key: cord-0930808-j607hh9t
authors: Pakzad, Reza; Malekifar, Pooneh; Shateri, Zainab; Zandi, Milad; Akhavan Rezayat, Sara; Soleymani, Maral; Karimi, Mohammad Reza; Ahmadi, Seyed Esmaeil; Shahbahrami, Ramin; Pakzad, Iraj; Abdi, Fatemeh; Farahani, Abbas; Soltani, Saber; Kesheh, Mina Mobini; Hosseini, Parastoo
title: Worldwide prevalence of microbial agents’ coinfection among COVID‐19 patients: A comprehensive updated systematic review and meta‐analysis
date: 2021-12-01
journal: J Clin Lab Anal
DOI: 10.1002/jcla.24151
sha: 3bed18968597fe83eda3b3abdf867951d1c1ef4c
doc_id: 930808
cord_uid: j607hh9t

BACKGROUND: To provide information about pathogens’ coinfection prevalence with SARS‐CoV‐2 could be a real help to save patients’ lives. This study aims to evaluate the pathogens’ coinfection prevalence among COVID‐19 patients. METHOD: In order to find all of the relevant articles, we used systematic search approach. Research‐based databases including PubMed, Web of Science, Embase, and Scopus, without language restrictions, were searched to identify the relevant bacterial, fungal, and viral coinfections among COVID‐19 cases from December 1, 2019, to August 23, 2021. In order to dig deeper, other scientific repositories such as Medrxiv were probed. RESULTS: A total of 13,023 studies were found through systematic search. After thorough analysis, only 64 studies with 61,547 patients were included in the study. The most common causative agents of coinfection among COVID‐19 patients were bacteria (pooled prevalence: 20.97%; 95% CI: 15.95–26.46; I (2): 99.9%) and less frequent were virus coinfections (pooled prevalence: 12.58%; 95% CI: 7.31–18.96; I (2): 98.7%). The pooled prevalence of fungal coinfections was also 12.60% (95% CI: 7.84–17.36; I (2): 98.3%). Meta‐regression analysis showed that the age sample size and WHO geographic region did not influenced heterogeneity. CONCLUSION: We identified a high prevalence of pathogenic microorganism coinfection among COVID‐19 patients. Because of this rate of coinfection empirical use of antibacterial, antifungal, and antiviral treatment are advisable specifically at the early stage of COVID‐19 infection. We also suggest running simultaneously diagnostic tests to identify other microbiological agents’ coinfection with SARS‐CoV‐2.

COVID-19 was declared as the new respiratory pandemic in March 2020. 1 Microbial pathogens coinfections always played an important role in increasing mortality and morbidity rate in pandemics. Their coinfection with SARS-CoV-2 is not an exception. While countries applied different measures to limit spread of the virus, new wave still striking and quickly mutate and gain new feature which has made it more dangerous than ever. 2 Viral, bacterial, and fungal coinfections alter the pathophysiology of disease, also the patient recovery outcome. 3, 4 Respiratory viruses' including hRV, hMPV, and RSV are associated with majority respiratory viral coinfection. 5 Also, immunosuppression and immunodeficiency condition such as HIV infection could effect on COVID-19 disease. 6 Fungal infection plays a major threat to patient's life in intensive care units. 7 Fungal coinfections such as Aspergillus and Candida species could increase mortality rate, especially in critically ill patients. 8 One of the great challenges for clinicians is their detection. Fungal coinfection remained undetectable even after the death of the patients. 9 Similar clinical and radiological features between SARS-CoV-2 and fungal pathogens are the other difficulties that healthcare providers have to dealt with. 10 Among microbiological coinfections, bacterial pathogens are considered more important agents based on their previous record viral outbreaks and pandemics. 11 It also was reported people with bacterial coinfection showed high number of mortality. Critical ill patients showed greater percentage of coinfection compared to hospitalized patients. 12 One of the main importance of assessing bacterial coinfection prevalence is about applying empirical antibiotic treatment, in SARS-CoV-2 patients. Extensive use of antibiotics could lead to several such as antibacterial resistance. 13, 14 Some of the respiratory bacterial pathogen such as pneumococcal, staphylococcal, and Klebsiella with SARS-CoV-2 have common clinical manifestation; therefore, antibiotics treatment would be more difficult than regular situation. 15 This study aims to evaluate the microbiological coinfection prevalence among COVID-19 patients.

We performed our research based on PRISMA guideline studies 16 we registered our article search protocol in the International Prospective Register of Systemic Reviews with CRD42021277142.

We used related unique keywords to conduct our search strategy and retrieving all of the related articles.

We explored the online scientific repositories without setting any language barrier. PubMed, Web of Science, Embase, and Scopus were probed to find the relevant articles about pathogens' coinfection prevalence in COVID-19-infected persons between December 1, 2019, and August 23, 2021. Other knowledge-based databases such as Medrxiv and SSRN were also used to gather the off-the-record articles. We chose the keywords in this article based on MeSH Terms. The PICOTS in our study are available in Appendix 1.

To find other off-the-record publication, we probed Google Scholar. A microbiologist was asked to identify and validate the related articles. Simultaneously, we hand-searched our articles library to gather other relevant studies. We imported all of the gathered data to Endnote X6. The duplicated articles were removed.

We scanned the remained studies in three distinguished steps.

Firstly, we probed the articles based on their titles. Afterward, the abstract of the screened articles were reviewed, and the full text of the relevant ones were collected. We conducted the study selection procedure based on blinding and task separation. The mentioned procedure was done by two independent reviewers simultaneously. In case of any disagreement between reviewers (Inter-rater discrepancies), another rater were asked to resolve the problem. The kappa coefficient for agreement between two raters was equal to 93%. were virus coinfections (pooled prevalence: 12.58%; 95% CI: 7.31-18.96; I 2 : 98.7%).

The pooled prevalence of fungal coinfections was also 12.60% (95% CI: 7.84-17.36; I 2 : 98.3%). Meta-regression analysis showed that the age sample size and WHO geographic region did not influenced heterogeneity.

We identified a high prevalence of pathogenic microorganism coinfection among COVID-19 patients. Because of this rate of coinfection empirical use of antibacterial, antifungal, and antiviral treatment are advisable specifically at the early stage of COVID-19 infection. We also suggest running simultaneously diagnostic tests to identify other microbiological agents' coinfection with SARS-CoV-2.

coinfection, coronavirus, COVID-19, meta-analysis, systematic review

All the related studies including cross-sectional, case series, and cohort studies evaluating the prevalence of viral, bacterial, and fungal coinfections among COVID-19 cases were gathered. The case series and case report articles with <10 sample sizes did not reviewed in this study. We excluded the other types of articles including clinical trials, reviews, and case-control articles.

We extracted the necessary data from all of the studies including authors' name, study year, country, study design, sample size, gender, age, number, and type of coinfections.

Bacteria type were classified based on transmission way and clinical signs. Countries were categorized based on the latest WHO definition that includes the following six regions: Regional Office for Africa (AFRO), Regional Office for the Americas (AMRO), Regional

Office for the Eastern Mediterranean (EMRO), Regional Office for Europe (EURO), Regional Office for South-East Asia (SEARO), and the Regional Office for the Western Pacific (WPRO).

Newcastle-Ottawa Scale 17 evaluated the quality of the finalized studies. We assessed the studies based on three selection steps of this scale: 1-Selection 2-Confounder, and 3-Exposure. Two independent reviewers examined the articles based on the Newcastle-Ottawa criteria (RP and SS), and the total score for each study in the three steps was calculated. Afterward, the selected studies were categorized in the following groups: very good, good, satisfactory, and unsatisfactory studies. 18 

All statistical tests in this study were performed with Stata 14.0.

Just like previous researches, 18-21 the sample size, the coinfection prevalence in COVID-19 cases, and the coinfection causative agent's types and species were extracted. We applied Cochran's Q test to determine the heterogeneity. We also quantified it with the I 2 index. I 2 values above 0.7 were determined as high heterogeneity based on the Higgins classification approach. 22 Metaprop package were used to calculate the pooled prevalence with 95% confidence interval. Random-effects model was applied to estimate the pooled prevalence. This package applies double arcsine transformations to stabilize the variance in the meta-analyses. The effect of sample size, age, and WHO geographic regions on the studies heterogeneity were analyzed by meta-regression analysis. Publication bias evaluated by "metabias" command. In case of any publication bias, we adjusted the prevalence rate with "metatrim" command applying trim-and-fill approach. Statistical significance was considered 0.05.

We collected 13,241 articles probing the mentioned databases. We also found 151 articles through other resources. By removing the duplicated articles, 8838 articles remained. The remained articles were screened in three distinguished steps. First, we exclude the 6542 studies by analyzing their titles. Then After reviewing the abstracts, 1924 studies were removed from the library. In the third step, the full text of the 372 remained articles was comprehensively studied, and we exclude the 308 studies. A total of 64 studies 3,5,18,23-79 with 61,547 total sample size were included in our study. Selection process flow chart is available in Figure 1 , and Table 1 shows the studies' characteristics. The highest studies number belonged to Western Pacific (25 studies) area, Southeast Asia (three studies), and Eastern Mediterranean Region (three studies) was the lowest one.

All the included studies were published during 2020. The minimum and maximum age range of the subjects was for Wu et al. 28 article had the lowest age ranges (mean age = 6 years old) and Wang et al. 65 

Heterogeneity results are available in Table 2 . Cochran's Q test showed the included studies had high heterogeneity (p < 0.001).

The I 2 index for total coinfections and pathogen subtypes were up to 90%. Meta-regression analysis showed the age (Coefficient: 

Egger's test results (coefficient: −0.41, p: 0.899) exhibited that there was not any significant publication bias in this meta-analysis.

Our result elucidated that overall coinfection prevalence was 16.98.

The lowest coinfection prevalence was reported in the USA and the highest level of coinfection was in Iran. As we expected between pathogenic microorganisms, bacterial agents were the most frequent and viral coinfection had the lowest coinfection rate in COVID-19 patients. We also found out that EMRO region had the most prevalence of coinfection and compare to that SEARO region was the lowest coinfection area.

manifests clinical features similar to COVID-19, which is a potential threat for COVID-19-infected cases. 80,81 A systematic review and meta-analysis reported that influenza type A, rhinovirus, and non-SARS-CoV-2 coronaviruses are the most frequent viruses among coinfected patients 82 Another systematic review showed that 11.6% of SARS-CoV-2 patients had viral coinfection. 83 Malekifar et al. 84 showed the prevalence of 12.58% viral coinfection among COVID-19 patients.

Compare to other systematic review studies focused on coinfection question, we found a higher coinfection rate. Our result showed that 20.97%; of patients were infected with at least one bacterial pathogens which is much higher than other studies reported 7%-8% of coinfection prevalence among COVID-19 patients. 81 The rate of bacterial coinfection prevalence among critically ill patients is one of the important issues during pandemic, which related to higher comorbidity. A meta-analysis study showed 8.1% of coinfection among critically ill patients compared to 5.9% 

We faced some limitation in our study. One: we could not perform gender-specific estimation because of primary studies little data;

Two: pooled prevalence in this study were analyzed based on WHO regional office; therefore, we wanted to conduct the spatial analysis in geographic regions, 91-94 but because of infrequent studies number, we would not sure about robust results. Performing a through-full study probe search and estimating the different coinfections species pooled prevalence were our study's strengths.

Because of increasing rate of pathogens coinfection prevalence in COVID-19 patients, we suggest that a world registry will be developed in order to screen the pattern of coinfections. 95,96

In conclusion, we identified a higher level of pathogenic microorganism coinfection among COVID-19 patients. Because of this rate of coinfection, we support the empirical use of antibacterial, antifungal, and antiviral treatment specifically at the onset of the COVID-19 infection. We also encourage clinician to run diagnostic test for other pathogens simultaneously with SARS-CoV-2, which is important to properly patient's treatment.

We are sincerely thankful to Hormozgan University of Medical Sciences and Tehran University of Medical Sciences, Iran (G. no. 4000407).

The authors report no conflicts of interest in this work. 

Not applicable.

All data associated with this article are inclusive in this article. 

Initial COVID-19 outbreak: an epidemiological and socioeconomic case review of Iran

COVID-19: prevention and control measures in community

Evaluation of bacterial co-infections of the respiratory tract in COVID-19 patients admitted to ICU

SARS-CoV-2 respiratory co-infections: incidence of viral and bacterial co-pathogens

Rates of co-infection between SARS-CoV-2 and other respiratory pathogens

Impacts of immunosuppression and immunodeficiency on COVID-19: a systematic review and meta-analysis

International study of the prevalence and outcomes of infection in intensive care units

Fungal co-infections associated with global COVID-19 pandemic: a clinical and diagnostic perspective from China

Invasive fungal diseases during COVID-19: we should be prepared

The role of co-infections and secondary infections in patients with COVID-19

Critical illness from 2009 pandemic influenza A (H1N1) virus and bacterial co-infection in the United States

Bacterial and viral infections associated with influenza. Influenza Other Respir Viruses

SARS-CoV-2, bacterial coinfections, and AMR: the deadly trio in COVID-19?

How covid-19 is accelerating the threat of antimicrobial resistance

Collateral damage of the COVID-19 pandemic: exacerbation of antimicrobial resistance and disruptions to antimicrobial stewardship programmes?

Preferred reporting items for systematic reviews and meta-analyses: the PRISMA statement

The Newcastle-Ottawa Scale (NOS) for Assessing the Quality of Nonrandomised Studies in Metaanalyses. The Newcastle-Ottawa Scale (NOS) for assessing the quality of non randomised studies in meta-analyses

Global and regional prevalence of age-related cataract: a comprehensive systematic review and meta-analysis

The association between metabolic syndrome and its components with systemic lupus erythematosus: a comprehensive systematic review and meta-analysis of observational studies

Global and regional prevalence of strabismus: a comprehensive systematic review and metaanalysis

COVID-19 associated central nervous system manifestations, mental and neurological symptoms: a systematic review and meta-analysis

Measuring inconsistency in meta-analyses

Co-infection with respiratory pathogens among COVID-2019 cases

Risks and features of secondary infections in severe and critical ill COVID-19 patients

Clinical features and outcomes of adult COVID-19 patients co-infected with Mycoplasma pneumoniae

Low prevalence of bloodstream infection and high blood culture contamination rates in patients with COVID-19

Improving antibiotic stewardship in COVID-19: bacterial co-infection is less common than with influenza

Coinfection and other clinical characteristics of COVID-19 in children

Co-infections in COVID-19 critically ill and antibiotic management: a prospective cohort analysis

Traditional herbal remedies with a multifunctional therapeutic approach as an implication in COVID-19 associated co-infections

Active tuberculosis, sequelae and COVID-19 co-infection: first cohort of 49 cases

Previous and active tuberculosis increases risk of death and prolongs recovery in patients with COVID-19

SARS-CoV-2-related pneumonia cases in pneumonia picture in Russia in March-May 2020: secondary bacterial pneumonia and viral co-infections

Bacteremia and blood culture utilization during COVID-19 surge in New York City

Tuberculosis and COVID-19: an overlapping situation during pandemic

Rates of bacterial co-infections and antimicrobial use in COVID-19 patients: a retrospective cohort study in light of antibiotic stewardship

Secondary infections in patients hospitalized with COVID-19: incidence and predictive factors

Increased risk of acquisition of New Delhi metallo-beta-lactamase-producing carbapenem-resistant Enterobacterales (NDM-CRE) among a cohort of COVID-19 patients in a teaching hospital in Tuscany

Bacterial and fungal coinfections in COVID-19 patients hospitalized during the New York City pandemic surge

Tuberculosis, COVID-19 and migrants: preliminary analysis of deaths occurring in 69 patients from two cohorts

Respiratory microbial coinfection with SARS-CoV-2

Coinfection of SARS-CoV-2 and other respiratory pathogens

Clinical characteristics and co-infections of 354 hospitalized patients with COVID-19 in Wuhan, China: a retrospective cohort study

Effect of a previous history of antiretroviral treatment on the clinical picture of patients with co-infection of SARS-CoV-2 and HIV: a preliminary study

Il-6 inhibition in critically ill COVID-19 patients is associated with increased secondary infections

Few bacterial coinfections but frequent empiric antibiotic use in the early phase of hospitalized patients with COVID-19: results from a multicentre retrospective cohort study in The Netherlands

Bacterial and fungal colonization of the respiratory tract in COVID-19 patients should not be neglected

Bacterial and fungal coinfection among hospitalized patients with COVID-19: a retrospective cohort study in a UK secondary-care setting

Analysis of Covid-19 and non-Covid-19 viruses, including influenza viruses, to determine the influence of intensive preventive measures in Japan

Coinfections with SARS-CoV-2 and other respiratory pathogens

A profile of a retrospective cohort of 22 patients with COVID-19 and active/treated tuberculosis

Bacterial infections and patterns of antibiotic use in patients with COVID-19

Presenting characteristics, comorbidities, and outcomes of patients coinfected with COVID-19 and Mycoplasma pneumoniae in the USA

Incidence of co-infections and superinfections in hospitalized patients with COVID-19: a retrospective cohort study

Secondary bacterial infections in critical ill patients of COVID-19

Differentiating influenza from COVID-19 in patients presenting with suspected sepsis

Bacterial and viral coinfections in patients with severe SARS-CoV-2 pneumonia admitted to a French ICU

Primary respiratory bacterial coinfections in patients with COVID-19

Co-detection of respiratory pathogens in patients hospitalized with Coronavirus viral disease-2019 pneumonia

Clinical characteristics of hospitalized patients with SARS-CoV-2 and hepatitis B virus co-infection

Different patterns of Influenza A and B detected during early stages of COVID-19 in a university hospital in São Paulo

The clinical characteristics of pneumonia patients coinfected with 2019 novel coronavirus and influenza virus in Wuhan

Lack of MERS-CoV Co-infection among Hospitalized COVID-19 Patients in Saudi Arabia

High prevalence of SARS-CoV-2 and influenza A virus (H1N1) coinfection in dead patients in Northeastern Iran

Coinfection of SARS-CoV-2 and multiple respiratory pathogens in children

Epidemiology of severe acute respiratory syndrome coronavirus 2 emergence amidst community-acquired respiratory viruses

Co-infections of SARS-CoV-2 with multiple common respiratory pathogens in infected patients

Patients with SARS-CoV-2 and HBV co-infection are at risk of greater liver injury

Clinical characteristics of critically ill patients co-infected with SARS-CoV-2 and the influenza virus in Wuhan, China

Coinfection in SARS-CoV-2 infected patients: where are influenza virus and rhinovirus/enterovirus?

Clinical and biochemical parameters of COVID-19 patients with prior or active dengue fever

Empiric antibacterial therapy and community-onset bacterial co-infection in patients hospitalized with COVID-19: a multi-hospital cohort study

Does respiratory coinfection facilitate dispersal of SARS-CoV-2? investigation of a super-spreading event in an open-space office

Effect of SARS-CoV-2 coinfection was not apparent on the dynamics of chronic hepatitis B infection

The epidemiology and clinical characteristics of co-infection of SARS-CoV-2 and influenza viruses in patients during COVID-19 outbreak

Co-infection of SARS-CoV-2 and Influenza virus in early stage of the COVID-19 epidemic in Wuhan

Critically ill patients with COVID-19 and candidaemia: we must keep this in mind

Multidrug-resistant Candida auris infections in critically Ill coronavirus disease patients

Prevalence of opportunistic invasive aspergillosis in COVID-19 patients with severe pneumonia

The burden of respiratory syncytial virus in adults: a systematic review and metaanalysis

Co-infections in people with COVID-19: a systematic review and meta-analysis

Prevalence and outcomes of coinfection and superinfection with SARS-CoV-2 and other pathogens: a systematic review and meta-analysis

Viral and atypical respiratory co-infections in COVID-19: a systematic review and meta-analysis

Viral coinfection among COVID-19 PATIENT groups: an update systematic review and meta-analysis

Bacterial co-infection and secondary infection in patients with COVID-19: a living rapid review and meta-analysis

Bacterial co-infection among COVID-19 patient groups: an update systematic review and Metaanalysis

New threatening of SARS-CoV-2 co-infection and strategies to fight the current pandemic

Fatal invasive aspergillosis and coronavirus disease in an immunocompetent patient

COVID-19-associated candidiasis (CAC): an underestimated complication in the absence of immunological predispositions?

A national strategy to diagnose COVID-19 associated invasive fungal disease in the ICU

Spatial analysis of breast cancer incidence in Iran

Spatial analysis of colorectal cancer in Iran

Spatial analysis of skin cancer incidence in Iran

Spatial analysis of stomach cancer incidence in Iran

Design and development of a web-based registry for Coronavirus (COVID-19) disease

Determination of the most important diagnostic criteria for COVID-19: a step forward to design an intelligent clinical decision support system

Population: COVID-19 patients

Prevalence of coinfections. Time: from December 1

The search strategy is described in Appendix 1 that is applied based on PICOTS for MEDLINE (MeSH) and then used in other databases

BOX 1 Search strategy based on PICO for MEDLINE (MeSH, Medical Subject Headings) 1. COVID-19

SARS-CoV-2 infection [text word] OR SARS-CoV-2 infection

Mixed Infection [text word] OR Mixed Infection [Mesh term] 11. Polymicrobial Coinfection [text word] OR Polymicrobial Coinfection [Mesh term] 12. Bacterial Coinfection [text word] OR Bacterial Coinfection