Molina Diana, Carrión-Olmedo Julio C, Jarrín-V Pablo, Tenea Gabriela N
Biofood and Nutraceutics Research and Development Group, Faculty of Engineering in Agricultural and Environmental Sciences, Universidad Técnica del Norte, Ibarra, Ecuador.
Laboratorio de Secuenciamiento de Ácidos Nucleicos, Dirección de Innovación, Instituto Nacional de Biodiversidad (INABIO), Quito, Ecuador.
Front Microbiol. 2024 Jul 22;15:1392333. doi: 10.3389/fmicb.2024.1392333. eCollection 2024.
Foodborne infections, which are frequently linked to bacterial contamination, are a serious concern to public health on a global scale. Whether agricultural farming practices help spread genes linked to antibiotic resistance in bacteria associated with humans or animals is a controversial question.
This study applied a long-read Oxford Nanopore MinION-based sequencing to obtain the complete genome sequence of a multi-drug resistant strain (L1PEag1), isolated from commercial cape gooseberry fruits ( L.) in Ecuador. Using different genome analysis tools, the serotype, Multi Locus Sequence Typing (MLST), virulence genes, and antimicrobial resistance (AMR) genes of the L1PEag1 isolate were determined. Additionally, assays were performed to demonstrate functional genes.
The complete genome sequence of the L1PEag1 isolate was assembled into a circular chromosome of 4825.722 Kbp and one plasmid of 3.561 Kbp. The L1PEag1 isolate belongs to the B2 phylogroup, sequence type ST1170, and O1:H4 serotype based on genome analysis. The genome contains 4,473 genes, 88 tRNA, 8 5S rRNA, 7 16S rRNA, and 7 23S rRNA. The average GC content is 50.58%. The specific annotation consisted of 4,439 and 3,723 genes annotated with KEEG and COG respectively, 3 intact prophage regions, 23 genomic islands (GIs), and 4 insertion sequences (ISs) of the ISAs1 and IS630 families. The L1PEag1 isolate carries 25 virulence genes, and 4 perfect and 51 strict antibiotic resistant gene (ARG) regions based on VirulenceFinder and RGI annotation. Besides, the antibiotic profile indicated resistance to kanamycin (K30), azithromycin (AZM15), clindamycin (DA2), novobiocin (NV30), amikacin (AMK30), and other antibiotics. The L1PEag1 isolate was predicted as a human pathogen, matching 464 protein families (0.934 likelihood).
Our work emphasizes the necessity of monitoring environmental antibiotic resistance, particularly in commercial settings to contribute to develop early mitigation techniques for dealing with resistance diffusion.
食源性感染通常与细菌污染有关，是全球公共卫生领域的一个严重问题。农业种植 practices 是否有助于传播与人类或动物相关细菌中与抗生素耐药性相关的基因，这是一个有争议的问题。
本研究应用基于长读长牛津纳米孔MinION的测序技术，获得了从厄瓜多尔商业灯笼果果实中分离出的一株多重耐药菌株（L1PEag1）的完整基因组序列。使用不同的基因组分析工具，确定了L1PEag1分离株的血清型、多位点序列分型（MLST）、毒力基因和抗菌药物耐药性（AMR）基因。此外，还进行了实验以证明功能基因。
L1PEag1分离株的完整基因组序列组装成一个4825.722 Kbp的环状染色体和一个3.561 Kbp的质粒。基于基因组分析，L1PEag1分离株属于B2系统发育群、序列型ST1170和O1:H4血清型。该基因组包含4473个基因、88个tRNA、8个5S rRNA、7个16S rRNA和7个23S rRNA。平均GC含量为50.58%。具体注释包括分别用KEEG和COG注释的4439个和3723个基因、3个完整的前噬菌体区域、23个基因组岛（GIs）以及ISAs1和IS630家族的4个插入序列（ISs）。根据VirulenceFinder和RGI注释，L1PEag1分离株携带25个毒力基因以及4个完美和51个严格的抗生素耐药基因（ARG）区域。此外，抗生素谱显示对卡那霉素（K30）、阿奇霉素（AZM15）、克林霉素（DA2）、新生霉素（NV30）、阿米卡星（AMK30）和其他抗生素耐药。L1PEag1分离株被预测为人类病原体，与464个蛋白质家族匹配（可能性为0.934）。
我们的工作强调了监测环境抗生素耐药性的必要性，特别是在商业环境中，以有助于开发应对耐药性扩散的早期缓解技术。
