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.

本数据集对随机临床试验中，依据快速胸超声引导下氧四环素（OTC）与氟苯尼考（FF）治疗肺炎的疗效评估中，每个巴氏杆菌属分离株的抗菌敏感性测试结果以及全基因组测序（WGS）结果进行了详细概述。以最大实变深度小于1厘米作为治愈标准及抗菌治疗的终止依据。此外，研究还评估了治疗开始时实变深度与治愈及治疗持续时间之间的关联。试验纳入了320头肉牛，随机分配至两组之一：一组接受OTC治疗（n=160），另一组接受FF治疗（n=160），均在第1天（为期两天的预防性治疗）。在第1天及之后每48小时进行一次临床评分和快速胸超声检查，持续10天。自第1天起，仅对实变深度≥1厘米的牛进行进一步治疗。在每个时间点，最大实变深度被用于将牛分为四个快速胸超声类别：健康（无实变）、轻度肺炎（实变<1厘米）、中度肺炎（实变1-3厘米）和重度肺炎（实变≥3厘米）。比较两组治疗组的治愈率、治疗持续时间和抗菌药物剂量数（NAD）。此外，对非内窥镜支气管肺泡灌洗液中的分离株进行了病原体鉴定和抗菌敏感性测试。在第1天，30.0%（96/320）的牛存在实变≥1厘米，至第9天增至50.9%（162/318）。经单次预防性治疗，OTC组和FF组的治愈率分别为20.9%（9/43）和20.9%（9/43）。与中度肺炎的牛相比，重度肺炎的牛在首次治疗后治愈的可能性较低（优势比（OR）=0.17；95%置信区间（CI）：0.04 - 0.63）。至第9天，初始病例的最终治愈率在OTC组和FF组均为27.9%。两组在所有观察点上的治愈率相似（P>0.05）。总体而言，试验期间所有患有中度或重度肺炎的牛的最终治愈率分别为41.2%（52/102）和19.0%（12/63）（P=0.004）。中位治疗持续时间为4天（四分位数间距（IQR）=2-6；最小值（Min）=2；最大值（Max）=8），两组治疗持续时间相似（P=0.59）。中度肺炎牛的治疗持续时间（中位数=6；IQR=4-6；Min=2；Max=8）低于重度肺炎牛的中位治疗持续时间（中位数=8；IQR=4-8；Min=2；Max=8）（P=0.004）。与第1天轻度肺炎的牛相比，中度（P=0.01）和重度肺炎（P<0.001）的牛的治疗持续时间显著更长。在本研究中，治愈率较低，且两种抗菌药物之间的治愈率无显著差异。根据实变深度对牛进行分类似乎是有益的，因为轻度、中度和重度组的治愈率和治疗持续时间均存在差异。