Predictors of Severity and Co-Infection Resistance Profile in COVID-19 Patients: First Report from Upper Egypt

References

• Guo Y-R, Cao QD, Hong ZS, et al. The origin, transmission and clinical therapies on coronavirus disease 2019 (COVID-19) outbreak–an update on the status. Mil Med Res. 2020;7(1):1–10.31928528
   PubMed Web of Science ®Google Scholar
• Sohrabi C, Alsafi Z, O’Neill N, et al. World Health Organization declares global emergency: a review of the 2019 novel coronavirus (COVID-19). Int J Surg. 2020.
   Web of Science ®Google Scholar
• WHO. Coronavirus Disease (COVID-19) Dashboard; 2020.
   Google Scholar
• WHO. 2020 Available from: https://covid19.who.int/region/emro/country/eg. Accessed 923, 2020.
   Google Scholar
• Kumar Y, Singh H, Patel CN. In silico prediction of potential inhibitors for the main protease of SARS-CoV-2 using molecular docking and dynamics simulation based drug-repurposing. J Infect Public Health. 2020;13(9):1210–1223. doi:10.1016/j.jiph.2020.06.01632561274
   PubMed Web of Science ®Google Scholar
• Zhu N, Zhang D, Wang W, et al. A novel coronavirus from patients with pneumonia in China, 2019. N Engl J Med. 2020.
   Web of Science ®Google Scholar
• Chan JF, Yuan S, Kok KH, et al. A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster. Lancet. 2020;395(10223):514–523.31986261
   PubMed Web of Science ®Google Scholar
• Chen N, Zhou M, Dong X, et al. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study. Lancet. 2020;395(10223):507–513. doi:10.1016/S0140-6736(20)30211-732007143
   PubMed Web of Science ®Google Scholar
• Li T, Wei C, Li W, Hongwei F, Shi J. Beijing Union Medical College Hospital on “pneumonia of novel coronavirus infection” diagnosis and treatment proposal (V2. 0). Med J Peking Union Med Coll Hosp. 2020.
   Google Scholar
• Li Q, Guan X, Wu P, et al. Early transmission dynamics in Wuhan, China, of novel coronavirus–infected pneumonia. N Engl J Med. 2020;382(13):1199–1207. doi:10.1056/NEJMoa200131631995857
   PubMed Web of Science ®Google Scholar
• Ai T, Yang Z, Hou H, et al. Correlation of chest CT and RT-PCR testing in coronavirus disease 2019 (COVID-19) in China: a report of 1014 cases. Radiology. 2020;200642.
   PubMed Web of Science ®Google Scholar
• Favaloro EJ, Lippi G. Recommendations for Minimal Laboratory Testing Panels in Patients with COVID-19: Potential for Prognostic Monitoring. In Seminars in Thrombosis and Hemostasis. Thieme Medical Publishers; 2020.
   Google Scholar
• Mahdavi A, Khalili N, Davarpanah AH, et al. Radiologic management of COVID-19: preliminary experience of the Iranian Society of Radiology COVID-19 Consultant Group (ISRCC). Iran J Radiol. 2020;17(2). doi:10.5812/iranjradiol.102324
   Web of Science ®Google Scholar
• Organization, W.H. Clinical Management of Severe Acute Respiratory Infection (SARI) When COVID-19 Disease is Suspected: Interim Guidance, 13 March 2020. World Health Organization; 2020.
   Google Scholar
• Ruan Q, Yang K, Wang W, et al. Clinical predictors of mortality due to COVID-19 based on an analysis of data of 150 patients from Wuhan, China. Intensive Care Med. 2020;46(5):846–848. doi:10.1007/s00134-020-05991-x32125452
   PubMed Web of Science ®Google Scholar
• Rice TW, Rubinson L, Uyeki TM, et al. Critical illness from 2009 pandemic influenza A (H1N1) virus and bacterial co-infection in the United States. Crit Care Med. 2012;40(5):1487.22511131
   PubMed Web of Science ®Google Scholar
• Morris DE, Cleary DW, Clarke SC. Secondary bacterial infections associated with influenza pandemics. Front Microbiol. 2017;8:1041.28690590
   PubMed Web of Science ®Google Scholar
• Canning B, Senanayake V, Burns D, et al. Post-influenza Aspergillus ventriculitis. Clin Infect Pract. 2020;7–8:100026. doi:10.1016/j.clinpr.2020.100026
   Google Scholar
• Mulcahy ME, McLoughlin RMJM. Staphylococcus aureus and influenza A virus: partners in coinfection. MBio. 2016;7(6).
   Web of Science ®Google Scholar
• Bengoechea JA, Bamford CG. SARS-CoV-2, bacterial co-infections, and AMR: the deadly trio in COVID-19? EMBO Mol Med. 2020;12(7):e12560. doi:10.15252/emmm.20201256032453917
   PubMed Web of Science ®Google Scholar
• American Thoracic Society, Infectious Diseases Society of America. Guidelines for the management of adults with hospital-acquired, ventilator-associated, and healthcare-associated pneumonia. Am J Respir Crit Care Med. 2005;171(4):388.15699079
   PubMed Web of Science ®Google Scholar
• Wiegers HMG, van Nijen L, van Woensel JBM, et al. Bacterial co-infection of the respiratory tract in ventilated children with bronchiolitis; a retrospective cohort study. BMC Infect Dis. 2019;19(1):938. doi:10.1186/s12879-019-4468-331694565
   PubMed Web of Science ®Google Scholar
• Rubin GD, Ryerson CJ, Haramati LB, et al. The role of chest imaging in patient management during the COVID-19 pandemic: a multinational consensus statement from the Fleischner Society. Chest. 2020.
   Web of Science ®Google Scholar
• Guan W-J, Ni Z-Y, Hu Y, et al. Clinical characteristics of coronavirus disease 2019 in China. N Engl J Med. 2020;382(18):1708–1720. doi:10.1056/NEJMoa200203232109013
   PubMed Web of Science ®Google Scholar
• Li L-Q, Huang T, Wang Y-Q, et al. COVID-19 patients’ clinical characteristics, discharge rate, and fatality rate of meta-analysis. J Med Virol. 2020;92(6):577–583. doi:10.1002/jmv.2575732162702
   PubMed Web of Science ®Google Scholar
• Qian K, Deng Y, Tai Y, Peng J, Peng H, Jiang L. Clinical characteristics of 2019 novel infected coronavirus pneumonia: a systemic review and meta-analysis. medRxiv. 2020.
   PubMedGoogle Scholar
• Klein SL, Huber S. Sex Differences in Susceptibility to Viral Infection, in Sex Hormones and Immunity to Infection. Springer; 2010:93–122.
   Google Scholar
• Yang J, Zheng Y, Gou X, et al. Prevalence of comorbidities and its effects in patients infected with SARS-CoV-2: a systematic review and meta-analysis. Int J Infect Dis. 2020;94:91–95. doi:10.1016/j.ijid.2020.03.01732173574
   PubMed Web of Science ®Google Scholar
• Chew NWS, Lee GKH, Tan BYQ, et al. A multinational, multicentre study on the psychological outcomes and associated physical symptoms amongst healthcare workers during COVID-19 outbreak. Brain Behav Immun. 2020;88:559–565. doi:10.1016/j.bbi.2020.04.04932330593
   PubMed Web of Science ®Google Scholar
• Fu L, Wang B, Yuan T, et al. Clinical characteristics of coronavirus disease 2019 (COVID-19) in China: a systematic review and meta-analysis. J Infect. 2020;80(6):656–665. doi:10.1016/j.jinf.2020.03.04132283155
   PubMed Web of Science ®Google Scholar
• Zhang H, Shang W, Liu Q, Zhang X, Zheng M, Yue M. Clinical characteristics of 194 cases of COVID-19 in Huanggang and Taian, China. Infection. 2020;1–8.31919762
   PubMed Web of Science ®Google Scholar
• Zhang J, Wang X, Jia X, et al. Risk factors for disease severity, unimprovement, and mortality in COVID-19 patients in Wuhan, China. Clin Microbiol Infect. 2020;26(6):767–772. doi:10.1016/j.cmi.2020.04.01232304745
   PubMed Web of Science ®Google Scholar
• Peiris JSM, Chu CM, Cheng V, et al. Clinical progression and viral load in a community outbreak of coronavirus-associated SARS pneumonia: a prospective study. Lancet. 2003;361(9371):1767–1772. doi:10.1016/S0140-6736(03)13412-512781535
   PubMed Web of Science ®Google Scholar
• Assiri A, McGeer A, Perl TM, et al. Hospital outbreak of Middle East respiratory syndrome coronavirus. N Engl J Med. 2013;369(5):407–416. doi:10.1056/NEJMoa130674223782161
   PubMed Web of Science ®Google Scholar
• Chen G, Wu D, Guo W, et al. Clinical and immunologic features in severe and moderate forms of coronavirus disease. J Clin Invest. 2019;137244.
   Google Scholar
• Wang F, Hou H, Luo Y, et al. The laboratory tests and host immunity of COVID-19 patients with different severity of illness. JCI Insight. 2020;5(10). doi:10.1172/jci.insight.137799
   Web of Science ®Google Scholar
• Salehi S, Abedi A, Balakrishnan S, Gholamrezanezhad A, et al. Coronavirus disease 2019 (COVID-19): a systematic review of imaging findings in 919 patients. Am J Roentgenol. 2020:1–7. doi:10.2214/AJR.20.24425
   Web of Science ®Google Scholar
• Song F, Shi N, Shan F, et al. Emerging 2019 novel coronavirus (2019-nCoV) pneumonia. Radiology. 2020;295(1):210–217.32027573
   PubMed Web of Science ®Google Scholar
• Li X, Zeng X, Liu B, Yu Y. COVID-19 infection presenting with CT halo sign. Radiology. 2020;2(1):e200026.
   PubMed Web of Science ®Google Scholar
• Jin Y-H, Cai L, Cheng Z-S, et al. A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version). Mil Med Res. 2020;7(1):4. doi:10.1186/s40779-020-0233-632029004
   PubMed Web of Science ®Google Scholar
• Pan Y, Guan H, Zhou S, et al. Initial CT findings and temporal changes in patients with the novel coronavirus pneumonia (2019-nCoV): a study of 63 patients in Wuhan, China. Eur Radiol. 2020;1–4.31278580
   PubMed Web of Science ®Google Scholar
• Diao K, Han P, Pang T, et al. HRCT imaging features in representative imported cases of 2019 novel coronavirus pneumonia. Precis Clin Med. 2020;3(1):9–13. doi:10.1093/pcmedi/pbaa004
   Google Scholar
• Zhu X, Ge Y, Wu T, et al. Co-infection with respiratory pathogens among COVID-2019 cases. Virus Res. 2020;285:198005. doi:10.1016/j.virusres.2020.19800532408156
   PubMed Web of Science ®Google Scholar
• Cox MJ, Loman N, Bogaert D, et al. Co-infections: potentially lethal and unexplored in COVID-19. Lancet Microbe. 2020;1(1):e11. doi:10.1016/S2666-5247(20)30009-432835323
   PubMedGoogle Scholar
• Lansbury L, Lim B, Baskaran V, et al. Co-infections in people with COVID-19: a systematic review and meta-analysis. J Infect. 2020;81(2):266–275. doi:10.1016/j.jinf.2020.05.04632473235
   PubMed Web of Science ®Google Scholar
• Noviello S, Huang DB. The basics and the advancements in diagnosis of bacterial lower respiratory tract infections. Diagnostics. 2019;9(2):37.
   Web of Science ®Google Scholar
• Wu C, Chen X, Cai Y, et al. Risk factors associated with acute respiratory distress syndrome and death in patients with coronavirus disease 2019 pneumonia in Wuhan, China. JAMA Intern Med. 2020;180(7):934. doi:10.1001/jamainternmed.2020.099432167524
   PubMed Web of Science ®Google Scholar
• Wang Z, Yang B, Li Q, et al. Clinical features of 69 cases with coronavirus disease 2019 in Wuhan, China. Clin Infect Dis. 2020;71(15):769–777. doi:10.1093/cid/ciaa27232176772
   PubMed Web of Science ®Google Scholar
• Arentz M, Yim E, Klaff L, et al. Characteristics and outcomes of 21 critically Ill patients with COVID-19 in Washington State. JAMA. 2020;323(16):1612. doi:10.1001/jama.2020.432632191259
   PubMed Web of Science ®Google Scholar
• El-Mokhtar MA, Hassanein KM, Ahmed AS, et al. Antagonistic activities of cell-free supernatants of lactobacilli against extended-spectrum β-lactamase producing Klebsiella pneumoniae and Pseudomonas aeruginosa. Infect Drug Resist. 2020;13:543–552. doi:10.2147/IDR.S23560332110064
   PubMed Web of Science ®Google Scholar
• Elgendy SG, Abdel Hameed MR, El-Mokhtar MA. Tigecycline resistance among Klebsiella pneumoniae isolated from febrile neutropenic patients. J Med Microbiol. 2018;67(7):972–975. doi:10.1099/jmm.0.00077029799385
   PubMed Web of Science ®Google Scholar
• El-Mokhtar MA, Hetta HF. Ambulance vehicles as a source of multidrug-resistant infections: a multicenter study in Assiut City, Egypt. Infect Drug Resist. 2018;11:587–594. doi:10.2147/IDR.S15178329731647
   PubMed Web of Science ®Google Scholar
• Ahmed SH, Daef EA, Badary MS, et al. Nosocomial blood stream infection in intensive care units at Assiut University Hospitals (Upper Egypt) with special reference to extended spectrum β-lactamase producing organisms. BMC Res Notes. 2009;2(1):76. doi:10.1186/1756-0500-2-7619419535
   PubMedGoogle Scholar
• Drew RH, Gallis HA. Therapy, azithromycin—spectrum of activity, pharmacokinetics, and clinical applications. Pharmacotherapy. 1992;12(3):161–173.1319048
   PubMed Web of Science ®Google Scholar
• Hassan AT, Mohamed SA, Mohamed MS, El-Mokhtar MA. Acute exacerbations of chronic obstructive pulmonary disease: etiological bacterial pathogens and antibiotic resistance in Upper Egypt. Egypt J Bronchol. 2016;10(3):283.
   Google Scholar
• Daef EA, Mohamad IS, Ahmad AS, El-Gendy SG, Ahmed EH, Sayed IM. Relationship between clinical and environmental isolates of Acinetobacter baumannii in Assiut University hospitals. J Am Sci. 2013;9(11s):67–73.
   Google Scholar
• Enas AD, Ismail SM, Ahmed SA, et al. Detection of outbreak caused by multi-drug resistant Acinetobacter baumannii in Assiut University Hospitals. Afr J Microbiol Res. 2014;8(22):2238–2244. doi:10.5897/AJMR2014.6795
   Google Scholar
• Lin S-H, Kuo P-H, Hsueh P-R, et al. Sputum bacteriology in hospitalized patients with acute exacerbation of chronic obstructive pulmonary disease in Taiwan with an emphasis on Klebsiella pneumoniae and Pseudomonas aeruginosa. Respirology. 2007;12(1):81–87. doi:10.1111/j.1440-1843.2006.00999.x17207030
   PubMed Web of Science ®Google Scholar
• Kollef MH, Golan Y, Micek ST, et al. Appraising contemporary strategies to combat multidrug resistant gram-negative bacterial infections–proceedings and data from the gram-negative resistance summit. Clin Infect Dis. 2011;53(Suppl suppl_2):SS33–SS38. doi:10.1093/cid/cir475
   Web of Science ®Google Scholar
• Martins A, de Lourdes RS Cunha M. Methicillin resistance in Staphylococcus aureus and coagulase-negative staphylococci: epidemiological and molecular aspects. Microbiol Immunol. 2007;51(9):787–795.17895595
   PubMed Web of Science ®Google Scholar
• Eltwisy HO, Abdel-Fattah M, Elsisi AM, et al. Pathogenesis of Staphylococcus haemolyticus on primary human skin fibroblast cells. Virulence. 2020;11(1):1142–1157. doi:10.1080/21505594.2020.180996232799619
   PubMed Web of Science ®Google Scholar
• Abdel-Rahim MH, Mohammed AH, Ghandour AM, Shaaban LH, Hassan HA. Bacterial nosocomial pneumonia in respiratory intensive care unit of Assiut University Hospital. Egypt J Med Microbiol. 2019;28(4):113–139.
   Google Scholar
• Lincopan N, McCulloch JA, Reinert C, Cassettari VC, Gales AC, Mamizuka EM. First isolation of metallo-beta-lactamase-producing multiresistant Klebsiella pneumoniae from a patient in Brazil. J Clin Microbiol. 2005;43(1):516–519. doi:10.1128/JCM.43.1.516-519.200515635033
   PubMed Web of Science ®Google Scholar
• Rawson TM, Moore LS, Zhu N, et al. Bacterial and fungal co-infection in individuals with coronavirus: a rapid review to support COVID-19 antimicrobial prescribing. Clin Infect Dis. 2020. doi:10.1093/cid/ciaa530
   PubMed Web of Science ®Google Scholar
• Bills CB, Newberry JA, Rao GR, et al. Acute respiratory illness among a prospective cohort of pediatric patients using emergency medical services in India: demographic and prehospital clinical predictors of mortality. PLoS One. 2020;15(4):e0230911. doi:10.1371/journal.pone.023091132240227
   PubMed Web of Science ®Google Scholar
• Ruan Q, Yang K, Wang W, Jiang L, Song J. Clinical predictors of mortality due to COVID-19 based on an analysis of data of 150 patients from Wuhan, China. Intensive Care Med. 2020;1–3.
   Web of Science ®Google Scholar
• Fann RJ, Rani VR, Vaithlingam I. Clinical presentations and predictors of mortality for leptospirosis - a study from suburban area in Malaysia. Med J Malaysia. 2020;75(1):52–56.32008021
   PubMedGoogle Scholar
• Henry BM, De Oliveira MH, Benoit S, Plebani M, Lippi G. Hematologic, biochemical and immune biomarker abnormalities associated with severe illness and mortality in coronavirus disease 2019 (COVID-19): a meta-analysis. Clin Chem Lab Med. 2020;58(7):1021–1028.32286245
   PubMed Web of Science ®Google Scholar