Haemophilus influenzae is a common cause of mucosal infections that warrants accurate surveillance. We aimed to assess the prevalence of the species in clinical specimens, and characterise population structure and resistance to aminopenicillins by whole genome sequencing.We assessed the point prevalence by entering the database records of 1 day in Denmark and examined the genome sequences of nationwide, collected isolates from the same day. The prevalence of H. influenzae in clinical samples on the 10th of January 2018 was 1.78 per 100,000 person-days (all samples), and 2.47 per 1000 hospital bed-days (hospital samples). Of 2009 bacteria deemed clinically relevant and collected in a concerted action by the Danish departments of clinical microbiology, 62 (3.1%) were H. influenzae. All 62 isolates belonged to phylogenetic group I and were unencapsulated. Three strains from separate Danish regions had identical core genome sequences, but a small number of intergenic mutations testified to circulating clones, rather than individual cases of patient-to-patient transmission. The TEM-1 β-lactamase gene was present in 24 strains, while 13 strains were genetically categorised as ampicillin-resistant due to substitutions in penicillin-binding protein 3; shared patterns of amino acid substitutions in unrelated strains indicated putative lateral transfer of chromosomal resistance. Circulating clones of H. influenzae are frequent, and host factors, rather than direct transmission of epidemic strains, may be the primary cause of infection. The bleak presence of ampicillin resistance revealed by sequencing of point prevalence strains underscores the necessity for close examination of testing methods.

流感嗜血杆菌是粘膜感染的常见原因，需要进行准确监测。我们旨在评估临床标本中该物种的流行率，并通过全基因组测序来表征种群结构和对氨基青霉素的耐药性。 我们通过进入丹麦 1 天的数据库记录评估点流行率，并检查了全国范围内的基因组序列，收集从同一天隔离。2018 年 1 月 10 日临床样本中流感嗜血杆菌的流行率为每 100,000 人日（所有样本）1.78 例，每 1000 个医院床位日（医院样本）2.47 例。在 2009 年被丹麦临床微生物学部门一致认为具有临床相关性并收集的细菌中，62 种 (3.1%) 是流感嗜血杆菌. 所有 62 个分离株都属于系统发育组 I 并且没有被封装。来自丹麦不同地区的三个菌株具有相同的核心基因组序列，但少量基因间突变证明了循环克隆，而不是个别病例的患者间传播。TEM-1 β-内酰胺酶基因存在于 24 个菌株中，而 13 个菌株由于青霉素结合蛋白 3 的取代而被基因归类为氨苄青霉素抗性；无关菌株中氨基酸取代的共享模式表明染色体抗性的推定横向转移。流感嗜血杆菌的循环克隆是常见的，宿主因素，而不是流行菌株的直接传播，可能是感染的主要原因。点流行菌株的测序显示氨苄青霉素耐药性的暗淡存在强调了仔细检查测试方法的必要性。