Srednik Mariela E, Morningstar-Shaw Brenda R, Hicks Jessica A, Mackie Tonya A, Schlater Linda K
National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, United States Department of Agriculture, Ames, IA, United States.
Front Microbiol. 2022 Nov 3;13:979790. doi: 10.3389/fmicb.2022.979790. eCollection 2022.
In the USA, subspecies serovar Senftenberg is among the top five serovars isolated from food and the top 11 serovars isolated from clinically ill animals. Human infections are associated with exposure to farm environments or contaminated food. The objective of this study was to characterize Senftenberg isolates from production animals by analyzing phenotypic antimicrobial resistance profiles, genomic features and phylogeny. Senftenberg isolates (n = 94) from 20 US states were selected from NVSL submissions (2014-2017), tested against 14 antimicrobial drugs, and resistance phenotypes determined. Resistance genotypes were determined using whole genome sequencing analysis with AMRFinder and the NCBI and ResFinder databases with ABRicate. Plasmids were detected using PlasmidFinder. Integrons were detected using IntFinder and manual alignment with reference genes. Multilocus-sequence-typing (MLST) was determined using ABRicate with PubMLST database, and phylogeny was determined using vSNP. Among 94 isolates, 60.6% were resistant to at least one antimicrobial and 39.4% showed multidrug resistance. The most prevalent resistance findings were for streptomycin (44.7%), tetracycline (42.6%), ampicillin (36.2%) and sulfisoxazole (32.9%). The most commonly found antimicrobial resistance genes were (6')-Iaa (100%), (3″)-Ib and (6)-Id (29.8%) for aminoglycosides, followed by (26.6%) for penicillins, 1 (25.5%) and 2 (23.4%) for sulfonamides and A (23.4%) for tetracyclines. Quinolone-resistant isolates presented mutations in A and/or C genes. Class 1 integrons were found in 37 isolates. Thirty-six plasmid types were identified among 77.7% of the isolates. Phylogenetic analysis identified two distinct lineages of Senftenberg that correlated with the MLST results. Isolates were classified into two distinct sequence types (ST): ST14 (97.9%) and ST 185 (2.1%). The diversity of this serotype suggests multiple introductions into animal populations from outside sources. This study provided antimicrobial susceptibility and genomic characteristics of Senftenberg clinical isolates from production animals in the USA during 2014 to 2017. This study will serve as a base for future studies focused on the phenotypic and molecular antimicrobial characterization of Senftenberg isolates in animals. Monitoring of antimicrobial resistance to detect emergence of multidrug-resistant strains is critical.
在美国，森夫滕贝格血清型亚种是从食品中分离出的前五大血清型之一，也是从患病动物中分离出的前11种血清型之一。人类感染与接触农场环境或受污染食品有关。本研究的目的是通过分析表型抗菌药物耐药谱、基因组特征和系统发育来鉴定生产动物中的森夫滕贝格分离株。从美国国家兽医服务实验室（NVSL）2014 - 2017年提交的样本中选取来自美国20个州的94株森夫滕贝格分离株，对其进行14种抗菌药物测试并确定耐药表型。使用AMRFinder以及带有ABRicate的NCBI和ResFinder数据库通过全基因组测序分析确定耐药基因型。使用PlasmidFinder检测质粒。使用IntFinder并与参考基因进行手动比对检测整合子。使用带有PubMLST数据库的ABRicate确定多位点序列分型（MLST），并使用vSNP确定系统发育。在94株分离株中，60.6%对至少一种抗菌药物耐药，39.4%表现出多重耐药。最常见的耐药结果是对链霉素（44.7%）、四环素（42.6%）、氨苄青霉素（36.2%）和磺胺异恶唑（32.9%）。最常见的抗菌药物耐药基因是氨基糖苷类的(6')-Iaa（100%）、(3″)-Ib和(6)-Id（29.8%），其次是青霉素类的（26.6%）、磺胺类的1（25.5%）和2（23.4%）以及四环素类的A（23.4%）。耐喹诺酮分离株在A和/或C基因中出现突变。在37株分离株中发现了1类整合子。在77.7%的分离株中鉴定出36种质粒类型。系统发育分析确定了森夫滕贝格的两个不同谱系，这与MLST结果相关。分离株分为两种不同的序列类型（ST）：ST14（97.9%）和ST185（2.1%）。这种血清型的多样性表明有多种外部来源引入动物群体。本研究提供了2014年至2017年美国生产动物中森夫滕贝格临床分离株的抗菌药物敏感性和基因组特征。本研究将作为未来专注于动物中森夫滕贝格分离株表型和分子抗菌特征研究的基础。监测抗菌药物耐药性以检测多重耐药菌株的出现至关重要。
