摘要
      接触抗生素的食用动物粪便通常被用作土壤肥料，可能会向土壤中释放具有不同抗生素抗性基因（ARG）的抗生素抗性细菌（ARB）。为了确定鸡粪施用对土壤抗性的影响，使用全基因组测序和生物信息学工具，对从鸡粪和土壤改良前后收集的土壤样本中分离的肠球菌进行了表征。19株肠球菌。在Illumina Miseq平台上对来自三个来源的分离株进行测序，以确定分离株的抗性组、移动性组、病毒群、克隆性和系统发育关系。多基因座序列分型（MLST）分析揭示了八种新的序列类型（ST）（ST1700、ST1752、ST1753、ST1754、ST1755、ST1756、ST1004和ST1006）。这些分离株携带多种抗性基因，包括对大环内酯类林克酰胺链脲菌素（erm（B）、lnu（B），lnu（G），lsaA，lsaE，eat（A），msr（C）），四环素（tet（M），tet（L），tet（S）），氨基糖苷类（aac（6'）-Ii，aac（6'）-Iih，ant（6）-Ia，aph（3'）-III，ant（9）-Ia），氟喹诺酮类（efmA和emeA）产生抗性的基因，万古霉素（VanC{VanC-2，VanXY，VanXYC-3，VanXYC-4，VanRC}）和氯霉素（cat）。枯枝落叶改良土壤中含有新的ARB（特别是粪大肠杆菌）和ARG（蚂蚁（6）-Ia、aac（6’）-Ii、aph（3’）-III）、lnu（G）、msr（C）和eat（A）、efmA），这些都是以前在土壤中没有检测到的。所鉴定的ARGs与多种可移动遗传元件（MGE）相关，如插入序列（IS6、ISL3、IS256、IS30）、转座子（Tn3和Tn916）和质粒（repUS43、repUS1、rep9b和rep22）。在分离株的基因组中检测到28个编码粘附/生物膜形成（ebpA、ebpB、ebpC）、抗吞噬细胞增多症（elrA）和细菌性信息素（Ccf10、cOB1、cad和camE）的毒力基因。系统发育基因组分析揭示了来自枯枝落叶改良土壤的一些分离株与鸡枯枝落叶分离株之间的密切关系。枯枝落叶改良前后土壤中ARG和ARB剖面的差异及其与不同MGE的关系表明ARG和ARB从枯枝落叶向土壤的迁移和传递。
Abstract
Manure from food animals exposed to antibiotics is often used as soil fertiliser, potentially releasing antibiotic-resistant bacteria (ARB) with diverse antibiotic-resistance genes (ARGs) into the soil. To determine the impact of chicken litter application on the soil resistome, Enterococcus spp. isolated from chicken litter and soil samples collected before and after the soil amendment were characterised, using whole-genome sequencing and bioinformatics tools. Nineteen Enterococcus spp. isolates from the three sources were sequenced on Illumina Miseq platform to ascertain the isolates’ resistome, mobilome, virulome, clonality, and phylogenomic relationships. Multilocus sequence typing (MLST) analysis revealed eight novel sequence types (STs) (ST1700, ST1752, ST1753, ST1754, ST1755, ST1756, ST1004, and ST1006). The isolates harboured multiple resistance genes including those conferring resistance to inter alia macrolides-lincosamide-streptogramin (erm(B), lnu(B), lnu(G), lsaA, lsaE, eat(A), msr(C)), tetracycline (tet(M), tet(L), tet(S)), aminoglycosides (aac(6’)-Ii, aac(6’)-Iih, ant(6)-Ia, aph(3’)-III, ant(9)-Ia), fluoroquinolones (efmA, and emeA), vancomycin (VanC {VanC-2, VanXY, VanXYC-3, VanXYC-4, VanRC}), and chloramphenicol (cat). The litter-amended soil harboured new ARB (particularly E. faecium) and ARGs (ant(6)-Ia, aac(6’)-Ii, aph(3’)-III), lnu(G), msr(C), and eat(A), efmA) that were not previously detected in the soil. The identified ARGs were associated with diverse mobile genetic elements (MGEs) such as insertion sequences (IS6, ISL3, IS256, IS30), transposons (Tn3 and Tn916) and plasmids (repUS43, repUS1, rep9b, and rep 22). Twenty-eight virulence genes encoding adherence/biofilm formation (ebpA, ebpB, ebpC), antiphagocytosis (elrA) and bacterial sex pheromones (Ccf10, cOB1, cad, and camE), were detected in the genomes of the isolates. Phylogenomic analysis revealed a close relationship between a few isolates from litter-amended soil and the chicken litter isolates. The differences in the ARG and ARB profiles in the soil before and after the litter amendment and their association with diverse MGEs indicate the mobilisation and transmission of ARGs and ARB from the litter to the soil.

https://www.sciencedirect.com/science/article/abs/pii/S0301479721021630