Departamento de Microbiologia e Imunologia, Instituto de Biociências, Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP), Botucatu, SP, Brasil.
Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America.
PLoS Negl Trop Dis. 2020 Jun 1;14(6):e0008373. doi: 10.1371/journal.pntd.0008373. eCollection 2020 Jun.
Atypical enteropathogenic Escherichia coli (aEPEC) are one of the most frequent intestinal E. coli pathotypes isolated from diarrheal patients in Brazil. Isolates of aEPEC contain the locus of enterocyte effacement, but lack the genes of the bundle-forming pilus of typical EPEC, and the Shiga toxin of enterohemorrhagic E. coli (EHEC). The objective of this study was to evaluate the phylogeny and the gene content of Brazilian aEPEC genomes compared to a global aEPEC collection.
Single nucleotide polymorphism (SNP)-based phylogenomic analysis was used to compare 106 sequenced Brazilian aEPEC with 221 aEPEC obtained from other geographic origins. Additionally, Large-Scale BLAST Score Ratio was used to determine the shared versus unique gene content of the aEPEC studied.
Phylogenomic analysis demonstrated the 106 Brazilian aEPEC were present in phylogroups B1 (47.2%, 50/106), B2 (23.6%, 25/106), A (22.6%, 24/106), and E (6.6%, 7/106). Identification of EPEC and EHEC phylogenomic lineages demonstrated that 42.5% (45/106) of the Brazilian aEPEC were in four of the previously defined lineages: EPEC10 (17.9%, 19/106), EPEC9 (10.4%, 11/106), EHEC2 (7.5%, 8/106) and EPEC7 (6.6%, 7/106). Interestingly, an additional 28.3% (30/106) of the Brazilian aEPEC were identified in five novel lineages: EPEC11 (14.2%, 15/106), EPEC12 (4.7%, 5/106), EPEC13 (1.9%, 2/106), EPEC14 (5.7%, 6/106) and EPEC15 (1.9%, 2/106). We identified 246 genes that were more frequent among the aEPEC isolates from Brazil compared to the global aEPEC collection, including espG2, espT and espC (P<0.001). Moreover, the nleF gene was more frequently identified among Brazilian aEPEC isolates obtained from diarrheagenic patients when compared to healthy subjects (69.7% vs 41.2%, P<0.05).
The current study demonstrates significant genomic diversity among aEPEC from Brazil, with the identification of Brazilian aEPEC isolates to five novel EPEC lineages. The greater prevalence of some virulence genes among Brazilian aEPEC genomes could be important to the specific virulence strategies used by aEPEC in Brazil to cause diarrheal disease.
非典型肠致病性大肠杆菌（aEPEC）是从巴西腹泻患者中分离出的最常见的肠道大肠杆菌病原体之一。aEPEC 菌株含有肠上皮细胞消失的基因座，但缺乏典型 EPEC 的束形成菌毛基因和肠出血性大肠杆菌（EHEC）的志贺毒素。本研究的目的是评估巴西 aEPEC 基因组的系统发育和基因含量，与全球 aEPEC 集合进行比较。
基于单核苷酸多态性（SNP）的系统基因组分析用于比较 106 株从巴西分离的 aEPEC 与从其他地理来源获得的 221 株 aEPEC。此外，使用大规模 BLAST 得分比来确定所研究的 aEPEC 的共享和独特的基因含量。
系统基因组分析表明，106 株巴西 aEPEC 存在于 B1 （47.2%，50/106）、B2 （23.6%，25/106）、A （22.6%，24/106）和 E （6.6%，7/106）。鉴定出 EPEC 和 EHEC 系统发育谱系表明，42.5%（45/106）的巴西 aEPEC 属于之前定义的四个谱系之一：EPEC10 （17.9%，19/106）、EPEC9 （10.4%，11/106）、EHEC2 （7.5%，8/106）和 EPEC7 （6.6%，7/106）。有趣的是，另外 28.3%（30/106）的巴西 aEPEC 被鉴定为五个新谱系：EPEC11 （14.2%，15/106）、EPEC12 （4.7%，5/106）、EPEC13 （1.9%，2/106）、EPEC14 （5.7%，6/106）和 EPEC15 （1.9%，2/106）。与全球 aEPEC 集合相比，我们在巴西分离的 aEPEC 菌株中发现了 246 个更频繁的基因，包括 espG2、espT 和 espC（P<0.001）。此外，与健康受试者相比，从腹泻患者中获得的巴西 aEPEC 菌株中更频繁地鉴定出 nleF 基因（69.7%对 41.2%，P<0.05）。
本研究表明，巴西 aEPEC 具有显著的基因组多样性，鉴定出巴西 aEPEC 分离株属于五个新的 EPEC 谱系。巴西 aEPEC 基因组中某些毒力基因的更高流行率可能对 aEPEC 在巴西引起腹泻病的特定毒力策略很重要。
