Caracterização molecular e fenotípica de Acinetobacter baumannii em pacientes com COVID-19

Abstract

Introduction: Acinetobacter baumannii is a clinically relevant hospital opportunistic pathogen and one of the most resistant microorganisms found in healthcare settings worldwide. However, the characterization of isolates causing infection in COVID-19 patients remains incompletely explored. Objective: In this context, the central purpose of this study was to characterize phenotypically and molecularly isolates of A. baumannii causing infection in patients with COVID-19. Material and Method: Clinical samples from individuals with positive COVID-19 results, admitted to the Hospital de Base de São José do Rio Preto, from May to October 2020, were analyzed. Bacterial isolates underwent species identification and antimicrobial susceptibility evaluation using the automated BD PhoenixTM microbiology system. The isolates were then subjected to PCR analysis of resistance genes, molecular typing, and biofilm formation testing. Additionally, whole genome sequencing (WGS) was performed on four representative isolates. Simultaneously, a retrospective review of medical records for all patients was conducted. Results: A total of 91 isolates were recovered from 86 patients, with 78 (85.7%) originating from tracheal aspirate samples, 8 (8.79%) from urine, 4 (4.39%) from blood, and one (1%) from pleural fluid. Notably, the majority of patients (86.04%) presented comorbidities, and 99% required Intensive Care Unit (ICU) admission, resulting in a lethality rate of 63.95%. All isolates exhibited a multidrug-resistant (MDR) phenotype and demonstrated high frequency resistance to aminoglycosides, fluoroquinolones, and beta-lactams, while remaining susceptible to polymyxin B. OXA-23-producing strains were identified in all patients. Pulse Field Gel Electrophoresis (PFGE) analysis revealed the circulation of distinct A. baumannii clones among patients, with 66% of strains clustered into five main groups. Furthermore, the presence and persistence of clones were observed over a six-month investigation period. Multilocus Sequence Typing (MLST) identified four distinct sequence types (STs): ST1 (56.04%), ST15 (37.36%), ST730 (5.49%), and ST79 (1.09%). Additionally, 78 (85.71%) isolates were classified as biofilm producers. Core genome MLST (cgMLST) analysis demonstrated remarkable genetic proximity among the three sequenced ST1 strains. Whole Genome Sequencing (WGS) also revealed a wide range of genes associated with resistance and virulence, including multiple efflux xiii pump genes that play crucial roles in both characteristics. Conclusions: This study identified widespread dissemination of A. baumannii carrying the blaOXA-23 gene, exhibiting a multidrug-resistant phenotype. The ST1, ST15, and ST730 lineages predominated, with similar isolates observed over time. Biofilm formation was observed in the majority of isolates. The analyzed population displayed a predominantly high-risk profile, associated with a high occurrence of fatalities. Therefore, there is a highlighted need for targeted strategies to mitigate morbidity and mortality resulting from secondary infections, particularly in the post-COVID-19 pandemic context, aiming to prevent subsequent challenges and ensure patient safety.