Pathogens isolated in respiratory tract samples of recently hospitalized patients: Implications for primary care physicians

Abstract

Background. Little is known about the etiology of community-acquired lower respiratory tract infections (CA-LRTI), and treatment is largely empirical. We aimed to provide clinicians with microbiologic data of the more severe cases, i.e. those that result in hospital admission.Methods. A retrospective cohort study was conducted at a tertiary care hospital in Haifa, Israel. Consecutive respiratory tract samples obtained from admitted patients older than 12 years between 2014 and 2020 were included. Pathogen distribution and drug susceptibility were described, and factors associated with 14 day mortality rates were analyzed using a multivariable logistic regression with a stepwise model reduction.Results. A total of 1,395; 2,212; and 2,760 samples were included in the community-acquired LRTI with no healthcare exposure, community-acquired LRTI with recent healthcare exposure, and LRTI diagnosed 48 hours to 7 days within hospital admission LRTI groups, respectively. Gram negative bacteria were the most common bacteria isolated. Streptococcus pneumoniae was over represented in patients admitted to the intensive care unit in the first two study groups (accounting for 20% and 10.1% of patients admitted to the ICU versus 12.6% and 6.4% of patients in the entire cohort, p < 0.001). Streptococcus pneumoniae was susceptible to penicillin in around 50% of cases; to erythromycin in 65% of cases; and to fluoroquinolones and 3rd generation cephalosporins in more than 95% of cases. Twenty-five percent of other typical community pathogens were resistant to ampicillin. Susceptibility of Gram negative bacteria to penicillins with and without a β-lactamase inhibitor and to second generation cephalosporins was lower than 50%. In the multivariable analysis, factors that were associated with increased mortality in the entire cohort were: age, admission to an ICU or surgical department, healthcare-associated infections, and infections with gram negative bacteria, Staphylococcus aureus, and Stenotrophomonas or Acinetobacter baummannii. Conclusions. Our data shows that gram negative bacteria are the most common pathogens causing LRTI. Typical community acquired pathogens are proportionally more common in younger patients, although the vast majority occur in elderly patients. The susceptibility pattern of these pathogens suggests that for high-risk patients the choice of oral antibiotics is limited.