Clinical and etiological analysis of co‐infections and secondary infections in COVID‐19 patients: An observational study

Abstract

Background: Co-infections, secondary bacterial or fungal infections, are important risk factors for poor outcomes in viral infections. The prevalence of co-infection and secondary infection in patients infected with SARS-CoV-2 is not well understood. Aims: To investigate the role of co-infections and secondary infections in disease severity of hospitalized individuals with COVID-19. Materials and Methods: A retrospective study was carried out between 11 January 2020 and 1 March 2020 among 408 laboratory confirmed COVID-19 patients in China. These patients were divided into three groups based on disease severity: mild or moderate, severe, or critically ill. Microbiological pathogens in blood, urine, and respiratory tract specimens were detected by the combination of culture, serology, polymerase chain reaction, and metagenomic next-generation sequencing (mNGS). Results: The median age of participants was 48 years (IQR 34-60 years). Fifty-two patients (12.7%) had at least one additional pathogen, 8.1% were co-infected, and 5.1% had a secondary infection. There were 13 Mycoplasma pneumoniae cases, 8Haemophilus influenzae cases, 8 respiratory viruses, and 3 Streptococcus pneumoniae cases, primarily detected in mild and moderate COVID-19 patients. Hospitalacquired infection pathogens were more common in critically ill patients. Compared to those without additional pathogens, patients with co-infections and/or secondary infections were more likely to receive antibiotics (p < 0.001) and have elevated levels of d-dimer (p = 0.0012), interleukin-6 (p = 0.0027), and procalcitonin (p = 0.0002).The performance of conventional culture was comparable with that of mNGS in diagnosis of secondary infections. Conclusion: Co-infections and secondary infections existed in hospitalized COVID-19 patients and were relevant to the disease severity. Screening of common respiratory pathogens and hospital infection control should be strengthened.

Co-infection of SARS-CoV-2 and influenza viruses: A systematic review and meta-analysis

“…A total of 169 articles were processed for full text screening. Fifty-four articles met the inclusion criteria and were included in the qualitative synthesis of the systematic review and meta-analysis ( Figure 1 ) [5] , [6] , [7] , [8] , [9] , [10] , [11] , [12] , [13] , [14] , [15] , [16] , [17] , [18] , [19] , [20] , [21] , [22] , [23] , [24] , [25] , [26] , [27] , [28] , [29] , [30] , [31] , [32] , [33] , [34] , [35] , [36] , [37] , [38] , [39] , [40] , [41] , [42] , [43] , [44] , [45] , [46] , [47] , [48] , [49] , [50] , [51] , [52] , [53] , [54] , [55] , [56] , [57] , [58] .…”

Rapid Genomic Diagnosis of Fungal Infections in the Age of Next-Generation Sequencing

“…Pneumocystis jirovecii is the predominant fungus reported (~25% of the fungi detected), followed by Aspergillus species (~22%), Candida species (~16%), Cryptococcus species (~7%), Rhizopus species (~6%), Fusarium species (~4%), Alternaria species, Talaromyces marneffei and other Sordariomycetes (~3% each), Histoplasma capsulatum, other yeasts and Mucor species (~2% each), as well as some other rare fungal species (collectively~5%) (Figure 2). Excluding P. jirovecii, which is generally unculturable, out of the remaining 274 fungi detected by NGS, only 105 (~38%) were recovered by fungal culture from the same or different specimens from the respective patients [26,[29][30][31][32][33][34][35][36][37][38][39]43,45,46,49,52,54,57,59,62,64,66,67,71,73,76,77]. cies (~22%), Candida species (~16%), Cryptococcus species (~7%), Rhizopus species (~6%), Fusarium species (~4%), Alternaria species, Talaromyces marneffei and other Sordariomycetes (~3% each), Histoplasma capsulatum, other yeasts and Mucor species (~2% each), as well as some other rare fungal species (collectively ~5%) (Figure 2).…”

“…cies (~22%), Candida species (~16%), Cryptococcus species (~7%), Rhizopus species (~6%), Fusarium species (~4%), Alternaria species, Talaromyces marneffei and other Sordariomycetes (~3% each), Histoplasma capsulatum, other yeasts and Mucor species (~2% each), as well as some other rare fungal species (collectively ~5%) (Figure 2). Excluding P. jirovecii, which is generally unculturable, out of the remaining 274 fungi detected by NGS, only 105 (~38%) were recovered by fungal culture from the same or different specimens from the respective patients [26,[29][30][31][32][33][34][35][36][37][38][39]43,45,46,49,52,54,57,59,62,64,66,67,71,73,76,77]. The majority of P. jirovecii infections diagnosed by NGS were reported in case series [34,36,39,41,48,53,55,58,62,64,65,67,72,75].…”

“…Lastly, publications were searched using specific fungal names and after manual examination five extra articles were added. Therefore, in total 52 articles were included in this review [ 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 , 62 , 63 , 64 , 65 , 66 , 67 , 68 , 69 , 70 , 71 , 72 , 73 , 74 , 75 , 76 , 77 ].…”

“…It was a case of allergic bronchopulmonary mycosis where A. fumigatus and Schizophyllum commune sequences were detected in the homogenised sputum and mucoid plugs of the patient [ 26 ]. Since then, up to the time of writing, a total of 319 cases of fungal infections diagnosed by NGS were described in the literature, with some in case reports and others in case series or cohorts [ 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 , 62 , 63 , 64 , 65 , 66 , 67 , 68 , 69 , 70 , 71 , 72 , 73 , 74 , 75 , 76 , 77 ]. In 40 out of the 319 cases (12.5%), more than 1 fungus was detected by NGS [ 26 , ...…”