Supplementary file 1

Detailed overview of the antimicrobial susceptibility test results for each Pasteurellaceae isolate and WGS results from a randomized clinical trial evaluating the efficact of oxytetracycline (OTC) and florfenicol (FF) treatment for pneumonia guided by quick thoracic ultrasound. Regression of maximum consolidation depth <1cm was used as a criterion for cure and to stop antimicrobial treatment. Additionally, the study assessed the associations of consolidation depth at treatment initiation with cure and treatment duration. The trial involved 320 veal calves, randomly assigned into one of two groups: one receiving OTC (n=160) and the other FF (n=160) on day 1 (2-day metaphylaxis). Clinical scoring and qTUS were done on day 1 and every 48 hours for a 10-day period. After day 1, only calves with consolidations ≥1cm were given further treatment. On each time point, maximum consolidation depth was used to categorize calves into four qTUS categories: healthy (no consolidation), mild pneumonia (consolidation <1cm), moderate pneumonia (consolidation 1–3cm) and severe pneumonia (consolidation ≥3cm). Cure, treatment duration and the number of antimicrobial dosages (NAD) were compared between treatment groups. In addition, pathogen identification and antimicrobial susceptibility testing was performed on isolates from non-endoscopic broncho alveolar lavage fluid. On day 1, 30.0% (96/320) of the calves had consolidation ≥1cm, which increased to 50.9% (162/318) by day 9. After single metaphylactic treatment, cure was 20.9% (9/43) and 20.9% (9/43) in the OTC and FF group, respectively. Calves with severe pneumonia had lower odds to be cured after first treatment than calves with moderate pneumonia (Odds ratio (OR) = 0.17; 95% Confidence interval (CI): 0.04 - 0.63). By day 9, final cure of the initial cases was 27.9% in both the OTC- and FF-group. both groups, cure was similar at all observation points (P > 0.05). Overall, final cure of all calves with either moderate or severe pneumonia during the trial was 41.2% (52/102) and 19.0% (12/63), respectively (P = 0.004). Median treatment duration was 4 days (Interquartile range (IQR) = 2-6; Minimum (Min)=2; Maximum (Max)=8) and was similar in both treatment groups (P = 0.59). Treatment duration for calves with moderate pneumonia (Med=6; IQR= 4-6; Min=2; Max=8) was lower than the median treatment duration of calves with severe pneumonia (Med=8; IQR= 4-8; Min=2; Max=8) (P = 0.004). When compared to calves with mild pneumonia on day 1, calves with moderate (P = 0.01) and severe pneumonia (P < 0.001) had significantly longer treatment durations. In this study, cure was low and not different between both antimicrobials. Categorizing calves based on consolidation depth appears useful as both cure and treatment duration were different for the mild, moderate and severe group.