Atbexpression automatic bacterial identification instrument

Total nucleic acids were extracted from respiratory and blood samples using a NucliSens easyMAG apparatus (bioMerieux, Marcy l′Etoile, France). The presence of HRVs and other common respiratory pathogens were screened using the fast-track diagnostic respiratory pathogens 21 plus kit (2013 version, Fast-track diagnostics, Junglinster, Luxembourg), which included HRVs, IFVA and B, human coronaviruses (HCoV, OC43, 229E, NL63, and HKU1), parainfluenza viruses, human metapneumovirus (A and B), EV, RSV (A and B), adenovirus, bocavirus, parechovirus, Mycoplasma pneumoniae, Chlamydia pneumoniae, Streptococcus pneumoniae, Haemophilus influenzae B, and Staphylococcus aureus. Bacterial culture was performed on lower respiratory samples and acute sera using an ATBExpression automatic bacterial identification instrument (bioMerieux, Marcy l′Etoile, France).

Twenty-five COPD cases and nine non-COPD controls (not paired) were enrolled in this study. All COPD subjects were in a stable state (at least 8 weeks without exacerbation or use of antibiotics). The exclusion conditions included known cardiovascular diseases, renal or liver insufficiency, bronchiectasis, active pulmonary tuberculosis, bronchial asthma, pulmonary fibrosis, and lung cancer. Non-COPD controls had had no respiratory tract infection symptoms in the three months before submitting to bronchoscope examination. Clinical information was obtained for each enrolled patient (Table S1 in the supplemental material).
BALF samples were collected from each subject using a bronchoscope as part of normal clinical management. Two aliquots of 50 ml sterile isotonic saline solution were instilled, with 50% of the volume recovered on average. The BALF samples were immediately placed on ice and processed within 30 min. Bacterial culturing was performed on the BALF samples using an ATB Expression automatic bacterial identification instrument (bioMérieux, Marcy l’Etoile, France). The remnant samples were aliquoted and stored at −80°C before processing. Two negative controls (saline solution passed through a new bronchoscope and a reused sterilized bronchoscope) were collected and processed following the same library preparation protocol.