key: cord-0801289-woqoroha authors: Ruiz-Bastián, Mario; Falces-Romero, Iker; Ramos-Ramos, Juan Carlos; de Pablos, Manuela; García-Rodríguez, Julio title: BACTERIAL CO-INFECTIONS IN COVID-19 PNEUMONIA IN A TERTIARY CARE HOSPITAL: SURFING THE FIRST WAVE date: 2021-07-03 journal: Diagn Microbiol Infect Dis DOI: 10.1016/j.diagmicrobio.2021.115477 sha: 42ea55f182eea96cf8c837c19e9072010899bbc5 doc_id: 801289 cord_uid: woqoroha The aim of this study is to review bacterial isolates from respiratory samples of patients with severe COVID-19 disease during the first two months of the first wave of in our hospital. A single-centre retrospective observational study in critically ill adult patients was performed. A total of 1251 respiratory samples from 1195 patients were processed. Samples from 66 patients (5.52%) were determined to be microbiologically significant by a semi-quantitative culture. All patients received broad spectrum antibiotherapy as an empirical treatment. The isolated bacteria were mainly Enterobacterales followed by Staphylococcus aureus and Pseudomonas aeruginosa. Bacterial co-infections in ICU stay could seem not dependant on the virus that has produced the viral pneumonia similarly as with other respiratory viruses such as Influenza virus. The pandemic yield by SARS-CoV-2 has been ongoing for more than one year. Around 178 million cases and 3.8 million deaths have been reported up to June 2021 by the World Health Organization (WHO) (1) . This virus can cause community-acquired pneumonia and hospital-acquired pneumonia with an important rate of Intensive Care Unit (ICU) admissions (2, 3) . Due to the long-term intubation, bacterial and fungal infections (2) (3) (4) are a frequent complication of viral pneumonias as reported in Influenza virus infections (5) (6) and also in SARS-CoV-2 infections (5, 7, 8) . There are no guidelines for managing viral, bacterial or fungal co-infections with SARS-CoV-2, but 200 million viral community-acquired pneumonias occur every year (5) and many studies have addressed the issue of viral pneumonia and bacterial co-infections (2) (3) (4) (5) 7, 8, 10) . The aim of this study is to review bacterial isolates from respiratory samples of patients with severe COVID-19 during the first two months of the first wave of maximum incidence in our hospital. During this period the population attended in our hospital was only COVID patients as described by Borobia et al (11) . Multidrug-resistant isolates were defined when presenting resistance to more than one antibiotic. Gram stains were also reported to give a better interpretation of the samples. Universitario La Paz with the code HULP: PI-4193. During the period of the study 1251 respiratory samples from 1195 patients were processed. All patients admitted to our centre had diagnostic of COVID-19 by a positive RT-PCR. Respiratory samples in ICU patients were obtained and cultured for bacteria at least 48 hours after admission. Samples from 66 patients (5.52%) were determined to be microbiologically significant. Among them there were 62 BAS (93.9%), 1 BAL (1.5%) and 3 tracheal aspirates (4.5%). Fifty three patients were male (80.3%), 13 were female (19.7%). The age ranges were detailed in Table 1 Table 1 . β-lactams were administered as an empirical treatment for infections to all of our patients being ceftriaxone the most prescribed one. Linezolid was the second antibiotic more prescribed in these patients (16, 24 .2%). Fifty seven patients had monomicrobial cultures and nine had 2 significant bacterial isolates. Among them, there were thirty one (42%) Enterobacterales (Escherichia coli, Klebsiella spp., and others, fourteen ESBLproducers), eighteen S. aureus (eight of them methicillin-resistant), and seventeen P. aeruginosa (two of them carbapenem-resistant, though no carbapenemase was detected). Other multidrug-resistant species isolated were detailed in Table 1 . Nineteen patients had bacteremia related to their respiratory infections, with the same isolated microorganism in blood culture and in respiratory sample. The median length of stay in the ICU before the first positive significant respiratory isolate was 15 days and the mortality rate during this period was 54.5%. The first respiratory sample of the patients collected and cultured for bacteria was at least 48 hours after ICU admission. Comparing the number of bacterial co-infections in the study period were much lower than the approximately 40% of bacterial co-infections described by Falsey et al. (15) , even though the demographic and clinical features of our patients were similar. This might be due to the fact that during the first COVID-19 wave empirical treatment with broad spectrum antibiotics were prescribed in all patients. Broad spectrum antibiotic were prescribed as an empirical treatment and when clinically significant microorganisms were isolated in a respiratory sample. ICUs are a hotspot for isolating multidrug-resistant microorganisms as they have a high antimicrobial pressure. Antibiotic therapy should not be started until bacterial co-infection is suspected and it should be based on up-to-date antibiotic guidelines, host risk factors, prior microbiological and epidemiology resistant data and taking into account recommendations from the stewardship team. One of the factors for the selection of multidrug-resistant bacteria in our study (Chryseobacterium spp., Burkholderia spp., Stenotrophomonas spp…) could be the use of broad spectrum antibiotics. Few studies have approached bacterial co-infection based on quantitative culture of respiratory samples. Some have addressed this topic by PCR on throat swab samples (8, 9) with the limitation of not being able to distinguish colonization from actual infection and the possibility of not detecting pathogens not included in the PCR design. In our study, the clinically significant bacterial isolates associated to COVID-19 were very similar to those isolates found in other viral pneumonia co-infections such as Influenza virus (S. aureus and P. aeruginosa followed by pathogens of the Enterobacterales order (16) . Streptococcus peumoniae and other pathogens involved in community-acquired pneumonia such as Haemophilus spp. and Moraxella spp. were not isolated during our study (6) . This could have been due to the fact that we did not recover samples at admission, so our isolates were mainly nosocomial microorganisms. The main limitations of our study are that it is a single-centre study with small numbers, short time period of the study, sampling only reflects extended ICU stay, and the samples not obtained during admission reflecting more community acquired pathogens. Also impact of giving azithromycin on bacterial microbiome affecting culture results. Further multicentric studies addressing larger cohorts in other regions will clarify more the matter of bacterial co-infection in COVID-19 patients. In conclusion, we have observed that bacterial co-infections in ICU stay could seem not dependant on the virus that has produced the viral pneumonia in the first place such as with Influenza virus. It would seem that SARS-CoV-2 is no exception to this issue. World Health Organization. Coronavirus disease (COVID-19) Weekly Epidemiological Update and Weekly Operational Update COVID-19 Associated Pulmonary Aspergillosis Bacterial and fungal infections in COVID-19 patients: A matter of concern Invasive aspergillosis in patients admitted to the intensive care unit with severe influenza: a retrospective cohort study Viral pneumonia Bacterial Coinfection in Adults With Community-Acquired Pneumonia Admitted to Conventional Wards: Risk Factors Isolation of Aspergillus spp. in respiratory samples of patients with COVID-19 in a Spanish Tertiary Care Hospital Rates of Co-infection Between SARS-CoV-2 and Other Respiratory Pathogens Co-infection with respiratory pathogens among COVID-2019 cases Recognition and management of respiratory coinfection and secondary bacterial pneumonia in patients with COVID-19 A Cohort of Patients with COVID-19 in a Major Teaching Hospital in Europe Diagnóstico microbiológico de las infecciones bacterianas del tracto respiratorio inferior. Procedimientos en Microbiología clínica. Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica The European Committee on Antimicrobial Susceptibility Testing. Breakpoint tables for interpretation of MICs and zone diameters Spanish Agency of Medicines and Medical Devices recommendation guidelines Bacterial Complications of Respiratory Tract Viral Illness: A Comprehensive Evaluation List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ B has contributed in conceptualization, data curation, formal analysis, investigation, methodology, project administrations, resources, software, writing, supervision and validation, visualization R has contributed in data curation, formal analysis, methodology, supervision and visualization P has contributed in supervision and visualization Polimicrobial: 5 (7.5%) Staphylococcus aureus 18 (24.3%): 8 MRSA Pseudomonas aeruginosa 17 (23%): 2 carbapenem-resistant isolates* Enterobacterales 31 (42%): 14 ESBL producing isolates -Kebsiella pneumoniae Multidrug-resistant bacteria** (Achromobacter spp., Burkholderia spp., Stenotrophomonas spp., Chryseobacterium spp., Corynebacterium spp.) 8 (10.8%) ESBL: Extended spectrum beta-lactamase; ICU: Intensive Care Unit; MRSA: Methicillin-resistant Staphylococcus aureus *No carbapenemase-producing isolate ** Resistance to more than one antibiotic I.F.R has contributed in data curation, formal analysis, methodology, supervision and visualization.J.C.R.R and M.D.P has contributed in supervision and visualization.J.G.R has contributed in supervision, visualization and validation.