Abstract：
Shiga toxin-producing Escherichia coli (STEC) are globally significant foodborne pathogens. Dairy calves are a known reservoir of both O157 and non-O157 STEC. The objective of this study was to comprehensively evaluate the genomic attributes, diversity, virulence factors, and antimicrobial resistance gene (ARG) profiles of the STEC from preweaned and postweaned dairy calves in commercial dairy herds.
In total, 31 non-O157 STEC were identified as part of a larger study focused on the pangenome of >1000 E. coli isolates from the faeces of preweaned and postweaned dairy calves on commercial dairy farms. These 31 genomes were sequenced on an Illumina NextSeq500 platform.
Based on the phylogenetic analyses, the STEC isolates were determined to be polyphyletic, with at least three phylogroups: A (32%), B1 (58%), and G (3%). These phylogroups represented at least 16 sequence types and 11 serogroups, including two of the \'big six\' serogroups, O103 and O111. Several Shiga toxin gene subtypes were identified in the genomes, including stx1a, stx2a, stx2c, stx2d, and stx2g. Using the ResFinder database, the majority of the isolates (>50%) were determined to be multidrug-resistant strains because they harboured genes conferring resistance to three or more classes of antimicrobials, including some of human health significance (e.g., β-lactams, macrolides, and fosfomycin). Additionally, non-O157 STEC strain persistence and transmission within a farm was observed.
Dairy calves are a reservoir of phylogenomically diverse multidrug-resistant non-O157 STEC. Information from this study may inform assessments of public health risk and guide preharvest prevention strategies focusing on STEC reservoirs.
In total, 31 non-O157 STEC were identified as part of a larger study focused on the pangenome of >1000 E. coli isolates from the faeces of preweaned and postweaned dairy calves on commercial dairy farms. These 31 genomes were sequenced on an Illumina NextSeq500 platform.
Based on the phylogenetic analyses, the STEC isolates were determined to be polyphyletic, with at least three phylogroups: A (32%), B1 (58%), and G (3%). These phylogroups represented at least 16 sequence types and 11 serogroups, including two of the \'big six\' serogroups, O103 and O111. Several Shiga toxin gene subtypes were identified in the genomes, including stx1a, stx2a, stx2c, stx2d, and stx2g. Using the ResFinder database, the majority of the isolates (>50%) were determined to be multidrug-resistant strains because they harboured genes conferring resistance to three or more classes of antimicrobials, including some of human health significance (e.g., β-lactams, macrolides, and fosfomycin). Additionally, non-O157 STEC strain persistence and transmission within a farm was observed.
Dairy calves are a reservoir of phylogenomically diverse multidrug-resistant non-O157 STEC. Information from this study may inform assessments of public health risk and guide preharvest prevention strategies focusing on STEC reservoirs.
摘要：
目的：产志贺毒素的大肠杆菌（STEC）是全球重要的食源性致病菌，乳牛是O157和非O157STEC的已知储库。这项研究的目的是全面评估基因组属性，多样性,毒力因子（VFs），和商业奶牛群断奶前和断奶后小牛STEC的抗菌素抗性基因（ARG）谱。
方法：总共，31non-O157STEC被鉴定为一项更大的研究的一部分，该研究的重点是来自商业奶牛场断奶前和断奶后小牛粪便的>1000大肠杆菌分离株的pangenome。在IlluminaNextSeq500平台上对这31个基因组进行测序。
结果：基于系统发育分析，STEC分离株被确定为具有至少三个系统群的多系，即，A（32%），B1（58%），和G（3%），代表至少16种序列类型和11种血清群，包括“六大”血清群中的两个，O103和O111。在基因组中鉴定了几种志贺毒素基因亚型，包括stx1a，stx2a,stx2c,stx2d，和stx2g。根据对ResFinder数据库的分析，大多数分离株（>50％）是多药耐药（MDR），因为它们带有对三类或更多类抗菌药物具有抗性的基因，包括一些人类健康意义(例如，β-内酰胺,大环内酯类,和磷霉素）。此外,观察到非O157STEC菌株在农场内的持久性和传播。
结论：乳牛是系统发育多样的MDR非O157STEC的储库。这项研究的信息将有助于评估公共卫生风险，并可能有助于指导以STEC水库为重点的收获前预防策略。
方法：总共，31non-O157STEC被鉴定为一项更大的研究的一部分，该研究的重点是来自商业奶牛场断奶前和断奶后小牛粪便的>1000大肠杆菌分离株的pangenome。在IlluminaNextSeq500平台上对这31个基因组进行测序。
结果：基于系统发育分析，STEC分离株被确定为具有至少三个系统群的多系，即，A（32%），B1（58%），和G（3%），代表至少16种序列类型和11种血清群，包括“六大”血清群中的两个，O103和O111。在基因组中鉴定了几种志贺毒素基因亚型，包括stx1a，stx2a,stx2c,stx2d，和stx2g。根据对ResFinder数据库的分析，大多数分离株（>50％）是多药耐药（MDR），因为它们带有对三类或更多类抗菌药物具有抗性的基因，包括一些人类健康意义(例如，β-内酰胺,大环内酯类,和磷霉素）。此外,观察到非O157STEC菌株在农场内的持久性和传播。
结论：乳牛是系统发育多样的MDR非O157STEC的储库。这项研究的信息将有助于评估公共卫生风险，并可能有助于指导以STEC水库为重点的收获前预防策略。
