Co-infection in COVID-19, a cohort study

Co-infection in COVID-19 patients may inflence the outcome of the disease and needs more attention and investigations. In this journal, Lansbury and colleges reported a meta-analysis of co-infections in COVID-19 patients.1Lansbury L. Lim B. Baskaran V. Lim W.S. Co-infections in people with COVID-19: a systematic review and meta-analysis.J Infect. 2020; 81: 266-275https://doi.org/10.1016/j.jinf.2020.05.046Abstract Full Text Full Text PDF PubMed Scopus (981) Google Scholar In this study, we investigated a COVID-19 cohort in Shanghai, China. We screened viruses include Human parainfluenza virus 1, Human parainfluenza virus 2, Human parainfluenza virus 3, Human parainfluenza virus4, Influenza A virus, Influenza B virus, Human rhinovirus, Human metapneumovirus, Human respiratory syncytial virus, Human Bocavirus, Human adenovirus, Human Coronavirus 229E, Human Coronavirus NL63, Human Coronavirus HKU1, Human Coronavirus OC43; bacteria include Pseudomonas aeruginosa, Moraxella catarrhalis, Mycobacterium tuberculosis, Legionella pneumophila, Group A Streptococcus, Haemophilus influenza, Staphylococcus aureus, Acinetobacter baumannii, Streptococcus pneumonia, Klebsiella.peneumoniae, Escherichia coli and Mycoplasma pneumonia, Chlamydia pneumonia by a taqman-based real time PCR methods. Eighty-nine patients were enrolled with disease outcomes include mild, moderate, severe and critical (Chinese clinical guidance for COVID-19 pneumonia diagnosis and treatment (7th edition) published by China National Health Commission on March 4, 2020. http://www.gov.cn/zhengce/zhengceku/2020–03/04/content_5486705.htm). Nine patients showed severe or critical symptoms. As reported, age is a risk factor for severe symptoms (Table 1).2Mei X. Zhang Y. Zhu H. Ling Y. Zou Y. Zhang Z. et al.Observations about symptomatic and asymptomatic infections of 494 patients with COVID-19 in Shanghai, China.Am J Infect Control. 2020; 48: 1045-1050https://doi.org/10.1016/j.ajic.2020.06.221Abstract Full Text Full Text PDF PubMed Scopus (23) Google Scholar,3Zhang Xiaonan Tan Yun Ling Yun Lu Gang et al.Viral and host factors related to the clinical outcome of COVID-19.Nature. 2020; 583https://doi.org/10.1038/s41586-020-2355-0Crossref Scopus (595) Google Scholar Nucleic acids from the throat swab samples of the COVID-19 patients were used as template for Real-time PCR. Real-time PCR was performed by using One Step PrimeScript RT-PCR kit (Takara) in a 25µl reaction mixture as following: 2.5µl of nucleic acid was added in the mixture of 12.5µl of 2 × one step RT-PCR buffer, 0.5µl of EX Taq HS, 0.5μl of RT Enzyme, 1.6µl of primer mix (10µM each), 0.4µl of probe (10µM) and H2O up to 25µl. The R-PCR program was run with incubation at 42 °C for 10 min, followed by 40 cycles of a program (95 °C, 10 s; 95 °C 10 s, 60 °C, 1 min). The primers and probes for Influenza A virus were as following: sense (5′-CTT CTA ACC GAG GTC GAA ACG TA-3′), antisense: (5′-GGT GAC AGG ATT GGT CTT GTC TTT A-3′) and probe: (5′-FAM-TCA GGC CCC CTC AAA GCC GAG −3′-BHQ1); For E. coli were as flowing: sense (5′-GGA TAT CGT CTG GGA CTT CCG-3′), antisense (5′-GCG GAG CCA GAC CGA ATT T-3′) and probe (5′-FAM-GTG AAA TCG ATC AGT GCT TCA GGC CA −3′-BHQ1). Screening for other pathogens were performed by using real-time PCR detection kits from BioGerm (Shanghai, China) as following: human parainfluenza virus 1/human parainfluenza virus 3(PIV1/PIV3) (BioGerm, SJ-HX-215–2), human parainfluenza virus 2/human parainfluenza virus 4 (PIV2/PIV4)(BioGerm, SJ-HX-216–2), Influenza B virus (FLUB)(BioGerm, SJ-LG-006–2), human rhinovirus/human metapneumovirus/Human respiratory syncytial virus (HRV/HMPV/RSV)(BioGerm, SJ-HX-303–2), human Bocavirus/human adenovirus (HBOV/RADV)(BioGerm, SJ-HX-207–2), human Coronavirus 229E/human Coronavirus NL63 (BioGerm, SJ-HX-204–2), human Coronavirus HKU1/ human Coronavirus OC43 (BioGerm, SJ-HX-205–2), Pseudomonas aeruginosa (PA)(BioGerm, SJ-HX-039–2), Moraxella catarrhalis (MC)(BioGerm, SJ-HX-027–2), Mycobacterium tuberculosis (MTB)(BioGerm, SJ-HX-040–2), Mycoplasma pneumonia/Chlamydia pneumonia/Legionella pneumophila (MP/CP/LP)(BioGerm, SJ-HX-302–2), Group A Streptococcus/Haemophilus influenzae/Staphylococcus aureus (GA/HI/SA)(BioGerm, SJ-HX-319–2), Acinetobacter baumannii/Streptococcus pneumoniae/Klebsiella peneumoniae (AB/SP/KP)(BioGerm, SJ-HX-309–2).Table 1Patients in this study.AgePatients (Total number)Patients (Severe or critical symptom)15–6066161–75205>7533 Open table in a new tab As shown in the Table 2, we detected co-infections in 18 patients. We detected co-infection with Kp (Klebsiella.peneumoniae) in 6 patients, co-infection with EC (E. coli) in 5 patients, co-infection with Mcat (Moraxella catarrhalis) in 4 patients, co-infection with Hi (Haemophilus influenzae) in 4 patients, co-infection with Ab (Acinetobacter baumannii) in 2 patients, co-infection with Sa (Staphylococcus aureus) in 2 patients, co-infection with PA (Pseudomonas aeruginosa) in 1 patient, and co-infection with GAS (Group A Streptococcus) in 1 patients. Notably, 6 patients got coinfection with more than two bacteria. One patient with a moderate to severe disease and one patient with severe disease got co-infection with Mcat (Moraxella catarrhalis). One patient with a critical disease got co-infection with Ab (Acinetobacter baumannii). We didn't detect co-infection with any virus in these patients.Table 2Co-infection in the COVID-19 patients.PatientsPathogenAgeCt ValueDisease Severity277#PA, Pseudomonas aeruginosa1535.47Mild726#Mcat, Moraxella catarrhalis7635.14Moderate to Severe144#Kp, Klebsiella.peneumoniae3232.87Mild973#Hi, Haemophilus influenzae5730.52Moderate994#Mcat, Moraxella catarrhalis3524.16MildGAS, Group A Streptococcus32.46903#Hi, Haemophilus influenza2126.55MildKp, Klebsiella.peneumoniae35.82830#Ab, Acinetobacter baumannii6530.17Critical14#Mcat, Moraxella catarrhalis3734.49MildHi, Haemophilus influenza34.01Kp, Klebsiella.peneumoniae26.19743#Hi, Haemophilus influenza3635.13MildAb, Acinetobacter baumannii32.11952#Sa, Staphylococcus aureus3331.94ModerateEC, E. coli35.77976#Kp, Klebsiella.peneumoniae3235.42Mild75#EC, E. coli4526.40Mild1002#Sa, Staphylococcus aureus1934.68Moderate225#Mcat, Moraxella catarrhalis6728.62Severe63#Kp, Klebsiella.peneumoniae3432.02MildEC, E. coli27.3867#EC, E. coli2723.01Mild74#EC, E. coli6628.43Mild327#Kp, Klebsiella.peneumoniae6433.97Mild Open table in a new tab M. catarrhalis typically infect adults with a weakened immune system.4catarrhalis Moraxella J.C.Verhaegh Suzanne Schaar Viveka ChingSu Yu Riesbeck Kristian John P.Hays Molecular Medical Microbiology.2nd Edition. 2015: 1565-1586https://doi.org/10.1016/C2010-1-67744-9Crossref Google Scholar Elderly COVID-19 patients have impaired Cytotoxic CD8+ T Cell Responses, which may make them highly risk for infection.5Westmeier Jaana Paniskaki Krystallenia Karaköse Zehra Werner Tanja et al.Impaired cytotoxic CD8 1 + T cell response in elderly COVID-19 patients.MBio. Sep 2020; 18 (11-20): e02243https://doi.org/10.1128/mBio.02243-20Crossref Scopus (97) Google Scholar A. baumannii is a common pathogen in Intensive Care Units (ICU) and evolves rapidly to be resistant to many antibiotics and should be seriously considered for critical COVID-19 patients.6Nhu N.T.K. Lan N.P.H. Campbell J.I. Parry C.M. Thompson C. Tuyen H.T. et al.Emergence of carbapenem-resistant Acinetobacter baumannii as the major cause of ventilator-associated pneumonia in intensive care unit patients at an infectious disease hospital in southern Vietnam.J Med Microbiol. 2014; 63: 1386-1394https://doi.org/10.1099/jmm.0.076646-0Crossref PubMed Scopus (51) Google Scholar In summary, we carried out an extensive pathogen screening in a COVID-19 cohort. We didn't detect co-infection of SARS-CoV-2 with other viruses. Co-infection with bacteria was detected in 18 of the 89 patients. M. catarrhalis was detected in two patients with severe symptoms and A. baumannii was detected in one patient with critical symptoms. These bacterial co-infections should be taken care in managing the COVID-19 patients. This study was approved by the ethics committee of Shanghai public health clinical center under the study number YJ-2020-S077-02, and the procedures were carried out in accordance with approved guidelines. Informed consent was obtained from the subjects. YZ conceived the manuscript; SW and JX performed experiments; ZX, LY collected samples; YZ all authors performed litera- ture search; YZ wrote the first draft of the manuscript; all authors reviewed it. SW and JX contributed equally. The authors declare no conflicts of interest. This work was supported in part by the National Science and Technology Major Project of China (2017ZX10103009), Key Emergency Project of Shanghai Science and Technology Committee (20411950103).