Li Cong, Tyson Gregory H, Hsu Chih-Hao, Harrison Lucas, Strain Errol, Tran Thu-Thuy, Tillman Glenn E, Dessai Uday, McDermott Patrick F, Zhao Shaohua
Center for Veterinary Medicine, United States Food and Drug Administration, Laurel, MD, United States.
Food Safety and Inspection Service, United States Department of Agriculture, Athens, GA, United States.
Front Microbiol. 2021 Nov 19;12:777817. doi: 10.3389/fmicb.2021.777817. eCollection 2021.
is a significant and phylogenetically diverse zoonotic pathogen. To understand its genomic heterogeneity and antimicrobial resistance, we performed long-read sequencing on isolated from retail meats and food animals. A collection of 134 multidrug-resistant isolates belonging to 33 serotypes were subjected to PacBio sequencing. One major locus of diversity among these isolates was the presence and orientation of pathogenic islands (SPI), which varied across different serotypes but were largely conserved within individual serotypes. We also identified insertion of an IncQ resistance plasmid into the chromosome of fourteen strains of serotype I 4,[5],12:i:- and the genomic island 1 (SGI-1) in five serotypes. The presence of various SPIs, SGI-1 and integrated plasmids contributed significantly to the genomic variability and resulted in chromosomal resistance in 55.2% (74/134) of the study isolates. A total of 93.3% (125/134) of isolates carried at least one plasmid, with isolates carrying up to seven plasmids. We closed 233 plasmid sequences of thirteen replicon types, along with twelve hybrid plasmids. Some associations between isolate source, serotype, and plasmid type were seen. For instance, IncX plasmids were more common in serotype Kentucky from retail chicken. Plasmids IncC and IncHI had on average more than five antimicrobial resistance genes, whereas in IncX, it was less than one per plasmid. Overall, 60% of multidrug resistance (MDR) strains that carried >3 AMR genes also carried >3 heavy metal resistance genes, raising the possibility of co-selection of antimicrobial resistance in the presence of heavy metals. We also found nine isolates representing four serotypes that carried virulence plasmids with the operon. Together, these data demonstrate the power of long-read sequencing to reveal genomic arrangements and integrated plasmids with a high level of resolution for tracking and comparing resistant strains from different sources. Additionally, the findings from this study will help expand the reference set of closed genomes that can be used to improve genome assembly from short-read data commonly used in One Health antimicrobial resistance surveillance.
是一种重要且在系统发育上具有多样性的人畜共患病原体。为了解其基因组异质性和抗菌药物耐药性，我们对从零售肉类和食用动物中分离出的[病原体名称未给出]进行了长读长测序。对属于33种血清型的134株多重耐药分离株进行了PacBio测序。这些分离株之间一个主要的多样性位点是致病岛（SPI）的存在和方向，其在不同血清型中有所不同，但在单个血清型内基本保守。我们还鉴定出14株血清型I 4,[5],12:i:-菌株的染色体中插入了一个IncQ耐药质粒，以及5种血清型中存在基因组岛1（SGI-1）。各种SPI、SGI-1和整合质粒的存在显著促成了基因组变异性，并导致55.2%（74/134）的研究分离株产生染色体耐药性。总共93.3%（125/134）的分离株携带至少一个质粒，有些分离株携带多达七个质粒。我们完成了13种复制子类型的233个质粒序列以及12个杂交质粒的测序。观察到分离株来源、血清型和质粒类型之间存在一些关联。例如，IncX质粒在零售鸡肉的肯塔基血清型中更为常见。IncC和IncHI质粒平均携带超过五个抗菌药物耐药基因，而IncX质粒每个质粒携带的耐药基因少于一个。总体而言，携带>3个抗菌药物耐药（AMR）基因的60%多重耐药（MDR）菌株也携带>3个重金属耐药基因，这增加了在存在重金属的情况下共同选择抗菌药物耐药性的可能性。我们还发现代表四种血清型的9株分离株携带带有[未明确给出的操纵子名称]操纵子的毒力质粒。总之，这些数据证明了长读长测序在揭示基因组排列和整合质粒方面的强大能力，能够以高分辨率追踪和比较来自不同来源的耐药菌株。此外，本研究的结果将有助于扩大封闭基因组的参考集，可用于改进从“同一健康”抗菌药物耐药性监测中常用的短读长数据进行的基因组组装。
