1
|
Dimartino V, Venditti C, Messina F, D’Arezzo S, Selleri M, Butera O, Nisii C, Marani A, Arcangeli A, Gaziano R, Cosio T, Scanzano P, Fontana C. Screening of Klebsiella pneumoniae subsp. pneumoniae Strains with Multi-Drug Resistance and Virulence Profiles Isolated from an Italian Hospital between 2020 and 2023. Antibiotics (Basel) 2024; 13:561. [PMID: 38927227 PMCID: PMC11200418 DOI: 10.3390/antibiotics13060561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 06/07/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
Klebsiella pneumoniae strains that are resistant to multiple drugs (KPMDRs), which are often acquired in hospital settings and lead to healthcare-associated infections, pose a serious public health threat, as does hypervirulent K. pneumoniae (hvKp), which can also cause serious infections in otherwise healthy individuals. The widespread and often unnecessary use of antibiotics seen during the recent COVID-19 pandemic has exacerbated the challenges posed by antibiotic resistance in clinical settings. There is growing concern that hypervirulent (hvKp) strains may acquire genes that confer antimicrobial resistance, thus combining an MDR profile with their increased ability to spread to multiple body sites, causing difficult-to-treat infections. This study aimed to compare resistance and virulence profiles in KPC-3-producing K. pneumoniae isolates collected over four years (2020-2023). A genome-based surveillance of all MDR CRE-K. pneumoniae was used to identify genetic differences and to characterize the virulence and resistance profiles. Our results provide a picture of the evolution of resistance and virulence genes and contribute to avoiding the possible spread of isolates with characteristics of multi-drug resistance and increased virulence, which are thought to be one of the main global challenges to public health, within our hospital.
Collapse
Affiliation(s)
- Valentina Dimartino
- National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, 00149 Rome, Italy; (V.D.); (C.V.); (F.M.); (S.D.); (M.S.); (O.B.); (C.F.)
| | - Carolina Venditti
- National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, 00149 Rome, Italy; (V.D.); (C.V.); (F.M.); (S.D.); (M.S.); (O.B.); (C.F.)
| | - Francesco Messina
- National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, 00149 Rome, Italy; (V.D.); (C.V.); (F.M.); (S.D.); (M.S.); (O.B.); (C.F.)
| | - Silvia D’Arezzo
- National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, 00149 Rome, Italy; (V.D.); (C.V.); (F.M.); (S.D.); (M.S.); (O.B.); (C.F.)
| | - Marina Selleri
- National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, 00149 Rome, Italy; (V.D.); (C.V.); (F.M.); (S.D.); (M.S.); (O.B.); (C.F.)
| | - Ornella Butera
- National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, 00149 Rome, Italy; (V.D.); (C.V.); (F.M.); (S.D.); (M.S.); (O.B.); (C.F.)
| | - Carla Nisii
- National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, 00149 Rome, Italy; (V.D.); (C.V.); (F.M.); (S.D.); (M.S.); (O.B.); (C.F.)
| | - Alessandra Marani
- Health Direction, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, 00149 Rome, Italy; (A.M.); (A.A.); (P.S.)
| | - Alessia Arcangeli
- Health Direction, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, 00149 Rome, Italy; (A.M.); (A.A.); (P.S.)
| | - Roberta Gaziano
- Department of Experimental Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy;
| | - Terenzio Cosio
- Dermatology Unit, Department of Systems Medicine, Tor Vergata University Hospital, 00133 Rome, Italy;
| | - Pietro Scanzano
- Health Direction, National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, 00149 Rome, Italy; (A.M.); (A.A.); (P.S.)
| | - Carla Fontana
- National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, 00149 Rome, Italy; (V.D.); (C.V.); (F.M.); (S.D.); (M.S.); (O.B.); (C.F.)
| |
Collapse
|
2
|
Patel TS, Sati H, Lessa FC, Patel PK, Srinivasan A, Hicks LA, Neuhauser MM, Tong D, van der Heijden M, Alves SC, Getahun H, Park BJ. Defining access without excess: expanding appropriate use of antibiotics targeting multidrug-resistant organisms. THE LANCET. MICROBE 2024; 5:e93-e98. [PMID: 37837986 PMCID: PMC10789610 DOI: 10.1016/s2666-5247(23)00256-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 08/07/2023] [Accepted: 08/08/2023] [Indexed: 10/16/2023]
Abstract
Antimicrobial resistance remains a significant global public health threat. Although development of novel antibiotics can be challenging, several new antibiotics with improved activity against multidrug-resistant Gram-negative organisms have recently been commercialised. Expanding access to these antibiotics is a global public health priority that should be coupled with improving access to quality diagnostics, health care with adequately trained professionals, and functional antimicrobial stewardship programmes. This comprehensive approach is essential to ensure responsible use of these new antibiotics.
Collapse
Affiliation(s)
- Twisha S Patel
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
| | - Hatim Sati
- WHO AMR Division, WHO, Geneva, Switzerland
| | - Fernanda C Lessa
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Payal K Patel
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA; Division of Infectious Diseases, Intermountain Health, Salt Lake City, UT, USA
| | - Arjun Srinivasan
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Lauri A Hicks
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Melinda M Neuhauser
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | | | | | | | - Benjamin J Park
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| |
Collapse
|
3
|
Biedrzycka M, Urbanowicz P, Żabicka D, Hryniewicz W, Gniadkowski M, Izdebski R. Country-wide expansion of a VIM-1 carbapenemase-producing Klebsiella oxytoca ST145 lineage in Poland, 2009-2019. Eur J Clin Microbiol Infect Dis 2023; 42:1449-1457. [PMID: 37857919 PMCID: PMC10651708 DOI: 10.1007/s10096-023-04682-x] [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: 08/11/2023] [Accepted: 10/10/2023] [Indexed: 10/21/2023]
Abstract
PURPOSE To elucidate the role of the Klebsiella oxytoca species complex (KoSC) in epidemiology of VIM-type MBL-producing Enterobacterales in Poland. METHODS The study comprised all 106 VIM-positive KoSC isolates collected by the Polish National Reference Centre for Susceptibility Testing during 2009-2019 from 60 institutions in 35 towns. All isolates were sequenced by Illumina MiSeq, followed by MinION sequencing of selected organisms. Genomes were subjected to bioinformatic analysis, addressing taxonomy, clonality, phylogeny and structural characterisation of key resistance determinants within their chromosomal and plasmidic loci. RESULTS Among five species identified, K. oxytoca was predominant (n = 92), followed by Klebsiella michiganensis (n = 11). MLST distinguished 18 STs, with the most prevalent Klebsiella oxytoca ST145 (n = 83). The clone segregated a lineage with the In237-like integron [blaVIM-1-aacA4 genes; n = 78], recorded in 28 cities almost all over the country. The integron was located in a ~ 49-50 kb chromosomal mosaic region with multiple other resistance genes, linked to a ~ 51 kb phage-like element. The organism might have originated from Greece, and its evolution in Poland included several events of chromosomal ~ 54-258 kb deletions, comprising the natural β-lactamase blaOXY gene. A group of other isolates of various species and clones (n = 12) carried the integron In916 on self-transmissible IncA-type plasmids, effectively spreading in Italy, France and Poland. CONCLUSION KoSC has been one of the major VIM producers in Poland, owing largely to clonal expansion of the specific K. oxytoca-In237-like lineage. Its apparently enhanced epidemic potential may create a danger on international scale.
Collapse
Affiliation(s)
- M Biedrzycka
- Department of Molecular Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| | - P Urbanowicz
- Department of Molecular Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| | - D Żabicka
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| | - W Hryniewicz
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| | - M Gniadkowski
- Department of Molecular Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| | - R Izdebski
- Department of Molecular Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland.
| |
Collapse
|
4
|
Mendes de Almeida V, Engel DF, Ricci MF, Cruz CS, Lopes ÍS, Alves DA, d’ Auriol M, Magalhães J, Machado EC, Rocha VM, Carvalho TG, Lacerda LSB, Pimenta JC, Aganetti M, Zuccoli GS, Smith BJ, Carregari VC, da Silva Rosa E, Galvão I, Dantas Cassali G, Garcia CC, Teixeira MM, André LC, Ribeiro FM, Martins FS, Saia RS, Costa VV, Martins-de-Souza D, Hansbro PM, Marques JT, Aguiar ERGR, Vieira AT. Gut microbiota from patients with COVID-19 cause alterations in mice that resemble post-COVID symptoms. Gut Microbes 2023; 15:2249146. [PMID: 37668317 PMCID: PMC10481883 DOI: 10.1080/19490976.2023.2249146] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/19/2023] [Accepted: 08/14/2023] [Indexed: 09/06/2023] Open
Abstract
Long-term sequelae of coronavirus disease (COVID)-19 are frequent and of major concern. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection affects the host gut microbiota, which is linked to disease severity in patients with COVID-19. Here, we report that the gut microbiota of post-COVID subjects had a remarkable predominance of Enterobacteriaceae strains with an antibiotic-resistant phenotype compared to healthy controls. Additionally, short-chain fatty acid (SCFA) levels were reduced in feces. Fecal transplantation from post-COVID subjects to germ-free mice led to lung inflammation and worse outcomes during pulmonary infection by multidrug-resistant Klebsiella pneumoniae. transplanted mice also exhibited poor cognitive performance. Overall, we show prolonged impacts of SARS-CoV-2 infection on the gut microbiota that persist after subjects have cleared the virus. Together, these data demonstrate that the gut microbiota can directly contribute to post-COVID sequelae, suggesting that it may be a potential therapeutic target.
Collapse
Affiliation(s)
- Viviani Mendes de Almeida
- Laboratory of Microbiota and Immunomodulation - Department of Biochemistry and Immunology, Institute of Biological Sciences, Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, Brazil
| | - Daiane F. Engel
- Department of Clinical Analysis, School of Pharmacy, Universidade Federal de Ouro Preto - UFOP, Ouro Preto, Brazil
| | - Mayra F. Ricci
- Laboratory of Microbiota and Immunomodulation - Department of Biochemistry and Immunology, Institute of Biological Sciences, Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, Brazil
| | - Clênio Silva Cruz
- Laboratory of Microbiota and Immunomodulation - Department of Biochemistry and Immunology, Institute of Biological Sciences, Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, Brazil
| | - Ícaro Santos Lopes
- Laboratory of Virus Bioinformatics - Department of Biological Science, Center of Biotechnology and Genetics, Universidade Estadual de Santa Cruz - UESC, Ilhéus, Brazil
| | - Daniele Almeida Alves
- Laboratory of RNA Interference and Antiviral Immunity - Department of Biochemistry and Immunology, Institute of Biological Sciences, Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, Brazil
| | - Mirna d’ Auriol
- Laboratory of Toxicology - Department of Clinical and Toxicological Analysis, Faculty of Pharmacy, Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, Brazil
| | - João Magalhães
- Laboratory of Microbiota and Immunomodulation - Department of Biochemistry and Immunology, Institute of Biological Sciences, Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, Brazil
| | - Elayne C. Machado
- Laboratory of Microbiota and Immunomodulation - Department of Biochemistry and Immunology, Institute of Biological Sciences, Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, Brazil
| | - Victor M. Rocha
- Laboratory of Microbiota and Immunomodulation - Department of Biochemistry and Immunology, Institute of Biological Sciences, Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, Brazil
| | - Toniana G. Carvalho
- Laboratory of Neurobiochemistry - Department of Biochemistry and Immunology, Institute of Biological Sciences, Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, Brazil
| | - Larisse S. B. Lacerda
- Center for Research and Development of Drugs - Department of Morphology, Institute of Biological Sciences, Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, Brazil
| | - Jordane C. Pimenta
- Center for Research and Development of Drugs - Department of Morphology, Institute of Biological Sciences, Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, Brazil
| | - Mariana Aganetti
- Laboratory of Microbiota and Immunomodulation - Department of Biochemistry and Immunology, Institute of Biological Sciences, Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, Brazil
| | - Giuliana S. Zuccoli
- Laboratory of Neuroproteomics - Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade do Estado de Campinas - UNICAMP, Campinas, Brazil
| | - Bradley J. Smith
- Laboratory of Neuroproteomics - Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade do Estado de Campinas - UNICAMP, Campinas, Brazil
| | - Victor C. Carregari
- Laboratory of Neuroproteomics - Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade do Estado de Campinas - UNICAMP, Campinas, Brazil
| | - Erika da Silva Rosa
- Laboratory of Microbiota and Immunomodulation - Department of Biochemistry and Immunology, Institute of Biological Sciences, Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, Brazil
| | - Izabela Galvão
- Laboratory of Microbiota and Immunomodulation - Department of Biochemistry and Immunology, Institute of Biological Sciences, Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, Brazil
| | - Geovanni Dantas Cassali
- Laboratory of Comparative Pathology - Department of Pathology, Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, Brazil
| | - Cristiana C. Garcia
- Laboratory of Respiratory Viruses and Measles, Instituto Oswaldo Cruz - Fiocruz, Rio de Janeiro, Brazil
| | - Mauro Martins Teixeira
- Center for Research and Development of Drugs - Department of Morphology, Institute of Biological Sciences, Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, Brazil
| | - Leiliane C. André
- Laboratory of Toxicology - Department of Clinical and Toxicological Analysis, Faculty of Pharmacy, Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, Brazil
| | - Fabiola Mara Ribeiro
- Laboratory of Neurobiochemistry - Department of Biochemistry and Immunology, Institute of Biological Sciences, Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, Brazil
| | - Flaviano S. Martins
- Laboratory of Biotherapeutic Agents - Department of Microbiology, Institute of Biological Sciences, Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, Brazil
| | - Rafael Simone Saia
- Laboratory of Intestinal Physiology - Department of Physiology, Ribeirão Preto Medical School, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Vivian Vasconcelos Costa
- Center for Research and Development of Drugs - Department of Morphology, Institute of Biological Sciences, Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, Brazil
| | - Daniel Martins-de-Souza
- Laboratory of Neuroproteomics - Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade do Estado de Campinas - UNICAMP, Campinas, Brazil
- D’Or Institute for Research and Education, São Paulo, Brazil
- Experimental Medicine Research Cluster, Universidade do Estado de Campinas - UNICAMP, Campinas, Brazil
- National Institute of Biomarkers in Neuropsychiatry, National Council for Scientific and Technological Development, São Paulo, Brazil
| | - Philip M. Hansbro
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Sydney, Australia
| | - João Trindade Marques
- Laboratory of RNA Interference and Antiviral Immunity - Department of Biochemistry and Immunology, Institute of Biological Sciences, Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, Brazil
- CNRS UPR9022, University of Strasbourg, Strasbourg, France
| | - Eric R. G. R. Aguiar
- Laboratory of Virus Bioinformatics - Department of Biological Science, Center of Biotechnology and Genetics, Universidade Estadual de Santa Cruz - UESC, Ilhéus, Brazil
| | - Angélica T. Vieira
- Laboratory of Microbiota and Immunomodulation - Department of Biochemistry and Immunology, Institute of Biological Sciences, Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, Brazil
| |
Collapse
|
5
|
Ficik J, Andrezál M, Drahovská H, Böhmer M, Szemes T, Liptáková A, Slobodníková L. Carbapenem-Resistant Klebsiella pneumoniae in COVID-19 Era-Challenges and Solutions. Antibiotics (Basel) 2023; 12:1285. [PMID: 37627705 PMCID: PMC10451955 DOI: 10.3390/antibiotics12081285] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/25/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023] Open
Abstract
The COVID-19 era brought about new medical challenges, which, together with nosocomial bacterial infections, resulted in an enormous burden for the healthcare system. One of the most alarming nosocomial threats was carbapenem-resistant Klebsiella pneumoniae (CRKP). Monitoring CRKP incidence and antimicrobial resistance globally and locally is vitally important. In a retrospective study, the incidence of CRKP in the pre-COVID-19 period (2017-2019) and the COVID-19 pandemic (2020-2022) was investigated in the Central Military Hospital in Ružomberok, Slovak Republic. The relative incidence of CRKP significantly increased during the COVID-19 period-by 4.8 times, from 0.18 to 0.76%. At the same time, 47% of CRKP-positive patients also had COVID-19. Twenty-six KPC and sixty-nine NDM-producing isolates were identified. CRKPs isolated in the year 2022 were submitted to whole genome sequencing, and their susceptibility was tested to cefiderocol, ceftazidime-avibactam, imipenem-relebactam and meropenem-vaborbactam, with excellent results. KPC-producing isolates were also highly susceptible to colistin (92%). The NDM isolates revealed lower susceptibility rates, including only 57% colistin susceptibility. ST-307 prevailed in KPC and ST-11 in NDM isolates. Despite the excellent activity of new antimicrobials, rational antibiotic policy must be thoroughly followed, supported by complementary treatments and strict anti-epidemic precautions.
Collapse
Affiliation(s)
- Jozef Ficik
- Institute of Clinical Microbiology, Central Military Hospital, 034 26 Ružomberok, Slovakia;
- Institute of Microbiology, Faculty of Medicine, Comenius University and the University Hospital in Bratislava, 811 08 Bratislava, Slovakia;
| | - Michal Andrezál
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 842 15 Bratislava, Slovakia; (M.A.); (H.D.); (T.S.)
| | - Hana Drahovská
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 842 15 Bratislava, Slovakia; (M.A.); (H.D.); (T.S.)
| | - Miroslav Böhmer
- Comenius University Science Park, 841 02 Bratislava, Slovakia;
- Public Health Authority of the Slovak Republic, 826 45 Bratislava, Slovakia
| | - Tomáš Szemes
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 842 15 Bratislava, Slovakia; (M.A.); (H.D.); (T.S.)
- Comenius University Science Park, 841 02 Bratislava, Slovakia;
- Public Health Authority of the Slovak Republic, 826 45 Bratislava, Slovakia
| | - Adriána Liptáková
- Institute of Microbiology, Faculty of Medicine, Comenius University and the University Hospital in Bratislava, 811 08 Bratislava, Slovakia;
| | - Lívia Slobodníková
- Institute of Microbiology, Faculty of Medicine, Comenius University and the University Hospital in Bratislava, 811 08 Bratislava, Slovakia;
| |
Collapse
|
6
|
Villalva C, Patil G, Narayanan S, Chanda D, Ghimire R, Snider T, Ramachandran A, Channappanavar R, More S. Klebsiella pneumoniae C o-infection Leads to Fatal Pneumonia in SARS-CoV-2-infected Mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.28.551035. [PMID: 37577517 PMCID: PMC10418095 DOI: 10.1101/2023.07.28.551035] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
SARS-CoV-2 patients have been reported to have high rates of secondary Klebsiella pneumoniae infections. Klebsiella pneumoniae is a commensal that is typically found in the respiratory and gastrointestinal tracts. However, it can cause severe disease when a person's immune system is compromised. Despite a high number of K. pneumoniae cases reported in SARS-CoV-2 patients, a co-infection animal model evaluating the pathogenesis is not available. We describe a mouse model to study disease pathogenesis of SARS-CoV-2 and K. pneumoniae co-infection. BALB/cJ mice were inoculated with mouse-adapted SARS-CoV-2 followed by a challenge with K. pneumoniae . Mice were monitored for body weight change, clinical signs, and survival during infection. The bacterial load, viral titers, immune cell accumulation and phenotype, and histopathology were evaluated in the lungs. The co-infected mice showed severe clinical disease and a higher mortality rate within 48 h of K. pneumoniae infection. The co-infected mice had significantly elevated bacterial load in the lungs, however, viral loads were similar between co-infected and single-infected mice. Histopathology of co-infected mice showed severe bronchointerstitial pneumonia with copious intralesional bacteria. Flow cytometry analysis showed significantly higher numbers of neutrophils and macrophages in the lungs. Collectively, our results demonstrated that co-infection of SARS-CoV-2 with K. pneumoniae causes severe disease with increased mortality in mice.
Collapse
|
7
|
Slimene K, Ali AA, Mohamed EA, El Salabi A, Suliman FS, Elbadri AA, El-fertas FF, El-awjly A, Shokri SA, Rolain JM, Chouchani C. Isolation of Carbapenem and Colistin Resistant Gram-Negative Bacteria Colonizing Immunocompromised SARS-CoV-2 Patients Admitted to Some Libyan Hospitals. Microbiol Spectr 2023; 11:e0297222. [PMID: 37042782 PMCID: PMC10269485 DOI: 10.1128/spectrum.02972-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 03/16/2023] [Indexed: 04/13/2023] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has had a devastating effect, globally. We describe, for the first time, the occurrence of carbapenem-resistant bacteria colonizing SARS-CoV-2 patients who developed hospital-associated infections with carbapenemase-producing, Gram-negative bacteria at some isolation centers of SARS-CoV-2 in the eastern part of Libya. In total, at first, 109 samples were collected from 43 patients, with the samples being recovered from oral (n = 35), nasal (n = 45), and rectal (n = 29) cavities. Strain identification was performed via matrix assisted laser desorption ionization-time of flight (MALDI-TOF). Antibiotic susceptibility testing was carried out on Mueller-Hinton agar, using the standard disk diffusion method. MIC determination was confirmed via E-TEST and microdilution standard methods. A molecular study was carried out to characterize the carbapenem and colistin resistance in Gram-negative bacterial strains. All of the positive results were confirmed via sequencing. Klebsiella pneumoniae (n = 32), Citrobacter freundii (n = 21), Escherichia coli (n = 7), and Acinetobacter baumannii (n = 21) were the predominant isolated bacteria. Gram-negative isolates were multidrug-resistant and carried different carbapenem resistance-associated genes, including NDM-1 (56/119; 47.05%), OXA-48 (15/119; 12.60%), OXA-23 (19/119; 15.96%), VIM (10/119; 8.40%), and the colistin resistance mobile gene mcr-1 (4/119; 3.36%). The overuse of antimicrobials, particularly carbapenem antibiotics, during the SARS-CoV-2 pandemic has led to the emergence of multidrug-resistant bacteria, mainly K. pneumoniae, A. baumannii, and colistin-resistant E. coli strains. Increased surveillance as well as the rational use of carbapenem antibiotics and, recently, colistin are required to reduce the propagation of multidrug-resistant strains and to optimally maintain the efficacy of these antibiotics. IMPORTANCE In this work, we describe, for the first time, the occurrence of carbapenem-resistant bacteria colonizing COVID-19 patients who developed hospital-associated infections with carbapenemase-producing, Gram-negative bacteria at some isolation centers of COVID-19 in the eastern part of Libya. Our results confirmed that the overuse of antimicrobials, such as carbapenem antibiotics, during the COVID-19 pandemic has led to the emergence of multidrug-resistant bacteria, mainly K. pneumoniae and A. baumannii, as well as colistin resistance.
Collapse
Affiliation(s)
- Khouloud Slimene
- Université Aix-Marseille, IRD, APHM, MEPHI, Faculté de Médecine et de Pharmacie, Marseille Cedex 05, France
- IHU Méditerranée Infection, Marseille Cedex 05, France
- Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Campus Universitaire, 2098 El-Manar II, Université de Tunis El-Manar, Tunis, Tunisie
- Laboratoire de Recherche des Sciences et Technologies de l’Environnement, Institut Supérieur des Sciences et Technologies de l’Environnement de Borj-Cedria, BP-1003, Hammam-Lif 2050, Université de Carthage, Tunisie
- Unité de Service en Commun pour la Recherche Plateforme Génomique Institut Supérieur des Sciences et Technologies de l’Environnement de Borj-Cedria, BP-1003, Hammam-Lif 2050, Université de Carthage, Tunisie
| | - Asrra A. Ali
- Department of Environmental Health, Faculty of Public Health, University of Benghazi, Benghazi, Libya
| | - Elhussan A. Mohamed
- Department of Community Medicine, Omar Al-Mukhtar University, El-Beyda, Libya
| | - Allaaeddin El Salabi
- Department of Environmental Health, Faculty of Public Health, University of Benghazi, Benghazi, Libya
| | - Faraj S. Suliman
- Department of Community Medicine, Omar Al-Mukhtar University, El-Beyda, Libya
- Almansoura Isolation Department of COVID-19 Patients, Shahat Teaching Hospital for Chest Diseases and Tuberculosis, Shahat, Libya
| | - Agela A. Elbadri
- Department of Medicine, Faculty of Medicine, University of Benghazi, Benghazi, Libya
- Alhawari Hospital, Benghazi, Libya
| | | | - Ahmed El-awjly
- Sterilization Service Department, Benghazi Medical Center, Benghazi, Libya
| | - Salah A. Shokri
- Department of Microbiology, Faculty of Science, Misurata University, Misurata, Libya
| | - Jean-Marc Rolain
- Université Aix-Marseille, IRD, APHM, MEPHI, Faculté de Médecine et de Pharmacie, Marseille Cedex 05, France
- IHU Méditerranée Infection, Marseille Cedex 05, France
| | - Chedly Chouchani
- Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Campus Universitaire, 2098 El-Manar II, Université de Tunis El-Manar, Tunis, Tunisie
- Laboratoire de Recherche des Sciences et Technologies de l’Environnement, Institut Supérieur des Sciences et Technologies de l’Environnement de Borj-Cedria, BP-1003, Hammam-Lif 2050, Université de Carthage, Tunisie
- Unité de Service en Commun pour la Recherche Plateforme Génomique Institut Supérieur des Sciences et Technologies de l’Environnement de Borj-Cedria, BP-1003, Hammam-Lif 2050, Université de Carthage, Tunisie
| |
Collapse
|
8
|
Arun N, Saurabh K, Muni S, Kumari N, Dev A. A Comparative Study of Bacterial Infections Between COVID-19 and Non-COVID-19 Patients With Respect to Different Isolates and Their Antibiotic Sensitivity Pattern. Cureus 2023; 15:e40387. [PMID: 37456417 PMCID: PMC10344732 DOI: 10.7759/cureus.40387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2023] [Indexed: 07/18/2023] Open
Abstract
Background Following the pandemic caused by SARS-CoV-2, the emergence of and following the pandemic has required major modifications to healthcare systems and frameworks. Antimicrobials have more than a few potential roles in managing COVID-19. Experimental cures for the treatment of SARS-CoV-2 are being explored. The availability of limited data suggests that nosocomial infections are associated with a higher risk of death and severity of COVID-19. To fill this knowledge gap, we conducted a study to assess the spectrum of bacteriological isolates in different samples from COVID-19 patients. Our study aimed to evaluate the antibiotic resistance pattern of these bacterial isolates and compare the spectrum of bacteriological isolates in different samples and their antibiotic sensitivity pattern between COVID-19 and non-COVID-19 patients. Methodology An observational cross-sectional, partly retrospective, and partly prospective study was carried out in the bacteriology section of the Department of Microbiology, Indira Gandhi Institute of Medical Sciences (IGIMS), Patna, Bihar, for a total duration of six months from February 2021 to July 2021. The profile of pathogens isolated from 105 clinical samples from COVID-19 patients was studied. To detect COVID-19, RT-PCR was performed. All clinical specimens (urine, blood, pus, respiratory sample, etc.) were processed and cultured on different media to support the growth of the bacteria as per our standard operating procedures (SOP) for bacteriology samples. Antimicrobial susceptibility testing was carried out based on the Clinical and Laboratory Standards Institute. Results A total of 105 clinical samples were received in the bacteriology section of the Department of Microbiology, IGIMS, Patna, Bihar, from admitted COVID-19 patients. The mean age of study participants was 51.57 ± 14.76 years, and males (66.7%, 70/105) were more than females (33.3%, 35/105). The majority of the patients were 91 out of 105 (86.67%) from the ward and 14 from the ICU (13.33%). Of the total samples tested, 62 (59%) were urine samples, 26 (24.8%) were respiratory specimens, 13 (12.4%) were pus samples, 3 (2.9%) were body fluids, and 1 (1%) were tissue samples. Among the total pathogen isolates (n=57) obtained from patients with SARS-CoV-2 admitted to the ward and ICU, 56.14% (32) were gram-negative, 26.31% (15) were Candida, and 17.54% (10) were gram-positive pathogens. The most isolated pathogen was Escherichia coli (39.02%, 16/41) followed by Klebsiella pneumoniae (29.26%, 12/41), Acinetobacter baumannii (7.31%, 3/41), and Enterobacter cloacae (2.43%, 1/41). Enterococcus spp. as gram-positive bacteria were isolated in 21.95% (9/41) of patients. Among the gram-negative bacteria (Enterobacterales), the highest resistance was seen in ampicillin (100%,29/29). For non-Enterobacterales, the highest resistance was seen in ceftriaxone (66.66%,2/3). Enterococcus spp. showed maximum ciprofloxacin, and gentamicin (high level) resistance was 100% (9/9). Conclusion Secondary infections with resistant pathogens in COVID-19 patients highlight the importance of antimicrobial management programs focused on the optimal selection of empirical treatments based on culture reports.
Collapse
Affiliation(s)
- Nitali Arun
- Microbiology, Indira Gandhi Institute of Medical Sciences, Patna, IND
| | - Kumar Saurabh
- Microbiology, Indira Gandhi Institute of Medical Sciences, Patna, IND
| | - Sweta Muni
- Microbiology, Indira Gandhi Institute of Medical Sciences, Patna, IND
| | - Namrata Kumari
- Microbiology, Indira Gandhi Institute of Medical Sciences, Patna, IND
| | - Anand Dev
- Emergency Medicine, Indira Gandhi Institute of Medical Sciences, Patna, IND
| |
Collapse
|
9
|
Yahya RO. Problems Associated with Co-Infection by Multidrug-Resistant Klebsiella pneumoniae in COVID-19 Patients: A Review. Healthcare (Basel) 2022; 10:2412. [PMID: 36553936 PMCID: PMC9778403 DOI: 10.3390/healthcare10122412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 11/25/2022] [Accepted: 11/26/2022] [Indexed: 12/02/2022] Open
Abstract
To date, coronavirus disease 2019 (COVID-19) and its variants have been reported as a novel public health concern threatening us worldwide. The presence of Klebsiella pneumoniae in COVID-19-infected patients is a major problem due to its resistance to multiple antibiotics, and it can possibly make the management of COVID-19 in patients more problematic. The impact of co-infection by K. pneumoniae on COVID-19 patients was explored in the current review. The spread of K. pneumoniae as a co-infection among critically ill COVID-19 patients, particularly throughout hospitalization, was identified and recorded via numerous reports. Alarmingly, the extensive application of antibiotics in the initial diagnosis of COVID-19 infection may reduce bacterial co-infection, but it increases the antibiotic resistance of bacteria such as the strains of K. pneumoniae. The correct detection of multidrug-resistant K. pneumoniae can offer a supportive reference for the diagnosis and therapeutic management of COVID-19 patients. Furthermore, the prevention and control of K. pneumoniae are required to minimize the risk of COVID-19. The aim of the present review is, therefore, to report on the virulence factors of the K. pneumonia genotypes, the drug resistance of K. pneumonia, and the impact of K. pneumoniae co-infection with COVID-19 on patients through a study of the published scientific papers, reports, and case studies.
Collapse
Affiliation(s)
- Reham Omar Yahya
- Basic Sciences Department, College of Sciences and Health Professions, King Saud Bin Abdulaziz University for Health Sciences, Riyadh 11671, Saudi Arabia;
- King Abduallah International Medical Research Center, Riyadh 11481, Saudi Arabia
| |
Collapse
|
10
|
Rahmati M, Babapoor E, Dezfulian M. Amikacin-loaded niosome nanoparticles improve amikacin activity against antibiotic-resistant Klebsiella pneumoniae strains. World J Microbiol Biotechnol 2022; 38:230. [PMID: 36184645 PMCID: PMC9527143 DOI: 10.1007/s11274-022-03405-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 08/27/2022] [Indexed: 11/30/2022]
Abstract
Amikacin is an aminoglycoside antibiotic used in drug-resistant bacterial infections. The spread of bacterial infections has become a severe concern for the treatment system because of the simultaneous drug resistance bacteria and SARS-CoV-2 hospitalized patients. One of the most common bacteria in the development of drug resistance is Klebsiella strains, which is a severe threat due to the possibility of biofilm production. In this regard, recent nanotechnology studies have proposed using nanocarriers as a practical proposal to improve the performance of antibiotics and combat drug resistance. Among drug nanocarriers, niosomes are considered for their absorption mechanism, drug coverage, and biocompatibility. In this study, niosomal formulations were synthesized by the thin-layer method. After optimizing the synthesized niosomes, their properties were evaluated in terms of stability and drug release rate. The toxicity of the optimal formulation was then analyzed. The effect of free amikacin and amikacin encapsulated in niosome on biofilm inhibition were compared in multi-drug resistant isolated Klebsiella strains, and the mrkD gene expression was calculated. The MIC and MBC were measured for the free drug and amikacin loaded in the noisome. The particle size of synthesized amikacin-loaded niosomes ranged from 175.2 to 248.3 nm. The results showed that the amount of lipid and the molar ratio of tween 60 to span 60 has a positive effect on particle size, while the molar ratio of surfactant to cholesterol has a negative effect. The highest release rate in amikacin-loaded niosomes is visible in the first 8 h, and then a slower release occurs up to 72 h. The cytotoxicity induced by amikacin-loaded niosome is significantly less than the cytotoxicity of free amikacin in HFF cells (***p < 0.001, **p < 0.01). The mrkD mRNA expression level in the studied strains was significantly reduced after treatment with niosome-containing amikacin compared to free amikacin (***p < 0.001). It was confirmed that in the presence of the niosome, the amikacin antibacterial activity increased while the concentration of the drug used decreased, the formation of biofilm inhibited, and reduced antibiotics resistance in MDR Klebsiella strains.
Collapse
Affiliation(s)
- Mohamad Rahmati
- Department of Microbiology, Karaj Branch, Islamic Azad University, Karaj, Iran
| | - Ebrahim Babapoor
- Biotechnology Research Center, Karaj Branch, Islamic Azad University, Karaj, Iran
| | - Mehrouz Dezfulian
- Biotechnology Research Center, Karaj Branch, Islamic Azad University, Karaj, Iran.
| |
Collapse
|
11
|
Teklemariam AD, Hashem AM, Saber SH, Almuhayawi MS, Haque S, Abujamel TS, Harakeh S. Bacterial co-infections and antimicrobial resistance associated with the Coronavirus Disease 2019 infection. Biotechnol Genet Eng Rev 2022:1-22. [PMID: 36123822 DOI: 10.1080/02648725.2022.2122297] [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: 06/18/2022] [Accepted: 08/03/2022] [Indexed: 12/15/2022]
Abstract
Bacterial co-infections are typically associated with viral respiratory tract infections and pose a significant public health problem around the world. COVID-19 infection damages tissues lining the respiratory track and regulates immune cells/cytokines leading to microbiome dysbiosis and facilitating the area to be colonized by pathogenic bacterial agents. There have been reports of different types of bacterial co-infection in COVID-19 patients. Some of these reports showed despite geographical differences and differences in hospital settings, bacterial co-infections are a major cause of morbidity and mortality in COVID-19 patients. The inappropriate use of antibiotics for bacterial infections, particularly broad-spectrum antibiotics, can also further complicate the infection process, often leading to multi drug resistance, clinical deterioration, poor prognosis, and eventually death. To this end, researchers must establish a new therapeutic approach to control SARS-CoV-2 and the associated microbial coinfections. Hence, the aim of this review is to highlight the bacterial co-infection that has been recorded in COVID-19 patients and the status of antimicrobial resistance associated with the dual infections.
Collapse
Affiliation(s)
- Addisu D Teklemariam
- Department of Biology, Faculty of sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Anwar M Hashem
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Vaccines and immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Saber H Saber
- Molecular Cell Biology Laboratory, Department of Zoology, Faculty of Science, Assiut University, Asyut, Egypt
| | - Mohammed S Almuhayawi
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Turki S Abujamel
- Vaccines and immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Steve Harakeh
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| |
Collapse
|
12
|
Impact of the COVID-19 Pandemic on the Prevalence of HAIs and the Use of Antibiotics in an Italian University Hospital. Healthcare (Basel) 2022; 10:healthcare10091597. [PMID: 36141209 PMCID: PMC9498585 DOI: 10.3390/healthcare10091597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/19/2022] [Accepted: 08/20/2022] [Indexed: 12/04/2022] Open
Abstract
The COVID-19 pandemic has massively affected healthcare systems globally, causing a possible reduction in attention to traditional infection prevention programs. The objective of this study was to estimate the prevalence of healthcare-associated infections (HAIs) and the use of antimicrobials in an Italian University Hospital and to investigate whether the intensification of hospital infection control measures during the COVID-19 pandemic has affected the prevalence of bacterial HAIs. A point prevalence survey was conducted according to the simplified ECDC protocol. The survey identified a local HAI prevalence of 9.0%, revealing an increase compared to pre-pandemic values (7.3%). The survey also identified an antimicrobial exposure of 40.8%, revealing a decrease in their use compared to the study carried out in the pre-pandemic era (44.6%). Among the organizational challenges experienced during the COVID-19 pandemic, despite the greater attention paid to infection prevention measures aimed at reducing SARS-CoV-2, many healthcare facilities had to contend with the controlled availability of personnel, physical space limitations and a large number of patients. Active surveillance in hospital wards and the consequent reporting by personnel specialized in infection control is fundamental for hospitals to recognize gaps in prevention and report any observed increases in HAIs.
Collapse
|
13
|
Wong Fok Lung T, Charytonowicz D, Beaumont KG, Shah SS, Sridhar SH, Gorrie CL, Mu A, Hofstaedter CE, Varisco D, McConville TH, Drikic M, Fowler B, Urso A, Shi W, Fucich D, Annavajhala MK, Khan IN, Oussenko I, Francoeur N, Smith ML, Stockwell BR, Lewis IA, Hachani A, Upadhyay Baskota S, Uhlemann AC, Ahn D, Ernst RK, Howden BP, Sebra R, Prince A. Klebsiella pneumoniae induces host metabolic stress that promotes tolerance to pulmonary infection. Cell Metab 2022; 34:761-774.e9. [PMID: 35413274 PMCID: PMC9081115 DOI: 10.1016/j.cmet.2022.03.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/18/2022] [Accepted: 03/22/2022] [Indexed: 12/21/2022]
Abstract
K. pneumoniae sequence type 258 (Kp ST258) is a major cause of healthcare-associated pneumonia. However, it remains unclear how it causes protracted courses of infection in spite of its expression of immunostimulatory lipopolysaccharide, which should activate a brisk inflammatory response and bacterial clearance. We predicted that the metabolic stress induced by the bacteria in the host cells shapes an immune response that tolerates infection. We combined in situ metabolic imaging and transcriptional analyses to demonstrate that Kp ST258 activates host glutaminolysis and fatty acid oxidation. This response creates an oxidant-rich microenvironment conducive to the accumulation of anti-inflammatory myeloid cells. In this setting, metabolically active Kp ST258 elicits a disease-tolerant immune response. The bacteria, in turn, adapt to airway oxidants by upregulating the type VI secretion system, which is highly conserved across ST258 strains worldwide. Thus, much of the global success of Kp ST258 in hospital settings can be explained by the metabolic activity provoked in the host that promotes disease tolerance.
Collapse
Affiliation(s)
| | - Daniel Charytonowicz
- Department of Genetics and Genomic Sciences, Mt. Sinai Icahn School of Medicine, New York, NY 10029, USA
| | - Kristin G Beaumont
- Department of Genetics and Genomic Sciences, Mt. Sinai Icahn School of Medicine, New York, NY 10029, USA
| | - Shivang S Shah
- Department of Pediatrics, Columbia University, New York, NY 10032, USA
| | - Shwetha H Sridhar
- Department of Genetics and Genomic Sciences, Mt. Sinai Icahn School of Medicine, New York, NY 10029, USA
| | - Claire L Gorrie
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Andre Mu
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Casey E Hofstaedter
- Department of Microbial Pathogenesis, University of Maryland, Baltimore, MD 21201, USA
| | - David Varisco
- Department of Microbial Pathogenesis, University of Maryland, Baltimore, MD 21201, USA
| | | | - Marija Drikic
- Department of Biological Sciences, University of Calgary, Calgary, T2N 1N4, Canada
| | - Brandon Fowler
- Microbiome & Pathogen Genomics Collaborative Center, Columbia University, New York, NY 10032, USA
| | - Andreacarola Urso
- Department of Pediatrics, Columbia University, New York, NY 10032, USA
| | - Wei Shi
- Department of Pediatrics, Columbia University, New York, NY 10032, USA
| | - Dario Fucich
- Department of Pediatrics, Columbia University, New York, NY 10032, USA
| | - Medini K Annavajhala
- Department of Medicine, Columbia University, New York, NY 10032, USA; Microbiome & Pathogen Genomics Collaborative Center, Columbia University, New York, NY 10032, USA
| | - Ibrahim N Khan
- Department of Pediatrics, Columbia University, New York, NY 10032, USA
| | - Irina Oussenko
- Department of Genetics and Genomic Sciences, Mt. Sinai Icahn School of Medicine, New York, NY 10029, USA
| | - Nancy Francoeur
- Department of Genetics and Genomic Sciences, Mt. Sinai Icahn School of Medicine, New York, NY 10029, USA
| | - Melissa L Smith
- Department of Genetics and Genomic Sciences, Mt. Sinai Icahn School of Medicine, New York, NY 10029, USA
| | - Brent R Stockwell
- Department of Chemistry, Columbia University, New York, NY 10027, USA; Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Ian A Lewis
- Department of Biological Sciences, University of Calgary, Calgary, T2N 1N4, Canada
| | - Abderrahman Hachani
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | | | - Anne-Catrin Uhlemann
- Department of Medicine, Columbia University, New York, NY 10032, USA; Microbiome & Pathogen Genomics Collaborative Center, Columbia University, New York, NY 10032, USA
| | - Danielle Ahn
- Department of Pediatrics, Columbia University, New York, NY 10032, USA
| | - Robert K Ernst
- Department of Microbial Pathogenesis, University of Maryland, Baltimore, MD 21201, USA
| | - Benjamin P Howden
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Mt. Sinai Icahn School of Medicine, New York, NY 10029, USA; Sema4: A Mount Sinai Venture, Stamford, CT 06902, USA
| | - Alice Prince
- Department of Pediatrics, Columbia University, New York, NY 10032, USA.
| |
Collapse
|
14
|
SATHYAKAMALA RAVICHANDRAN, PEACE ALICER, SHANMUGAM PRIYADARSHINI. A Comparative Study on Bacterial Co-Infections and Prevalence of Multidrug Resistant Organisms among Patients in COVID and Non-COVID Intensive Care Units. JOURNAL OF PREVENTIVE MEDICINE AND HYGIENE 2022; 63:E19-E26. [PMID: 35647371 PMCID: PMC9121664 DOI: 10.15167/2421-4248/jpmh2022.63.1.2175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 02/22/2022] [Indexed: 11/05/2022]
Abstract
Introduction Secondary bacterial infections have been reported in majority of patients hospitalized with coronavirus disease 2019 (COVID-19). A study of the antimicrobial susceptibility profiles of these bacterial strains revealed that they were multidrug resistant, demonstrating their resistance to at least three classes of antimicrobial agents including beta-lactams, fluoroquinolones and aminoglycosides. Bacterial co-infection remains as an important cause for high mortality in patients hospitalized with COVID-19. Methods In our study, we conducted a retrospective comparative analysis of bacterial co-infections and the antimicrobial resistance profile of bacterial isolates obtained from inpatients admitted in COVID-19 and non-COVID-19 intensive care units. The goal was to obtain the etiology and antimicrobial resistance of these infections for more accurate use of antimicrobials in clinical settings. This study involved a total of 648 samples collected from 356 COVID-19 positive patients and 292 COVID-19 negative patients admitted in the intensive care unit over a period of six months from May to October 2020. Results Among the co-infections found, maximum antimicrobial resistance was found in Acinetobacter species followed by Klebsiella species in both the ICU’s. Incidence of bacterial co-infection was found to be higher in COVID-19 intensive care patients and most of these isolates were multidrug resistant strains. Conclusion Therefore, it is important that co-infections should not be underestimated and instead be made part of an integrated plan to limit the global burden of morbidity and mortality during the SARS-CoV-2 pandemic and beyond.
Collapse
Affiliation(s)
| | - ALICE R. PEACE
- Department of Microbiology, Chettinad Hospital and Research Institute
| | - PRIYADARSHINI SHANMUGAM
- Department of Microbiology, Chettinad Hospital and Research Institute
- Correspondence: Priyadarshini Shanmugam, Professor and Head, Chettinad Hospital and Research Institute, Kelambakkam –Tel. #9841551891 - E-mail:
| |
Collapse
|
15
|
Complete Genome Sequence of Klebsiella quasipneumoniae MMCC7, Isolated from an Eclectus Parrot (Eclectus roratus). Microbiol Resour Announc 2022; 11:e0017122. [PMID: 35467363 PMCID: PMC9119098 DOI: 10.1128/mra.00171-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Klebsiella quasipneumoniae MMCC7 is a multidrug- and heavy metal-resistant strain isolated from the feces of a pet shop eclectus parrot in Hong Kong. The complete genome, a single chromosome and circular plasmid (5,382,488 bp; G+C content, 57.79%), was determined by hybrid assembly.
Collapse
|
16
|
Association between Virulence Factors and Antimicrobial Resistance of Klebsiella pneumoniae Clinical Isolates from North Kerala. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2022. [DOI: 10.22207/jpam.16.2.06] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Klebsiella pneumoniae is a common bacterial pathogen causes wide range of infections all over the world. The antimicrobial resistance of K. pneumoniae is a global concern and expresses several virulence factors contributing to the pathogenesis. The incidences of bacterial co-infection in viral pneumonia are common. Increased risk of K. pneumoniae co-infection in viral respiratory tract infection should be alerted in COVID-19 pandemic period. The study aims to detect the association between antimicrobial resistance and factors causing pathogenicity of K. pneumoniae. For the current study, 108 K. pneumoniae clinical isolates were included. Antimicrobial susceptibility test was done by Kirby-Bauer disc diffusion method according to CLSI guidelines. Virulence factors such as biofilm formation, haemagglutination, haemolysins, hypermucoviscocity, siderophore, amylase, and gelatinase production were determined by phenotypic method. In this study K. pneumoniae showed high level of antimicrobial resistance towards ampicillin (92.59%) followed by amoxicillin-clavulanic acid (67.59%) and cotrimoxazole (47,22%). An important association between biofilm formation and antimicrobial resistance was found to be statistically significant for cotrimoxazole (P-value 0.036) and amoxicillin-clavulanic acid (P-value 0.037). Other virulence factors like hypermucoviscocity, haemagglutination, amylase, and siderophore production were also showed a statistically significant relation (P-value <0.05) with antimicrobial resistance. Further molecular studies are necessary for the identification of virulence and antimicrobial resistance genes, for the effective control of drug-resistant bacteria.
Collapse
|
17
|
Ayoub Moubareck C, Hammoudi Halat D. The Collateral Effects of COVID-19 Pandemic on the Status of Carbapenemase-Producing Pathogens. Front Cell Infect Microbiol 2022; 12:823626. [PMID: 35372126 PMCID: PMC8968076 DOI: 10.3389/fcimb.2022.823626] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 01/27/2022] [Indexed: 12/28/2022] Open
Abstract
The serious challenge of antimicrobial resistance continues to threaten public health and lingers in the era of the coronavirus disease 2019 (COVID-19), declared pandemic by the World Health Organization. While the pandemic has triggered the importance of infection control practices and preventive measures such as physical distancing, hand hygiene, travel reduction and quarantine, the ongoing alarm of antimicrobial resistance seems to accompany the pandemic too. Antimicrobial resistance has been fostered during COVID-19, possibly due to high rate of empirical antibiotic utilization in COVID-19 patients, increased use of biocides, and the disruption of proper healthcare for other conditions. Specifically, carbapenemase-producing Gram-negative bacteria have shown to cause secondary bacterial infections in patients hospitalized for COVID-19. Clinical and microbiological evidence of such infections is accumulating in different parts of the world. With the resilient nature of carbapenemases, their association with mortality, and the limited treatment options available, concerns regarding this group of antibiotic-hydrolyzing enzymes during the pandemic are expected to upsurge. While the additional burden carbapenemases exert on healthcare is worrisome, it remains hidden or abandoned among the various health consequences of the pandemic. The purpose of this minireview is to shed a light on carbapenemase-associated infections during such unprecedented time of COVID-19. A focused insight shall be made into carbapenemases, their implications for COVID-19 patients, and the features and consequences of co-infection, with a review of available evidence from pertinent literature. The importance of increased surveillance for carbapenemase-producers and optimizing their management in relation to the pandemic, shall be addressed as well.
Collapse
Affiliation(s)
| | - Dalal Hammoudi Halat
- Department of Pharmaceutical Sciences, School of Pharmacy, Lebanese International University, Bekaa, Lebanon
| |
Collapse
|
18
|
Bianco G, Boattini M, Bondi A, Comini S, Zaccaria T, Cavallo R, Costa C. Outbreak of ceftazidime-avibactam resistant KPC-producing Klebsiella pneumoniae in a COVID-19 Intensive Care Unit, Italy: urgent need for updating diagnostic protocols of surveillance cultures. J Hosp Infect 2022; 122:217-219. [PMID: 35139426 PMCID: PMC8818127 DOI: 10.1016/j.jhin.2022.02.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 02/02/2022] [Indexed: 11/29/2022]
|
19
|
Wang Y, Li J, Zhang L, Sun HX, Zhang Z, Xu J, Xu Y, Lin Y, Zhu A, Luo Y, Zhou H, Wu Y, Lin S, Sun Y, Xiao F, Chen R, Wen L, Chen W, Li F, Ou R, Zhang Y, Kuo T, Li Y, Li L, Sun J, Sun K, Zhuang Z, Lu H, Chen Z, Mai G, Zhuo J, Qian P, Chen J, Yang H, Wang J, Xu X, Zhong N, Zhao J, Li J, Zhao J, Jin X. Plasma cell-free RNA characteristics in COVID-19 patients. Genome Res 2022; 32:228-241. [PMID: 35064006 PMCID: PMC8805721 DOI: 10.1101/gr.276175.121] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 12/21/2021] [Indexed: 12/15/2022]
Abstract
The pathogenesis of COVID-19 is still elusive, which impedes disease progression prediction, differential diagnosis, and targeted therapy. Plasma cell-free RNAs (cfRNAs) carry unique information from human tissue and thus could point to resourceful solutions for pathogenesis and host-pathogen interactions. Here, we performed a comparative analysis of cfRNA profiles between COVID-19 patients and healthy donors using serial plasma. Analyses of the cfRNA landscape, potential gene regulatory mechanisms, dynamic changes in tRNA pools upon infection, and microbial communities were performed. A total of 380 cfRNA molecules were up-regulated in all COVID-19 patients, of which seven could serve as potential biomarkers (AUC > 0.85) with great sensitivity and specificity. Antiviral (NFKB1A, IFITM3, and IFI27) and neutrophil activation (S100A8, CD68, and CD63)–related genes exhibited decreased expression levels during treatment in COVID-19 patients, which is in accordance with the dynamically enhanced inflammatory response in COVID-19 patients. Noncoding RNAs, including some microRNAs (let 7 family) and long noncoding RNAs (GJA9-MYCBP) targeting interleukin (IL6/IL6R), were differentially expressed between COVID-19 patients and healthy donors, which accounts for the potential core mechanism of cytokine storm syndromes; the tRNA pools change significantly between the COVID-19 and healthy group, leading to the accumulation of SARS-CoV-2 biased codons, which facilitate SARS-CoV-2 replication. Finally, several pneumonia-related microorganisms were detected in the plasma of COVID-19 patients, raising the possibility of simultaneously monitoring immune response regulation and microbial communities using cfRNA analysis. This study fills the knowledge gap in the plasma cfRNA landscape of COVID-19 patients and offers insight into the potential mechanisms of cfRNAs to explain COVID-19 pathogenesis.
Collapse
|
20
|
Arcari G, Oliva A, Sacco F, Di Lella FM, Raponi G, Tomolillo D, Curtolo A, Venditti M, Carattoli A. Interplay between Klebsiella pneumoniae producing KPC-31 and KPC-3 under treatment with high dosage meropenem: a case report. Eur J Clin Microbiol Infect Dis 2022; 41:495-500. [PMID: 34988712 PMCID: PMC8731190 DOI: 10.1007/s10096-021-04388-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 11/29/2021] [Indexed: 12/28/2022]
Abstract
The objective was to study ceftazidime-avibactam resistant and susceptible Klebsiella pneumoniae isolated from a patient admitted to the Policlinico Umberto I of Rome for SARS-CoV2. Data on the evolution of patient's conditions, antimicrobial therapies, and microbiological data were collected. Whole-genome sequencing performed by Illumina and Nanopore sequencing methods were used to type the strains. During the hospitalization, a SARS-CoV2-infected patient was colonized by a KPC-producing K. pneumoniae strain and empirically treated with ceftazidime-avibactam (CZA) when presenting spiking fever symptoms. Successively, ST2502 CZA-resistant strain producing the KPC-31 variant gave a pulmonary infection to the patient. The infection was treated with high doses of meropenem. The KPC-31-producing strain disappeared but the patient remained colonized by a KPC-3-producing K. pneumoniae strain. An interplay between highly conserved KPC-31- and KPC-3-producing ST2502 strains occurred in the SARS-CoV2 patient during the hospitalization, selected by CZA and carbapenem treatments, respectively.
Collapse
Affiliation(s)
- Gabriele Arcari
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Alessandra Oliva
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Federica Sacco
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy.,Microbiology and Virology Unit, University Hospital Policlinico Umberto I, Rome, Italy
| | | | - Giammarco Raponi
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy.,Microbiology and Virology Unit, University Hospital Policlinico Umberto I, Rome, Italy
| | - Dario Tomolillo
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Ambrogio Curtolo
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Mario Venditti
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | | |
Collapse
|
21
|
Silvester R, Madhavan A, Kokkat A, Parolla A, B M A, M H, Abdulla MH. Global surveillance of antimicrobial resistance and hypervirulence in Klebsiella pneumoniae from LMICs: An in-silico approach. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 802:149859. [PMID: 34464800 DOI: 10.1016/j.scitotenv.2021.149859] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 08/19/2021] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
The global emergence of antimicrobial resistance (AMR) among pathogens is a major public health crisis that might soon lead to a post-antibiotic era. Klebsiella pneumoniae, included in the World Health Organization list of critical priority pathogens, is an emerging threat to global health owing to the rapid rise of convergent AMR and hypervirulent strains. Comprehensive epidemiology of AMR-hypervirulent determinants in K. pneumoniae from Low-and Middle-Income Countries (LMICs) is still lacking. As part of rapid risk assessment, an in-silico approach was employed to characterize the AMR and hypervirulence determinants in K. pneumoniae from LMICs. Genomic data of 2432 K. pneumoniae strains were obtained from 33 LMICs representing 4 continents; Asia (n = 12), Africa (n = 18), N. America (n = 2) and Europe (n = 1). All the analysed strains were multiple-drug resistant and 13.6% of them were hypervirulent as well. The co-existence of antibiotic resistant genes conferring concomitant resistance towards life-saving drugs (carbapenems, colistin, fluoroquinolones and fosfomycin) were also observed among the strains, thereby challenging the efficacy of current treatment strategies. The emergence of convergent strains of K. pneumoniae carrying both multi-drug resistance and hypervirulence-associated genes in 12 LMICs is highlighted in this study. Asian region was identified as the major hotspot for convergent strains, especially being confined to 3 countries (India, Pakistan and Vietnam), further exacerbating the situation. This represents a major challenge to disease treatment and public health management in the LMICs. Regular surveillance for emergence of convergence and necessary interventions in the high-risk regions are strongly recommended.
Collapse
Affiliation(s)
- Reshma Silvester
- School of Industrial Fisheries, Cochin University of Science and Technology (CUSAT), 682016, India.
| | - Ajin Madhavan
- Department of Marine Biology, Microbiology and Biochemistry, Cochin University of Science and Technology (CUSAT), 682016, India
| | - Aswin Kokkat
- National Geophysical Research Institute, Uppal, Hyderabad, 500007, India
| | - Ajilesh Parolla
- Department of Atmospheric Sciences, Cochin University of Science and Technology (CUSAT), 682016, India
| | - Adarsh B M
- Department of Marine Biology, Microbiology and Biochemistry, Cochin University of Science and Technology (CUSAT), 682016, India
| | - Harikrishnan M
- School of Industrial Fisheries, Cochin University of Science and Technology (CUSAT), 682016, India
| | - Mohamed Hatha Abdulla
- Department of Marine Biology, Microbiology and Biochemistry, Cochin University of Science and Technology (CUSAT), 682016, India
| |
Collapse
|
22
|
Pustake M, Tambolkar I, Giri P, Gandhi C. SARS, MERS and CoVID-19: An overview and comparison of clinical, laboratory and radiological features. J Family Med Prim Care 2022; 11:10-17. [PMID: 35309670 PMCID: PMC8930171 DOI: 10.4103/jfmpc.jfmpc_839_21] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/30/2021] [Accepted: 07/04/2021] [Indexed: 11/04/2022] Open
Abstract
In the 21st century, we have seen a total of three outbreaks by members of the coronavirus family. Although the first two outbreaks did not result in a pandemic, the third and the latest outbreak of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) culminated in a pandemic. This pandemic has been extremely significant on a social and international level. As these viruses belong to the same family, they are closely related. Despite their numerous similarities, they have slight distinctions that render them distinct from one another. The Severe Acute Respiratory Distress Syndrome and Middle East Respiratory Syndrome (MERS) cases were reported to have a very high case fatality rate of 9.5 and 34.4% respectively. In contrast, the CoVID-19 has a case fatality rate of 2.13%. Also, there are no clear medical countermeasures for these coronaviruses yet. We can cross information gaps, including cultural weapons for fighting and controlling the spread of MERS-CoV and SARS-CoV-2, and plan efficient and comprehensive defensive lines against coronaviruses that might arise or reemerge in the future by gaining a deeper understanding of these coronaviruses and the illnesses caused by them. The review thoroughly summarises the state-of-the-art information and compares the biochemical properties of these deadly coronaviruses with the clinical characteristics, laboratory features and radiological manifestations of illnesses induced by them, with an emphasis on comparing and contrasting their similarities and differences.
Collapse
Affiliation(s)
- Manas Pustake
- Department of Internal Medicine, Grant Government Medical College and Sir JJ Group of Hospitals, Mumbai, India
| | - Isha Tambolkar
- Department of Internal Medicine, BJ Government Medical College and Sassoon Hospital, Pune, India
| | - Purushottam Giri
- Department of Community Medicine, IIMSR Medical College, Badnapur, District. Jalna, Maharashtra, India
| | - Charmi Gandhi
- Department of Internal Medicine, Grant Government Medical College and Sir JJ Group of Hospitals, Mumbai, India
| |
Collapse
|
23
|
Rahaman MM, Sarkar MMH, Rahman MS, Islam MR, Islam I, Saha O, Akter S, Banu TA, Jahan I, Habib MA, Goswami B, Bari L, Malek MA, Khan MS. Genomic characterization of the dominating Beta variant carrying vaccinated (Oxford-AstraZeneca) and non-vaccinated COVID-19 patient samples in Bangladesh: A metagenomics and whole genome approach. J Med Virol 2021; 94:1670-1688. [PMID: 34939673 DOI: 10.1002/jmv.27537] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 12/17/2021] [Accepted: 12/20/2021] [Indexed: 11/11/2022]
Abstract
Bangladesh experiences a second wave of COVID-19 since March 2021, despite the nationwide vaccination drive with ChAdOx1 (Oxford-AstraZeneca) vaccine from early February 2021. Here, we characterized 19 nasopharyngeal swab (NPS) samples from COVID-19 suspect patients using genomic and metagenomic approach. Screening for SARS-CoV-2 by RT-PCR and metagenomic sequencing revealed 17 samples of COVID-19 positive (vaccinated=10, non-vaccinated=7) and 2 samples of COVID-19 negative. We did not find any significant correlation between associated factors including vaccination status, age or sex of the patients, diversity or abundance of the co-infected organisms/pathogens, and the abundance of SARS-CoV-2. Though the first wave of the pandemic was dominated by clade 20B, Beta,V2 (South African variant) dominated the second wave (January 2021 to May 2021), while the third wave (May 2021 to September 2021) was responsible for Delta variants of the epidemic in Bangladesh including both vaccinated and unvaccinated infections. Noteworthy, the RBD region of S protein of all the isolates harbored similar substitutions including K417N, E484K and N501Y that signify the Beta, while D614G, D215G, D80A, A67V, L18F and A701V substitutions were commonly found in the non-RBD region of Spike proteins. ORF7b and ORF3a genes underwent a positive selection (dN/dS ratio 1.77 and 1.24, respectively), while the overall S protein of the Bangladeshi SARS-CoV-2 isolates underwent negative selection pressure (dN/dS=0.621). Furthermore, we found different bacterial co-infection like Streptococcus agalactiae, Neisseria meningitidis, Elizabethkingia anophelis, Stenotrophomonas maltophilia, Klebsiella pneumoni and Pseudomonas plecoglossicida, expressing a number of antibiotic resistance genes such as tetA and tetM. Overall, this approach provides valuable insights on the SARS-CoV-2 genomes and microbiome composition from both vaccinated and non-vaccinated patients in Bangladesh. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
| | - Md Murshed Hasan Sarkar
- Genomics Research Laboratory, Bangladesh Council of Scientific and Industrial Research, BCSIR, Dhaka, Bangladesh
| | - M Shaminur Rahman
- Department of Microbiology, Jashore University of Science Technology, Jashore, Bangladesh
| | - M Rafiul Islam
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - Israt Islam
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - Otun Saha
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - Shahina Akter
- Genomics Research Laboratory, Bangladesh Council of Scientific and Industrial Research, BCSIR, Dhaka, Bangladesh
| | - Tanjian Akhtar Banu
- Genomics Research Laboratory, Bangladesh Council of Scientific and Industrial Research, BCSIR, Dhaka, Bangladesh
| | - Iffat Jahan
- Genomics Research Laboratory, Bangladesh Council of Scientific and Industrial Research, BCSIR, Dhaka, Bangladesh
| | - Md Ahasan Habib
- Genomics Research Laboratory, Bangladesh Council of Scientific and Industrial Research, BCSIR, Dhaka, Bangladesh
| | - Barna Goswami
- Genomics Research Laboratory, Bangladesh Council of Scientific and Industrial Research, BCSIR, Dhaka, Bangladesh
| | - Latiful Bari
- Centre for Advanced Research in Sciences, University of Dhaka, Dhaka, Bangladesh
| | - Md Abdul Malek
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh.,Centre for Advanced Research in Sciences, University of Dhaka, Dhaka, Bangladesh
| | - Md Salim Khan
- Genomics Research Laboratory, Bangladesh Council of Scientific and Industrial Research, BCSIR, Dhaka, Bangladesh
| |
Collapse
|
24
|
Amarsy R, Trystram D, Cambau E, Monteil C, Fournier S, Oliary J, Junot H, Sabatier P, Porcher R, Robert J, Jarlier V. Surging bloodstream infections and antimicrobial resistance during the first wave of COVID-19: a study in a large multihospital institution in the Paris region. Int J Infect Dis 2021; 114:90-96. [PMID: 34688945 PMCID: PMC8531236 DOI: 10.1016/j.ijid.2021.10.034] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 09/22/2021] [Accepted: 10/15/2021] [Indexed: 01/08/2023] Open
Abstract
Objectives This study measured the impact of the first wave of COVID-19 pandemic (COVID-19) (March–April 2020) on the incidence of bloodstream infections (BSIs) at Assistance Publique – Hôpitaux de Paris (APHP), the largest multisite public healthcare institution in France. Methods The number of patient admission blood cultures (BCs) collected, number of positive BCs, and antibiotic resistance and consumption were analysed retrospectively for the first quarter of 2020, and also for the first quarter of 2019 for comparison, in 25 APHP hospitals (ca. 14 000 beds). Results Up to a fourth of patients admitted in March–April 2020 in these hospitals had COVID-19. The BSI rate per 100 admissions increased overall by 24% in March 2020 and 115% in April 2020, and separately for the major pathogens (Escherichia coli, Klebsiella pneumoniae, enterococci, Staphylococcus aureus, Pseudomonas aeruginosa, yeasts). A sharp increase in the rate of BSIs caused by microorganisms resistant to third-generation cephalosporins (3GC) was also observed in March–April 2020, particularly in K. pneumoniae, enterobacterial species naturally producing inducible AmpC (Enterobacter cloacae...), and P. aeruginosa. A concomitant increase in 3GC consumption occurred. Conclusions The COVID-19 pandemic had a strong impact on hospital management and also unfavourable effects on severe infections, antimicrobial resistance, and laboratory work diagnostics.
Collapse
Affiliation(s)
- Rishma Amarsy
- Groupe hospitalo-universitaire APHP Nord-Université de Paris, Site Lariboisière et Fernand Widal, Infection Prevention and Control Team and CIMI-Paris, Inserm U1135, Sorbonne Université, Paris, France
| | - David Trystram
- Groupe hospitalo-universitaire APHP Sorbonne Université, Site Pitié-Salpêtrière, Laboratoire de Bactériologie-Hygiène, Paris, France and Direction des Systèmes d'Information de l'Assistance Publique - Hôpitaux de Paris, Paris, France
| | - Emmanuelle Cambau
- Groupe hospitalo-universitaire APHP Nord -Université de Paris, Site Lariboisière, Laboratoire de Microbiologie-Hygiène and Inserm UMR1137 IAME, Paris, France
| | - Catherine Monteil
- Central Infection Control Team, Assistance Publique - Hôpitaux de Paris, Paris, France
| | - Sandra Fournier
- Central Infection Control Team, Assistance Publique - Hôpitaux de Paris, Paris, France
| | - Juliette Oliary
- Groupe hospitalo-universitaire APHP Nord-Université de Paris, Site Lariboisière, Pharmacie, Paris, France
| | - Helga Junot
- Groupe hospitalo-universitaire APHP Sorbonne Université, Site Pitié-Salpêtrière, Pharmacie, Paris, France
| | - Pierre Sabatier
- Agence Générale des Equipements et Produits de Santé, Assistance Publique - Hôpitaux de Paris, Pharmacie, Paris, France
| | - Raphaël Porcher
- Groupe hospitalo-universitaire APHP Centre-Université de Paris, Site Hôtel-Dieu, Centre for Clinical Epidemiology, Paris, France; Université de Paris, CRESS UMR1153, INSERM, INRAE, Paris, France
| | - Jérôme Robert
- Groupe hospitalo-universitaire APHP Sorbonne Université, Site Pitié-Salpêtrière, Laboratoire de Bactériologie-Hygiène and CIMI-Paris, Inserm U1135, Sorbonne Université, Paris, France
| | - Vincent Jarlier
- Groupe hospitalo-universitaire APHP Sorbonne Université, Site Pitié-Salpêtrière, Laboratoire de Bactériologie-Hygiène and CIMI-Paris, Inserm U1135, Sorbonne Université, Paris, France.
| | | |
Collapse
|
25
|
Amikacin in combination with zinc pyrithione prevents growth of a multidrug-resistant carbapenem-resistant Klebsiella pneumoniae isolate. Int J Antimicrob Agents 2021; 58:106442. [PMID: 34551357 PMCID: PMC9371889 DOI: 10.1016/j.ijantimicag.2021.106442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 09/06/2021] [Accepted: 09/12/2021] [Indexed: 11/24/2022]
|
26
|
Sreenath K, Batra P, Vinayaraj EV, Bhatia R, SaiKiran KVP, Singh V, Singh S, Verma N, Singh UB, Mohan A, Bhatnagar S, Trikha A, Guleria R, Chaudhry R. Coinfections with Other Respiratory Pathogens among Patients with COVID-19. Microbiol Spectr 2021; 9:e0016321. [PMID: 34287033 PMCID: PMC8552727 DOI: 10.1128/spectrum.00163-21] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 06/22/2021] [Indexed: 12/23/2022] Open
Abstract
Emerging evidence indicates that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected individuals are at an increased risk for coinfections; therefore, physicians need to be cognizant about excluding other treatable respiratory pathogens. Here, we report coinfection with SARS-CoV-2 and other respiratory pathogens in patients admitted to the coronavirus disease (COVID) care facilities of an Indian tertiary care hospital. From June 2020 through January 2021, we tested 191 patients with SARS-CoV-2 for 33 other respiratory pathogens using an fast track diagnostics respiratory pathogen 33 (FTD-33) assay. Additionally, information regarding other relevant respiratory pathogens was collected by reviewing their laboratory data. Overall, 13 pathogens were identified among patients infected with SARS-CoV-2, and 46.6% (89/191) of patients had coinfection with one or more additional pathogens. Bacterial coinfections (41.4% [79/191]) were frequent, with Staphylococcus aureus being the most common, followed by Klebsiella pneumoniae. Coinfections with SARS-CoV-2 and Pneumocystis jirovecii or Legionella pneumophila were also identified. The viral coinfection rate was 7.3%, with human adenovirus and human rhinovirus being the most common. Five patients in our cohort had positive cultures for Acinetobacter baumannii and K. pneumoniae, and two patients had active Mycobacterium tuberculosis infection. In total, 47.1% (90/191) of patients with coinfections were identified. The higher proportion of patients with coinfections in our cohort supports the systemic use of antibiotics in patients with severe SARS-CoV-2 pneumonia with rapid de-escalation based on respiratory PCR/culture results. The timely and simultaneous identification of coinfections can contribute to improved health of COVID-19 patients and enhanced antibiotic stewardship during the pandemic. IMPORTANCE Coinfections in COVID-19 patients may worsen disease outcomes and need further investigation. We found that a higher proportion of patients with COVID-19 were coinfected with one or more additional pathogens. A better understanding of the prevalence of coinfection with other respiratory pathogens in COVID-19 patients and the profile of pathogens can contribute to effective patient management and antibiotic stewardship during the current pandemic.
Collapse
Affiliation(s)
- K. Sreenath
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Priyam Batra
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - E. V. Vinayaraj
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Ridhima Bhatia
- Department of Anaesthesiology, Pain Medicine and Critical Care, All India Institute of Medical Sciences, New Delhi, India
| | - KVP SaiKiran
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Vishwajeet Singh
- Department of Geriatric Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Sheetal Singh
- Department of Hospital Administration, National Cancer Institute, Jhajjar, Haryana, India
| | - Nishant Verma
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Urvashi B. Singh
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Anant Mohan
- Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Sushma Bhatnagar
- Department of Onco-Anaesthesia and Palliative Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Anjan Trikha
- Department of Anaesthesiology, Pain Medicine and Critical Care, All India Institute of Medical Sciences, New Delhi, India
| | - Randeep Guleria
- Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Rama Chaudhry
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| |
Collapse
|
27
|
Contamination of Hospital Surfaces with Bacterial Pathogens under the Current COVID-19 Outbreak. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18179042. [PMID: 34501634 PMCID: PMC8431522 DOI: 10.3390/ijerph18179042] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/18/2021] [Accepted: 08/23/2021] [Indexed: 12/23/2022]
Abstract
The SARS-CoV-2 pandemic remains a global health issue for several reasons, such as the low vaccination rates and a lack of developed herd immunity to the evolution of SARS-CoV-2, as well as its potential inclination to elude neutralizing antibodies. It should be noted that the severity of the COVID-19 disease is significantly affected by the presence of co-infections. Comorbid conditions are caused not only by pathogenic and opportunistic microorganisms but also by some representatives of the environmental microbiome. The presence of patients with moderate and severe forms of the disease in hospitals indicates the need for epidemiological monitoring of (1) bacterial pathogens circulating in hospitals, especially the ESKAPE group pathogens, and (2) the microbiome of various surfaces in hospitals. In our study, we used combined methods based on PCR and NGS sequencing, which are widely used for epidemiological monitoring. Through this approach, we identified the DNA of pathogenic bacteria (Klebsiella pneumoniae, Pseudomonas aeruginosa, Staphylococcus aureus, CoNS, and Achromobacter spp.) on various surfaces. We also estimated the microbiome diversity of surfaces and identified the potential reservoirs of infections using 16S rRNA profiling. Although we did not assess the viability of identified microorganisms, our results indicate the possible risks of insufficient regular disinfection of surfaces, regardless of department, at the Infectious Diseases Hospital. Controlling the transmission of nosocomial diseases is critical to the successful treatment of COVID-19 patients, the rational use of antimicrobial drugs, and timely decontamination measures.
Collapse
|
28
|
Pintado V, Ruiz-Garbajosa P, Escudero-Sanchez R, Gioia F, Herrera S, Vizcarra P, Fortún J, Cobo J, Martín-Dávila P, Morosini MI, Cantón R, Moreno S. Carbapenemase-producing Enterobacterales infections in COVID-19 patients. Infect Dis (Lond) 2021; 54:36-45. [PMID: 34382910 PMCID: PMC8425444 DOI: 10.1080/23744235.2021.1963471] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Background Carbapenemase-producing Enterobacterales (CPE) infections have been occasionally described in patients with coronavirus disease-19 (COVID-19). We assess the clinical features and outcome of these infections. Methods In this retrospective single-centre, case-control study, we included 54 patients with CPE infection: 30 case-patients (COVID-19) and 24 controls (non-COVID-19), collected between March and May 2020. We compared the epidemiological, clinical features, and outcome between cases and controls. Results CPE infection was more frequent in COVID-19 patients than in controls (1.1 vs. 0.5%, p = .005). COVID-19 patients were younger, had a lower frequency of underlying diseases (p = .01), and a lower median Charlson score (p = .002). Predisposing factors such as antimicrobial use, mechanical ventilation, or ICU admission, were more frequent in COVID-19 patients (p < .05). There were 73 episodes of infection (42 cases and 31 controls) that were more frequently hospital-acquired and diagnosed at the ICU in COVID-19 patients (p < .001). Urinary tract was the most common source of infection (47.9%), followed by pneumonia (23.3%). The frequency of severe sepsis or shock (p = .01) as well as the median SOFA score (p = .04) was higher in cases than in controls. Klebsiella pneumoniae (80.8%), Serratia marcescens (11%) and Enterobacter cloacae (4.1%) were the most common bacteria in both groups (KPC 56.2%, OXA-48 26% and VIM 17.8%). Overall 30-d mortality rate of COVID-19 patients and controls was 30 and 16.7%, respectively (p = .25). Conclusions COVID-19 patients have an increased risk of CPE infections, which usually present as severe, nosocomial infections, appearing in critically-ill patients and associated with a high mortality.
Collapse
Affiliation(s)
- Vicente Pintado
- Infectious Diseases Department, Hospital Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Patricia Ruiz-Garbajosa
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Rosa Escudero-Sanchez
- Infectious Diseases Department, Hospital Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Francesca Gioia
- Infectious Diseases Department, Hospital Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Sabina Herrera
- Infectious Diseases Department, Hospital Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Pilar Vizcarra
- Infectious Diseases Department, Hospital Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Jesús Fortún
- Infectious Diseases Department, Hospital Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Javier Cobo
- Infectious Diseases Department, Hospital Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Pilar Martín-Dávila
- Infectious Diseases Department, Hospital Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - María Isabel Morosini
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Rafael Cantón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Santiago Moreno
- Infectious Diseases Department, Hospital Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| |
Collapse
|
29
|
Predisposition of COVID-19 patients to secondary infections: set in stone or subject to change? Curr Opin Infect Dis 2021; 34:357-364. [PMID: 34039879 DOI: 10.1097/qco.0000000000000736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
PURPOSE OF REVIEW There likely are several predisposing factors to secondary infections in patients with Coronavirus disease 2019 (COVID-19), some of which may be preventable. The aim of this review is to explore the literature, summarize potential predisposing factors to secondary infections and their incidence. It also summarizes a variety of healthcare scenarios in which different kinds of secondary infections occur. RECENT FINDINGS Apart from immune dysregulation, severe resource limitations in healthcare settings have made COVID-19 units conducive to a variety of secondary infections. Long-term effect of excess antibiotic use in COVID-19 patients is yet to be studied. Very few studies have assessed secondary infections as the primary outcome measure making it difficult to know the true incidence. Mortality attributable to secondary infections in COVID-19 patients is also unclear. SUMMARY Incidence of secondary infections in COVID-19 patients is likely higher than what is reported in the literature. Well designed studies are needed to understand the incidence and impact of secondary infections in this patient population. Many of these may be preventable especially now, as personal protective equipment and other healthcare resources are recovering. Infection prevention and control (IPC) and antimicrobial stewardship programmes (ASP) must reassess current situation to correct any breaches that could potentially cause more harm in these already vulnerable patients as we brace for a future surge with another pandemic wave.
Collapse
|
30
|
Hao H, Liu Y, Cao J, Gao K, Lu Y, Wang W, Wang P, Lu S, Hu L, Tong Z, Li W. Genomic New Insights Into Emergence and Clinical Therapy of Multidrug-Resistant Klebsiella pneumoniae in Infected Pancreatic Necrosis. Front Microbiol 2021; 12:669230. [PMID: 34248878 PMCID: PMC8269854 DOI: 10.3389/fmicb.2021.669230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 05/07/2021] [Indexed: 11/13/2022] Open
Abstract
Infected pancreatic necrosis (IPN) is a key risk factor in the progression of severe acute pancreatitis, and use of antibiotics is one of the main clinical actions. However, early prophylactic or unreasonable use of antibiotics promotes drug resistance in bacteria and also delays optimum treatment. To explore genomic evidence of rational antibiotic use in intensive care units, we isolated Klebsiella pneumoniae from IPN samples that showed the highest positive-culture rate in 758 patients. Based on whole-genome sequencing from eight strains, 42 antibiotic-resistant genes were identified in the chromatin and 27 in the plasmid, which included classic resistance-mechanism factors such as β-lactamases [16.67% (7/42) in the chromatin and 25.93% (7/27) in the plasmid]. The K. pneumoniae isolates were identified to be resistant to multiple antibiotics used in clinics. In vivo and in vitro, ceftazidime-avibactam (CZA) plus aztreonam (ATM) (2.5:1) showed more significant antibacterial effectiveness than CZA alone. The isolated K. pneumoniae were of three different types according to the resistance phenotypes for CZA and ATM. Those co-harboring bla NDM-5, bla CTX-M-15, bla OXA-1, and bla SHV-187 showed higher resistance to CAZ than bla NDM-5. Those co-harboring bla CTX-M-65, bla SHV-182, and bla TEM-181 were significantly less resistant to β-lactam than to other extended-spectrum β-lactamases. However, β-lactamases were inhibited by avibactam (AVI), except for NDM-5. ATM plus AVI showed a significant inhibitory effect on K. pneumoniae, and the minimum dosage of ATM was < 1 mg/L. In conclusion, we propose that ATM plus AVI could be a major therapy for complex infectious diseases caused by multidrug-resistant K. pneumoniae.
Collapse
Affiliation(s)
- Haibin Hao
- Department of Critical Care Medicine, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Yang Liu
- Department of Critical Care Medicine, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Jin Cao
- Laboratory of Microbiology, Basic Medical Laboratory, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Kun Gao
- Department of Critical Care Medicine, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China.,School of Medicine, Nanjing Medical University, Nanjing, China
| | - Yingying Lu
- Department of Critical Care Medicine, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China.,School of Medicine, Southeast University, Nanjing, China
| | - Weiping Wang
- Laboratory of Microbiology, Basic Medical Laboratory, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Peng Wang
- Department of Critical Care Medicine, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Sida Lu
- Department of Critical Care Medicine, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Long Hu
- Department of Bioinformatics, Hugobiotech Co., Ltd., Beijing, China
| | - Zhihui Tong
- Department of Critical Care Medicine, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Weiqin Li
- Department of Critical Care Medicine, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China.,National Institut of Healthcare Data Science at Nanjing University, Nanjing, China.,State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| |
Collapse
|
31
|
Diagnostic, Clinical and Post-SARS-CoV-2 Scenarios in Cancer Patients with SARS-CoV-2: Retrospective Analysis in Three German Cancer Centers. Cancers (Basel) 2021; 13:cancers13122917. [PMID: 34208007 PMCID: PMC8230714 DOI: 10.3390/cancers13122917] [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] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/01/2021] [Accepted: 06/08/2021] [Indexed: 12/30/2022] Open
Abstract
Simple Summary The study investigated diagnostic, clinical and post-SARS-CoV-2 scenarios in cancer patients with SARS-CoV-2 aiming to improve management of SARS-CoV-2 infections and cancer afterwards. Around half of patients were initially asymptomatic and were diagnosed with SARS-CoV-2 during routine or contact tracing screening. Of them, 33% developed COVID-19 lately. Eventually, predominant part of patients had asymptomatic SARS-CoV-2 or mild COVID-19 course. Lymphocytopenia preceding SARS-CoV-2 was associated with a significantly increased risk for severe or critical COVID-19 course. Commonly patients experienced a treatment delay post-SARS-CoV-2; one fifth developed progressive disease (PD) within that time and/or had to undergo therapy modifications following deterioration of the performance status or PD post-COVID-19. This study provides knowledge of real-life clinical courses of SARS-CoV-2 in oncology and contributes to improving therapeutic strategies for cancer patients in the COVID-19 pandemic. Abstract Oncologists face challenges in the management of SARS-CoV-2 infections and post-SARS-CoV-2 cancer treatment. We analyzed diagnostic, clinical and post-SARS-CoV-2 scenarios in patients from three German cancer centers with RT-PCR confirmed SARS-CoV-2 infection. Sixty-three patients with SARS-CoV-2 and hematologic or solid neoplasms were included. Thirty patients were initially asymptomatic, 10 of whom developed COVID-19 symptoms subsequently. Altogether 20 (32%) patients were asymptomatic, 18 (29%) had mild, 12 (19%) severe and 13 (20%) critical courses. Lymphocytopenia increased risk of severe/critical COVID-19 three-fold (p = 0.015). Asymptomatic course was not associated with age, remission status, therapies or co-morbidities. Secondary bacterial infection accompanied more than one third of critical COVID-19 cases. Treatment was delayed post-SARS-CoV-2 in 46 patients, 9 of whom developed progressive disease (PD). Cancer therapy was modified in 8 SARS-CoV-2 survivors because of deteriorating performance or PD. At the last follow-up, 17 patients had died from COVID-19 (n = 8) or PD (n = 9) giving an estimated 73% four-month overall survival rate. SARS-CoV-2 infection has a heterogenous course in cancer patients. Lymphocytopenia carries a significant risk of severe/critical COVID-19. SARS-CoV-2 disruption of therapy is as serious as SARS-CoV-2 infection itself. Careful surveillance will allow early restart of the anti-cancer treatment.
Collapse
|
32
|
Comparison of clinical features and outcomes in COVID-19 and influenza pneumonia patients requiring intensive care unit admission. Infection 2021; 49:965-975. [PMID: 34036458 PMCID: PMC8149291 DOI: 10.1007/s15010-021-01624-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 05/03/2021] [Indexed: 01/14/2023]
Abstract
BACKGROUND Little is known in distinguishing clinical features and outcomes between coronavirus disease-19 (COVID-19) and influenza (FLU). MATERIALS/METHODS Retrospective, single-centre study including patients with COVID-19 or FLU pneumonia admitted to the Intensive care Unit (ICU) of Policlinico Umberto I (Rome). Aims were: (1) to assess clinical features and differences of patients with COVID-19 and FLU, (2) to identify clinical and/or laboratory factors associated with FLU or COVID-19 and (3) to evaluate 30-day mortality, bacterial superinfections, thrombotic events and invasive pulmonary aspergillosis (IPA) in patients with FLU versus COVID-19. RESULTS Overall, 74 patients were included (19, 25.7%, FLU and 55, 74.3%, COVID-19), median age 67 years (58-76). COVID-19 patients were more male (p = 0.013), with a lower percentage of COPD (Chronic Obstructive Pulmonary Disease) and chronic kidney disease (CKD) (p = 0.001 and p = 0.037, respectively) than FLU. SOFA score was higher (p = 0.020) and lymphocytes were significantly lower in FLU than in COVID-19 [395.5 vs 770.0 cells/mmc, p = 0.005]. At multivariable analysis, male sex (OR 6.1, p < 0.002), age > 65 years (OR 2.4, p = 0.024) and lymphocyte count > 725 cells/mmc at ICU admission (OR 5.1, p = 0.024) were significantly associated with COVID-19, whereas CKD and COPD were associated with FLU (OR 0.1 and OR 0.16, p = 0.020 and p < 0.001, respectively). No differences in mortality, bacterial superinfections and thrombotic events were observed, whereas IPA was mostly associated with FLU (31.5% vs 3.6%, p = 0.0029). CONCLUSIONS In critically ill patients, male sex, age > 65 years and lymphocytes > 725 cells/mmc are related to COVID-19. FLU is associated with a significantly higher risk of IPA than COVID-19.
Collapse
|
33
|
Ahmed OB, Asghar AH, Bahwerth FS. Increasing frequency of Aminoglycoside-Resistant Klebsiella pneumoniae during the era of pandemic COVID-19. MATERIALS TODAY. PROCEEDINGS 2021:S2214-7853(21)03943-2. [PMID: 34075332 PMCID: PMC8160573 DOI: 10.1016/j.matpr.2021.05.344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 05/18/2021] [Indexed: 01/10/2023]
Abstract
The emergence of multidrug resistance to aminoglycosides in K. pneumoniae isolates is a growing concern, especially during pandemic Coronavirus disease 2019 (COVID-19). The study identifies antibiotic resistance in K. pneumoniae isolated from tertiary hospitals during pandemic COVID-19. Among 220 clinical isolates, the total rate of K. pneumoniae was found to be 89 (40.5%). Phenotyping results confirmed the resistance of aminoglycoside antibiotics in 51 (23.2%) of K. pneumoniae isolates. PCR results confirmed the existence of one or more aminoglycoside genes in 82.3% of the 51 isolates. The rmtD gene was the highest-detected gene (66.7%), followed by aac(6')-Ib (45.1%), aph(3')-Ia (45.1%), rmtB (29.4%), armA (21.6%), aac(3)-II (7.8%), and rmtA (3) (11.8%). Significantly, higher resistance strains showed a higher prevalence (61.5%) of aminoglycoside genes (p < 0.05). During COVID-19, there is a higher risk of acquiring MDR bacterial infections, so the monitoring of multidrug resistant bacteria must be continuously undertaken to implement effective measures in infection control and prevention.
Collapse
Affiliation(s)
- Omar B Ahmed
- Department of Environmental and Health Research, The Custodian of the Two Holy Mosques Institute for Hajj and Umrah Research, Umm Al-Qura University, Saudi Arabia
| | - Atif H Asghar
- Department of Environmental and Health Research, The Custodian of the Two Holy Mosques Institute for Hajj and Umrah Research, Umm Al-Qura University, Saudi Arabia
| | - Fayez S Bahwerth
- King Faisal Hospital Makkah, Ministry of Health, Makkah, Saudi Arabia
| |
Collapse
|
34
|
Mędrzycka-Dąbrowska W, Lange S, Zorena K, Dąbrowski S, Ozga D, Tomaszek L. Carbapenem-Resistant Klebsiella pneumoniae Infections in ICU COVID-19 Patients-A Scoping Review. J Clin Med 2021; 10:jcm10102067. [PMID: 34066031 PMCID: PMC8150615 DOI: 10.3390/jcm10102067] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/08/2021] [Accepted: 05/10/2021] [Indexed: 02/06/2023] Open
Abstract
Introduction: The spread of multidrug-resistant pathogens is a serious problem and challenge for the whole medical community. Carbapenem-resistant Klebsiella pneumoniae (CRKP) infections in immunocompromised patients have a severe course and may be fatal. Increasingly, these bacteria are exhibiting resistance to carbapenem antibiotics, which have been used as so-called drugs of last resort. The emergence of the new coronavirus and the pandemic that it has caused require changes to protect against the spread of the new SARS-CoV-2. These changes paradoxically may contribute to the spread of other infections. Methods: PubMed, Cochrane Library databases were searched using relevant keywords. A literature review of carbapenem-resistant Klebsiella pneumoniae infection in patients hospitalized for COVID-19 was conducted according to PRISMA recommendations. A written review protocol was not prepared. Results: 1016 studies in scientific databases were searched. After rejecting duplicate studies, 964 results were obtained. Inclusion and exclusion criteria were then applied, and studies were qualitatively analyzed. Finally, 11 studies were included in the review. The results of infected patients were from six countries. The prevalence of CRKP in Covid-19 patients ranged from 0.35–53%. The majority of CRKP infected patients were male (85%), with a mean age of 61 years. Among isolates, the predominant genes were KPC, OXY-48, CTX-M, TEM, NDM and SHV. Conclusion: The results presented in our review indicate the necessity of paying attention to carbapenem-resistant Klebsiella pneumoniae infections in patients with COVID-19. In order to prevent the increase of bacterial resistance, rational antibiotic therapy should be used, as well as continuous control and surveillance of hospital infections caused by multidrug-resistant organisms.
Collapse
Affiliation(s)
- Wioletta Mędrzycka-Dąbrowska
- Department of Anaesthesiology Nursing & Intensive Care, Faculty of Health Sciences, Medical University of Gdańsk, Dębinki 7, 80-211 Gdańsk, Poland
- Correspondence:
| | - Sandra Lange
- Department of Anesthesiology and Intensive Care, Hospitals Tczewskie SA, 30 Stycznia 57, 83-110 Tczew, Poland;
| | - Katarzyna Zorena
- Department of Immunobiology and Environment Microbiology, Faculty of Health Sciences, Medical University of Gdańsk, Dębinki 7, 80-211 Gdańsk, Poland;
| | - Sebastian Dąbrowski
- Departament of Medical Rescue, Faculty of Health Sciences, Medical University of Gdańsk, Dębinki 7, 80-211 Gdańsk, Poland;
| | - Dorota Ozga
- Institute of Health Sciences, College of Medical Sciences of the University of Rzeszow, St. Warzywna1A, 35-310 Rzeszow, Poland;
| | - Lucyna Tomaszek
- Department of Specialist Nursing, Faculty of Medicine and Health Sciences, Kraków Academy of Andrzej Frycz Modrzewski, St. Gustawa Herlinga-Grudzińskiego 1, 30-705 Kraków, Poland;
| |
Collapse
|
35
|
Westblade LF, Simon MS, Satlin MJ. Bacterial coinfections in coronavirus disease 2019. Trends Microbiol 2021; 29:930-941. [PMID: 33934980 PMCID: PMC8026275 DOI: 10.1016/j.tim.2021.03.018] [Citation(s) in RCA: 119] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/28/2021] [Accepted: 03/29/2021] [Indexed: 02/07/2023]
Abstract
Bacterial coinfections increase the severity of respiratory viral infections and were frequent causes of mortality in influenza pandemics but have not been well characterized in patients with coronavirus disease 2019 (COVID-19). The aim of this review was to identify the frequency and microbial etiologies of bacterial coinfections that are present upon admission to the hospital and that occur during hospitalization for COVID-19. We found that bacterial coinfections were present in <4% of patients upon admission and the yield of routine diagnostic tests for pneumonia was low. When bacterial coinfections did occur, Staphylococcus aureus, Streptococcus pneumoniae, and Haemophilus influenzae were the most common pathogens and atypical bacteria were rare. Although uncommon upon admission, bacterial infections frequently occurred in patients with prolonged hospitalization, and Pseudomonas aeruginosa, Klebsiella spp., and S. aureus were common pathogens. Antibacterial therapy and diagnostic testing for bacterial infections are unnecessary upon admission in most patients hospitalized with COVID-19, but clinicians should be vigilant for nosocomial bacterial infections.
Collapse
Affiliation(s)
- Lars F Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA; Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Matthew S Simon
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Michael J Satlin
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA; Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
| |
Collapse
|
36
|
Rothe K, Lahmer T, Rasch S, Schneider J, Spinner CD, Wallnöfer F, Wurst M, Schmid RM, Waschulzik B, Fuest K, Kriescher S, Schneider G, Busch DH, Feihl S, Heim M. Dexamethasone therapy and rates of secondary pulmonary and bloodstream infections in critically ill COVID-19 patients. Multidiscip Respir Med 2021; 16:793. [PMID: 34760275 PMCID: PMC8567088 DOI: 10.4081/mrm.2021.793] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 10/01/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Coronavirus disease 2019 (COVID-19) has become a pandemic. Bacterial superinfections seem to be associated with higher mortality in COVID-19 patients in intensive care units (ICUs). However, details on the prevalence and species distribution of secondary infections are limited. Moreover, the increasing use of dexamethasone may pose an additional risk of superinfections. METHODS We performed a single-center retrospective study of the clinical and microbiological characteristics of 154 COVID-19 patients admitted to the ICU between March 2020 and January 2021, focusing on bacterial infections, use of antimicrobial agents and dexamethasone therapy. RESULTS The median age was 68 years; 67.5% of the patients were men. Critically ill COVID-19 patients were treated with dexamethasone since July 2020 (second wave), which was not common during the first wave of the pandemic. In the dexamethasone group (n=90, 58.4%), respiratory pathogens were detected more frequently, as were multidrugresistant pathogens. The number of patients with polymicrobial detection of respiratory pathogens was significantly increased (p=0.013). The most frequently detected species were Enterobacterales, Staphylococcus aureus, and Aspergillus fumigatus. The rates of bloodstream infections did not differ between the groups. The use of dexamethasone in ICU COVID-19 patients was associated with higher rates of respiratory infectious complications. CONCLUSIONS Secondary infections are present in a substantial fraction of critically ill COVID-19 patients. Respiratory pathogens were detectable in the majority of COVID-19 ICU patients. The use of dexamethasone poses a potential risk of secondary pulmonary infections. Infectious complications in patients with dexamethasone therapy could be associated with worse outcomes.
Collapse
Affiliation(s)
- Kathrin Rothe
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, School of Medicine, Munich
| | - Tobias Lahmer
- Department of Internal Medicine II, Technical University of Munich, School of Medicine, Munich
| | - Sebastian Rasch
- Department of Internal Medicine II, Technical University of Munich, School of Medicine, Munich
| | - Jochen Schneider
- Department of Internal Medicine II, Technical University of Munich, School of Medicine, Munich
| | - Christoph D. Spinner
- Department of Internal Medicine II, Technical University of Munich, School of Medicine, Munich
- German Center for Infection Research (DZIF), Partner Site Munich, Munich
| | - Fabian Wallnöfer
- Department of Internal Medicine II, Technical University of Munich, School of Medicine, Munich
| | - Milena Wurst
- Department of Internal Medicine II, Technical University of Munich, School of Medicine, Munich
| | - Roland M. Schmid
- Department of Internal Medicine II, Technical University of Munich, School of Medicine, Munich
| | - Birgit Waschulzik
- Institute of Medical Informatics, Statistics and Epidemiology, Technical University of Munich, School of Medicine, Munich
| | - Kristina Fuest
- Department of Anaesthesiology and Intensive Care Medicine, Technical University of Munich, School of Medicine, Munich, Germany
| | - Silja Kriescher
- Department of Anaesthesiology and Intensive Care Medicine, Technical University of Munich, School of Medicine, Munich, Germany
| | - Gerhard Schneider
- Department of Anaesthesiology and Intensive Care Medicine, Technical University of Munich, School of Medicine, Munich, Germany
| | - Dirk H. Busch
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, School of Medicine, Munich
- German Center for Infection Research (DZIF), Partner Site Munich, Munich
| | - Susanne Feihl
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, School of Medicine, Munich
| | - Markus Heim
- Department of Anaesthesiology and Intensive Care Medicine, Technical University of Munich, School of Medicine, Munich, Germany
| |
Collapse
|