Antibiotic susceptibility of pathogens isolated in respiratory tract samples of recently hospitalized patients

Community-acquired lower respiratory tract infections (CA-LRTIs) treatment is largely empirical as microbiologic testing is rarely performed. Here, we provide microbiologic data of severe CA-LRTI cases requiring hospitalization. We aim to describe the distribution and susceptibility patterns of pathogens causing severe CA-LRTI. We analyzed respiratory samples from recently admitted patients with CA-LRTIs to assess pathogen distribution and antibiotic susceptibility patterns. We divided patients into three groups: CA-LRTI and no prior healthcare exposure, CA-LRTI with healthcare exposure, and patients diagnosed with LRTI 48 to 7 days of hospital admission. In a sub-cohort, we assessed the bacteria's susceptibility to cefditoren. A total of 1,395, 2,212, and 2,760 samples were included in the three study groups. Gram-negative bacteria were the most common bacteria isolated. Streptococcus pneumoniae was over-represented in patients admitted to the intensive care unit (ICU) in the first two study groups, and was fully susceptible to penicillin in only ~50% of cases, and to fluoroquinolones and third-generation cephalosporins including cefditoren in >95% of cases. Susceptibility of Gram-negative bacteria to penicillins and to second-generation cephalosporins was lower than 50%. Age, admission to an ICU or surgical department, healthcare-associated infections, and infections with Gram-negative bacteria, Staphylococcus aureus, and Stenotrophomonas/Acinetobacter baumannii were associated with increased mortality. These results highlight pathogen diversity and concerning antibiotic susceptibility patterns in LRTI. These findings emphasize the importance of improving diagnostics and addressing antibiotic resistance in the effective management of LRTI.IMPORTANCEThis survey aims to describe the microbiologic aspects of community-acquired lower respiratory tract infections (CA-LRTI) in a large cohort of patients recently admitted to hospital. In a small sub-study, we assessed antibiotic susceptibility to cefditoren, an oral third-generation cephalosporin not used in Israel. By analyzing specimens from recently admitted patients with CA-LRTI, we aim to provide physicians with the relevant microbiologic data of the more severe CA-LRTI cases, i.e., those that resulted in hospital admission. Such microbiological data would provide primary care and emergency room physicians with additional insights as to the causative agents of severe CA-LRTI.