#FEMSmicroBlog: When Covid-19 meets ESKAPE pathogens in hospitals


Northern Greece was struck by an intense second Covid-19 epidemic wave during the fall of 2020. At the same time, a silent epidemic of multi-drug resistant organisms was and is going on. Hence, handling Covid-19 patients became even more challenging. The research article “Microbiological characteristics of bacteremias among Covid-19 hospitalized patients in a tertiary referral hospital in Northern Greece during the second epidemic wave” published in FEMS Microbes focuses on this problem. Together with the team from the University Hospital of Thessaloniki, Sarah Wettstadt explores for the #FEMSmicroBlog how antimicrobial-resistant bacteria challenge the course of Covid-19 in patients. #FascinatingMicrobes


When bacterial infections coincide with Covid-19

By the end of November 2021, SARS-CoV-2 is responsible for more than 5 million deaths worldwide and 260 million confirmed infections. In some severe cases, patients are co-infected with other pathogens, which worsens their course of the disease.

As such, bacterial co-infections in Covid-19 are associated with extended stays in the intensive care unit, mechanical ventilation, higher occurrence of acute respiratory distress syndrome and higher mortality. Plus, the chance of a bacterial co-infection seems to increase with the severity of Covid-19 infection.

Especially bacteremias–the presence of bacteria in blood–are most clinically important and life-threatening. Up to 40% of Covid-19 patients carry viable bacteria causing bacteremia, as shown in various studies.

Up to 40% of Covid-19 patients carry viable pathogenic bacteria that caus blood infections.

A new study published in FEMS Microbes now characterizes bacteremias in confirmed cases of hospitalized Covid-19 patients in a hospital in Northern Greece. The work reviews data from patients hospitalized between September and December 2020. It focuses on the frequency of bloodstream infections as well as the epidemiology and the antibiotic susceptibility profiles of the causative bacteria.


Antibiotic resistance profiles in secondary bacterial infections

The study shows that about 10% of Covid-19 patients developed bacteremia in this setting. Unfortunately, when patients were co-infected with a bacterial pathogen, their time of hospitalization was longer as well as the in-hospital mortality rate increased.

a hand reaching out for blood samples from covid-19 patients.
Positive blood culture bottles for evaluation. From Efthymia et al. (2021).

Interestingly, the isolated microorganisms represent bacterial species that were already present in the hospital before the Covid-19 pandemic. Of the identified pathogens, 114 are Gram-negative and 52 Gram-positive bacteria.

Identified bacteria belong to the ESKAPE group of bacteria, as such Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. Of these, Covid-19 patients most frequently carried strains of A. baumannii, K. pneumoniae or E. faecium.

ESKAPE bacteria are known for their virulent as well as their multi-drug resistant profiles. This is why the study further compares the profiles of antibiotic susceptibility of the identified pathogens and finds that many resistances indeed increased.

Most of these pathogens carry resistances to major antibiotics like gentamicin, piperacillin, fosfomycin or colistin. The study further shows that most carbapenem-resistant strains produced carbapenemase as their main protective mechanism. As expected, the type of genes encoding for carbapenem resistance did not change over the course of the Covid-19 pandemic.


ESKAPE pathogens cause secondary infections

The increased prevalence of ESKAPE pathogens in hospital settings and especially in Covid-19 patients is extremely worrying. However, this rise could be explained by the extended stay of patients in hospitals.

The increased prevalence of ESKAPE pathogens in hospital settings and especially Covid-19 patients is extremely worrying.

Many patients further received extensive antimicrobial treatments increasing the risk of settlement by sturdier pathogens. Secondly, personnel in the hospital that is generally responsible for infection control was constrained. Thus, ESKAPE pathogens might have had an easy time spreading to new hosts and settling in already immuno-compromised patients.

Overall, the study reveals high rates of bacteremias caused by ESKAPE pathogens in Covid-19 patients. Its results should be used to optimize hospital infection practices as well as administer the appropriate antibiotic therapies for secondary infections in Covid-19 patients.



About the authors of this blog

Landscape picture of the University hospital in ThessalonikiGeorgios Meletis is a Medical Microbiologist at the Microbiology Department of AHEPA University Hospital of Thessaloniki that has a long clinical and research history. Especially over the last decade, the institute’s research work focused on understanding, monitoring and combating antibiotic resistance. From the very beginning of the current pandemic, the Hospital has served as a referral center of Northern Greece for COVID-19.


headshot of Dr Sarah Wettstadt: science writer and science communicatorDr Sarah Wettstadt is a microbiologist-turned science writer and communicator working on various outreach projects and helping researchers talk and write about their scientific results. Her overall vision is to empower through learning: she shares scientific knowledge with both scientists and non-scientists and coaches scientists in writing about their research. Sarah is blog commissioner for the FEMSmicroBlog and was a social media editor for FEMS for 1.5 years. Previous to her science communication career, she worked as a postdoc in Marían Llamas’ lab on Pseudomonas aeruginosa’s ability to use heterologous iron sources and completed her PhD with Alain Filloux investigating the type 6 secretion system in Pseudomonas aeruginosa.

About this blog section

The section #FascinatingMicrobes for the #FEMSmicroBlog explains the science behind a paper and highlights the significance and broader context of a recent finding. One of the main goals is to share the fascinating spectrum of microbes across all fields of microbiology.

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