Bacterial Resistance to Antibiotics and Clonal Spread in COVID-19-Positive Patients on a Tertiary Hospital Intensive Care Unit, Czech Republic

Abstract

This observational retrospective study aimed to analyze whether/how the spectrum of bacterial pathogens and their resistance to antibiotics changed during the worst part of the COVID-19 pandemic (1 November 2020 to 30 April 2021) among intensive care patients in University Hospital Olomouc, Czech Republic, as compared with the pre-pandemic period (1 November 2018 to 30 April 2019). A total of 789 clinically important bacterial isolates from 189 patients were cultured during the pre-COVID-19 period. The most frequent etiologic agents causing nosocomial infections were strains of Klebsiella pneumoniae (17%), Pseudomonas aeruginosa (11%), Escherichia coli (10%), coagulase-negative staphylococci (9%), Burkholderia multivorans (8%), Enterococcus faecium (6%), Enterococcus faecalis (5%), Proteus mirabilis (5%) and Staphylococcus aureus (5%). Over the comparable COVID-19 period, a total of 1500 bacterial isolates from 372 SARS-CoV-2-positive patients were assessed. While the percentage of etiological agents causing nosocomial infections increased in Enterococcus faecium (from 6% to 19%, p < 0.0001), Klebsiella variicola (from 1% to 6%, p = 0.0004) and Serratia marcescens (from 1% to 8%, p < 0.0001), there were significant decreases in Escherichia coli (from 10% to 3%, p < 0.0001), Proteus mirabilis (from 5% to 2%, p = 0.004) and Staphylococcus aureus (from 5% to 2%, p = 0.004). The study demonstrated that the changes in bacterial resistance to antibiotics are ambiguous. An increase in the frequency of ESBL-positive strains of some species (Serratia marcescens and Enterobacter cloacae) was confirmed; on the other hand, resistance decreased (Escherichia coli, Acinetobacter baumannii) or the proportion of resistant strains remained unchanged over both periods (Klebsiella pneumoniae, Enterococcus faecium). Changes in pathogen distribution and resistance were caused partly due to antibiotic selection pressure (cefotaxime consumption increased significantly in the COVID-19 period), but mainly due to clonal spread of identical bacterial isolates from patient to patient, which was confirmed by the pulse field gel electrophoresis methodology. In addition to the above shown results, the importance of infection prevention and control in healthcare facilities is discussed, not only for dealing with SARS-CoV-2 but also for limiting the spread of bacteria.

Bacterial Community- and Hospital-Acquired Pneumonia in Patients with Critical COVID-19—A Prospective Monocentric Cohort Study

“…This may be due to the high severity of the clinical condition of critical COVID-19 patients, who may have been colonized easily and quickly by hospital pathogens. The spread of multi-drug resistant clones in the hospital environment that has been adapted to the dramatic wave of a viral pandemic is also likely to play a role [73]. This conjecture is supported by the results of microbiological findings in HAP patients with a high prevalence of multi-drug-resistant Enterobacterales strains.…”

“…However, environmental issues also play a significant role. Previous studies by our authors' team, utilizing genetic methods, demonstrated clonal spread of identical bacterial strains in the ICU during the pandemic, leading to exogenous nosocomial infections, including respiratory tract infections caused by Klebsiella pneumoniae, Serratia marcescens, and Burkholderia cepacia complex, as well as colitis caused by Clostridioides difficile [72,73]. The reasons for this can be attributed to the predominantly open-space layout of the ward, where most rooms are open-plan, with few enclosed spaces for the isolation of patients, many of whom were connected to an HFOT device via a nasal mask.…”

“…The potential for spreading infected aerosols through this route has been a topic of extensive discussion in the literature [74][75][76][77][78]. Furthermore, it is plausible that during the initial months of the pandemic, when the DARIC department underwent restructuring, the influx of beds, staff, and patients played a significant role in the dissemination of bacteria within the ICU [72,73]. Hygienic epidemiological regimes were effective against SARS-CoV-2 infections in healthcare workers but were not sufficiently effective against the clonal spread of bacterial strains.…”

Bacterial coinfection and antibiotic resistance in hospitalized COVID-19 patients: a systematic review and meta-analysis

“…The included studies were published from 2020 to 2022 from regions of Africa (Egypt) ( Ramadan et al, 2020 ), America (United States, Peru, and Brazil) ( Baggs et al, 2022 ; Copaja-Corzo et al, 2021 ; da Costa et al, 2022 ; Kubin et al, 2021 ; Nori et al, 2021 ), Asia (Pakistan, Saudi Arabia, Qatar, India, Iran, Iraq, China, Indonesia, and Korea) ( Ahmed et al, 2022 ; Alqahtani et al, 2022 ; Baiou et al, 2021 ; Bazaid et al, 2022 ; Bhaskaran, 2022 ; Boorgula et al, 2022 ; Jabir, 2022 ; Jamnani et al, 2022 ; Khurana et al, 2021 ; Li et al, 2020 ; Mahmoudi, 2020 ; Moradi et al, 2021 ; Palanisamy et al, 2021 ; Pourajam et al, 2022 ; Rao et al, 2022 ; Rizvi et al, 2022 ; Said et al, 2022 ; Sathyakamala, Peace & Shanmugam, 2022 ; Sharifipour et al, 2020 ; Sharma et al, 2021 ; Sinto et al, 2022 ; Son et al, 2021 ; Vijay et al, 2021 ; Zeshan et al, 2022 ) and Europe (Turkey, United Kingdoms, Italy, France, Czech Republic, Switzerland, Germany, Greece, and Spain) ( Bahce, Acer & Ozudogru, 2022 ; Baskaran et al, 2021 ; Bentivegna et al, 2021 ; Ceccarelli et al, 2022 ; Contou et al, 2020 ; Cultrera et al, 2021 ; Doubravska et al, 2022 ; Floridia et al, 2022 ; Fontana et al, 2021 ; Foschi et al, 2021 ; Gysin et al, 2021 ; Karataş et al, 2021 ; Karruli et al, 2021 ; Lingscheid et al, 2022 ; Mazzariol et al, 2021 ; Posteraro et al, 2021 ; Protonotariou et al, 2021 ; Suarez-de-la-Rica et al, 2021 ; Temperoni, Caiazzo & Barchiesi, 2021 ...…”

A case report of fatal COVID-19 complicated by rapidly progressive sepsis caused by Klebsiella variicola

“…The causative organism was initially reported as K. pneumoniae , but genetic analysis revealed that it was indeed K. variicola . K. variicola have been reported among patients with immunocompromising conditions such as malignancy and diabetes [ 6 ], and a recent study in Czech Republic reported that the percentage of K. variicola as an etiological agent causing nosocomial infections increased significantly (from 1 to 6%, p = 0.0004) in COVID-19 patients compared to the pre-COVID-19 period [ 9 ]. But the impact of co-infection or secondary infection among COVID-19 patients remain uncertain.…”