Draft Genome Sequence of Escherichia coli Strain M15-4, a Typical Enteropathogenic E. coli Strain Isolated in Mexico.

We present here the first draft genome sequence of a typical enteropathogenic Escherichia coli serotype O55:H51 strain, M15-4, isolated from a 2-month-old infant girl with acute diarrhea. The study of this Mexican isolate will provide insights to the virulence and drug resistance traits involved in its pathogenic potential.

GENOME ANNOUNCEMENT

According to the World Health Organization, diarrheal disease is the second leading cause of death in children under 5 years old and kills around 525,000 children every year (http://www.who.int/mediacentre/factsheets/fs330/en). Typical enteropathogenic Escherichia coli (tEPEC) strains, which belong to one of the diarrheagenic E. coli pathotypes, remain a significant public health concern in low-income countries owing to their high rates of hospitalization and mortality in infants with moderate to severe diarrhea, particularly in children under the age of 12 months (1). Here, we report the draft genome sequence of tEPEC strain M15-4, isolated from a 2-month-old infant girl with acute diarrhea. Identification of strain M15-4 was completed on the Vitek system and classified as a tEPEC strain based on the positive PCR amplification of the eaeA and bfpA determinants (2).

The genome sequencing of E. coli M15-4 was performed using Ion Torrent PGM technology (Life Technologies, Inc., Carlsbad, CA, USA) with 200-bp chemistry on a 316 chip. The sequencing generated 369,712 reads with a mean length of 204 bp. De novo assembly was performed with SPAdes version 3.11 (3), resulting in 192 contigs with a maximum length of 283,282 bp, an N50 of 71,091 bp, a G+C content of 50.48%, and a predicted genome size of 5,082,644 bp. Gene prediction and genome annotation were performed with the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) version 4.2 (4) and the Rapid Annotations using Subsystems Technology (RAST) server (5). SeroTypeFinder version 1.1, VirulenceFinder version 1.5, and ResFinder version 3.0 were used to determine serotype, virulence factors, and antibiotic resistance genes in this isolate, respectively (6–8). PGAP analysis revealed 5,513 genes, 5,420 protein-coding sequences, and 93 RNA genes (16 rRNAs, 71 tRNAs, and 6 noncoding RNAs). According to the RAST nearest-neighbor analysis, the closest genome is that of E. coli AA86. Furthermore, 101 features corresponded to resistance to antibiotics (beta-lactams, fluoroquinolones, and aminoglycosides), and toxic substances (copper, cobalt, zinc, cadmium, and mercury) were found. The isolate displayed an O55:H51 serotype, and the tEPEC pathotype was confirmed by the presence of eae, tir, perA (EPEC adherence factor), bfpA, and several pathogenicity-related genes in its genome. Interestingly, we found a sequence corresponding to capU, a gene belonging to a plasmid-associated cap cluster, which is involved in the biofilm formation of the enteroaggregative E. coli (EAEC) pathotype (9). Moreover, genes conferring aminoglycoside, beta-lactam, sulfonamide, tetracycline, and trimethoprim resistance [aadA1, blaTEM-1B, sul1, tet(A), and dfrA15, respectively] were identified. To the best of our knowledge, this is the first reported sequence of an E. coli serotype O55:H51 strain. Likewise, this is the first time that the capU gene has been identified in a tEPEC strain.

Accession number(s).

This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number PDCE00000000. The version described in this paper is the first version, PDCE01000000.