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Duan Y, Wang J, Wang S, Zhang R, Hu J, Li W, Chen B. Risk factors, outcomes, and epidemiological and etiological study of hospitalized COVID-19 patients with bacterial co-infection and secondary infections. Eur J Clin Microbiol Infect Dis 2024; 43:577-586. [PMID: 38246947 PMCID: PMC10917871 DOI: 10.1007/s10096-024-04755-5] [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: 12/13/2023] [Accepted: 01/10/2024] [Indexed: 01/23/2024]
Abstract
BACKGROUND As a common complication of viral respiratory tract infection, bacterial infection was associated with higher mortality and morbidity. Determining the prevalence, culprit pathogens, outcomes, and risk factors of co-infection and secondary infection occurring in hospitalized patients with coronavirus disease 2019 (COVID-19) will be beneficial for better antibiotic management. METHODS In this retrospective cohort research, we assessed clinical characteristics, laboratory parameters, microbiologic results, and outcomes of laboratory-confirmed COVID-19 patients with bacterial co-infection and secondary infection in West China Hospital from 2022 December 2nd to 2023 March 15th. RESULTS The incidence of bacterial co-infection and secondary infection, as defined by positive culture results of clinical specimens, was 16.3% (178/1091) and 10.1% (110/1091) respectively among 1091 patients. Acinetobacter, Klebsiella, and Pseudomonas were the most commonly identified bacteria in respiratory tract samples of COVID-19 patients. In-hospital mortality of COVID-19 patients with co-infection (17.4% vs 9.5%, p = 0.003) and secondary infection (28.2% vs 9.5%, p < 0.001) greatly exceeded that of COVID-19 patients without bacterial infection. Cardiovascular disease (1.847 (1.202-2.837), p = 0.005), severe COVID-19 (1.694 (1.033-2.778), p = 0.037), and critical COVID-19 (2.220 (1.196-4.121), p = 0.012) were proved to be risk factors for bacterial co-infection, while only critical COVID-19 (1.847 (1.202-2.837), p = 0.005) was closely related to secondary infection. CONCLUSIONS Bacterial co-infection and secondary infection could aggravate the disease severity and worsen clinical outcomes of COVID-19 patients. Notably, only critical COVID-19 subtype was proved to be an independent risk factor for both co-infection and secondary infection. Therefore, standard empirical antibiotics was recommended for critically ill COVID-19 rather than all the inpatients according to our research.
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Affiliation(s)
- Yishan Duan
- Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, Chengdu, 610041, Sichuan Province, China
| | - Jing Wang
- Precision Medicine Center, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Suyan Wang
- Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan Province, China
| | - Rui Zhang
- Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, Chengdu, 610041, Sichuan Province, China
| | - Jinrui Hu
- Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, Chengdu, 610041, Sichuan Province, China
| | - Weimin Li
- Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, Chengdu, 610041, Sichuan Province, China
- Precision Medicine Center, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, 610041, China
- Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan Province, China
- The Research Units of West China, Chinese Academy of Medical Sciences, West China Hospital, Chengdu, 610041, Sichuan, China
- State Key Laboratory of Respiratory Health and Multimorbidity, West China Hospital, Chengdu, 610041, Sichuan, China
| | - Bojiang Chen
- Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, Chengdu, 610041, Sichuan Province, China.
- Precision Medicine Center, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, 610041, China.
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Zhang Y, Ma Y, Sun W, Zhou X, Wang R, Xie P, Dai L, Gao Y, Li J. Exploring gut-lung axis crosstalk in SARS-CoV-2 infection: Insights from a hACE2 mouse model. J Med Virol 2024; 96:e29336. [PMID: 38193530 DOI: 10.1002/jmv.29336] [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: 10/08/2023] [Revised: 11/27/2023] [Accepted: 12/11/2023] [Indexed: 01/10/2024]
Abstract
Based on the forefront of clinical research, there is a growing recognition that the gut microbiota, which plays a pivotal role in shaping both the innate and adaptive immune systems, may significantly contribute to the pathogenesis of coronavirus disease 2019 (COVID-19). Although an association between altered gut microbiota and COVID-19 pathogenesis has been established, the causative mechanisms remain incompletely understood. Additionally, the validation of the precise functional alterations within the gut microbiota relevant to COVID-19 pathogenesis has been limited by a scarcity of suitable animal experimental models. In the present investigation, we employed a newly developed humanized ACE2 knock-in (hACE2-KI) mouse model, capable of recapitulating critical aspects of pulmonary and intestinal infection, to explore the modifications in the gut microbiota following severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Examination of fecal samples using 16S rRNA gene profiling unveiled a notable reduction in species richness and conspicuous alterations in microbiota composition at 6 days postinfection (dpi). These alterations were primarily characterized by a decline in beneficial bacterial species and an escalation in certain opportunistic pathogens. Moreover, our analysis entailed a correlation study between the gut microbiota and plasma cytokine concentrations, revealing the potential involvement of the Lachnospiraceae_NK4A136_group and unclassified_f_Lachnospiraceae genera in attenuating hyperinflammatory responses triggered by the infection. Furthermore, integration of gut microbiota data with RNA-seq analysis results suggested that the increased presence of Staphylococcus in fecal samples may signify the potential for bacterial coinfection in lung tissues via gut translocation. In summary, our hACE2-KI mouse model effectively recapitulated the observed alterations in the gut microbiota during SARS-CoV-2 infection. This model presents a valuable tool for elucidating gut microbiota-targeted strategies aimed at mitigating COVID-19.
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Affiliation(s)
- Yu Zhang
- Department of Biosafety, School of Basic Medicine, Army Medical University, Chongqing, China
| | - Yifang Ma
- Department of Biosafety, School of Basic Medicine, Army Medical University, Chongqing, China
| | - Weiyang Sun
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Xiaoyang Zhou
- Department of Biosafety, School of Basic Medicine, Army Medical University, Chongqing, China
| | - Ruixuan Wang
- Department of Biosafety, School of Basic Medicine, Army Medical University, Chongqing, China
| | - Peng Xie
- Department of Biosafety, School of Basic Medicine, Army Medical University, Chongqing, China
| | - Lu Dai
- Department of Biosafety, School of Basic Medicine, Army Medical University, Chongqing, China
| | - Yuwei Gao
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Jintao Li
- Department of Biosafety, School of Basic Medicine, Army Medical University, Chongqing, China
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Bordi L, Vulcano A, Sberna G, Nonis M, Giacomini P, Maggi F, Fontana C, Lalle E. Co-Circulation of SARS-CoV-2 and Other Respiratory Pathogens in Upper and Lower Respiratory Tracts during Influenza Season 2022-2023 in Lazio Region. Microorganisms 2023; 11:2239. [PMID: 37764083 PMCID: PMC10536072 DOI: 10.3390/microorganisms11092239] [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: 08/25/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
Lower respiratory tract infections (LRTIs) occur when there is a lower airway tract infection. They are well-known for increasing the susceptibility of patients to bacterial/fungal co-infections and super-infections. In this study, we present the results of our investigation, which involved 381 consecutive patients admitted to our hospital during the Influenza season from October 2022 to April 2023. Among the 381 specimens, 75 were bronchoalveolar (BAL), and 306 were nasopharyngeal swabs (NPSs). Notably, 34.4% of the examined samples tested positive for SARS-CoV-2. Of these, we observed that 7.96% of NPSs showed positivity only for other respiratory viruses, while a substantial percentage (77%) of BAL specimens exhibited positive results only for bacterial co-infections. The results of our study not only confirm the importance of co-infections in COVID-19 but also emphasize the significance of utilizing rapid diagnostic tests (RDTs) for the timely diagnosis of LRTIs. In fact, RDTs allow for the identification of multiple pathogens, providing clinicians with useful and timely information to establish effective therapy.
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Affiliation(s)
- Licia Bordi
- Laboratory of Virology and Biosafety Laboratories, National Institute of Infectious Diseases "L. Spallanzani" IRCCS, 00149 Rome, Italy
| | - Antonella Vulcano
- Laboratory of Microbiology and Biological Bank, National Institute of Infectious Diseases "L. Spallanzani" IRCCS, 00149 Rome, Italy
| | - Giuseppe Sberna
- Laboratory of Virology and Biosafety Laboratories, National Institute of Infectious Diseases "L. Spallanzani" IRCCS, 00149 Rome, Italy
| | - Marino Nonis
- Health Management Direction, National Institute of Infectious Diseases "L. Spallanzani" IRCCS, 00149 Rome, Italy
| | - Paolo Giacomini
- Health Management Direction, National Institute of Infectious Diseases "L. Spallanzani" IRCCS, 00149 Rome, Italy
| | - Fabrizio Maggi
- Laboratory of Virology and Biosafety Laboratories, National Institute of Infectious Diseases "L. Spallanzani" IRCCS, 00149 Rome, Italy
| | - Carla Fontana
- Laboratory of Microbiology and Biological Bank, National Institute of Infectious Diseases "L. Spallanzani" IRCCS, 00149 Rome, Italy
| | - Eleonora Lalle
- Laboratory of Virology and Biosafety Laboratories, National Institute of Infectious Diseases "L. Spallanzani" IRCCS, 00149 Rome, Italy
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