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Co-infected Covid-19 patients have longer hospital stays and higher mortality rates.
Secondary infections with bacterial and viral pathogens are well described Data on Covid-19 patients are still emerging in influenza, SARS, MERS and other respiratory viral diseases. Concurrent infection with two or more pathogens, called coinfection, can lead to more severe disease and higher mortality.
During the 1918 Spanish flu pandemic, most deaths were thought to be due to bacterial pneumonia rather than the H1N1 virus itself.This phenomenon was also observed during 1957, 1968 and 2009 flu pandemic. During the 2009 swine flu pandemic, bacterial infections were associated with 29% to 55% of deaths.
recent meta-analysis Twenty-seven studies including 3,214 influenza patients showed bacterial coinfection rates between 11% and 35%.The most common pathogens are Streptococcus pneumoniae and Staphylococcus aureus, accounted for 35% and 28% of infections, respectively, with the remainder caused by a variety of other pathogens.
Co-infection is also common in Covid-19 patients, which is related to 3.3 times higher risk of death. one meta-analysis Although 71.9% of patients received antibiotics, acute bacterial co-infections were found in 4.9% of the 7,100 patients.in another meta-analysis In 118 studies, the prevalence of coinfection was 19%. Bacterial infections (6.9%) were more common than viral and fungal pathogens. The authors concluded that better diagnostic tests are needed to identify and treat respiratory coinfections in Covid-19 patients.
Covid-19 patients are at higher risk of contracting multidrug-resistant pathogens
report from Southeast Asia and Europe In critically ill Covid-19 patients, more frequent infections are suggested multidrug resistant bacteria carbapenem-resistant Acinetobacter baumannii and produce carbapenemase Klebsiella pneumoniae. In general, a type of multidrug resistant bacteria Cultivated from Covid-19 patients worldwide various rates include Klebsiella pneumoniae, Pseudomonas aeruginosa, Serratia marcescens, Enterobacter cloacae, Acinetobacter baumannii, Escherichia coli, and Staphylococcus aureus.
Diagnostic Challenges of Respiratory Infections
Even with the best diagnostic efforts, the etiology of respiratory infections is often elusive. CDC EPIC research team conducts landmark trial of 2,250 people adults and 2,222 children Community-acquired pneumonia (CAP). Despite extensive diagnostic workup, including culture, multiplex PCR, and urine antigen testing, the pathogen was detected in only 38% of adult and 81% of pediatric patients, highlighting the need for new assays to improve diagnostic yields.
Imaging studies such as invasive diagnostic procedures (such as bronchoscopy that allow testing of samples of the lower respiratory tract (site of infection)) and CT scans complement routine laboratory testing, but expose health care providers to airborne pathogens, And its use is discouraged in Covid-19 patients. This further limits diagnostic options and may reduce the yield of diagnostic tests.
Metagenomics can identify co-infections, including Covid-19 patients
Metagenomics offers advances in infectious disease diagnosis by providing diagnostic techniques to detect potentially unlimited numbers of known and novel microorganisms from a single sample in a single test. one Several studies have shown that metagenomic sequencing Nasopharyngeal swab Not only can detect the overall SARS-CoV-2 Genomes and emerging mutations/variations, but also identify co-infections with human parainfluenza virus 3, Moraxella and other organisms more easily than traditional methods. also, metagenomics Identified candidate etiologies SARS-CoV-2 PCR negative samples, otherwise the cause of the patient’s symptoms remains unknown.
In addition to detecting hundreds of pathogens, a Commercially available metagenomics analysis More than 2,100 markers of antimicrobial resistance (AMR) can also be comprehensively tested within 24 hours.This test, called precision metagenomics, is a very broad metagenomic next-generation sequencing (mNGS), much like Shotgun Metagenomics, and can correct all pathogen types in one test. Furthermore, Precision Metagenomics requires only modest depths compared to shotgun tests, as the enrichment step removes host background more efficiently, making the results very sensitive and specific. Importantly, Precision Metagenomics can reliably provide insight into a very broad range of AMR markers, faster hands-on turnaround times, and a more cost-effective price point than shotgun metagenomics.
These results demonstrate the value of metagenomics in identifying pathogens that may evade detection, including co-infections that may put Covid-19 patients at increased risk of adverse outcomes. By analyzing circulating strains, routine metagenomics-based broad and rapid pathogen detection and AMR analysis can also aid in real-time monitoring of circulating strains and preparation and early identification of future viral pandemics.
In conclusion, we still have a lot to learn from the Covid-19 pandemic, and the role of improved diagnostic rates and antimicrobial resistance testing for co-infections is critical.
Photo: Anastasia Usenko, Getty Images
