Antimicrobial Resistance Genes, Cassettes, and Plasmids Present in Salmonella enterica Associated With United States Food Animals
Antimicrobial Resistance Genes, Cassettes, and Plasmids Present in Salmonella enterica Associated With United States Food Animals
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DOI：
10.3389/fmicb.2019.00832
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发表时间：
2019-04-17
影响因子：
5.2
通讯作者：
Frye, Jonathan G.
中科院分区：
文献类型：
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作者：
McMillan, Elizabeth A.;Gupta, Sushim K.;Frye, Jonathan G.
抗菌素耐药性（AR）在细菌间通过移动的遗传元件（MGE）转移的能力，可导致动物源细菌快速建立多药耐药性（MDR），从而对人类健康造成食源性风险。为了研究肠道沙门氏菌的耐药性及其与质粒的关系，对193株沙门氏菌进行了全基因组序列（WGS）分析。在1998年至2011年期间，从与美国食用动物相关的来源中分离出的肠道菌; 119种对至少一种抗生素具有耐药性。分离株代表86种血清型和变异体，以及不同的表型耐药谱。共检测到923个AR基因和212个质粒。每个分离株都含有至少一个AR基因。在157株分离株中检测到至少一种质粒。鉴定了对氨基糖苷类（n = 472）、β-内酰胺类（n = 84）、四环素类（n = 171）、磺胺类（n = 91）、非尼考类（n = 42）、甲氧苄啶（n = 8）、大环内酯类（n = 5）、磷霉素（n = 48）和利福平（n = 2）的耐药基因。在分离株中检测到的质粒复制子类型为NC（n = 32）、ColE（n = 76）、F（n = 43）、HI 1（n = 4）、HI 2（n = 20）、I1（n = 62）、N（n = 4）、Q（n = 7）和X（n = 35）。表型耐药与95.4%的病例中确定的AR基因相关。大多数AR基因位于质粒上，许多质粒携带多个AR基因。鉴定出6个抗生素耐药盒结构（ARC）和1个假盒。ARC含有1至5个抗性基因（ARC 1：sul2、strAB、tetAR; ARC 2：aac3-iid; ARC 3：aph、sph; ARC 4：cmy-2; ARC 5：floR; ARC 6：tetB;伪ARC：aadA、aac3-Vla、sull）。这些ARC存在于多个分离株和多个复制子类型的质粒上。为了确定这些ARC的当前分布和频率，分析了公共NCBI数据库，包括2014年至2018年美国农业部食品安全和检验局（FSIS）收集的分离株的WGS数据。ARC 1、ARC 4和ARCS与牛分离株显著相关，而ARC 6与鸡分离株显著相关。这项研究表明，携带AR基因的一组不同的质粒负责从美国食用动物分离的沙门氏菌中观察到的表型抗性。还确定许多质粒携带类似的ARC。
The ability of antimicrobial resistance (AR) to transfer, on mobile genetic elements (MGEs) between bacteria, can cause the rapid establishment of multidrug resistance (MDR) in bacteria from animals, thus creating a foodborne risk to human health. To investigate MDR and its association with plasmids in Salmonella enterica, whole genome sequence (WGS) analysis was performed on 193 S. enterica isolated from sources associated with United States food animals between 1998 and 2011; 119 were resistant to at least one antibiotic tested. Isolates represented 86 serotypes and variants, as well as diverse phenotypic resistance profiles. A total of 923 AR genes and 212 plasmids were identified among the 193 strains. Every isolate contained at least one AR gene. At least one plasmid was detected in 157 isolates. Genes were identified for resistance to aminoglycosides (n = 472), beta-lactams (n = 84), tetracyclines (n = 171), sulfonamides (n = 91), phenicols (n = 42), trimethoprim (n = 8), macrolides (n = 5), fosfomycin (n = 48), and rifampicin (n = 2). Plasmid replicon types detected in the isolates were NC (n = 32), ColE (n = 76), F (n = 43), HI1 (n = 4), HI2 (n = 20), I1 (n = 62), N (n = 4), Q (n = 7), and X (n = 35). Phenotypic resistance correlated with the AR genes identified in 95.4% of cases. Most AR genes were located on plasmids, with many plasmids harboring multiple AR genes. Six antibiotic resistance cassette structures (ARCs) and one pseudocassette were identified. ARCs contained between one and five resistance genes (ARC1: sul2, strAB, tetAR; ARC2: aac3-iid; ARC3: aph, sph; ARC4: cmy-2; ARCS: floR; ARC6: tetB; pseudo-ARC: aadA, aac3-Vla, sull). These ARCs were present in multiple isolates and on plasmids of multiple replicon types. To determine the current distribution and frequency of these ARCs, the public NCBI database was analyzed, including WGS data on isolates collected by the USDA Food Safety and Inspection Service (FSIS) from 2014 to 2018. ARC1, ARC4, and ARCS were significantly associated with cattle isolates, while ARC6 was significantly associated with chicken isolates. This study revealed that a diverse group of plasmids, carrying AR genes, are responsible for the phenotypic resistance seen in Salmonella isolated from United States food animals. It was also determined that many plasmids carry similar ARCs.