.)
- Correspondence: ; Tel.: +49-761-270-82150
| |
Collapse
|
46
|
Adebisi YA, Jimoh ND, Ogunkola IO, Uwizeyimana T, Olayemi AH, Ukor NA, Lucero-Prisno DE. The use of antibiotics in COVID-19 management: a rapid review of national treatment guidelines in 10 African countries. Trop Med Health 2021; 49:51. [PMID: 34162445 PMCID: PMC8220112 DOI: 10.1186/s41182-021-00344-w] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 06/09/2021] [Indexed: 12/12/2022] Open
Abstract
Antimicrobial resistance is a hidden threat lurking behind the COVID-19 pandemic which has claimed thousands of lives prior to the emergence of the global outbreak. With a pandemic on the scale of COVID-19, antimicrobial resistance has the potential to become a double-edged sword with the overuse of antibiotics having the potential of taking us back to the pre-antibiotic era. Antimicrobial resistance is majorly attributed to widespread and unnecessary use of antibiotics, among other causes, which has facilitated the emergence and spread of resistant pathogens. Our study aimed to conduct a rapid review of national treatment guidelines for COVID-19 in 10 African countries (Ghana, Kenya, Uganda, Nigeria, South Africa, Zimbabwe, Botswana, Liberia, Ethiopia, and Rwanda) and examined its implication for antimicrobial resistance response on the continent. Our findings revealed that various antibiotics, such as azithromycin, doxycycline, clarithromycin, ceftriaxone, erythromycin, amoxicillin, amoxicillin-clavulanic acid, ampicillin, gentamicin, benzylpenicillin, piperacillin/tazobactam, ciprofloxacin, ceftazidime, cefepime, vancomycin, meropenem, and cefuroxime among others, were recommended for use in the management of COVID-19. This is worrisome in that COVID-19 is a viral disease and only a few COVID-19 patients would have bacterial co-infection. Our study highlighted the need to emphasize prudent and judicious use of antibiotics in the management of COVID-19 in Africa.
Collapse
Affiliation(s)
- Yusuff Adebayo Adebisi
- Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria
- Medical Research Center, Kateb University, Kabul, Afghanistan
| | | | | | | | | | | | - Don Eliseo Lucero-Prisno
- Department of Global Health and Development, London School of Hygiene and Tropical Medicine, London, UK
| |
Collapse
|