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Lubkin A, Bernard-Raichon L, DuMont AL, Valero Jimenez AM, Putzel GG, Gago J, Zwack EE, Olusanya O, Boguslawski KM, Dallari S, Dyzenhaus S, Herrmann C, Ilmain JK, Isom GL, Pawline M, Perault AI, Perelman S, Sause WE, Shahi I, St. John A, Tierce R, Zheng X, Zhou C, Noval MG, O'Keeffe A, Podkowik M, Gonzales S, Inglima K, Desvignes L, Hochman SE, Stapleford KA, Thorpe LE, Pironti A, Shopsin B, Cadwell K, Dittmann M, Torres VJ. SARS-CoV-2 infection predisposes patients to coinfection with Staphylococcus aureus. mBio 2024; 15:e0166724. [PMID: 39037272 PMCID: PMC11323729 DOI: 10.1128/mbio.01667-24] [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: 05/31/2024] [Accepted: 06/27/2024] [Indexed: 07/23/2024] Open
Abstract
Severe COVID-19 has been associated with coinfections with bacterial and fungal pathogens. Notably, patients with COVID-19 who develop Staphylococcus aureus bacteremia exhibit higher rates of mortality than those infected with either pathogen alone. To understand this clinical scenario, we collected and examined S. aureus blood and respiratory isolates from a hospital in New York City during the early phase of the pandemic from both SARS-CoV-2+ and SARS-CoV-2- patients. Whole genome sequencing of these S. aureus isolates revealed broad phylogenetic diversity in both patient groups, suggesting that SARS-CoV-2 coinfection was not associated with a particular S. aureus lineage. Phenotypic characterization of the contemporary collection of S. aureus isolates from SARS-CoV-2+ and SARS-CoV-2- patients revealed no notable differences in several virulence traits examined. However, we noted a trend toward overrepresentation of S. aureus bloodstream strains with low cytotoxicity in the SARS-CoV-2+ group. We observed that patients coinfected with SARS-CoV-2 and S. aureus were more likely to die during the acute phase of infection when the coinfecting S. aureus strain exhibited high or low cytotoxicity. To further investigate the relationship between SARS-CoV-2 and S. aureus infections, we developed a murine coinfection model. These studies revealed that infection with SARS-CoV-2 renders mice susceptible to subsequent superinfection with low cytotoxicity S. aureus. Thus, SARS-CoV-2 infection sensitizes the host to coinfections, including S. aureus isolates with low intrinsic virulence. IMPORTANCE The COVID-19 pandemic has had an enormous impact on healthcare across the globe. Patients who were severely infected with SARS-CoV-2, the virus causing COVID-19, sometimes became infected with other pathogens, which is termed coinfection. If the coinfecting pathogen is the bacterium Staphylococcus aureus, there is an increased risk of patient death. We collected S. aureus strains that coinfected patients with SARS-CoV-2 to study the disease outcome caused by the interaction of these two important pathogens. We found that both in patients and in mice, coinfection with an S. aureus strain lacking toxicity resulted in more severe disease during the early phase of infection, compared with infection with either pathogen alone. Thus, SARS-CoV-2 infection can directly increase the severity of S. aureus infection.
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Affiliation(s)
- Ashira Lubkin
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Lucie Bernard-Raichon
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Ashley L. DuMont
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Ana Mayela Valero Jimenez
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Gregory G. Putzel
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
- Antimicrobial-Resistant Pathogens Program, Microbial Genomics Core Lab, New York University Langone Health, New York, New York, USA
| | - Juan Gago
- Department of Population Health, New York University Grossman School of Medicine, New York, New York, USA
| | - Erin E. Zwack
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Olufolakemi Olusanya
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
- Antimicrobial-Resistant Pathogens Program, Microbial Genomics Core Lab, New York University Langone Health, New York, New York, USA
| | - Kristina M. Boguslawski
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Simone Dallari
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Sophie Dyzenhaus
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Christin Herrmann
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Juliana K. Ilmain
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Georgia L. Isom
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Miranda Pawline
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
- Department of Medicine, NYU Grossman School of Medicine, New York, New York, USA
| | - Andrew I. Perault
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
- Antimicrobial-Resistant Pathogens Program, Microbial Genomics Core Lab, New York University Langone Health, New York, New York, USA
| | - Sofya Perelman
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
| | - William E. Sause
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Ifrah Shahi
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Amelia St. John
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Rebecca Tierce
- Division of Comparative Medicine, New York University Langone Health, New York, New York, USA
| | - Xuhui Zheng
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Chunyi Zhou
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
- Department of Medicine, NYU Grossman School of Medicine, New York, New York, USA
| | - Maria G. Noval
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Anna O'Keeffe
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Magda Podkowik
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
- Antimicrobial-Resistant Pathogens Program, Microbial Genomics Core Lab, New York University Langone Health, New York, New York, USA
| | - Sandra Gonzales
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Kenneth Inglima
- Department of Medicine, NYU Grossman School of Medicine, New York, New York, USA
| | - Ludovic Desvignes
- Department of Medicine, NYU Grossman School of Medicine, New York, New York, USA
- High Containment Laboratories, Office of Science and Research, NYU Langone Health, New York, New York, USA
| | - Sarah E. Hochman
- Antimicrobial-Resistant Pathogens Program, Microbial Genomics Core Lab, New York University Langone Health, New York, New York, USA
- Department of Medicine, NYU Grossman School of Medicine, New York, New York, USA
| | - Kenneth A. Stapleford
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Lorna E. Thorpe
- Department of Population Health, New York University Grossman School of Medicine, New York, New York, USA
| | - Alejandro Pironti
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
- Antimicrobial-Resistant Pathogens Program, Microbial Genomics Core Lab, New York University Langone Health, New York, New York, USA
| | - Bo Shopsin
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
- Antimicrobial-Resistant Pathogens Program, Microbial Genomics Core Lab, New York University Langone Health, New York, New York, USA
- Department of Medicine, NYU Grossman School of Medicine, New York, New York, USA
| | - Ken Cadwell
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Meike Dittmann
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Victor J. Torres
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
- Antimicrobial-Resistant Pathogens Program, Microbial Genomics Core Lab, New York University Langone Health, New York, New York, USA
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2
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Ntziora F, Giannitsioti E. Bloodstream infections in the era of the COVID-19 pandemic: Changing epidemiology of antimicrobial resistance in the intensive care unit. JOURNAL OF INTENSIVE MEDICINE 2024; 4:269-280. [PMID: 39035613 PMCID: PMC11258508 DOI: 10.1016/j.jointm.2023.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/20/2023] [Accepted: 12/22/2023] [Indexed: 07/23/2024]
Abstract
The Coronavirus disease 2019 (COVID-19) pandemic increased the burden of critically ill patients who required hospitalization in the intensive care unit (ICU). Bacterial and fungal co-infections, including bloodstream infections (BSIs), increased significantly in ICU patients with COVID-19; this had a significant negative impact on patient outcomes. Reported data pertaining to BSI episodes from the ICU setting during the COVID-19 pandemic were collected and analyzed for this narrative review. We searched the PubMed database for articles published between March 2020 and October 2023; the terms "COVID-19" AND "bloodstream infections" AND "ICU" were used for the search. A total of 778 articles were retrieved; however, only 27 were exclusively related to BSIs in ICU patients with COVID-19. Data pertaining to the epidemiological characteristics, risk factors, characteristics of bacterial and fungal BSIs, patterns of antimicrobial resistance, and comparisons between ICU and non-ICU patients during and before the COVID-19 pandemic were obtained. Data on antimicrobial stewardship and infection-control policies were also included. The rates of BSI were found to have increased among ICU patients with COVID-19 than in non-COVID-19 patients and those admitted during the pre-pandemic period. Male gender, 60-70 years of age, increased body mass index, high Sequential Organ Failure Assessment scores at admission, prolonged hospital and ICU stay, use of central lines, invasive ventilation, and receipt of extracorporeal membrane oxygenation were all defined as risk factors for BSI. The use of immune modulators for COVID-19 appeared to increase the risk of BSI; however, the available data are conflicting. Overall, Enterococci, Acinetobacter baumannii, and Candida spp. emerged as prominent infecting organisms during the pandemic; along with Enterobacterales and Pseudomonas aeruginosa they had a significant impact on mortality. Multidrug-resistant organisms prevailed in the ICU, especially if antimicrobial resistance was established before the COVID-19 pandemic and were significantly associated with increased mortality rates. The unnecessary and widespread use of antibiotics further increased the prevalence of multidrug-resistant organisms during COVID-19. Notably, the data indicated a significant increase in contaminants in blood cultures; this highlighted the decline in compliance with infection-control measures, especially during the initial waves of the pandemic. The implementation of infection-control policies along with antibiotic stewardship succeeded in significantly reducing the rates of blood contamination and BSI pathogens. BSIs considerably worsened outcomes in patients with COVID-19 who were admitted to ICUs. Further studies are needed to evaluate adequate preventive and control measures that may increase preparedness for the future.
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Affiliation(s)
- Fotinie Ntziora
- 1st Department of Propaedeutic Internal Medicine, Medical School, National and Kapodistrian University of Athens, Laiko General Hospital, Athens, Greece
| | - Efthymia Giannitsioti
- 1st Department of Propaedeutic Internal Medicine, Medical School, National and Kapodistrian University of Athens, Laiko General Hospital, Athens, Greece
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Barra ALC, Ullah N, Brognaro H, Gutierrez RF, Wrenger C, Betzel C, Nascimento AS. Structure and dynamics of the staphylococcal pyridoxal 5-phosphate synthase complex reveal transient interactions at the enzyme interface. J Biol Chem 2024; 300:107404. [PMID: 38782204 PMCID: PMC11237949 DOI: 10.1016/j.jbc.2024.107404] [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: 10/31/2023] [Revised: 05/03/2024] [Accepted: 05/04/2024] [Indexed: 05/25/2024] Open
Abstract
Infectious diseases are a significant cause of death, and recent studies estimate that common bacterial infectious diseases were responsible for 13.6% of all global deaths in 2019. Among the most significant bacterial pathogens is Staphylococcus aureus, accounting for more than 1.1 million deaths worldwide in 2019. Vitamin biosynthesis has been proposed as a promising target for antibacterial therapy. Here, we investigated the biochemical, structural, and dynamic properties of the enzyme complex responsible for vitamin B6 (pyridoxal 5-phosphate, PLP) biosynthesis in S. aureus, which comprises enzymes SaPdx1 and SaPdx2. The crystal structure of the 24-mer complex of SaPdx1-SaPdx2 enzymes indicated that the S. aureus PLP synthase complex forms a highly dynamic assembly with transient interaction between the enzymes. Solution scattering data indicated that SaPdx2 typically binds to SaPdx1 at a substoichiometric ratio. We propose a structure-based view of the PLP synthesis mechanism initiated with the assembly of SaPLP synthase complex that proceeds in a highly dynamic interaction between Pdx1 and Pdx2. This interface interaction can be further explored as a potentially druggable site for the design of new antibiotics.
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Affiliation(s)
- Angélica Luana C Barra
- São Carlos Institute of Physics, University of São Paulo, São Carlos, Brazil; Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, Hamburg, Germany
| | - Najeeb Ullah
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, Hamburg, Germany; Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Hévila Brognaro
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, Hamburg, Germany
| | - Raissa F Gutierrez
- São Carlos Institute of Physics, University of São Paulo, São Carlos, Brazil
| | - Carsten Wrenger
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
| | - Christian Betzel
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, Hamburg, Germany; Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
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Fowora MA, Aiyedogbon A, Omolopo I, Tajudeen AO, Onyeaghasiri F, Edu-Muyideen I, Olanlege ALO, Abioye A, Bamidele TA, Raheem T, Adesesan A, Iwalokun B, Salako BL. Nasal carriage of virulent and multidrug resistant Staphylococcus aureus: a possible comorbidity of COVID-19. Mol Biol Rep 2024; 51:665. [PMID: 38777940 DOI: 10.1007/s11033-024-09578-3] [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: 02/05/2024] [Accepted: 04/22/2024] [Indexed: 05/25/2024]
Abstract
BACKGROUND Staphylococcus aureus (S. aureus) associated with COVID-19 has not been well documented. This cross-sectional study evaluated the association between nasal S. aureus carriage and COVID-19. METHODS AND RESULTS Nasopharyngeal samples were collected from 391 participants presenting for COVID-19 test in Lagos, Nigeria, and S. aureus was isolated from the samples. Antimicrobial susceptibility test was done by disc diffusion method. All S. aureus isolates were screened for the presence of mecA, panton-valentine leucocidin (PVL) and toxic shock syndrome toxin (TSST) virulence genes by polymerase chain reaction. Staphylococcal protein A (spa) typing was conducted for all the isolates. Participants with COVID-19 had double the prevalence of S. aureus (42.86%) compared to those who tested negative (20.54%). A significant association was seen between S. aureus nasal carriage and COVID-19 (p = 0.004). Antimicrobial sensitivity results showed resistance to oxacillin (100%), cefoxitin (53%), and vancomycin (98.7%). However, only 41% of the isolates harbored the mecA gene, with SCCmecV being the most common SCCmec type. There was no association between the carriage of virulence genes and COVID-19. A total of 23 Spa types were detected, with t13249 and t095 being the two most common spa types. CONCLUSION This study examined the association between nasal S. aureus carriage and SARS-COV-2 infection. Further research is required to fully explore the implications of S. aureus co-infection with COVID-19.
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Affiliation(s)
- Muinah Adenike Fowora
- Department of Molecular Biology and Biotechnology, Nigerian Institute of Medical Research, Lagos, Nigeria.
| | - Adenike Aiyedogbon
- Department of Molecular Biology and Biotechnology, Nigerian Institute of Medical Research, Lagos, Nigeria
| | - Ibilola Omolopo
- Department of Molecular Biology and Biotechnology, Nigerian Institute of Medical Research, Lagos, Nigeria
| | - Ahmed Oluwasegun Tajudeen
- Department of Molecular Biology and Biotechnology, Nigerian Institute of Medical Research, Lagos, Nigeria
| | | | - Idowu Edu-Muyideen
- Department of Microbiology, Nigerian Institute of Medical Research, Lagos, Nigeria
| | | | | | - Tajudeen Akanji Bamidele
- Department of Molecular Biology and Biotechnology, Nigerian Institute of Medical Research, Lagos, Nigeria
| | - Toyosi Raheem
- Department of Molecular Biology and Biotechnology, Nigerian Institute of Medical Research, Lagos, Nigeria
| | - Adesegun Adesesan
- Department of Microbiology, Nigerian Institute of Medical Research, Lagos, Nigeria
| | - Bamidele Iwalokun
- Department of Molecular Biology and Biotechnology, Nigerian Institute of Medical Research, Lagos, Nigeria
| | - Babatunde Lawal Salako
- Department of Molecular Biology and Biotechnology, Nigerian Institute of Medical Research, Lagos, Nigeria
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Li N, Zhang L, Gao Y, Lai Q, Tang Y, Du X, Chen P, Yue C, Zhao M, Yu K, Kang K. Changes in clinical parameters and inflammatory markers after blood culture collection facilitate early identification of positive culture in adult patients with COVID-19 and clinically suspected bloodstream infection. J Int Med Res 2024; 52:3000605241238134. [PMID: 38630560 PMCID: PMC11025435 DOI: 10.1177/03000605241238134] [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: 07/11/2023] [Accepted: 02/22/2024] [Indexed: 04/19/2024] Open
Abstract
OBJECTIVE We explored whether changes in clinical parameters and inflammatory markers can facilitate early identification of positive blood culture in adult patients with COVID-19 and clinically suspected bloodstream infection (BSI). METHODS This single-center retrospective study enrolled 20 adult patients with COVID-19 admitted to the intensive care unit who underwent blood culture for clinically suspected BSI (February 2020-November 2021). We divided patients into positive (Pos) and negative blood culture groups. Clinical parameters and inflammatory markers were obtained from medical records between blood culture collection and the first positive or negative result and compared between groups on different days. RESULTS Patients in the positive culture group had significantly older age and higher D-dimer, immunoglobulin 6 (IL-6), and Sequential Organ Failure Assessment score as well as lower albumin (ALB). The area under the receiver operating characteristic curve (AUC) was 0.865 for IL-6, D-dimer and ALB on the first day after blood culture collection; the AUC was 0.979 for IL-6, IL-10, D-dimer, and C-reactive protein on the second day after blood culture collection. CONCLUSION Changes in clinical parameters and inflammatory markers after blood culture collection may facilitate early identification of positive culture in adult patients with COVID-19 and clinically suspected BSI.
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Affiliation(s)
- Nana Li
- Department of Critical Care Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Long Zhang
- Department of Critical Care Medicine, The Shanghai Baoshan Luodian Hospital, Shanghai, China
| | - Yang Gao
- Department of Critical Care Medicine, The Sixth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
- Institute of Critical Care Medicine, The Sino Russian Medical Research Center of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Qiqi Lai
- Department of Critical Care Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Yujia Tang
- Department of Critical Care Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Xue Du
- Department of Critical Care Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Pengfei Chen
- Department of Critical Care Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Chuangshi Yue
- Department of Critical Care Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Mingyan Zhao
- Department of Critical Care Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Kaijiang Yu
- Department of Critical Care Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
- Institute of Critical Care Medicine, The Sino Russian Medical Research Center of Harbin Medical University, Harbin, Heilongjiang Province, China
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, Harbin, Heilongjiang Province, China
- Key Laboratory of Cell Transplantation, National Health Commission, Harbin, Heilongjiang Province, China
| | - Kai Kang
- Department of Critical Care Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
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Papic I, Bistrovic P, Cikara T, Busic N, Keres T, Ortner Hadziabdic M, Lucijanic M. Corticosteroid Dosing Level, Incidence and Profile of Bacterial Blood Stream Infections in Hospitalized COVID-19 Patients. Viruses 2024; 16:86. [PMID: 38257786 PMCID: PMC10820464 DOI: 10.3390/v16010086] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/30/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
COVID-19 patients with severe or critical symptoms are often treated with corticosteroids, per contemporary guidelines. Due to their immunosuppressive and immunomodulatory properties, corticosteroids are associated with the development of superinfections. We aimed to retrospectively assess patterns of corticosteroid use and the profiles of bacterial blood stream infections associated with exposure to different dosing levels, in a cohort of 1558 real-life adult COVID-19 patients. A total of 1391 (89.3%) patients were treated with corticosteroids, with 710 (45.6%) patients receiving low, 539 (34.6%) high and 142 (9.1%) very high corticosteroid doses. Bacteremia developed in a total of 178 (11.4%) patients. The risk of bacteremia was of similar magnitude between the no and low-dose corticosteroid treatments (p = 0.352), whereas it progressively increased with high (OR 6.18, 95% CI (2.66-14.38), p < 0.001) and very high corticosteroid doses (OR 8.12, 95% CI (3.29-20.05), p < 0.001), compared to no corticosteroid treatment. These associations persisted after multivariate adjustments and were present independently of sex, comorbidity burden, and mechanical ventilation. The profiles of individual bacterial pathogens differed depending on the used corticosteroid doses. High and very high corticosteroid doses are frequently used for real-life COVID-19 patients with severe and critical clinical presentations and are associated with a higher risk of bacteremia independently of sex, comorbidity burden, and mechanical ventilation use.
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Affiliation(s)
- Ivan Papic
- Pharmacy Department, University Hospital Dubrava, 10000 Zagreb, Croatia
| | - Petra Bistrovic
- Cardiology Department, University Hospital Dubrava, 10000 Zagreb, Croatia
| | - Tomislav Cikara
- Cardiology Department, University Hospital Dubrava, 10000 Zagreb, Croatia
| | - Nikolina Busic
- Department of Internal Medicine, University Hospital Dubrava, 10000 Zagreb, Croatia
| | - Tatjana Keres
- Department of Internal Medicine, University Hospital Dubrava, 10000 Zagreb, Croatia
| | - Maja Ortner Hadziabdic
- Centre for Applied Pharmacy, Faculty of Pharmacy and Biochemistry, University of Zagreb, 10000 Zagreb, Croatia
| | - Marko Lucijanic
- Hematology Department, University Hospital Dubrava, 10000 Zagreb, Croatia
- School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
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Dar S, Erickson D, Manca C, Lozy T, Shashkina E, Kordalewska M, Mediavilla JR, Chen L, Rojtman A, Kreiswirth BN. The impact of COVID on bacterial sepsis. Eur J Clin Microbiol Infect Dis 2023; 42:1173-1181. [PMID: 37597051 DOI: 10.1007/s10096-023-04655-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 08/10/2023] [Indexed: 08/21/2023]
Abstract
PURPOSE To identify the predictors of morbidity and mortality in matched COVID-19 positive and negative patients who were septic with Gram positive or Gram negative infections. METHODS We conducted a retrospective review, from March to October 2020, of matched septic patients at five Hackensack Meridian Health hospitals who had bacteremia with Staphylococcus aureus, Klebsiella pneumoniae or Escherichia coli with and without COVID-19. We extracted patient demographics, comorbidities and clinical outcomes data using ICD-10 codes. Bacterial isolates were compared by whole genome sequencing analysis. Multivariate logistic regression was used to analyze independent predictors of morbidity and mortality. RESULTS A total of 208 patients were grouped by positive bloodstream infection (BSI) with COVID-19 (n = 104) and without COVID-19 (n = 104). Most patients were over age 50 (90% vs. 89%) and Caucasian (78% vs. 86%). Inpatient mortality was higher in patients with COVID-19 for both GP (35% vs. 8%, p < 0.05) and GN (28% vs. 10%, p < 0.05) BSIs. Patients with Gram positive (GP) BSIs had a significant increase in mortality risk (OR 4.5, CI 1.4-14.5, p < 0.05) in contrast to those with Gram negative (GN) infections (OR 0.4, CI 0.4-4.0, p = 0.4). CONCLUSION Concurrent COVID-19 infection is associated with a significant increase in morbidity and mortality in patients with GP and GN BSIs. Patients with S. aureus BSIs with COVID-19 are more likely to develop shock and respiratory failure and have higher rates and odds of mortality than those without COVID-19. These findings provide an essential insight into the care of these patients, especially those co-infected with Staphylococcus aureus.
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Affiliation(s)
- Sophia Dar
- Hackensack Meridian School of Medicine, Nutley, NJ, 07110, USA
- Long Island Jewish Medical Center-Northshore University Hospital, Manhasset, NY, 11030, USA
| | - Daniel Erickson
- Hackensack Meridian School of Medicine, Nutley, NJ, 07110, USA
| | - Claudia Manca
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, 07110, USA
| | - Tara Lozy
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, 07110, USA
| | - Elena Shashkina
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, 07110, USA
| | - Milena Kordalewska
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, 07110, USA
| | - Jose R Mediavilla
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, 07110, USA
| | - Liang Chen
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, 07110, USA
| | - Albert Rojtman
- Jersey Shore University Medical Center, Neptune, NJ, 07753, USA
| | - Barry N Kreiswirth
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, 07110, USA.
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8
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Parisini A, Boni S, Vacca EB, Bobbio N, Puente FD, Feasi M, Prinapori R, Lattuada M, Sartini M, Cristina ML, Usiglio D, Pontali E. Impact of the COVID-19 Pandemic on Epidemiology of Antibiotic Resistance in an Intensive Care Unit (ICU): The Experience of a North-West Italian Center. Antibiotics (Basel) 2023; 12:1278. [PMID: 37627698 PMCID: PMC10451647 DOI: 10.3390/antibiotics12081278] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/25/2023] [Accepted: 07/30/2023] [Indexed: 08/27/2023] Open
Abstract
The SARS-CoV-2 pandemic caused an increase in intensive care unit (ICU) hospitalizations with a rise in morbidity and mortality; nevertheless, there is still little evidence on the impact of the pandemic on antibiotic resistance in ICUs. This is a retrospective, monocentric epidemiological study. The aim of the study was to describe and analyze the impact of the SARS-CoV-2 pandemic on ICU bacterial resistance patterns. All bacteria isolated from all patients admitted to the E.O. Galliera ICU from January 2018 to December 2022 were included. Antibiotic resistance (AR) profiles were evaluated. A total of 1021 microorganisms were identified, of which 221 (12.47%) had a resistance pattern (resistant organisms; ROs). In this time, there were 1679 patients with a total of 12,030 hospitalization days. The majority of microorganisms were Gram-negative (79.66% in 2018, 77.29% in 2019, 61.83% in 2020, 62.56% in 2021, and 60.75% in 2022), but an increase in Gram-positive microorganisms was observed (20.34 to 39.25% between 2018 and 2022). The prevalence of AR was 19.44% in 2018, 11.54% in 2019, 38.04% in 2020, 34.15% in 2021, and 39.29% in 2022 for Gram-positive microorganisms and 19.86% in 2018, 13.56% in 2019, 18.12% in 2020, 12.41% in 2021, and 12.31% in 2012 for Gram-negative microorganisms. The incidence of ROs showed a COVID-19-related increase in 2020-2021, followed by a lowering trend since 2021, and a new increase in 2022. Possible explanations are antibiotic overtreatment and a decrease in containment measures. An interesting finding was the cumulative lowering trend of carbapenem-resistant K. pneumoniae and P. aeruginosa, probably due to different patient features.
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Affiliation(s)
- Andrea Parisini
- Department of Infectious Diseases, Galliera Hospital, Mura delle Cappuccine 14, 16128 Genoa, Italy; (A.P.); (S.B.); (E.B.V.); (N.B.); (F.D.P.); (M.F.); (R.P.)
| | - Silvia Boni
- Department of Infectious Diseases, Galliera Hospital, Mura delle Cappuccine 14, 16128 Genoa, Italy; (A.P.); (S.B.); (E.B.V.); (N.B.); (F.D.P.); (M.F.); (R.P.)
| | - Elisabetta Blasi Vacca
- Department of Infectious Diseases, Galliera Hospital, Mura delle Cappuccine 14, 16128 Genoa, Italy; (A.P.); (S.B.); (E.B.V.); (N.B.); (F.D.P.); (M.F.); (R.P.)
| | - Nicoletta Bobbio
- Department of Infectious Diseases, Galliera Hospital, Mura delle Cappuccine 14, 16128 Genoa, Italy; (A.P.); (S.B.); (E.B.V.); (N.B.); (F.D.P.); (M.F.); (R.P.)
| | - Filippo Del Puente
- Department of Infectious Diseases, Galliera Hospital, Mura delle Cappuccine 14, 16128 Genoa, Italy; (A.P.); (S.B.); (E.B.V.); (N.B.); (F.D.P.); (M.F.); (R.P.)
| | - Marcello Feasi
- Department of Infectious Diseases, Galliera Hospital, Mura delle Cappuccine 14, 16128 Genoa, Italy; (A.P.); (S.B.); (E.B.V.); (N.B.); (F.D.P.); (M.F.); (R.P.)
| | - Roberta Prinapori
- Department of Infectious Diseases, Galliera Hospital, Mura delle Cappuccine 14, 16128 Genoa, Italy; (A.P.); (S.B.); (E.B.V.); (N.B.); (F.D.P.); (M.F.); (R.P.)
| | - Marco Lattuada
- Anaesthesia and Intensive Care Unit, E.O. Ospedali Galliera, Mura delle Cappuccine 14, 16128 Genoa, Italy;
| | - Marina Sartini
- Department of Health Sciences, University of Genova, Via Pastore 1, 16132 Genoa, Italy; (M.S.); (M.L.C.)
- Operating Unit (S.S.D.U.O.) Hospital Hygiene Unit, Galliera Hospital, Mura delle Cappuccine 14, 16128 Genoa, Italy
| | - Maria Luisa Cristina
- Department of Health Sciences, University of Genova, Via Pastore 1, 16132 Genoa, Italy; (M.S.); (M.L.C.)
- Operating Unit (S.S.D.U.O.) Hospital Hygiene Unit, Galliera Hospital, Mura delle Cappuccine 14, 16128 Genoa, Italy
| | - David Usiglio
- Department of Laboratory and Microbiological Analysis, Galliera Hospital, 16128 Genoa, Italy;
| | - Emanuele Pontali
- Department of Infectious Diseases, Galliera Hospital, Mura delle Cappuccine 14, 16128 Genoa, Italy; (A.P.); (S.B.); (E.B.V.); (N.B.); (F.D.P.); (M.F.); (R.P.)
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9
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Goyal N, Saini V, Gangar S, Mohapatra S, Singh NP, Saha R. Are we missing the silver lining of COVID-19 pandemic: An analytical study to determine effects of three COVID-19 peaks on antimicrobial susceptibility of Staphylococcus aureus isolates. J Family Med Prim Care 2023; 12:1424-1429. [PMID: 37649748 PMCID: PMC10465057 DOI: 10.4103/jfmpc.jfmpc_2420_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 05/09/2023] [Accepted: 05/24/2023] [Indexed: 09/01/2023] Open
Abstract
Background Given the evolving nature of COVID-19, for better understanding of its effect on antimicrobial resistance of Staphylococcus aureus (S. aureus), it becomes crucial that we follow the resistance patterns across different surges of COVID-19 cases. Methods This prospective surveillance study extended over two years from January 2020-March 2022 and was conducted in a healthcare center of North India. Susceptibility patterns of Staphylococcus aureus during January-March 2020 were considered as prepandemic patterns. Processing of clinical specimens, identification of S. aureus, and in-vitro antibiotic susceptibility testing were performed in accordance with standard microbiological testing procedures and Clinical Laboratory Standard Institute guidelines. Results Lowest prevalence (38.9%) of Methicillinresistant S. aureus was reported during January-March 2021 and July-September 2021. More than 50% S. aureus isolates were susceptible to linezolid, cotrimoxazole, tetracycline, and gentamicin in January-March 2020. In January-March 2021, ≥50% of S. aureus isolates from clinical specimens were additionally susceptible to clindamycin and erythromycin. Antibiotic agents of linezolid, tetracycline, clindamycin, and cotrimoxazole were susceptible in ≥50% of S. aureus isolates in January-March 2022. Conclusions This study reveals a sharp decline in overall resistance to commonly prescribed antibiotic agents for S. aureus isolates after first peak of COVID-19 cases. However, same trend was not observed in subsequent peaks and probably we are approaching the same resistance levels that were seen prior to COVID-19 pandemic.
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Affiliation(s)
- Nisha Goyal
- Department of Microbiology, University College of Medical Sciences and Guru Teg Bahadur Hospital, Delhi, India
| | - Vikas Saini
- Department of Microbiology, National Cancer Institute- All India Institute of Medical Sciences, BADSA Jhajjar, Haryana, India
| | - Seema Gangar
- Department of Microbiology, University College of Medical Sciences and Guru Teg Bahadur Hospital, Delhi, India
| | - Subhashree Mohapatra
- Department of Microbiology, University College of Medical Sciences and Guru Teg Bahadur Hospital, Delhi, India
| | - Narendra Pal Singh
- Department of Microbiology, University College of Medical Sciences and Guru Teg Bahadur Hospital, Delhi, India
| | - Rumpa Saha
- Department of Microbiology, University College of Medical Sciences and Guru Teg Bahadur Hospital, Delhi, India
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10
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Gatica S, Fuentes B, Rivera-Asín E, Ramírez-Céspedes P, Sepúlveda-Alfaro J, Catalán EA, Bueno SM, Kalergis AM, Simon F, Riedel CA, Melo-Gonzalez F. Novel evidence on sepsis-inducing pathogens: from laboratory to bedside. Front Microbiol 2023; 14:1198200. [PMID: 37426029 PMCID: PMC10327444 DOI: 10.3389/fmicb.2023.1198200] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/05/2023] [Indexed: 07/11/2023] Open
Abstract
Sepsis is a life-threatening condition and a significant cause of preventable morbidity and mortality globally. Among the leading causative agents of sepsis are bacterial pathogens Escherichia coli, Klebsiella pneumoniae, Staphylococcus aureus, Pseudomonas aeruginosa, and Streptococcus pyogenes, along with fungal pathogens of the Candida species. Here, we focus on evidence from human studies but also include in vitro and in vivo cellular and molecular evidence, exploring how bacterial and fungal pathogens are associated with bloodstream infection and sepsis. This review presents a narrative update on pathogen epidemiology, virulence factors, host factors of susceptibility, mechanisms of immunomodulation, current therapies, antibiotic resistance, and opportunities for diagnosis, prognosis, and therapeutics, through the perspective of bloodstream infection and sepsis. A list of curated novel host and pathogen factors, diagnostic and prognostic markers, and potential therapeutical targets to tackle sepsis from the research laboratory is presented. Further, we discuss the complex nature of sepsis depending on the sepsis-inducing pathogen and host susceptibility, the more common strains associated with severe pathology and how these aspects may impact in the management of the clinical presentation of sepsis.
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Affiliation(s)
- Sebastian Gatica
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
| | - Brandon Fuentes
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
| | - Elizabeth Rivera-Asín
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
| | - Paula Ramírez-Céspedes
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
| | - Javiera Sepúlveda-Alfaro
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Eduardo A. Catalán
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Susan M. Bueno
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alexis M. Kalergis
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Millennium Institute on Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, Santiago, Chile
- Departamento de Endocrinología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Felipe Simon
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
| | - Claudia A. Riedel
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
| | - Felipe Melo-Gonzalez
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
- Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
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11
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Falces-Romero I, Bloise I, García-Rodríguez J, Cendejas-Bueno E. Staphylococcus aureus bacteremia in patients with SARS-CoV-2 infection. MEDICINA CLINICA (ENGLISH ED.) 2023; 160:495-498. [PMID: 37311167 PMCID: PMC10250598 DOI: 10.1016/j.medcle.2023.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 01/18/2023] [Indexed: 06/15/2023]
Abstract
Objectives The aim was to compare the incidence of Staphylococcus aureus bacteremia in COVID-19 and non-COVID-19 adult patients during the pandemic period versus the previous two years. Also, we described the characteristics of both cohorts of patients in pandemic period to find differences. Material and methods Retrospective study in our tertiary-care centre reviewing S. aureus bacteremia episodes in COVID-19 and non-COVID-19 patients through clinical records and the Microbiology Department database. Results In 2018 and 2019, the incidence of S. aureus bacteremia episodes was 1.95 and 1.63 per 1000 admissions respectively. In the pandemic period, global incidence was 1.96 episodes per 1000 non-COVID-19 admissions and 10.59 episodes per 1000 COVID-19 admissions. A total of 241 bacteremia was registered during this pandemic period in 74 COVID-19 patients and in 167 non-COVID-19 patients. Methicillin resistance was detected in 32.4% and 13.8% of isolates from COVID-19 and non-COVID-19 patients respectively. In COVID-19 patients, mortality rates were significantly higher. Conclusions We showed a significantly high rates of S. aureus bacteremia incidence in COVID-19 patients and higher methicillin resistance and 15-day mortality rates than in non-COVID-19 patients.
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Affiliation(s)
- Iker Falces-Romero
- Clinical Microbiology and Parasitology Department, Hospital Universitario La Paz, IdiPaz, Madrid, Spain
- CIBERINFEC, Instituto de Salud Carlos III, Madrid, Spain
| | - Iván Bloise
- Clinical Microbiology and Parasitology Department, Hospital Universitario La Paz, IdiPaz, Madrid, Spain
| | - Julio García-Rodríguez
- Clinical Microbiology and Parasitology Department, Hospital Universitario La Paz, IdiPaz, Madrid, Spain
- CIBERINFEC, Instituto de Salud Carlos III, Madrid, Spain
| | - Emilio Cendejas-Bueno
- Clinical Microbiology and Parasitology Department, Hospital Universitario La Paz, IdiPaz, Madrid, Spain
- CIBERINFEC, Instituto de Salud Carlos III, Madrid, Spain
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12
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Loyola-Cruz MÁ, Gonzalez-Avila LU, Martínez-Trejo A, Saldaña-Padilla A, Hernández-Cortez C, Bello-López JM, Castro-Escarpulli G. ESKAPE and Beyond: The Burden of Coinfections in the COVID-19 Pandemic. Pathogens 2023; 12:pathogens12050743. [PMID: 37242413 DOI: 10.3390/pathogens12050743] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 05/15/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023] Open
Abstract
The ESKAPE group constitute a threat to public health, since these microorganisms are associated with severe infections in hospitals and have a direct relationship with high mortality rates. The presence of these bacteria in hospitals had a direct impact on the incidence of healthcare-associated coinfections in the SARS-CoV-2 pandemic. In recent years, these pathogens have shown resistance to multiple antibiotic families. The presence of high-risk clones within this group of bacteria contributes to the spread of resistance mechanisms worldwide. In the pandemic, these pathogens were implicated in coinfections in severely ill COVID-19 patients. The aim of this review is to describe the main microorganisms of the ESKAPE group involved in coinfections in COVID-19 patients, addressing mainly antimicrobial resistance mechanisms, epidemiology, and high-risk clones.
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Affiliation(s)
- Miguel Ángel Loyola-Cruz
- Laboratorio de Investigación Clínica y Ambiental, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Carpio y Plan de Ayala, Col. Casco de Santo Tomás, Ciudad de México 11340, Mexico
- División de Investigación, Hospital Juárez de México, Av. Instituto Politécnico Nacional 5160, Magdalena de las Salinas, Gustavo A. Madero, Ciudad de México 07760, Mexico
| | - Luis Uriel Gonzalez-Avila
- Laboratorio de Investigación Clínica y Ambiental, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Carpio y Plan de Ayala, Col. Casco de Santo Tomás, Ciudad de México 11340, Mexico
| | - Arturo Martínez-Trejo
- Laboratorio de Investigación Clínica y Ambiental, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Carpio y Plan de Ayala, Col. Casco de Santo Tomás, Ciudad de México 11340, Mexico
| | - Andres Saldaña-Padilla
- Laboratorio de Investigación Clínica y Ambiental, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Carpio y Plan de Ayala, Col. Casco de Santo Tomás, Ciudad de México 11340, Mexico
- Laboratorio de Bioquímica Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Carpio y Plan de Ayala, Col. Casco de Santo Tomás, Mexico City 11340, Mexico
| | - Cecilia Hernández-Cortez
- Laboratorio de Bioquímica Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Carpio y Plan de Ayala, Col. Casco de Santo Tomás, Mexico City 11340, Mexico
| | - Juan Manuel Bello-López
- División de Investigación, Hospital Juárez de México, Av. Instituto Politécnico Nacional 5160, Magdalena de las Salinas, Gustavo A. Madero, Ciudad de México 07760, Mexico
| | - Graciela Castro-Escarpulli
- Laboratorio de Investigación Clínica y Ambiental, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Carpio y Plan de Ayala, Col. Casco de Santo Tomás, Ciudad de México 11340, Mexico
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13
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Micheli G, Sangiorgi F, Catania F, Chiuchiarelli M, Frondizi F, Taddei E, Murri R. The Hidden Cost of COVID-19: Focus on Antimicrobial Resistance in Bloodstream Infections. Microorganisms 2023; 11:1299. [PMID: 37317274 DOI: 10.3390/microorganisms11051299] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 05/08/2023] [Accepted: 05/10/2023] [Indexed: 06/16/2023] Open
Abstract
Antibiotic resistance is one of the greatest growing public health threats and a worldwide priority. According to the WHO, drug-resistant diseases may cause 10 million deaths a year by 2050 and have a substantial impact on the global economy, driving up to 24 million people into poverty. The ongoing COVID-19 pandemic has exposed the fallacies and vulnerability of healthcare systems worldwide, displacing resources from existing programs and reducing funding for antimicrobial resistance (AMR) fighting efforts. Moreover, as already seen for other respiratory viruses, such as flu, COVID-19 is often associated with superinfections, prolonged hospital stays, and increased ICU admissions, further aggravating healthcare disruption. These events are accompanied by widespread antibiotic use, misuse, and inappropriate compliance with standard procedures with a potential long-term impact on AMR. Still, COVID-19-related measures such as increasing personal and environmental hygiene, social distancing, and decreasing hospital admissions could theoretically help the AMR cause. However, several reports have shown increased antimicrobial resistance during the COVID-19 pandemic. This narrative review focuses on this "twindemic", assessing the current knowledge of antimicrobial resistance in the COVID-19 era with a focus on bloodstream infections and provides insights into the lessons learned in the COVID-19 field that could be applied to antimicrobial stewardship initiatives.
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Affiliation(s)
- Giulia Micheli
- Dipartimento di Sicurezza e Bioetica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Flavio Sangiorgi
- Dipartimento di Sicurezza e Bioetica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Francesca Catania
- Dipartimento di Sicurezza e Bioetica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Marta Chiuchiarelli
- Dipartimento di Sicurezza e Bioetica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Federico Frondizi
- Dipartimento di Sicurezza e Bioetica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Eleonora Taddei
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
| | - Rita Murri
- Dipartimento di Sicurezza e Bioetica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
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14
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Sivapornnukul P, Chitcharoen S, Sawaswong V, Tachaboon S, Dinhuzen J, Srisawat N, Payungporn S. Comparison of circulating bacterial profiles between mild and severe COVID-19 patients. Exp Biol Med (Maywood) 2023; 248:866-873. [PMID: 36946423 PMCID: PMC10034557 DOI: 10.1177/15353702231157931] [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: 09/28/2022] [Accepted: 01/18/2023] [Indexed: 03/23/2023] Open
Abstract
Recent reports revealed that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected patients can develop bacteremia; however, the circulating bacterial profile is not well studied. Therefore, this study has aimed to investigate circulating bacterial profile in mild (n = 15) and severe (n = 13) SARS-CoV-2-infected patients as well as healthy controls (n = 10), using 16S rDNA (V4) sequencing approach. The alpha diversity indexes and Bray-Curtis dissimilarity matrix revealed that the bacterial profiles between the two conditions are significantly different. Correspondingly, the relative abundance indicates that the predominant bacterial phylum in both conditions was Proteobacteria. At genus level, the dominant bacterial genera in the mild patients belonged to Sphingomonas, Stenotrophomonas, and Achromobacter, while bacterial genera belonging to Enhydrobacter, Comamonas, and Acinetobacter were dominant in the severe patients. Furthermore, Linear discriminant analysis (LDA) Effect Size (LEfSe). revealed that Stenotrophomonas, Delftia, Achromobacter, and Neisseria were enriched in the mild condition, while Agrobacterium, Comamonas, Pseudomonas, Corynebacterium, Alkaliphilus, and Kocuria were enriched in the severe patients. These results revealed a distinct circulating bacterial profile in the mild and severe SARS-CoV-2-infected patients, which may provide an insight for further therapeutic strategy.
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Affiliation(s)
- Pavaret Sivapornnukul
- Center of Excellence in Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Suwalak Chitcharoen
- Center of Excellence in Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand
| | - Vorthon Sawaswong
- Center of Excellence in Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand
| | - Sasipha Tachaboon
- Division of Pulmonary Disease and Pulmonary Critical Care, Department of Medicine, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Bangkok 10330, Thailand
- Excellence Center for Critical Care Nephrology, King Chulalongkorn Memorial Hospital, Bangkok 10330, Thailand
| | - Janejira Dinhuzen
- Division of Pulmonary Disease and Pulmonary Critical Care, Department of Medicine, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Bangkok 10330, Thailand
- Excellence Center for Critical Care Nephrology, King Chulalongkorn Memorial Hospital, Bangkok 10330, Thailand
| | - Nattachai Srisawat
- Division of Pulmonary Disease and Pulmonary Critical Care, Department of Medicine, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Bangkok 10330, Thailand
- Excellence Center for Critical Care Nephrology, King Chulalongkorn Memorial Hospital, Bangkok 10330, Thailand
- Critical Care Nephrology Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
- Tropical Medicine Cluster, Chulalongkorn University, Bangkok 10330, Thailand
- Division of Nephrology, Department of Medicine, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Bangkok 10330, Thailand
- Academy of Science, Royal Society of Thailand, Bangkok 10300, Thailand
- Center for Critical Care Nephrology, The CRISMA Center, Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Sunchai Payungporn
- Center of Excellence in Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
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15
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Khan A, El Hosseiny A, Siam R. Assessing and Reassessing the Association of Comorbidities and Coinfections in COVID-19 Patients. Cureus 2023; 15:e36683. [PMID: 37113367 PMCID: PMC10126732 DOI: 10.7759/cureus.36683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/25/2023] [Indexed: 03/28/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) has posed an enormous global health and economic burden. To date, 324 million confirmed cases and over 5.5 million deaths have been reported. Several studies have reported comorbidities and coinfections associated with complicated and serious COVID-19 infections. Data from retrospective, prospective, case series, and case reports from various geographical locations were assessed, which included ~ 2300 COVID-19 patients with varying comorbidities and coinfection. We report that Enterobacterales with Staphylococcus aureus was the most while Mycoplasma pneumoniae was the least prevalent coinfection in COVID-19 patients with a comorbidity. In this order, hypertension, diabetes, cardiovascular disease, and pulmonary disease were the prevalent comorbidities observed in COVID-19 patients. There was a statistically significant difference in the prevalent comorbidities observed in patients coinfected with Staphylococcus aureus and COVID-19 and a statistically non-significant difference in the prevalent comorbidities in patients coinfected with Mycoplasma pneumoniae and COVID-19 as compared to similar infections in non-COVID-19 coinfection. We report a significant difference in the prevalent comorbidities recorded in COVID-19 patients with varying coinfections and varying geographic study regions. Our study provides informative data on the prevalence of comorbidities and coinfections in COVID-19 patients to aid in evidence-based patient management and care.
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16
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Bongiovanni M, Barda B. Pseudomonas aeruginosa Bloodstream Infections in SARS-CoV-2 Infected Patients: A Systematic Review. J Clin Med 2023; 12:jcm12062252. [PMID: 36983256 PMCID: PMC10056033 DOI: 10.3390/jcm12062252] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/07/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023] Open
Abstract
Bacterial co-infections increase the severity of respiratory viral infections and are frequent causes of mortality in COVID-19 infected subjects. During the COVID-19 period, especially at the beginning of the pandemic, an inappropriate use of broad-spectrum antibiotic treatments has been frequently described, mainly due to prolonged hospitalization, especially in intensive care unit departments, and the use of immune-suppressive treatments as steroids. This misuse has finally led to the occurrence of infections by multi-drug resistant (MDR) bacteria in hospitalized COVID-19 patients. Although different reports assessed the prevalence of Gram-negative infections in COVID-19 infected patients, scarce data are currently available on bloodstream infections caused by Pseudomonas aeruginosa in hospitalized COVID-19 patients. The aim of our systematic review is to describe data on this specific population and to discuss the possible implications that these co-infections could have in the management of COVID-19 pandemics in the future. We systematically analysed the current literature to find all the relevant articles that describe the occurrence of P. aeruginosa bloodstream infections in COVID-19 patients. We found 40 papers that described in detail P. aeruginosa HAIs-BSI in COVID-19 patients, including 756,067 patients overall. The occurrence of severe infections due to MDR bacteria had a significant impact in the management of hospitalized patients with COVID-19 infections, leading to a prolonged time of hospitalization and to a consequent increase in mortality. In the near future, the increased burden of MDR bacteria due to the COVID-19 pandemic might partially be reduced by maintaining the preventive measures of infection control implemented during the acute phase of the COVID-19 pandemic. Finally, we discuss how the COVID-19 pandemic changed the role of antimicrobial stewardship in healthcare settings, according to the isolation of MDR bacteria and how to restore on a large scale the optimization of antibiotic strategies in COVID-19 patients.
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17
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Falces-Romero I, Bloise I, García-Rodríguez J, Cendejas-Bueno E. Staphylococcus aureus bacteremia in patients with SARS-CoV-2 infection. Med Clin (Barc) 2023:S0025-7753(23)00029-5. [PMID: 36841646 PMCID: PMC9884619 DOI: 10.1016/j.medcli.2023.01.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 01/16/2023] [Accepted: 01/18/2023] [Indexed: 02/03/2023]
Abstract
OBJECTIVES The aim was to compare the incidence of Staphylococcus aureus bacteremia in COVID-19 and non-COVID-19 adult patients during the pandemic period versus the previous two years. Also, we described the characteristics of both cohorts of patients in pandemic period to find differences. MATERIAL AND METHODS Retrospective study in our tertiary-care centre reviewing S. aureus bacteremia episodes in COVID-19 and non-COVID-19 patients through clinical records and the Microbiology Department database. RESULTS In 2018 and 2019, the incidence of S. aureus bacteremia episodes was 1.95 and 1.63 per 1000 admissions respectively. In the pandemic period, global incidence was 1.96 episodes per 1000 non-COVID-19 admissions and 10.59 episodes per 1000 COVID-19 admissions. A total of 241 bacteremia was registered during this pandemic period in 74 COVID-19 patients and in 167 non-COVID-19 patients. Methicillin resistance was detected in 32.4% and 13.8% of isolates from COVID-19 and non-COVID-19 patients respectively. In COVID-19 patients, mortality rates were significantly higher. CONCLUSIONS We showed a significantly high rates of S. aureus bacteremia incidence in COVID-19 patients and higher methicillin resistance and 15-day mortality rates than in non-COVID-19 patients.
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Affiliation(s)
- Iker Falces-Romero
- Clinical Microbiology and Parasitology Department, Hospital Universitario La Paz, IdiPaz, Madrid, Spain; CIBERINFEC, Instituto de Salud Carlos III, Madrid, Spain.
| | - Iván Bloise
- Clinical Microbiology and Parasitology Department, Hospital Universitario La Paz, IdiPaz, Madrid, Spain
| | - Julio García-Rodríguez
- Clinical Microbiology and Parasitology Department, Hospital Universitario La Paz, IdiPaz, Madrid, Spain,CIBERINFEC, Instituto de Salud Carlos III, Madrid, Spain
| | - Emilio Cendejas-Bueno
- Clinical Microbiology and Parasitology Department, Hospital Universitario La Paz, IdiPaz, Madrid, Spain,CIBERINFEC, Instituto de Salud Carlos III, Madrid, Spain
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18
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Development of a Multiplex Polymerase Chain Reaction-Based DNA Lateral Flow Assay as a Point-of-Care Diagnostic for Fast and Simultaneous Detection of MRSA and Vancomycin Resistance in Bacteremia. Diagnostics (Basel) 2022; 12:diagnostics12112691. [DOI: 10.3390/diagnostics12112691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/26/2022] [Accepted: 11/02/2022] [Indexed: 11/06/2022] Open
Abstract
To reduce high mortality and morbidity rates, timely and proper treatment of methicillin-resistant Staphylococcus aureus (MRSA) bloodstream infection is required. A multiplex polymerase reaction (mPCR)-based DNA lateral flow assay (MBDLFA) was developed as a point-of-care diagnostic for simultaneous identification of S. aureus, methicillin resistance, and vancomycin resistance directly from blood or blood cultures. A mPCR was developed to detect nuc, mecA, and vanA/B; its sensitivity, specificity, and limit of detection (LOD) were determined. The developed reaction was further modified for use in MBDLFA and its sensitivity for detection of target genes from artificially inoculated blood samples was checked. The optimized mPCR successfully detected nuc, mecA, and vanA/B from genomic DNA of bacterial colonies with LODs of 107, 107, and 105 CFU/mL, respectively. The reaction was sensitive and specific. The optimized mPCR was used in MBDLFA that detected nuc, mecA, and vanA/B with LODs of 107, 108, and 104 CFU/mL, respectively, directly from artificially inoculated blood. The developed MBDLFA can be used as a rapid, cheap point-of-care diagnostic for detecting S. aureus, MRSA, and vancomycin resistance directly from blood and blood cultures in ~2 h with the naked eye. This will reduce morbidity, mortality, and treatment cost in S. aureus bacteremia.
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Espinosa Perez M, García Fenoll R, Mormeneo Bayo S, Martínez Álvarez RM, Frutos Millán V, Villuendas Usón MC, Palacián Ruiz MP, Arbonés Mainar JM, Martínez Jiménez MC, Ramos Paesa C. [Impact of Staphylococcus aureus bacteremia in COVID-19 patients]. REVISTA ESPANOLA DE QUIMIOTERAPIA : PUBLICACION OFICIAL DE LA SOCIEDAD ESPANOLA DE QUIMIOTERAPIA 2022; 35:468-474. [PMID: 35866373 PMCID: PMC9548065 DOI: 10.37201/req/022.2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 06/24/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
OBJECTIVE The disease caused by SARS-CoV-2 (COVID-19) has been a challenge for healthcare professionals since its appearance. Staphylococcus aureus has been described as one of the main pathogens causing bacterial infections in viral pandemics. However, co- infection with S. aureus causing bacteremia in patients with COVID-19 has yet to be well studied. METHODS We performed a e study of S. aureus bacteremia (SAB) at Hospital Miguel Servet (Zaragoza) from March 2020 to February 2021. The clinical characteristics, mortality and risk factors of adults hospitalized patients with BSA associated COVID-19 compared to patients without COVID-19. RESULTS A total of 95 patients with SAB were identified. 27.3% were positive for SARS-CoV-2. SAB represented 9.9% of bacteremia, being the second agent in frequency after E. coli. Nosocomial bacteremia was more frequent in the group of COVID-19 patients. The most frequent source of BSA in these patients was the respiratory source (26.9% vs 0%; P<0.001) followed by the skin (15.5% vs 15.9%; P=1). The development of sepsis was more frequent in COVID-19 patients (61,5% vs 7,8%; P=0,336) and among them, who received dexamethasone at doses > 6 mg/day (62.5% vs. 37.5%, P<0.05). CONCLUSIONS Our data suggest that BSA has a negative impact on the evolution of patients with COVID-19. However, further and preferably prospective studies are required to obtain solid data on the impact of BSA on coronavirus patients.
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Affiliation(s)
- M Espinosa Perez
- María Espinosa Pérez. Hospital Universitario Miguel Servet, Servicio de Medicina Interna. P.º Isabel la Católica, 1-3, 50009 Zaragoza, Spain.
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20
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Lu L, Liu LP, Gui R, Dong H, Su YR, Zhou XH, Liu FX. Discovering common pathogenetic processes between COVID-19 and sepsis by bioinformatics and system biology approach. Front Immunol 2022; 13:975848. [PMID: 36119022 PMCID: PMC9471316 DOI: 10.3389/fimmu.2022.975848] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 08/04/2022] [Indexed: 11/17/2022] Open
Abstract
Corona Virus Disease 2019 (COVID-19), an acute respiratory infectious disease caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has spread rapidly worldwide, resulting in a pandemic with a high mortality rate. In clinical practice, we have noted that many critically ill or critically ill patients with COVID-19 present with typical sepsis-related clinical manifestations, including multiple organ dysfunction syndrome, coagulopathy, and septic shock. In addition, it has been demonstrated that severe COVID-19 has some pathological similarities with sepsis, such as cytokine storm, hypercoagulable state after blood balance is disrupted and neutrophil dysfunction. Considering the parallels between COVID-19 and non-SARS-CoV-2 induced sepsis (hereafter referred to as sepsis), the aim of this study was to analyze the underlying molecular mechanisms between these two diseases by bioinformatics and a systems biology approach, providing new insights into the pathogenesis of COVID-19 and the development of new treatments. Specifically, the gene expression profiles of COVID-19 and sepsis patients were obtained from the Gene Expression Omnibus (GEO) database and compared to extract common differentially expressed genes (DEGs). Subsequently, common DEGs were used to investigate the genetic links between COVID-19 and sepsis. Based on enrichment analysis of common DEGs, many pathways closely related to inflammatory response were observed, such as Cytokine-cytokine receptor interaction pathway and NF-kappa B signaling pathway. In addition, protein-protein interaction networks and gene regulatory networks of common DEGs were constructed, and the analysis results showed that ITGAM may be a potential key biomarker base on regulatory analysis. Furthermore, a disease diagnostic model and risk prediction nomogram for COVID-19 were constructed using machine learning methods. Finally, potential therapeutic agents, including progesterone and emetine, were screened through drug-protein interaction networks and molecular docking simulations. We hope to provide new strategies for future research and treatment related to COVID-19 by elucidating the pathogenesis and genetic mechanisms between COVID-19 and sepsis.
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Affiliation(s)
- Lu Lu
- Department of Blood Transfusion, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Le-Ping Liu
- Department of Blood Transfusion, The Third Xiangya Hospital of Central South University, Changsha, China
- Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Rong Gui
- Department of Blood Transfusion, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Hang Dong
- Department of Blood Transfusion, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Yan-Rong Su
- Department of Laboratory Medicine, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Xiong-Hui Zhou
- Department of Blood Transfusion, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Feng-Xia Liu
- Department of Blood Transfusion, The Third Xiangya Hospital of Central South University, Changsha, China
- *Correspondence: Feng-Xia Liu,
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21
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Andrade BGN, Cuadrat RRC, Tonetti FR, Kitazawa H, Villena J. The role of respiratory microbiota in the protection against viral diseases: respiratory commensal bacteria as next-generation probiotics for COVID-19. BIOSCIENCE OF MICROBIOTA, FOOD AND HEALTH 2022; 41:94-102. [PMID: 35846832 PMCID: PMC9246420 DOI: 10.12938/bmfh.2022-009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 03/05/2022] [Indexed: 12/21/2022]
Abstract
On March 11, 2020, the World Health Organization declared a pandemic of coronavirus infectious disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and imposed the biggest public health challenge for our civilization, with unforeseen impacts in the subsequent years. Similar to other respiratory infections, COVID-19 is associated with significant changes in the composition of the upper respiratory tract microbiome. Studies have pointed to a significant reduction of diversity and richness of the respiratory microbiota in COVID-19 patients. Furthermore, it has been suggested that Prevotella, Staphylococcus, and Streptococcus are associated with severe COVID-19 cases, while Dolosigranulum and Corynebacterium are significantly more abundant in asymptomatic subjects or with mild disease. These results have stimulated the search for new microorganisms from the respiratory microbiota with probiotic properties that could alleviate symptoms and even help in the fight against COVID-19. To date, the potential positive effects of probiotics in the context of SARS-CoV-2 infection and COVID-19 pandemics have been extrapolated from studies carried out with other viral pathogens, such as influenza virus and respiratory syncytial virus. However, scientific evidence has started to emerge demonstrating the capacity of immunomodulatory bacteria to beneficially influence the resistance against SARS-CoV-2 infection. Here we review the scientific knowledge regarding the role of the respiratory microbiota in viral infections in general and in the infection caused by SARS-CoV-2 in particular. In addition, the scientific work that supports the use of immunomodulatory probiotic microorganisms as beneficial tools to reduce the severity of respiratory viral infections is also reviewed. In particular, our recent studies that evaluated the role of immunomodulatory Dolosigranulum pigrum strains in the context of SARS-CoV-2 infection are highlighted.
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Affiliation(s)
- Bruno G N Andrade
- Adapt Centre, Munster Technological University (MTU), T12 P928 Cork, Ireland
| | - Rafael R C Cuadrat
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), 13125 Berlin, Germany.,Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbrücke, 14558 Nuthetal, Germany
| | - Fernanda Raya Tonetti
- Laboratory of Immunobiotechnology, Reference Centre for Lactobacilli (CERELA-CONICET), 4000 Tucumán, Argentina
| | - Haruki Kitazawa
- Food and Feed Immunology Group, Laboratory of Animal Food Function, Graduate School of Agricultural Science, Tohoku University, 1-1 Amamiya-machi, Tsutsumidori, Aoba-ku, Sendai, Miyagi 981-8555, Japan.,Livestock Immunology Unit, International Education and Research Center for Food and Agricultural Immunology (CFAI), Graduate School of Agricultural Science, Tohoku University, 1-1 Amamiya-machi, Tsutsumidori, Aoba-ku, Sendai, Miyagi 981-8555, Japan
| | - Julio Villena
- Laboratory of Immunobiotechnology, Reference Centre for Lactobacilli (CERELA-CONICET), 4000 Tucumán, Argentina.,Food and Feed Immunology Group, Laboratory of Animal Food Function, Graduate School of Agricultural Science, Tohoku University, 1-1 Amamiya-machi, Tsutsumidori, Aoba-ku, Sendai, Miyagi 981-8555, Japan
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22
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Giannitsioti E, Louka C, Mamali V, Kousouli E, Velentza L, Papadouli V, Loizos G, Mavroudis P, Kranidiotis G, Rekleiti N, Stamati A, Speggos I, Daniil I, Kouvatsos P, Sidiropoulou C, Linardaki G, Gerakari S, Chrysos G, Themeli-Digalaki K, Zarkotou O. Bloodstream Infections in a COVID-19 Non-ICU Department: Microbial Epidemiology, Resistance Profiles and Comparative Analysis of Risk Factors and Patients' Outcome. Microorganisms 2022; 10:1314. [PMID: 35889033 PMCID: PMC9318208 DOI: 10.3390/microorganisms10071314] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/05/2022] [Accepted: 06/24/2022] [Indexed: 12/23/2022] Open
Abstract
Background: Bloodstream infections (BSI) caused by highly resistant pathogens in non-ICU COVID-19 departments pose important challenges. Methods: We performed a comparative analysis of incidence and microbial epidemiology of BSI in COVID-19 vs. non-COVID-19, non-ICU departments between 1 September 2020-31 October 2021. Risk factors for BSI and its impact on outcome were evaluated by a case-control study which included COVID-19 patients with/without BSI. Results: Forty out of 1985 COVID-19 patients developed BSI. The mean monthly incidence/100 admissions was 2.015 in COVID-19 and 1.742 in non-COVID-19 departments. Enterococcus and Candida isolates predominated in the COVID-19 group (p < 0.001 and p = 0.018, respectively). All Acinetobacter baumannii isolates were carbapenem-resistant (CR). In the COVID-19 group, 33.3% of Klebsiella pneumoniae was CR, 50% of Escherichia coli produced ESBL and 19% of Enterococcus spp. were VRE vs. 74.5%, 26.1% and 8.8% in the non-COVID-19 group, respectively. BSI was associated with prior hospitalization (p = 0.003), >2 comorbidities (p < 0.001), central venous catheter (p = 0.015), severe SARS-CoV-2 pneumonia and lack of COVID-19 vaccination (p < 0.001). In the multivariate regression model also including age and multiple comorbidities, only BSI was significantly associated with adverse in-hospital outcome [OR (CI95%): 21.47 (3.86−119.21), p < 0.001]. Conclusions: BSI complicates unvaccinated patients with severe SARS-CoV-2 pneumonia and increases mortality. BSI pathogens and resistance profiles differ among COVID-19/non-COVID-19 departments, suggesting various routes of pathogen acquisition.
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Affiliation(s)
- Efthymia Giannitsioti
- COVID-19 Department, Tzaneio General Hospital, 18536 Piraeus, Greece; (L.V.); (G.L.); (P.M.); (G.K.); (A.S.); (I.S.); (P.K.); (C.S.); (G.L.); (S.G.); (G.C.)
- Fourth Department of Internal Medicine, NKUA, ATTIKON University General Hospital, 12462 Athens, Greece
| | - Christina Louka
- Department of Microbiology, Tzaneio General Hospital, 18536 Piraeus, Greece; (C.L.); (V.M.); (V.P.); (N.R.); (I.D.); (K.T.-D.); (O.Z.)
| | - Vasiliki Mamali
- Department of Microbiology, Tzaneio General Hospital, 18536 Piraeus, Greece; (C.L.); (V.M.); (V.P.); (N.R.); (I.D.); (K.T.-D.); (O.Z.)
| | - Elisavet Kousouli
- Infection Control Action Team, Tzaneio General Hospital, 18536 Piraeus, Greece;
| | - Lemonia Velentza
- COVID-19 Department, Tzaneio General Hospital, 18536 Piraeus, Greece; (L.V.); (G.L.); (P.M.); (G.K.); (A.S.); (I.S.); (P.K.); (C.S.); (G.L.); (S.G.); (G.C.)
- Emergency Department, Tzaneio General Hospital, 18536 Piraeus, Greece
| | - Vaia Papadouli
- Department of Microbiology, Tzaneio General Hospital, 18536 Piraeus, Greece; (C.L.); (V.M.); (V.P.); (N.R.); (I.D.); (K.T.-D.); (O.Z.)
| | - Georgios Loizos
- COVID-19 Department, Tzaneio General Hospital, 18536 Piraeus, Greece; (L.V.); (G.L.); (P.M.); (G.K.); (A.S.); (I.S.); (P.K.); (C.S.); (G.L.); (S.G.); (G.C.)
- Second Department of Internal Medicine, Tzaneio General Hospital, 18536 Piraeus, Greece
| | - Panagiotis Mavroudis
- COVID-19 Department, Tzaneio General Hospital, 18536 Piraeus, Greece; (L.V.); (G.L.); (P.M.); (G.K.); (A.S.); (I.S.); (P.K.); (C.S.); (G.L.); (S.G.); (G.C.)
- Second Department of Internal Medicine, Tzaneio General Hospital, 18536 Piraeus, Greece
| | - Georgios Kranidiotis
- COVID-19 Department, Tzaneio General Hospital, 18536 Piraeus, Greece; (L.V.); (G.L.); (P.M.); (G.K.); (A.S.); (I.S.); (P.K.); (C.S.); (G.L.); (S.G.); (G.C.)
| | - Nektaria Rekleiti
- Department of Microbiology, Tzaneio General Hospital, 18536 Piraeus, Greece; (C.L.); (V.M.); (V.P.); (N.R.); (I.D.); (K.T.-D.); (O.Z.)
| | - Alexandra Stamati
- COVID-19 Department, Tzaneio General Hospital, 18536 Piraeus, Greece; (L.V.); (G.L.); (P.M.); (G.K.); (A.S.); (I.S.); (P.K.); (C.S.); (G.L.); (S.G.); (G.C.)
| | - Ioannis Speggos
- COVID-19 Department, Tzaneio General Hospital, 18536 Piraeus, Greece; (L.V.); (G.L.); (P.M.); (G.K.); (A.S.); (I.S.); (P.K.); (C.S.); (G.L.); (S.G.); (G.C.)
- Second Department of Internal Medicine, Tzaneio General Hospital, 18536 Piraeus, Greece
| | - Ioannis Daniil
- Department of Microbiology, Tzaneio General Hospital, 18536 Piraeus, Greece; (C.L.); (V.M.); (V.P.); (N.R.); (I.D.); (K.T.-D.); (O.Z.)
| | - Panagiotis Kouvatsos
- COVID-19 Department, Tzaneio General Hospital, 18536 Piraeus, Greece; (L.V.); (G.L.); (P.M.); (G.K.); (A.S.); (I.S.); (P.K.); (C.S.); (G.L.); (S.G.); (G.C.)
| | - Chrysanthi Sidiropoulou
- COVID-19 Department, Tzaneio General Hospital, 18536 Piraeus, Greece; (L.V.); (G.L.); (P.M.); (G.K.); (A.S.); (I.S.); (P.K.); (C.S.); (G.L.); (S.G.); (G.C.)
- Second Department of Internal Medicine, Tzaneio General Hospital, 18536 Piraeus, Greece
| | - Garifallia Linardaki
- COVID-19 Department, Tzaneio General Hospital, 18536 Piraeus, Greece; (L.V.); (G.L.); (P.M.); (G.K.); (A.S.); (I.S.); (P.K.); (C.S.); (G.L.); (S.G.); (G.C.)
- Second Department of Internal Medicine, Tzaneio General Hospital, 18536 Piraeus, Greece
| | - Styliani Gerakari
- COVID-19 Department, Tzaneio General Hospital, 18536 Piraeus, Greece; (L.V.); (G.L.); (P.M.); (G.K.); (A.S.); (I.S.); (P.K.); (C.S.); (G.L.); (S.G.); (G.C.)
- Emergency Department, Tzaneio General Hospital, 18536 Piraeus, Greece
| | - Georgios Chrysos
- COVID-19 Department, Tzaneio General Hospital, 18536 Piraeus, Greece; (L.V.); (G.L.); (P.M.); (G.K.); (A.S.); (I.S.); (P.K.); (C.S.); (G.L.); (S.G.); (G.C.)
- Infection Control Action Team, Tzaneio General Hospital, 18536 Piraeus, Greece;
- Second Department of Internal Medicine, Tzaneio General Hospital, 18536 Piraeus, Greece
| | - Katina Themeli-Digalaki
- Department of Microbiology, Tzaneio General Hospital, 18536 Piraeus, Greece; (C.L.); (V.M.); (V.P.); (N.R.); (I.D.); (K.T.-D.); (O.Z.)
- Infection Control Action Team, Tzaneio General Hospital, 18536 Piraeus, Greece;
| | - Olympia Zarkotou
- Department of Microbiology, Tzaneio General Hospital, 18536 Piraeus, Greece; (C.L.); (V.M.); (V.P.); (N.R.); (I.D.); (K.T.-D.); (O.Z.)
- Infection Control Action Team, Tzaneio General Hospital, 18536 Piraeus, Greece;
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23
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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.
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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
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24
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Zhang Y, Shi F, Wang Y, Meng Y, Zhang Q, Wang K, Zeng P, Diao H. Comparative Analysis of Long Non-Coding RNA Expression and Immune Response in Mild and Severe COVID-19. Front Mol Biosci 2022; 9:835590. [PMID: 35573725 PMCID: PMC9094366 DOI: 10.3389/fmolb.2022.835590] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/21/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Coronavirus disease 2019 (COVID-19) is a worldwide emergency, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Long non-coding RNAs (lncRNAs) do not encode proteins but could participate in immune response.Methods: In our study, 39 COVID-19 patients were enrolled. The microarray of peripheral blood mononuclear cells from healthy and COVID-19 patients was applied to identify the expression profiles of lncRNAs and mRNAs. Identified differentially expressed (DE) lncRNAs were validated by qRT-PCR. Then, the lncRNA–mRNA network was constructed and visualized using Cytoscape (3.6.1) based on the Pearson correlation coefficient. The enrichment of DE mRNAs was analyzed using Metascape. The difference in frequencies of immune cells and cytokines was detected using CIBERSORT and ImmPort based on DE mRNAs.Results: All patients with COVID-19 displayed lymphopenia, especially in T cells, and hyper-inflammatory responses, including IL-6 and TNF-α. Four immune-related lncRNAs in COVID-19 were found and further validated, including AC136475.9, CATG00000032642.1, G004246, and XLOC_013290. Functional analysis enriched in downregulation of the T-cell receptor and the antigen processing and presentation as well as increased apoptotic proteins, which could lead to T-cell cytopenia. In addition, they participated in monocyte remodeling, which contributed to releasing cytokines and chemokines and then recruiting more monocytes and aggravating the clinical severity of COVID-19 patients.Conclusion: Taken together, four lncRNAs were in part of immune response in COVID-19, which was involved in the T-cell cytopenia by downregulating the antigen processing and presentation, the T-cell receptor, and an increased proportion of monocytes, with a distinct change in cytokines and chemokines.
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Abstract
PURPOSE OF REVIEW Some patients with coronavirus disease 2019 (COVID-19) may develop pulmonary bacterial coinfection or superinfection, that could unfavorably impact their prognosis. RECENT FINDINGS The exact burden of methicillin-resistant Staphylococcus aureus (MRSA) lung infection in peculiar populations such as patients with COVID-19 remains somewhat elusive, possibly because of wide heterogeneity in methods and endpoints across studies. SUMMARY There was important heterogeneity in the retrieved literature on the epidemiology of MRSA lung infection in patients with COVID-19, both when considering all other bacteria as the denominator (relative prevalence ranging from 2% to 29%) and when considering only S. aureus as the denominator (relative prevalence ranging from 11% to 65%). Overall, MRSA is among the most frequent causative agents of pulmonary infection in patients with COVID-19. Improving our ability to rapidly reach etiological diagnosis of bacterial lung infection in COVID-19 patients remains fundamental if we are to improve the rates of appropriate antibiotic therapy in patients with COVID-19 and concomitant/superimposed MRSA infection, at the same time avoiding antibiotic overuse in line with antimicrobial stewardship principles.
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Givirovskaia D, Givirovskiy G, Haapakoski M, Hokkanen S, Ruuskanen V, Salo S, Marjomäki V, Ahola J, Repo E. Modification of face masks with zeolite imidazolate framework-8: A tool for hindering the spread of COVID-19 infection. MICROPOROUS AND MESOPOROUS MATERIALS : THE OFFICIAL JOURNAL OF THE INTERNATIONAL ZEOLITE ASSOCIATION 2022; 334:111760. [PMID: 35221784 PMCID: PMC8858792 DOI: 10.1016/j.micromeso.2022.111760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 06/14/2023]
Abstract
The worldwide spread of the SARS-CoV-2 virus has continued to accelerate, putting a considerable burden on public health, safety, and the global economy. Taking into consideration that the main route of virus transmission is via respiratory particles, the face mask represents a simple and efficient barrier between potentially infected and healthy individuals, thus reducing transmissibility per contact by reducing transmission of infected respiratory particles. However, long-term usage of a face mask leads to the accumulation of significant amounts of different pathogens and viruses onto the surface of the mask and can result in dangerous bacterial and viral co-infections. Zeolite imidazolate framework-8 (ZIF-8) has recently emerged as an efficient water-stable photocatalyst capable of generating reactive oxygen species under light irradiation destroying dangerous microbial pathogens. The present study investigates the potential of using ZIF-8 as a coating for face masks to prevent the adherence of microbial/viral entities. The results show that after 2 h of UV irradiation, a polypropylene mask coated with ZIF-8 nanostructures is capable of eliminating S. Aureus and bacteriophage MS2 with 99.99% and 95.4% efficiencies, respectively. Furthermore, low-pathogenic HCoV-OC43 coronavirus was eliminated by a ZIF-8-modified mask with 100% efficiency already after 1 h of UV irradiation. As bacteriophage MS2 and HCoV-OC43 coronavirus are commonly used surrogates of the SARS-CoV-2 virus, the revealed antiviral properties of ZIF-8 can represent an important step in designing efficient protective equipment for controlling and fighting the current COVID-19 pandemic.
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Affiliation(s)
| | | | - Marjo Haapakoski
- University of Jyväskylä, P.O. Box 35, FI-40014, Jyväskylä, Finland
| | - Sanna Hokkanen
- LUT University, P.O. Box 20, FI-53851, Lappeenranta, Finland
| | - Vesa Ruuskanen
- LUT University, P.O. Box 20, FI-53851, Lappeenranta, Finland
| | - Satu Salo
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, FI-02044, ESPOO, Finland
| | - Varpu Marjomäki
- University of Jyväskylä, P.O. Box 35, FI-40014, Jyväskylä, Finland
| | - Jero Ahola
- LUT University, P.O. Box 20, FI-53851, Lappeenranta, Finland
| | - Eveliina Repo
- LUT University, P.O. Box 20, FI-53851, Lappeenranta, Finland
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McCormick TS, Hejal RB, Leal LO, Ghannoum MA. GM-CSF: Orchestrating the Pulmonary Response to Infection. Front Pharmacol 2022; 12:735443. [PMID: 35111042 PMCID: PMC8803133 DOI: 10.3389/fphar.2021.735443] [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: 07/02/2021] [Accepted: 12/13/2021] [Indexed: 01/18/2023] Open
Abstract
This review summarizes the structure and function of the alveolar unit, comprised of alveolar macrophage and epithelial cell types that work in tandem to respond to infection. Granulocyte-macrophage colony-stimulating factor (GM-CSF) helps to maintain the alveolar epithelium and pulmonary immune system under physiological conditions and plays a critical role in restoring homeostasis under pathologic conditions, including infection. Given the emergence of novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and global spread of coronavirus disease 2019 (COVID-19), with subsequent acute respiratory distress syndrome, understanding basic lung physiology in infectious diseases is especially warranted. This review summarizes clinical and preclinical data for GM-CSF in respiratory infections, and the rationale for sargramostim (yeast-derived recombinant human [rhu] GM-CSF) as adjunctive treatment for COVID-19 and other pulmonary infectious diseases.
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Affiliation(s)
- Thomas S. McCormick
- Center for Medical Mycology, Department of Dermatology, Case Western Reserve University, Cleveland, OH, United States
| | - Rana B. Hejal
- Medical Intensive Care Unit, University Hospitals Cleveland Medical Center, Cleveland, OH, United States
- Pulmonary and Critical Care Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - Luis O. Leal
- Partner Therapeutics, Lexington, MA, United States
| | - Mahmoud A. Ghannoum
- Center for Medical Mycology, Department of Dermatology, Case Western Reserve University, Cleveland, OH, United States
- University Hospitals Cleveland Medical Center, Cleveland, OH, United States
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Alhaddad O, Elsabaawy M, Edrees A, Elshimy E, Elsabaawy D, Mansour T. A case report of COVID-19 evoked cholangitic liver abscess. EGYPTIAN LIVER JOURNAL 2022; 12:5. [PMID: 35036011 PMCID: PMC8750645 DOI: 10.1186/s43066-021-00169-6] [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: 07/20/2021] [Accepted: 12/30/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Lately, the humanity has been being threatened by the coronavirus disease (COVID-19). The virus-related destructive motives can damage not only the lungs but also the brain, blood vessels, kidneys, and the heart. CASE PRESENTATION A middle-aged female presented with jaundice post-COVID-19 pneumonia. The patient had past history of cholecystectomy 20 years ago. Both laboratory and imaging data revealed a picture of cholestasis with right lobe liver abscess. Despite drainage and culture-based antibiotics, no improvement ensued. Endoscopic retrograde cholangiopancreatography was done revealing mildly dilated common bile duct (CBD), multiple large stones, mildly dilated central biliary radicals, and an old overlooked stent inside the dilated CBD. Papillotomy and papilloplasty were undertaken followed by stones' extraction with insertion of 2 plastic stents (10 cm× 10 f), and a flow of thick dark bile was inspected. The patient was finally improved and safely discharged. CONCLUSION Herein, we present the first case of long-retained quiescent biliary stent which was over-headed by a cholangitic abscess in the vicinity of COVID pneumonia.
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Affiliation(s)
- Omkolsoum Alhaddad
- Department Of Hepatology and Gastroenterology, National Liver Institute, Menoufia University, Shebeen El-Kom, 32511 Egypt
| | - Maha Elsabaawy
- Department Of Hepatology and Gastroenterology, National Liver Institute, Menoufia University, Shebeen El-Kom, 32511 Egypt
| | - Ahmed Edrees
- Department Of Hepatology and Gastroenterology, National Liver Institute, Menoufia University, Shebeen El-Kom, 32511 Egypt
| | - Essam Elshimy
- Department Of Hepatology and Gastroenterology, National Liver Institute, Menoufia University, Shebeen El-Kom, 32511 Egypt
| | - Dalia Elsabaawy
- Department Of Clinical Pharmacy, National Liver Institute, Menoufia University, Shebeen El-Kom, 32511 Egypt
| | - Tarek Mansour
- Department Of Internal Medicine, Faculty of medicine, Ain Shams University, Cairo, Egypt
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Markovskaya Y, Gavioli EM, Cusumano JA, Glatt AE. Coronavirus disease 2019 (COVID-19): Secondary bacterial infections and the impact on antimicrobial resistance during the COVID-19 pandemic. ANTIMICROBIAL STEWARDSHIP & HEALTHCARE EPIDEMIOLOGY : ASHE 2022; 2:e114. [PMID: 36483429 PMCID: PMC9726554 DOI: 10.1017/ash.2022.253] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/30/2022] [Accepted: 05/31/2022] [Indexed: 05/16/2023]
Abstract
Secondary bacterial infections and bacterial coinfections are an important complication of coronavirus disease 2019 (COVID-19), leading to antibiotic overuse and increased rates of antimicrobial resistance (AMR) during the COVID-19 pandemic. In this literature review, we summarize the reported rates of secondary bacterial infections and bacterial coinfections in patients with COVID-19, the impact on patient outcomes, the antibiotic treatment approaches employed, and the resistance patterns observed. The reported data suggest that although the incidence of secondary bacterial infections or bacterial coinfections is relatively low, they are associated with worse outcomes such as prolonged hospitalization, intensive care unit admission, mechanical ventilator use, and increased mortality. Interestingly, antibiotic prescription rates are typically higher than secondary bacterial and bacterial coinfection rates, and reports of AMR are common. These findings highlight the need for an improved understanding of secondary bacterial and bacterial coinfection in patients with COVID-19, as well as improved treatment options, to mitigate inappropriate antibiotic prescribing and AMR.
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Affiliation(s)
- Yelena Markovskaya
- Department of Medicine, Mount Sinai South Nassau, Oceanside, NY, United States
- Icahn School of Medicine at Mount Sinai, New York, New York
| | - Elizabeth M. Gavioli
- Department of Pharmacy Practice, Arnold and Marie Schwartz College of Pharmacy and Health Sciences, Brooklyn, New York
| | - Jaclyn A. Cusumano
- Department of Pharmacy Practice, Arnold and Marie Schwartz College of Pharmacy and Health Sciences, Brooklyn, New York
- Department of Pharmacy, Mount Sinai Queens, Queens, New York
| | - Aaron E. Glatt
- Department of Medicine, Mount Sinai South Nassau, Oceanside, NY, United States
- Icahn School of Medicine at Mount Sinai, New York, New York
- Author for correspondence: Aaron E. Glatt, MD, Mount Sinai South Nassau, Oceanside, NY 11791. E-mail:
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Mairpady Shambat S, Gómez-Mejia A, Schweizer TA, Huemer M, Chang CC, Acevedo C, Bergada-Pijuan J, Vulin C, Hofmaenner DA, Scheier TC, Hertegonne S, Parietti E, Miroshnikova N, Wendel Garcia PD, Hilty MP, Buehler PK, Schuepbach RA, Brugger SD, Zinkernagel AS. Hyperinflammatory environment drives dysfunctional myeloid cell effector response to bacterial challenge in COVID-19. PLoS Pathog 2022; 18:e1010176. [PMID: 35007290 PMCID: PMC8782468 DOI: 10.1371/journal.ppat.1010176] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 01/21/2022] [Accepted: 12/06/2021] [Indexed: 02/06/2023] Open
Abstract
COVID-19 displays diverse disease severities and symptoms including acute systemic inflammation and hypercytokinemia, with subsequent dysregulation of immune cells. Bacterial superinfections in COVID-19 can further complicate the disease course and are associated with increased mortality. However, there is limited understanding of how SARS-CoV-2 pathogenesis and hypercytokinemia impede the innate immune function against bacterial superinfections. We assessed the influence of COVID-19 plasma hypercytokinemia on the functional responses of myeloid immune cells upon bacterial challenges from acute-phase COVID-19 patients and their corresponding recovery-phase. We show that a severe hypercytokinemia status in COVID-19 patients correlates with the development of bacterial superinfections. Neutrophils and monocytes derived from COVID-19 patients in their acute-phase showed an impaired intracellular microbicidal capacity upon bacterial challenges. The impaired microbicidal capacity was reflected by abrogated MPO and reduced NETs production in neutrophils along with reduced ROS production in both neutrophils and monocytes. Moreover, we observed a distinct pattern of cell surface receptor expression on both neutrophils and monocytes, in line with suppressed autocrine and paracrine cytokine signaling. This phenotype was characterized by a high expression of CD66b, CXCR4 and low expression of CXCR1, CXCR2 and CD15 in neutrophils and low expression of HLA-DR, CD86 and high expression of CD163 and CD11b in monocytes. Furthermore, the impaired antibacterial effector function was mediated by synergistic effect of the cytokines TNF-α, IFN-γ and IL-4. COVID-19 patients receiving dexamethasone showed a significant reduction of overall inflammatory markers in the plasma as well as exhibited an enhanced immune response towards bacterial challenge ex vivo. Finally, broad anti-inflammatory treatment was associated with a reduction in CRP, IL-6 levels as well as length of ICU stay and ventilation-days in critically ill COVID-19 patients. Our data provides insights into the transient functional dysregulation of myeloid immune cells against subsequent bacterial infections in COVID-19 patients and describe a beneficial role for the use of dexamethasone in these patients.
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Affiliation(s)
- Srikanth Mairpady Shambat
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Alejandro Gómez-Mejia
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Tiziano A. Schweizer
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Markus Huemer
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Chun-Chi Chang
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Claudio Acevedo
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Judith Bergada-Pijuan
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Clément Vulin
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Daniel A. Hofmaenner
- Institute of Intensive Care, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Thomas C. Scheier
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Sanne Hertegonne
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Elena Parietti
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Nataliya Miroshnikova
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Pedro D. Wendel Garcia
- Institute of Intensive Care, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Matthias P. Hilty
- Institute of Intensive Care, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Philipp Karl Buehler
- Institute of Intensive Care, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Reto A. Schuepbach
- Institute of Intensive Care, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Silvio D. Brugger
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Annelies S. Zinkernagel
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
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The interface between COVID-19 and bacterial healthcare-associated infections. Clin Microbiol Infect 2021; 27:1772-1776. [PMID: 34111586 PMCID: PMC8182977 DOI: 10.1016/j.cmi.2021.06.001] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/27/2021] [Accepted: 06/01/2021] [Indexed: 01/08/2023]
Abstract
BACKGROUND A wide range of bacterial infections occur in coronavirus disease 2019 (COVID-19) patients, particularly in those with severe coronaviral disease. Some of these are community-acquired co-infections. OBJECTIVE To review recent data that indicate the occurrence of hospital-onset bacterial infections, including with antibiotic-resistant isolates, in COVID-19 patients. SOURCES Using PubMed, the literature was searched using terms including: 'COVID-19'; 'SARS-CoV-2'; 'bacterial infection'; 'healthcare-associated infection'; 'antibiotic resistance'; 'antimicrobial resistance'; 'multi-drug resistance'; 'Streptococcus'; 'Staphylococcus'; 'Pseudomonas'; 'Escherichia'; 'Klebsiella'; 'Enterococcus'; 'Acinetobacter'; 'Haemophilus'; 'MRSA'; 'VRE'; 'ESBL'; 'NDM-CRE'; 'CR-Ab'; 'VRSA'; 'MDR'. CONTENT There is a growing number of reports of bacterial infections acquired by patients with severe COVID-19 after hospital admission. Antibiotic-resistant pathogens found to cause healthcare-associated infections (HAIs) in COVID-19 patients include methicillin-resistant Staphylococcus aureus, New Delhi metallo-β-lactamase-producing carbapenem-resistant Enterobacterales, carbapenem-resistant Acinetobacter baumannii, extended-spectrum β-lactamase Klebsiella pneumoniae and vancomycin-resistant enterococci. COVID-19 has impacted bacterial HAIs in a number of ways with an increase in the incidence of New Delhi metallo-β-lactamase-producing carbapenem-resistant Enterobacterales and carbapenem-resistant A. baumannii reported at some hospital sites compared with before the pandemic. Recommended guidelines for antimicrobial stewardship in COVID-19 patient treatment are discussed regarding minimization of empiric broad-spectrum antibiotic use. Other studies have reported a decrease in methicillin-resistant S. aureus and vancomycin-resistant enterococci cases, which has been attributed to enhanced infection prevention and control practices introduced to minimize intra-hospital spread of COVID-19. IMPLICATIONS Poorer outcomes have been observed in hospitalized COVID-19 patients with an antibiotic-resistant infection. Although heightened IPC measures have been accompanied by a reduction in some HAIs at specific sites, in other situations, COVID-19 has been associated with an increase in bacterial HAI incidence. Further research is needed to define the cost-benefit relationship of maintaining COVID-19-related infection prevention and control protocols beyond the pandemic to reduce the burden of HAIs. In addition, the longer-term impact of high usage of certain broad-spectrum antibiotics during the COVID-19 pandemic requires evaluation.
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32
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Rattanaburi S, Sawaswong V, Chitcharoen S, Sivapornnukul P, Nimsamer P, Suntronwong N, Puenpa J, Poovorawan Y, Payungporn S. Bacterial microbiota in upper respiratory tract of COVID-19 and influenza patients. Exp Biol Med (Maywood) 2021; 247:409-415. [PMID: 34775842 DOI: 10.1177/15353702211057473] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The upper respiratory tract is inhabited by diverse range of commensal microbiota which plays a role in protecting the mucosal surface from pathogens. Alterations of the bacterial community from respiratory viral infections could increase the susceptibility to secondary infections and disease severities. We compared the upper respiratory bacterial profiles among Thai patients with influenza or COVID-19 by using 16S rDNA high-throughput sequencing based on MiSeq platform. The Chao1 richness was not significantly different among groups, whereas the Shannon diversity of Flu A and Flu B groups were significantly lower than Non-Flu & COVID-19 group. The beta diversity revealed that the microbial communities of influenza (Flu A and Flu B), COVID-19, and Non-Flu & COVID-19 were significantly different; however, the comparison of the community structure was similar between Flu A and Flu B groups. The bacterial classification revealed that Enterobacteriaceae was predominant in influenza patients, while Staphylococcus and Pseudomonas were significantly enriched in the COVID-19 patients. These implied that respiratory viral infections might be related to alteration of upper respiratory bacterial community and susceptibility to secondary bacterial infections. Moreover, the bacteria that observed in Non-Flu & COVID-19 patients had high abundance of Streptococcus, Prevotella, Veillonella, and Fusobacterium. This study provides the basic knowledge for further investigation of the relationship between upper respiratory microbiota and respiratory disease which might be useful for better understanding the mechanism of viral infectious diseases.
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Affiliation(s)
- Somruthai Rattanaburi
- Interdisciplinary Program of Biomedical Sciences, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand.,Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Vorthon Sawaswong
- Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Suwalak Chitcharoen
- Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pavaret Sivapornnukul
- Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand.,Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pattaraporn Nimsamer
- Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Nungruthai Suntronwong
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Jiratchaya Puenpa
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Sunchai Payungporn
- Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand.,Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
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33
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Ohki R, Fukui Y, Morishita N, Iwata K. Increase of blood culture contamination during COVID-19 pandemic. A retrospective descriptive study. Am J Infect Control 2021; 49:1359-1361. [PMID: 34464662 PMCID: PMC8403069 DOI: 10.1016/j.ajic.2021.08.025] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/22/2021] [Accepted: 08/23/2021] [Indexed: 12/22/2022]
Abstract
Background Secondary bacterial infection during the care of coronavirus disease 2019 (COVID-19) patients poses risks to the patients, but there are concerns of an increase in blood culture contamination. Methods A retrospective comparative study was conducted from April 1 to December 31, 2020, when the patients with COVID-19 were taken care of (pandemic period, PP), and it was compared with the same period in 2019 (pre-pandemic period, pre-PP). Results A total of 346 patients with COVID-19 were hospitalized during the study period in 2020. A total of 1,040 and 918 blood cultures were taken during PPP and PP respectively. 38 and 56 contaminations occurred during pre-PP and PP respectively (3.7% [95% CI 2.6%-5.0%], vs 6.1% [95% CI 4.6%-7.8%], P = .015). For the ICU, 10 and 32 contaminations occurred during the same periods (5.0% [95% CI 2.4%-9.0%], vs 12.5% [95% CI 8.7%-17.1%], P = .0097). True bacteremia in the ICU per patient-day also increased during the PP. Conclusions We found a significant increase in blood culture contamination during the COVID-19 pandemic in the ICU setting, while true bacteremia also increased. A safe and effective way to obtain blood cultures from patients with COVID-19 should be sought.
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Pandey A, Davies WR, Calvert PA. A fatal case of infective endocarditis complicated by acute COVID-19 pneumonia. Oxf Med Case Reports 2021; 2021:omab123. [PMID: 34987853 PMCID: PMC8713583 DOI: 10.1093/omcr/omab123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 10/28/2021] [Accepted: 11/08/2021] [Indexed: 01/13/2023] Open
Abstract
A 74-year-old man with no co-morbidities presented to hospital with a 3-day history of diarrhoea and vomiting. He met the modified Duke’s criteria for definite infective endocarditis and was immediately started on an intravenous antibiotic. Over Days 1–9, he developed renal failure. On Day 10, he was transferred to a tertiary hospital for mitral valve replacement. However, he tested positive for SARS-CoV-2 on arrival at the tertiary hospital, which delayed his surgery. He underwent bi-weekly nasopharyngeal swabs for SARS-CoV-2 with a plan to operate as soon as he tested negative, or as soon as his incubation period for COVID-19 pneumonia had elapsed. Unfortunately, he died on Day 31 from acute respiratory distress syndrome secondary to COVID-19 pneumonia. We describe the challenges in deciding on the optimal timing for valve replacement. We conclude by suggesting that earlier valve replacement may result in better outcomes.
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Affiliation(s)
- Anmol Pandey
- North West Anglia NHS Foundation Trust, Peterborough City Hospital, Peterborough, UK
| | - William R Davies
- Royal Papworth Hospital NHS Foundation Trust, Royal Papworth Hospital and University of Cambridge, Cambridge, UK
| | - Patrick A Calvert
- Royal Papworth Hospital NHS Foundation Trust, Royal Papworth Hospital and University of Cambridge, Cambridge, UK
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35
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Segala FV, Bavaro DF, Di Gennaro F, Salvati F, Marotta C, Saracino A, Murri R, Fantoni M. Impact of SARS-CoV-2 Epidemic on Antimicrobial Resistance: A Literature Review. Viruses 2021; 13:2110. [PMID: 34834917 PMCID: PMC8624326 DOI: 10.3390/v13112110] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/12/2021] [Accepted: 10/15/2021] [Indexed: 01/08/2023] Open
Abstract
Antimicrobial resistance is an urgent threat to public health and global development; in this scenario, the SARS-CoV2 pandemic has caused a major disruption of healthcare systems and practices. A narrative review was conducted on articles focusing on the impact of COVID-19 on multidrug-resistant gram-negative, gram-positive bacteria, and fungi. We found that, worldwide, multiple studies reported an unexpected high incidence of infections due to methicillin-resistant S. aureus, carbapenem-resistant A. baumannii, carbapenem-resistant Enterobacteriaceae, and C. auris among COVID-19 patients admitted to the intensive care unit. In this setting, inappropriate antimicrobial exposure, environmental contamination, and discontinuation of infection control measures may have driven selection and diffusion of drug-resistant pathogens.
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Affiliation(s)
- Francesco Vladimiro Segala
- Clinic of Infectious Diseases, Catholic University of the Sacred Heart, 00168 Rome, Italy; (F.S.); (R.M.); (M.F.)
| | - Davide Fiore Bavaro
- Clinic of Infectious Diseases, University of Bari, 70121 Bari, Italy; (D.F.B.); (F.D.G.); (A.S.)
| | - Francesco Di Gennaro
- Clinic of Infectious Diseases, University of Bari, 70121 Bari, Italy; (D.F.B.); (F.D.G.); (A.S.)
| | - Federica Salvati
- Clinic of Infectious Diseases, Catholic University of the Sacred Heart, 00168 Rome, Italy; (F.S.); (R.M.); (M.F.)
| | - Claudia Marotta
- General Directorate of Health Prevention, Ministry of Health, 00144 Rome, Italy;
| | - Annalisa Saracino
- Clinic of Infectious Diseases, University of Bari, 70121 Bari, Italy; (D.F.B.); (F.D.G.); (A.S.)
| | - Rita Murri
- Clinic of Infectious Diseases, Catholic University of the Sacred Heart, 00168 Rome, Italy; (F.S.); (R.M.); (M.F.)
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
| | - Massimo Fantoni
- Clinic of Infectious Diseases, Catholic University of the Sacred Heart, 00168 Rome, Italy; (F.S.); (R.M.); (M.F.)
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
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Adalbert JR, Varshney K, Tobin R, Pajaro R. Clinical outcomes in patients co-infected with COVID-19 and Staphylococcus aureus: a scoping review. BMC Infect Dis 2021; 21:985. [PMID: 34548027 PMCID: PMC8453255 DOI: 10.1186/s12879-021-06616-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 08/10/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Endemic to the hospital environment, Staphylococcus aureus (S. aureus) is a leading bacterial pathogen that causes deadly infections such as bacteremia and endocarditis. In past viral pandemics, it has been the principal cause of secondary bacterial infections, significantly increasing patient mortality rates. Our world now combats the rapid spread of COVID-19, leading to a pandemic with a death toll greatly surpassing those of many past pandemics. However, the impact of co-infection with S. aureus remains unclear. Therefore, we aimed to perform a high-quality scoping review of the literature to synthesize the existing evidence on the clinical outcomes of COVID-19 and S. aureus co-infection. METHODS A scoping review of the literature was conducted in PubMed, Scopus, Ovid MEDLINE, CINAHL, ScienceDirect, medRxiv, and the WHO COVID-19 database using a combination of terms. Articles that were in English, included patients infected with both COVID-19 and S. aureus, and provided a description of clinical outcomes for patients were eligible. From these articles, the following data were extracted: type of staphylococcal species, onset of co-infection, patient sex, age, symptoms, hospital interventions, and clinical outcomes. Quality assessments of final studies were also conducted using the Joanna Briggs Institute's critical appraisal tools. RESULTS Searches generated a total of 1922 publications, and 28 articles were eligible for the final analysis. Of the 115 co-infected patients, there were a total of 71 deaths (61.7%) and 41 discharges (35.7%), with 62 patients (53.9%) requiring ICU admission. Patients were infected with methicillin-sensitive and methicillin-resistant strains of S. aureus, with the majority (76.5%) acquiring co-infection with S. aureus following hospital admission for COVID-19. Aside from antibiotics, the most commonly reported hospital interventions were intubation with mechanical ventilation (74.8 %), central venous catheter (19.1 %), and corticosteroids (13.0 %). CONCLUSIONS Given the mortality rates reported thus far for patients co-infected with S. aureus and COVID-19, COVID-19 vaccination and outpatient treatment may be key initiatives for reducing hospital admission and S. aureus co-infection risk. Physician vigilance is recommended during COVID-19 interventions that may increase the risk of bacterial co-infection with pathogens, such as S. aureus, as the medical community's understanding of these infection processes continues to evolve.
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Affiliation(s)
- Jenna R Adalbert
- Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA.
- Jefferson College of Population Health, 901 Walnut St., Philadelphia, PA, 19107, USA.
| | - Karan Varshney
- Jefferson College of Population Health, 901 Walnut St., Philadelphia, PA, 19107, USA
- Deakin University School of Medicine, Geelong, Victoria, Australia
| | - Rachel Tobin
- Deakin University School of Medicine, Geelong, Victoria, Australia
| | - Rafael Pajaro
- Morristown Medical Center of Atlantic Health System, Morristown, New Jersey, USA
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Merenstein C, Liang G, Whiteside SA, Cobián-Güemes AG, Merlino MS, Taylor LJ, Glascock A, Bittinger K, Tanes C, Graham-Wooten J, Khatib LA, Fitzgerald AS, Reddy S, Baxter AE, Giles JR, Oldridge DA, Meyer NJ, Wherry EJ, McGinniss JE, Bushman FD, Collman RG. Signatures of COVID-19 Severity and Immune Response in the Respiratory Tract Microbiome. mBio 2021; 12:e0177721. [PMID: 34399607 PMCID: PMC8406335 DOI: 10.1128/mbio.01777-21] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 07/14/2021] [Indexed: 01/12/2023] Open
Abstract
Viral infection of the respiratory tract can be associated with propagating effects on the airway microbiome, and microbiome dysbiosis may influence viral disease. Here, we investigated the respiratory tract microbiome in coronavirus disease 2019 (COVID-19) and its relationship to disease severity, systemic immunologic features, and outcomes. We examined 507 oropharyngeal, nasopharyngeal, and endotracheal samples from 83 hospitalized COVID-19 patients as well as non-COVID patients and healthy controls. Bacterial communities were interrogated using 16S rRNA gene sequencing, and the commensal DNA viruses Anelloviridae and Redondoviridae were quantified by qPCR. We found that COVID-19 patients had upper respiratory microbiome dysbiosis and greater change over time than critically ill patients without COVID-19. Oropharyngeal microbiome diversity at the first time point correlated inversely with disease severity during hospitalization. Microbiome composition was also associated with systemic immune parameters in blood, as measured by lymphocyte/neutrophil ratios and immune profiling of peripheral blood mononuclear cells. Intubated patients showed patient-specific lung microbiome communities that were frequently highly dynamic, with prominence of Staphylococcus. Anelloviridae and Redondoviridae showed more frequent colonization and higher titers in severe disease. Machine learning analysis demonstrated that integrated features of the microbiome at early sampling points had high power to discriminate ultimate level of COVID-19 severity. Thus, the respiratory tract microbiome and commensal viruses are disturbed in COVID-19 and correlate with systemic immune parameters, and early microbiome features discriminate disease severity. Future studies should address clinical consequences of airway dysbiosis in COVID-19, its possible use as biomarkers, and the role of bacterial and viral taxa identified here in COVID-19 pathogenesis. IMPORTANCE COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection of the respiratory tract, results in highly variable outcomes ranging from minimal illness to death, but the reasons for this are not well understood. We investigated the respiratory tract bacterial microbiome and small commensal DNA viruses in hospitalized COVID-19 patients and found that each was markedly abnormal compared to that in healthy people and differed from that in critically ill patients without COVID-19. Early airway samples tracked with the level of COVID-19 illness reached during hospitalization, and the airway microbiome also correlated with immune parameters in blood. These findings raise questions about the mechanisms linking SARS-CoV-2 infection and other microbial inhabitants of the airway, including whether the microbiome might regulate severity of COVID-19 disease and/or whether early microbiome features might serve as biomarkers to discriminate disease severity.
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Affiliation(s)
- Carter Merenstein
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Guanxiang Liang
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Samantha A. Whiteside
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Ana G. Cobián-Güemes
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Madeline S. Merlino
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Louis J. Taylor
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Abigail Glascock
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Ceylan Tanes
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jevon Graham-Wooten
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Layla A. Khatib
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Ayannah S. Fitzgerald
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Shantan Reddy
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Amy E. Baxter
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Josephine R. Giles
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Derek A. Oldridge
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Nuala J. Meyer
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - E. John Wherry
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - John E. McGinniss
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Frederic D. Bushman
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Ronald G. Collman
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
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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.
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Codina-Jiménez C, Marin S, Álvarez M, Quesada MD, Rodríguez-Ponga B, Valls E, Quiñones C. Risk factors for nosocomial bloodstream infections in COVID-19 affected patients: protocol for a case-control study. Eur J Hosp Pharm 2021; 29:e2-e5. [PMID: 34400550 PMCID: PMC8899639 DOI: 10.1136/ejhpharm-2021-002776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 07/05/2021] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND Nosocomial bloodstream infection (nBSI) is an important clinical concern among COVID-19 hospitalised patients. It can cause sepsis and septic shock leading to high morbidity, mortality, and the emergence of antibiotic resistance. The aim of this case-control study is to identify the risk factors associated with the nBSI development in COVID-19 hospitalised patients and its incidence. METHODS AND ANALYSIS A retrospective case-control study will be performed. Cases will include nBSI episodes of adult patients (≥18 years) admitted to Hospital Universitari Germans Trias i Pujol, Barcelona, Spain, from April to December 2020 with a diagnosis of SARS-CoV-2 pneumonia. Patients transferred from other hospitals will be excluded. Controls will include hospitalisation episodes of COVID-19 patients without nBSI. We will recruit a minimum of 74 nBSI episodes (cases) and 74 controls (according to sample size calculation). We will collect data on sociodemographics, clinical status at admission, hospital admission, in-hospital mortality, and exposure data (use of antivirals, glucocorticoids or immunomodulatory agents, length of hospitalisation, and use of medical devices such as intravenous catheters). A bivariate and a subsequent multivariate regression analysis will be performed to assess the independent effect of the associated risk factors after adjusting for confounders. The nBSI incidence rate will be estimated according to the number of nBSI episodes in admitted COVID-19 patients among the total person-month of follow-up. ETHICS AND DISSEMINATION The protocol of this study was approved by the Ethical Committee for Drug Investigation of the Hospital Universitari Germans Trias i Pujol. The results of this case-control study will be published in a peer reviewed journal.
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Affiliation(s)
- Carla Codina-Jiménez
- Pharmacy Department, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Sergio Marin
- Pharmacy Department, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Marlene Álvarez
- Pharmacy Department, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Maria Dolores Quesada
- Microbiology Department, Clinical Laboratory North Metropolitan Area, Autonomous University of Barcelona, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Beatriz Rodríguez-Ponga
- Microbiology Department, Clinical Laboratory North Metropolitan Area, Autonomous University of Barcelona, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Ester Valls
- Pharmacy Department, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Carles Quiñones
- Pharmacy Department, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
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40
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Chen K, Malik AA, Sheng YJ, Ahmed S, Sun C, Deng CL, Ojha SC. Clinical Utility of Molecular Tests for Guiding Therapeutic Decisions in Bloodstream Staphylococcal Infections: A Meta-Analysis. Front Pediatr 2021; 9:713447. [PMID: 34422731 PMCID: PMC8374148 DOI: 10.3389/fped.2021.713447] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 07/12/2021] [Indexed: 12/14/2022] Open
Abstract
Background: Treatment of bloodstream staphylococcal infections (BSI) necessitates the prompt initiation of appropriate antimicrobial agents and the rapid de-escalation of excessive broad-spectrum coverage to reduce the risk of mortality. We, therefore, aimed to demonstrate the diagnostic accuracy of nucleic acid amplification tests (NAAT) for the identification of methicillin-resistant S. aureus (MRSA) and methicillin-sensitive S. aureus (MSSA) in clinically suspected patients. Methods: Until November 23, 2020, databases including PubMed, Scopus, Embase, and Web of Science were scanned for eligible studies. A bivariate random-effects model was used for meta-analysis of the 33 included studies obtained from 1606 citations, and pooled summary estimates with 95% confidence intervals (CI) were generated. Results: Twenty-three studies (n = 8,547) assessed NAAT accuracy for MSSA detection, while three studies (n = 479) evaluated MRSA detection in adults. The pooled NAAT sensitivity and specificity for MRSA in adults was higher [sensitivity: 0.83 (95% CI 0.59-0.96), specificity: 0.99 (95% CI 0.98-1.0)] as compared to MSSA [sensitivity: 0.76 (95% CI 0.69-0.82), specificity: 0.98 (95% CI 0.98-0.99)]. Similarly, eight studies (n = 4,089) investigating MSSA in pediatric population reported higher NAAT accuracy [sensitivity: 0.89 (95% CI 0.76-0.96), specificity: 0.98 (95% CI 0.97-0.98)] compared to adults. Among NAA tests, SeptiFast (real-time PCR, commercial) was frequently applied, and its diagnostic accuracy corresponded well to the overall summary estimates. A meta-regression and subgroup analysis of study design, sample condition, and patient selection method could not explain the heterogeneity (P > 0.05) in the diagnostic efficiency. Conclusions: NAAT could be applied as the preferred initial tests for timely diagnosis and BSI management.
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Affiliation(s)
- Ke Chen
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Southwest Medical University, Luzhou, China
| | - Aijaz Ahmad Malik
- Faculty of Medical Technology, Center of Data Mining and Biomedical Informatics, Mahidol University, Bangkok, Thailand
| | - Yun-Jian Sheng
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Southwest Medical University, Luzhou, China
| | - Sarfraz Ahmed
- Department of Basic Sciences, University of Veterinary and Animal Sciences Lahore, Narowal, Pakistan
| | - Changfeng Sun
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Southwest Medical University, Luzhou, China
| | - Cun-Liang Deng
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Suvash Chandra Ojha
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Southwest Medical University, Luzhou, China
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Russell CD, Fairfield CJ, Drake TM, Turtle L, Seaton RA, Wootton DG, Sigfrid L, Harrison EM, Docherty AB, de Silva TI, Egan C, Pius R, Hardwick HE, Merson L, Girvan M, Dunning J, Nguyen-Van-Tam JS, Openshaw PJM, Baillie JK, Semple MG, Ho A. Co-infections, secondary infections, and antimicrobial use in patients hospitalised with COVID-19 during the first pandemic wave from the ISARIC WHO CCP-UK study: a multicentre, prospective cohort study. THE LANCET. MICROBE 2021; 2:e354-e365. [PMID: 34100002 PMCID: PMC8172149 DOI: 10.1016/s2666-5247(21)00090-2] [Citation(s) in RCA: 200] [Impact Index Per Article: 66.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
BACKGROUND Microbiological characterisation of co-infections and secondary infections in patients with COVID-19 is lacking, and antimicrobial use is high. We aimed to describe microbiologically confirmed co-infections and secondary infections, and antimicrobial use, in patients admitted to hospital with COVID-19. METHODS The International Severe Acute Respiratory and Emerging Infections Consortium (ISARIC) WHO Clinical Characterisation Protocol UK (CCP-UK) study is an ongoing, prospective cohort study recruiting inpatients from 260 hospitals in England, Scotland, and Wales, conducted by the ISARIC Coronavirus Clinical Characterisation Consortium. Patients with a confirmed or clinician-defined high likelihood of SARS-CoV-2 infection were eligible for inclusion in the ISARIC WHO CCP-UK study. For this specific study, we excluded patients with a recorded negative SARS-CoV-2 test result and those without a recorded outcome at 28 days after admission. Demographic, clinical, laboratory, therapeutic, and outcome data were collected using a prespecified case report form. Organisms considered clinically insignificant were excluded. FINDINGS We analysed data from 48 902 patients admitted to hospital between Feb 6 and June 8, 2020. The median patient age was 74 years (IQR 59-84) and 20 786 (42·6%) of 48 765 patients were female. Microbiological investigations were recorded for 8649 (17·7%) of 48 902 patients, with clinically significant COVID-19-related respiratory or bloodstream culture results recorded for 1107 patients. 762 (70·6%) of 1080 infections were secondary, occurring more than 2 days after hospital admission. Staphylococcus aureus and Haemophilus influenzae were the most common pathogens causing respiratory co-infections (diagnosed ≤2 days after admission), with Enterobacteriaceae and S aureus most common in secondary respiratory infections. Bloodstream infections were most frequently caused by Escherichia coli and S aureus. Among patients with available data, 13 390 (37·0%) of 36 145 had received antimicrobials in the community for this illness episode before hospital admission and 39 258 (85·2%) of 46 061 patients with inpatient antimicrobial data received one or more antimicrobials at some point during their admission (highest for patients in critical care). We identified frequent use of broad-spectrum agents and use of carbapenems rather than carbapenem-sparing alternatives. INTERPRETATION In patients admitted to hospital with COVID-19, microbiologically confirmed bacterial infections are rare, and more likely to be secondary infections. Gram-negative organisms and S aureus are the predominant pathogens. The frequency and nature of antimicrobial use are concerning, but tractable targets for stewardship interventions exist. FUNDING National Institute for Health Research (NIHR), UK Medical Research Council, Wellcome Trust, UK Department for International Development, Bill & Melinda Gates Foundation, EU Platform for European Preparedness Against (Re-)emerging Epidemics, NIHR Health Protection Research Unit (HPRU) in Emerging and Zoonotic Infections at University of Liverpool, and NIHR HPRU in Respiratory Infections at Imperial College London.
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Affiliation(s)
- Clark D Russell
- University of Edinburgh Centre for Inflammation Research, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, UK
| | - Cameron J Fairfield
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Thomas M Drake
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Lance Turtle
- Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
- Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
| | - R Andrew Seaton
- Department of Infectious Diseases, Queen Elizabeth University Hospital, Glasgow, UK
| | - Dan G Wootton
- Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
- Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
| | - Louise Sigfrid
- ISARIC Global Support Centre, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Ewen M Harrison
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Annemarie B Docherty
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Thushan I de Silva
- South Yorkshire Regional Department of Infection and Tropical Medicine, Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
- Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, UK
| | - Conor Egan
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Riinu Pius
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Hayley E Hardwick
- Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Laura Merson
- ISARIC Global Support Centre, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Michelle Girvan
- Liverpool Clinical Trials Centre, University of Liverpool, Liverpool, UK
| | - Jake Dunning
- Emerging Infections and Zoonoses Unit, National Infection Service, Public Health England, Colindale, London, UK
| | - Jonathan S Nguyen-Van-Tam
- Division of Epidemiology and Public Health, University of Nottingham School of Medicine, Nottingham, UK
- UK Department of Health and Social Care, London, UK
| | | | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, UK
| | - Malcolm G Semple
- Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
- Department of Respiratory Medicine, Alder Hey Children's Hospital, Liverpool, UK
| | - Antonia Ho
- Medical Research Council—University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
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Alhumaid S, Al Mutair A, Al Alawi Z, Alshawi AM, Alomran SA, Almuhanna MS, Almuslim AA, Bu Shafia AH, Alotaibi AM, Ahmed GY, Rabaan AA, Al-Tawfiq JA, Al-Omari A. Coinfections with Bacteria, Fungi, and Respiratory Viruses in Patients with SARS-CoV-2: A Systematic Review and Meta-Analysis. Pathogens 2021; 10:pathogens10070809. [PMID: 34202114 PMCID: PMC8308492 DOI: 10.3390/pathogens10070809] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 06/23/2021] [Accepted: 06/23/2021] [Indexed: 01/08/2023] Open
Abstract
Background: Coinfection with bacteria, fungi, and respiratory viruses in SARS-CoV-2 is of particular importance due to the possibility of increased morbidity and mortality. In this meta-analysis, we calculated the prevalence of such coinfections. Methods: Electronic databases were searched from 1 December 2019 to 31 March 2021. Effect sizes of prevalence were pooled with 95% confidence intervals (CIs). To minimize heterogeneity, we performed sub-group analyses. Results: Of the 6189 papers that were identified, 72 articles were included in the systematic review (40 case series and 32 cohort studies) and 68 articles (38 case series and 30 cohort studies) were included in the meta-analysis. Of the 31,953 SARS-CoV-2 patients included in the meta-analysis, the overall pooled proportion who had a laboratory-confirmed bacterial infection was 15.9% (95% CI 13.6–18.2, n = 1940, 49 studies, I2 = 99%, p < 0.00001), while 3.7% (95% CI 2.6–4.8, n = 177, 16 studies, I2 = 93%, p < 0.00001) had fungal infections and 6.6% (95% CI 5.5–7.6, n = 737, 44 studies, I2 = 96%, p < 0.00001) had other respiratory viruses. SARS-CoV-2 patients in the ICU had higher co-infections compared to ICU and non-ICU patients as follows: bacterial (22.2%, 95% CI 16.1–28.4, I2 = 88% versus 14.8%, 95% CI 12.4–17.3, I2 = 99%), and fungal (9.6%, 95% CI 6.8–12.4, I2 = 74% versus 2.7%, 95% CI 0.0–3.8, I2 = 95%); however, there was an identical other respiratory viral co-infection proportion between all SARS-CoV-2 patients [(ICU and non-ICU) and the ICU only] (6.6%, 95% CI 0.0–11.3, I2 = 58% versus 6.6%, 95% CI 5.5–7.7, I2 = 96%). Funnel plots for possible publication bias for the pooled effect sizes of the prevalence of coinfections was asymmetrical on visual inspection, and Egger’s tests confirmed asymmetry (p values < 0.05). Conclusion: Bacterial co-infection is relatively high in hospitalized patients with SARS-CoV-2, with little evidence of S. aureus playing a major role. Knowledge of the prevalence and type of co-infections in SARS-CoV-2 patients may have diagnostic and management implications.
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Affiliation(s)
- Saad Alhumaid
- Administration of Pharmaceutical Care, Al-Ahsa Health Cluster, Ministry of Health, Al-Ahsa 31982, Saudi Arabia
- Correspondence: ; Tel.: +966-561-522-581
| | - Abbas Al Mutair
- Research Center, Almoosa Specialist Hospital, Al-Ahsa 36342, Saudi Arabia; (A.A.M.); (G.Y.A.)
- College of Nursing, Princess Norah Bint Abdul Rahman University, Riyadh 11564, Saudi Arabia
- School of Nursing, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Zainab Al Alawi
- Division of Allergy and Immunology, College of Medicine, King Faisal University, Al-Ahsa 31982, Saudi Arabia;
| | - Abeer M. Alshawi
- Department of Pharmacy, King Fahad Hofuf Hospital, Al-Ahsa 36441, Saudi Arabia; (A.M.A.); (S.A.A.)
| | - Salamah A. Alomran
- Department of Pharmacy, King Fahad Hofuf Hospital, Al-Ahsa 36441, Saudi Arabia; (A.M.A.); (S.A.A.)
| | - Mohammed S. Almuhanna
- Department of Pharmacy, Maternity and Children Hospital, Al-Ahsa 36422, Saudi Arabia; (M.S.A.); (A.A.A.)
| | - Anwar A. Almuslim
- Department of Pharmacy, Maternity and Children Hospital, Al-Ahsa 36422, Saudi Arabia; (M.S.A.); (A.A.A.)
| | | | - Abdullah M. Alotaibi
- Department of Pharmacy, Prince Sultan Cardiac Center, Al-Ahsa 36441, Saudi Arabia;
| | - Gasmelseed Y. Ahmed
- Research Center, Almoosa Specialist Hospital, Al-Ahsa 36342, Saudi Arabia; (A.A.M.); (G.Y.A.)
| | - Ali A. Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia;
| | - Jaffar A. Al-Tawfiq
- Infectious Disease Unit, Specialty Internal Medicine, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia;
- Infectious Disease Division, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Infectious Disease Division, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Awad Al-Omari
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia;
- Research Center, Dr. Sulaiman Al Habib Medical Group, Riyadh 11372, Saudi Arabia
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43
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Chandran S, Avari M, Cherian BP, Suarez C. COVID-19-associated Staphylococcus aureus cavitating pneumonia. BMJ Case Rep 2021; 14:14/6/e243726. [PMID: 34117003 PMCID: PMC8201979 DOI: 10.1136/bcr-2021-243726] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Affiliation(s)
- Shruthi Chandran
- Microbiology and Infectious Diseases, The Royal London Hospital, London, UK
| | - Malcolm Avari
- Intensive Care Unit, The Royal London Hospital, London, UK
| | - Benny P Cherian
- Microbiology and Infectious Diseases, The Royal London Hospital, London, UK
| | - Cristina Suarez
- Microbiology and Infectious Diseases, The Royal London Hospital, London, UK
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44
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De Pascale G, De Maio F, Carelli S, De Angelis G, Cacaci M, Montini L, Bello G, Cutuli SL, Pintaudi G, Tanzarella ES, Xhemalaj R, Grieco DL, Tumbarello M, Sanguinetti M, Posteraro B, Antonelli M. Staphylococcus aureus ventilator-associated pneumonia in patients with COVID-19: clinical features and potential inference with lung dysbiosis. CRITICAL CARE : THE OFFICIAL JOURNAL OF THE CRITICAL CARE FORUM 2021; 25:197. [PMID: 34099016 PMCID: PMC8182737 DOI: 10.1186/s13054-021-03623-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 05/31/2021] [Indexed: 12/28/2022]
Abstract
Background Hospitalized patients with COVID-19 admitted to the intensive care unit (ICU) and requiring mechanical ventilation are at risk of ventilator-associated bacterial infections secondary to SARS-CoV-2 infection. Our study aimed to investigate clinical features of Staphylococcus aureus ventilator-associated pneumonia (SA-VAP) and, if bronchoalveolar lavage samples were available, lung bacterial community features in ICU patients with or without COVID-19. Methods We prospectively included hospitalized patients with COVID-19 across two medical ICUs of the Fondazione Policlinico Universitario A. Gemelli IRCCS (Rome, Italy), who developed SA-VAP between 20 March 2020 and 30 October 2020 (thereafter referred to as cases). After 1:2 matching based on the simplified acute physiology score II (SAPS II) and the sequential organ failure assessment (SOFA) score, cases were compared with SA-VAP patients without COVID-19 (controls). Clinical, microbiological, and lung microbiota data were analyzed. Results We studied two groups of patients (40 COVID-19 and 80 non-COVID-19). COVID-19 patients had a higher rate of late-onset (87.5% versus 63.8%; p = 0.01), methicillin-resistant (65.0% vs 27.5%; p < 0.01) or bacteremic (47.5% vs 6.3%; p < 0.01) infections compared with non-COVID-19 patients. No statistically significant differences between the patient groups were observed in ICU mortality (p = 0.12), clinical cure (p = 0.20) and microbiological eradication (p = 0.31). On multivariable logistic regression analysis, SAPS II and initial inappropriate antimicrobial therapy were independently associated with ICU mortality. Then, lung microbiota characterization in 10 COVID-19 and 16 non-COVID-19 patients revealed that the overall microbial community composition was significantly different between the patient groups (unweighted UniFrac distance, R2 0.15349; p < 0.01). Species diversity was lower in COVID-19 than in non COVID-19 patients (94.4 ± 44.9 vs 152.5 ± 41.8; p < 0.01). Interestingly, we found that S. aureus (log2 fold change, 29.5), Streptococcus anginosus subspecies anginosus (log2 fold change, 24.9), and Olsenella (log2 fold change, 25.7) were significantly enriched in the COVID-19 group compared to the non–COVID-19 group of SA-VAP patients. Conclusions In our study population, COVID-19 seemed to significantly affect microbiological and clinical features of SA-VAP as well as to be associated with a peculiar lung microbiota composition. Supplementary Information The online version contains supplementary material available at 10.1186/s13054-021-03623-4.
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Affiliation(s)
- Gennaro De Pascale
- Dipartimento Di Scienze Biotecnologiche Di Base, Cliniche Intensivologiche E Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy. .,Dipartimento Di Scienze Dell'Emergenza, Anestesiologiche e della Rianimazione, Fondazione Policlinico Universitario A. Gemelli IRCCS - Università Cattolica del Sacro Cuore Largo A. Gemelli 8, 00168, Rome, Italy.
| | - Flavio De Maio
- Dipartimento Di Scienze Biotecnologiche Di Base, Cliniche Intensivologiche E Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy.,Dipartimento Di Scienze Di Laboratorio E Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Simone Carelli
- Dipartimento Di Scienze Dell'Emergenza, Anestesiologiche e della Rianimazione, Fondazione Policlinico Universitario A. Gemelli IRCCS - Università Cattolica del Sacro Cuore Largo A. Gemelli 8, 00168, Rome, Italy
| | - Giulia De Angelis
- Dipartimento Di Scienze Biotecnologiche Di Base, Cliniche Intensivologiche E Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy.,Dipartimento Di Scienze Di Laboratorio E Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Margherita Cacaci
- Dipartimento Di Scienze Biotecnologiche Di Base, Cliniche Intensivologiche E Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy.,Dipartimento Di Scienze Di Laboratorio E Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Luca Montini
- Dipartimento Di Scienze Dell'Emergenza, Anestesiologiche e della Rianimazione, Fondazione Policlinico Universitario A. Gemelli IRCCS - Università Cattolica del Sacro Cuore Largo A. Gemelli 8, 00168, Rome, Italy
| | - Giuseppe Bello
- Dipartimento Di Scienze Dell'Emergenza, Anestesiologiche e della Rianimazione, Fondazione Policlinico Universitario A. Gemelli IRCCS - Università Cattolica del Sacro Cuore Largo A. Gemelli 8, 00168, Rome, Italy
| | - Salvatore Lucio Cutuli
- Dipartimento Di Scienze Dell'Emergenza, Anestesiologiche e della Rianimazione, Fondazione Policlinico Universitario A. Gemelli IRCCS - Università Cattolica del Sacro Cuore Largo A. Gemelli 8, 00168, Rome, Italy
| | - Gabriele Pintaudi
- Dipartimento Di Scienze Dell'Emergenza, Anestesiologiche e della Rianimazione, Fondazione Policlinico Universitario A. Gemelli IRCCS - Università Cattolica del Sacro Cuore Largo A. Gemelli 8, 00168, Rome, Italy
| | - Eloisa Sofia Tanzarella
- Dipartimento Di Scienze Dell'Emergenza, Anestesiologiche e della Rianimazione, Fondazione Policlinico Universitario A. Gemelli IRCCS - Università Cattolica del Sacro Cuore Largo A. Gemelli 8, 00168, Rome, Italy
| | - Rikardo Xhemalaj
- Dipartimento Di Scienze Dell'Emergenza, Anestesiologiche e della Rianimazione, Fondazione Policlinico Universitario A. Gemelli IRCCS - Università Cattolica del Sacro Cuore Largo A. Gemelli 8, 00168, Rome, Italy
| | - Domenico Luca Grieco
- Dipartimento Di Scienze Dell'Emergenza, Anestesiologiche e della Rianimazione, Fondazione Policlinico Universitario A. Gemelli IRCCS - Università Cattolica del Sacro Cuore Largo A. Gemelli 8, 00168, Rome, Italy
| | - Mario Tumbarello
- Dipartimento Di Scienze Di Laboratorio E Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy.,Dipartimento Di Sicurezza E Bioetica, Università Cattolica del Sacro Cuore, Rome, Italy.,Dipartimento Di Biotecnologie Mediche, Università Di Siena, Siena, Italy
| | - Maurizio Sanguinetti
- Dipartimento Di Scienze Biotecnologiche Di Base, Cliniche Intensivologiche E Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy.,Dipartimento Di Scienze Di Laboratorio E Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Brunella Posteraro
- Dipartimento Di Scienze Biotecnologiche Di Base, Cliniche Intensivologiche E Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy.,Dipartimento Di Scienze Mediche E Chirurgiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Massimo Antonelli
- Dipartimento Di Scienze Biotecnologiche Di Base, Cliniche Intensivologiche E Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy.,Dipartimento Di Scienze Dell'Emergenza, Anestesiologiche e della Rianimazione, Fondazione Policlinico Universitario A. Gemelli IRCCS - Università Cattolica del Sacro Cuore Largo A. Gemelli 8, 00168, Rome, Italy
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Abstract
The current frequency of COVID-19 in a pandemic era ensures that co-infections with a variety of co-pathogens will occur. Generally, there is a low rate of bonafide co-infections in early COVID-19 pulmonary infection as currently appreciated. Reports of high co-infection rates must be tempered by limitations in current diagnostic methods since amplification technologies do not necessarily confirm live pathogen and may be subject to considerable laboratory variation. Some laboratory methods may not exclude commensal microbes. Concurrent serodiagnoses have long been of concern for accuracy in these contexts. Presumed virus co-infections are not specific to COVID-19. The association of influenza viruses and SARS-CoV-2 in co-infection has been considerably variable during influenza season. Other respiratory virus co-infections have generally occurred in less than 10% of COVID-19 patients. Early COVID-19 disease is more commonly associated with bacterial co-pathogens that typically represent usual respiratory micro-organisms. Late infections, especially among severe clinical presentations, are more likely to be associated with nosocomial or opportunistic pathogens given the influence of treatments that can include antibiotics, antivirals, immunomodulating agents, blood products, immunotherapy, steroids, and invasive procedures. As anticipated, hospital care carries risk for multi-resistant bacteria. Overall, co-pathogen identification is linked with longer hospital stay, greater patient complexity, and adverse outcomes. As for other viral infections, a general reduction in the use of empiric antibiotic treatment is warranted. Further insight into co-infections with COVID-19 will contribute overall to effective antimicrobial therapies and disease control.
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Affiliation(s)
- Nevio Cimolai
- Faculty of Medicine, The University of British Columbia, Vancouver, Canada.,Children's and Women's Health Centre of British Columbia, 4480 Oak Street, Vancouver, B.C. V6H3V4 Canada
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46
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Risk Factors for Mortality in Adult COVID-19 Patients Who Develop Bloodstream Infections Mostly Caused by Antimicrobial-Resistant Organisms: Analysis at a Large Teaching Hospital in Italy. J Clin Med 2021; 10:jcm10081752. [PMID: 33920701 PMCID: PMC8073579 DOI: 10.3390/jcm10081752] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/13/2021] [Accepted: 04/15/2021] [Indexed: 11/24/2022] Open
Abstract
The aim of this study was to characterize COVID-19 (SARS-CoV-2-infected) patients who develop bloodstream infection (BSI) and to assess risk factors associated with in-hospital mortality. We conducted a retrospective observational study of adult patients admitted for ≥48 h to a large Central Italy hospital for COVID-19 (1 March to 31 May 2020) who had or had not survived at discharge. We included only patients having blood cultures drawn or other inclusion criteria satisfied. Kaplan–Meier survival or Cox regression analyses were performed of 293 COVID-19 patients studied, 46 patients (15.7%) had a hospital-acquired clinically relevant BSI secondary to SARS-CoV-2 infection, accounting for 58 episodes (49 monomicrobial and 9 polymicrobial) in total. Twelve episodes (20.7%) occurred at day 3 of hospital admission. Sixty-nine species were isolated, including Staphylococcus aureus (32.8%), Enterobacterales (20.7%), Enterococcus faecalis (17.2%), Candida (13.8%) and Pseudomonas aeruginosa (10.3%). Of 69 isolates, 27 (39.1%) were multidrug-resistant organisms. Twelve (54.5%) of 22 patients for whom empirical antimicrobial therapy was inappropriate were infected by a multidrug-resistant organism. Of 46 patients, 26 (56.5%) survived and 20 (43.5%) died. Exploring variables for association with in-hospital mortality identified > 75-year age (HR 2.97, 95% CI 1.15–7.68, p = 0.02), septic shock (HR 6.55, 95% CI 2.36–18.23, p < 0.001) and BSI onset ≤ 3 days (HR 4.68, 95% CI 1.40–15.63, p = 0.01) as risk factors independently associated with death. In our hospital, mortality among COVID-19 patients with BSI was high. While continued vigilance against these infections is essential, identification of risk factors for mortality may help to reduce fatal outcomes in patients with COVID-19.
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47
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Merenstein C, Liang G, Whiteside SA, Cobián-Güemes AG, Merlino MS, Taylor LJ, Glascock A, Bittinger K, Tanes C, Graham-Wooten J, Khatib LA, Fitzgerald AS, Reddy S, Baxter AE, Giles JR, Oldridge DA, Meyer NJ, Wherry EJ, McGinniss JE, Bushman FD, Collman RG. Signatures of COVID-19 severity and immune response in the respiratory tract microbiome. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.04.02.21254514. [PMID: 33851179 PMCID: PMC8043476 DOI: 10.1101/2021.04.02.21254514] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Rationale Viral infection of the respiratory tract can be associated with propagating effects on the airway microbiome, and microbiome dysbiosis may influence viral disease. Objective To define the respiratory tract microbiome in COVID-19 and relationship disease severity, systemic immunologic features, and outcomes. Methods and Measurements We examined 507 oropharyngeal, nasopharyngeal and endotracheal samples from 83 hospitalized COVID-19 patients, along with non-COVID patients and healthy controls. Bacterial communities were interrogated using 16S rRNA gene sequencing, commensal DNA viruses Anelloviridae and Redondoviridae were quantified by qPCR, and immune features were characterized by lymphocyte/neutrophil (L/N) ratios and deep immune profiling of peripheral blood mononuclear cells (PBMC). Main Results COVID-19 patients had upper respiratory microbiome dysbiosis, and greater change over time than critically ill patients without COVID-19. Diversity at the first time point correlated inversely with disease severity during hospitalization, and microbiome composition was associated with L/N ratios and PBMC profiles in blood. Intubated patients showed patient-specific and dynamic lung microbiome communities, with prominence of Staphylococcus. Anelloviridae and Redondoviridae showed more frequent colonization and higher titers in severe disease. Machine learning analysis demonstrated that integrated features of the microbiome at early sampling points had high power to discriminate ultimate level of COVID-19 severity. Conclusions The respiratory tract microbiome and commensal virome are disturbed in COVID-19, correlate with systemic immune parameters, and early microbiome features discriminate disease severity. Future studies should address clinical consequences of airway dysbiosis in COVID-19, possible use as biomarkers, and role of bacterial and viral taxa identified here in COVID-19 pathogenesis.
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Affiliation(s)
- Carter Merenstein
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Guanxiang Liang
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Samantha A Whiteside
- Pulmonary, Allergy and Critical Care Division; Department of Medicine; University of Pennsylvania Perelman School of Medicine; Philadelphia, PA 19104
| | - Ana G Cobián-Güemes
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Madeline S Merlino
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Louis J Taylor
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Abigail Glascock
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - Ceylan Tanes
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - Jevon Graham-Wooten
- Pulmonary, Allergy and Critical Care Division; Department of Medicine; University of Pennsylvania Perelman School of Medicine; Philadelphia, PA 19104
| | - Layla A Khatib
- Pulmonary, Allergy and Critical Care Division; Department of Medicine; University of Pennsylvania Perelman School of Medicine; Philadelphia, PA 19104
| | - Ayannah S Fitzgerald
- Pulmonary, Allergy and Critical Care Division; Department of Medicine; University of Pennsylvania Perelman School of Medicine; Philadelphia, PA 19104
| | - Shantan Reddy
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Amy E Baxter
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Josephine R Giles
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Derek A Oldridge
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Nuala J Meyer
- Pulmonary, Allergy and Critical Care Division; Department of Medicine; University of Pennsylvania Perelman School of Medicine; Philadelphia, PA 19104
| | - E John Wherry
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - John E McGinniss
- Pulmonary, Allergy and Critical Care Division; Department of Medicine; University of Pennsylvania Perelman School of Medicine; Philadelphia, PA 19104
| | - Frederic D Bushman
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
| | - Ronald G Collman
- Pulmonary, Allergy and Critical Care Division; Department of Medicine; University of Pennsylvania Perelman School of Medicine; Philadelphia, PA 19104
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48
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Malishev R, Salinas N, Gibson J, Eden AB, Mieres-Perez J, Ruiz-Blanco YB, Malka O, Kolusheva S, Klärner FG, Schrader T, Sanchez-Garcia E, Wang C, Landau M, Bitan G, Jelinek R. Inhibition of Staphylococcus aureus biofilm-forming functional amyloid by molecular tweezers. Cell Chem Biol 2021; 28:1310-1320.e5. [PMID: 33852903 DOI: 10.1016/j.chembiol.2021.03.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 01/19/2021] [Accepted: 03/19/2021] [Indexed: 02/07/2023]
Abstract
Biofilms are rigid and largely impenetrable three-dimensional matrices constituting virulence determinants of various pathogenic bacteria. Here, we demonstrate that molecular tweezers, unique supramolecular artificial receptors, modulate biofilm formation of Staphylococcus aureus. In particular, the tweezers affect the structural and assembly properties of phenol-soluble modulin α1 (PSMα1), a biofilm-scaffolding functional amyloid peptide secreted by S. aureus. The data reveal that CLR01, a diphosphate tweezer, exhibits significant S. aureus biofilm inhibition and disrupts PSMα1 self-assembly and fibrillation, likely through inclusion of lysine side chains of the peptide. In comparison, different peptide binding occurs in the case of CLR05, a tweezer containing methylenecarboxylate units, which exhibits lower affinity for the lysine residues yet disrupts S. aureus biofilm more strongly than CLR01. Our study points to a possible role for molecular tweezers as potent biofilm inhibitors and antibacterial agents, particularly against untreatable biofilm-forming and PSM-producing bacteria, such as methicillin-resistant S. aureus.
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Affiliation(s)
- Ravit Malishev
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Nir Salinas
- Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - James Gibson
- Center for Biotechnology and Interdisciplinary Studies, Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Angela Bailey Eden
- Center for Biotechnology and Interdisciplinary Studies, Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Joel Mieres-Perez
- Department of Computational Biochemistry, University of Duisburg-Essen, Universitätsstrasse 2, 45141 Essen, Germany
| | - Yasser B Ruiz-Blanco
- Department of Computational Biochemistry, University of Duisburg-Essen, Universitätsstrasse 2, 45141 Essen, Germany
| | - Orit Malka
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Sofiya Kolusheva
- Ilse Katz Institute for Nanotechnology, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
| | | | - Thomas Schrader
- Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Elsa Sanchez-Garcia
- Department of Computational Biochemistry, University of Duisburg-Essen, Universitätsstrasse 2, 45141 Essen, Germany
| | - Chunyu Wang
- Center for Biotechnology and Interdisciplinary Studies, Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Meytal Landau
- Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel; European Molecular Biology Laboratory (EMBL), 22607 Hamburg, Germany
| | - Gal Bitan
- Department of Neurology, David Geffen School of Medicine, Brain Research Institute, and Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Raz Jelinek
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva 84105, Israel; Ilse Katz Institute for Nanotechnology, Ben Gurion University of the Negev, Beer Sheva 84105, Israel.
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