Comprehensive Molecular Testing for Respiratory Pathogens in Community-Acquired Pneumonia

Gadsby, Naomi J.; Russell, Clark D.; McHugh, Martin P.; Mark, Harriet; Conway Morris, Andrew; Laurenson, Ian F.; Hill, Adam T.; Templeton, Kate E.

Patients presented to 2 tertiary care hospitals in Edinburgh, United Kingdom, over an 18-month period between September 2012 and February 2014. Consecutive cases with clinical and radiological evidence of CAP were identified through daily retrospective electronic review of all respiratory samples received by our microbiology laboratory. Inclusion criteria for the study included the following: adult (aged ≥18 years); LRT specimen obtained within 48 hours of admission to the hospital; new radiographic infiltrate as determined by radiologist or consultant respiratory physician; and 3 of more of the following signs or symptoms: new or worsening cough, new or worsening expectoration of sputum, hemoptysis, new or worsening dyspnea, pleuritic chest pain, fever, headache, or abnormalities on chest auscultation or percussion. Exclusion criteria included the following: bronchiectasis, cystic fibrosis, or healthcareassociated pneumonia (hospitalized in an acute care hospital for 2 or more days within 90 days of the infection or resided in a nursing home or long-term care facility) [34] . Radiology reports were reviewed for all patients, and only patients with radiological changes consistent with pneumonia were included. Where there was any uncertainty, the images were reviewed by an experienced respiratory physician (A. T. H.). Clinical data including comorbidities, outcomes, and antibiotic prescriptions were collected retrospectively from patient hospital records using a standard pro forma as part of a clinical audit of pneumonia management (approved by the Quality Improvement Team, Royal Infirmary of Edinburgh). Drug administration prior to hospitalization, including antibiotic prescription, was obtained from the electronic primary care prescription records on admission and later verified by a pharmacist.