If participants declined a clinical assessment or a swab, the data were coded as missing.
Any swab with visible secretions was coded as good.
Nasal swabs were labeled with a specific code containing the farm identification number, month, 2-letter state abbreviation, and nasal swab sample number.
22 Each pair of results (swab and tissue sample) will be coded as follows: swab and tissue sample report all the same isolates; swab reports same isolates as tissue sample plus extra isolates; tissue sample reports same isolates as swab plus extra isolates; tissue sample and swab report different isolates (with or without overlap in some isolates found).
Sample pairs will be further coded: results from the swab but not the tissue sample indicates change in therapy, results from the tissue sample but not the swab indicates a change in therapy, swab and tissue sample in agreement on change in therapy.
One of the swabs was transferred to Amies agar gel with charcoal, code 114C, from Copan Diagnostics Inc. (California, USA) for later bacteriological examinations.
All files of children who received a throat swab for GABHS culture with the following ICD-9 codes infectious mononucleosis (075), nasopharyngitis (460), pharyngitis (462), tonsillitis (463) and sore throat (784.1) were included for analysis.
Toxigenic C. ulcerans grew from culture of the nasal swab specimen; it was identified by biochemical differentiation (API Coryne code 0111326; bioMèrieux, Nürtingen, Germany), rpoB sequencing (6 ), and MALDI-TOF analysis (MALDI Biotyper; Bruker Daltonics, Bremen, Germany) (7 ).
For each resistant isolate the following codes will be created: resistant isolate reported by swab but not tissue sample, resistant isolate reported by tissue sample but not swab, swab and tissue sample results agree.
In addition, in order to further characterize the D8-VNM viruses, the complete coding region of the H gene from 8 throat swab samples with high viral copies was sequenced.
