Cell dyn sapphire

Routine hematological laboratory parameters were analyzed on an Abbott Cell-Dyn Sapphire hematology analyzer (Abbott Diagnostics Division, Santa Clara, CA, United States).

We extracted bacterial DNA directly from frozen BALF samples and amplified the V3–V4 hypervariable region of the bacterial 16S ribosomal RNA (rRNA) for sequencing on the Illumina Novaseq platform. Simultaneously, we performed quantitative PCR (qPCR) of the V3–V4 to obtain number of 16S rRNA gene copies per sample (surrogate for bacterial load). The default set of criteria was used to remove low-quality and chimeric reads. The remaining reads were subject to a close reference operational taxonomic unit (OTU) picking (97% identity cutoff). As for plasma biomarkers, we performed routine tests (white blood cells, neutrophils, red blood cell count, hemoglobin, platelets, alanine transaminase, etc.), inflammatory biomarkers (CRP, PCT, et al.) and correlated measurements. The WBC count, ANC, and ESR assays were performed on the CELL-DYN Sapphire (Abbott Diagnostics, Lake Forest, IL). CRP assays were performed on the Dimension Vista 1500 (Siemens Medical Solutions USA, Inc, Malvern, PA, USA) with a functional sensitivity of 0.29 mg/dl. Biomarkers were concentrations in blood measured at the Center for Clinical Research of Qilu Hospital of Shandong University.

Hematological indexes were performed by flow cytometry using the automatic analyzer CELL-DYN Sapphire (Abbott Diagnostics®, Abbott Laboratories. Abbott Park, Illinois, USA). Standard methods were used to assess biochemical metabolism parameters.
Determinations were performed at 0, 3, and 9 months and at the end of follow-up.
Proinflammatory ratios were calculated using Th1, Th17, and Th17.1 cells as numerators and Treg cells as denominators at month 0 and at the end of the follow-up. The Th1/Th2 ratio was also calculated. T cells were determined by flow cytometry in our immunology laboratory (Supplementary Methods 2).

White blood cell differential was immediately assessed in EDTA-treated blood via four angle optical flow cytometry on the Cell-Dyn Sapphire automated clinical hematology system using the Cell-Dyn WBC reagent pack (Abbott Diagnostics, Santa Clara, CA). Relative counts of leukocyte subpopulations were generated by dividing absolute subpopulation cell counts by the absolute total leukocyte count. The neutrophil-to-lymphocyte ratio was calculated as relative neutrophil count divided by relative lymphocyte count.

Anticoagulated whole blood from routine controls were processed on Sysmex XE2100 [TOA Medical Electronics, Kobe, Japan], Normal controls were analysed on Sysmex XN2000 (TOA Medical electronics Co, Kobe, Japan), Advia 2120 (Bayer Diagnostics, Tarritown, NY, USA), DXH800 (Beckman Coulter, Miami, FL USA), Cell-Dyn Sapphire (Abbott Diagnostics Santa Clara, CA, USA) for the determination of the complete blood cell counts and differential counts of leukocytes. The absolute neutrophil count was divided by the absolute lymphocyte count to calculate the NLR.