Table_1_Whole-Genome Sequencing of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli From Human Infections in Finland Revealed Isolates Belonging to Internationally Successful ST131-C1-M27 Subclade but Distinct From Non-human Sources.XLSX

Antimicrobial resistance (AMR) is a growing concern in public health, particularly for the clinically relevant extended-spectrum beta-lactamase (ESBL) and AmpC-producing Enterobacteriaceae. Studies describing ESBL-producing Escherichia coli clinical samples from Finland to the genomic level and investigation of possible zoonotic transmission routes are scarce. This study characterizes ESBL-producing E. coli from clinical samples in Finland using whole genome sequencing (WGS). Comparison is made between animal, food, and environmental sources in Finland to gain insight into potential zoonotic transmission routes and to recognize successful AMR genes, bacterial sequence types (STs), and plasmids. ESBL-producing E. coli isolates (n = 30) obtained from the Eastern Finland healthcare district between 2018 and 2020 underwent WGS and were compared to sequences from non-human and healthy human sources (n = 67) isolated in Finland between 2012 and 2018. A majority of the clinical isolates belonged to ST131 (n = 21; 70%), of which 19 represented O25:H4 and fimH30 allele, and 2 O16:H5 and fimH41 allele. Multidrug resistance was common, and the most common bla gene identified was blaCTX–M–27 (n = 14; 47%) followed by blaCTX–M–15 (n = 10; 33%). blaCTX–M–27 was identified in 13 out of 21 isolates representing ST131, with 12 isolates belonging to a recently discovered international E. coli ST131 C1-M27 subclade. Isolates were found to be genetically distinct from non-human sources with core genome multilocus sequence typing based analysis. Most isolates (n = 26; 87%) possessed multiple replicons, with IncF family plasmids appearing in 27 (90%) and IncI1 in 5 (17%) isolates. IncF[F1:A2:B20] replicon was identified in 11, and IncF[F-:A2:B20] in 4 isolates. The results indicate the ST131-C1-M27 clade gaining prevalence in Europe and provide further evidence of the concerning spread of this globally successful pathogenic clonal group. This study is the first to describe ESBL-producing E. coli in human infections with WGS in Finland and provides important information on global level of the spread of ESBL-producing E. coli belonging to the C1-M27 subclade. The results will help guide public health actions and guide future research.

抗菌药物耐药性（AMR）已成为公共卫生领域日益严重的关注焦点，尤其是对于临床相关的广谱β-内酰胺酶（ESBL）和AmpC酶产生的大肠杆菌。描述芬兰从临床样本到基因组水平的ESBL产生性大肠杆菌研究以及探讨可能的动物源性传播途径的研究为数不多。本研究利用全基因组测序（WGS）技术，对芬兰的临床样本中分离出的ESBL产生性大肠杆菌进行了特征描述。本研究对比了芬兰动物、食品和环境来源的样本，以洞察潜在的动物源性传播途径，并识别成功传播的抗菌药物耐药基因、细菌序列类型（STs）和质粒。2018年至2020年间，从芬兰东部医疗区获得的30株ESBL产生性大肠杆菌分离株经WGS测序后，与2012年至2018年在芬兰分离的非人类和健康人类来源的67个序列进行了比较。多数临床分离株属于ST131（n = 21；70%），其中19株代表O25:H4和fimH30等位基因，2株代表O16:H5和fimH41等位基因。多重耐药性普遍存在，最常见的bla基因是blaCTX–M–27（n = 14；47%），其次是blaCTX–M–15（n = 10；33%）。在21株代表ST131的分离株中，有13株携带blaCTX–M–27，其中12株属于最近发现的国际E. coli ST131 C1-M27亚克隆。通过核心基因组多座位点序列分型分析，发现分离株与非人类来源在遗传上存在差异。大多数分离株（n = 26；87%）具有多个复制子，其中IncF家族质粒出现在27株（90%）和IncI1在5株（17%）分离株中。在11株分离株中鉴定出IncF[F1:A2:B20]复制子，在4株分离株中鉴定出IncF[F-:A2:B20]复制子。结果表明，ST131-C1-M27克隆群在欧洲的流行趋势正在增加，并为这一在全球范围内成功传播的致病克隆群的担忧提供了进一步的证据。本研究首次描述了芬兰人类感染中利用WGS技术检测到的ESBL产生性大肠杆菌，并为全球C1-M27亚克隆群ESBL产生性大肠杆菌的传播水平提供了重要信息。研究结果将有助于指导公共卫生行动和未来的研究。