Draft Genomic Sequences of Three Escherichia coli Sequence Type 131 Isolates (H45, H43ii, and H43iii) from Patients in Lagos, Nigeria

Escherichia coli sequence type 131 (ST131) has recently emerged as a leading multidrug-resistant pathogen that causes urinary tract and bloodstream infections in humans. Here, we report the draft genomic sequences of three E. coli ST131 isolates, H45, H43ii, and H43iii, from urine samples of patients in Lagos, Nigeria.

ABSTRACT

Escherichia coli sequence type 131 (ST131) has recently emerged as a leading multidrug-resistant pathogen that causes urinary tract and bloodstream infections in humans. Here, we report the draft genomic sequences of three E. coli ST131 isolates, H45, H43ii, and H43iii, from urine samples of patients in Lagos, Nigeria.

ANNOUNCEMENT

Extraintestinal pathogenic Escherichia coli (ExPEC) is a common cause of urinary tract infections (UTIs), bacteremia, and neonatal meningitis in humans (1). The widespread use of antimicrobials to treat human and animal infections and to enhance livestock growth results in dissemination of multidrug-resistant ExPEC strains, among which sequence type 131 (ST131) is the most frequent isolate (2, 3). The prevalence of E. coli ST131 is possibly attributable to its increased antimicrobial resistance, enhanced virulence, and greater propensity to transfer genetic materials compared to non-ST131 E. coli (4–6).

Three E. coli ST131 strains, H45, H43ii, and H43iii, were isolated from urine samples of patients in Lagos, Nigeria (5). Prior to whole-genome sequencing, the phylogenetic group and virulence factors of the three E. coli strains were determined in our laboratory using PCR methods (7, 8), which confirmed that all these strains belonged to phylogenetic group B2 and that they were ExPEC strains.

For whole-genome sequencing, genomic DNA was extracted using the DNeasy blood and tissue kit (Qiagen, Valencia, CA, USA) from overnight cultures grown on Trypticase soy agar (TSA; Becton, Dickinson, and Company, Sparks, MD, USA) plates. The concentration of genomic DNA was determined using a Qubit 3.0 fluorometer (Thermo Fisher Scientific, Waltham, MA, USA) with Qubit double-stranded DNA (dsDNA) high-sensitivity (HS) assay kits (Thermo Fisher Scientific). Sequencing libraries were prepared using the Nextera DNA flex library prep kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. Prepared libraries were quantified, pooled, and denatured before paired-end sequencing (151 cycles with 150-bp read length) using the Illumina MiniSeq instrument. The quality of the sequence reads was assessed with FastQC version 1.0.0 (BaseSpace Labs, Illumina) (9), and the genome was de novo assembled using the SPAdes genome assembler version 3.9.0 (BaseSpace Labs) (10). Genome annotation was performed using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) version 4.10 (11). Default parameters were used for all software unless otherwise specified. Genome coverage, genome size, number of paired-end reads, GC content, and other characteristics are shown in Table 1.

TABLE 1.

Characteristics and accession numbers of three Escherichia coli sequence type 131 strains

Strain name	GenBank accession no.	BioProject no.	SRA no.	Genome coverage (×)	Genome size (bp)	No. of paired-end reads	GC content (%)	No. of contigs	N50a (bp)	Total no. of genes	No. of CDSsb	No. of tRNAs, rRNAs, ncRNAsc	No. of pseudogenes
H45	WMHN00000000	PRJNA589205	SRR10736389	270	5,245,824	9,442,758	50.79	208	173,083	5,201	5,102	78, 16, 5	147
H43ii	WMHL00000000	PRJNA589200	SRR10752474	237	5,235,471	8,293,283	50.79	216	161,311	5,183	5,090	71, 17, 5	147
H43iii	WMHM00000000	PRJNA589201	SRR10752475	216	5,246,794	7,568,529	50.78	230	142,020	5,201	5,103	77, 16, 5	147

^aThe N₅₀ value is the size of the shortest contig in the set of longest contigs that together cover at least 50% of the total genome size.

^bCDSs, coding DNA sequences.

^cncRNAs, noncoding RNAs.

Serotype, multilocus sequence types (MLST), virulence genes, and antimicrobial resistance were determined using the E. coli Serotyping Pipeline version 1.0.2 (BaseSpace Labs) and the Bacterial Analysis Pipeline version 1.0.4 (BaseSpace Labs). Based on the sequencing data, all three isolates were serotype O25:H4 and belonged to E. coli ST131. The virulence factors of the three isolates included genes encoding serum resistance (iss), glutamate decarboxylase (gad), secreted autotransporter toxin (sat), IrgA homologue adhesin (iha), and diffuse adherence fibrillar adhesion (nfaE). Antimicrobial resistance genes identified in all three isolates were a fluoroquinolone and aminoglycoside resistance gene [aac(6′)Ib-cr], aminoglycoside resistance genes [aac(3)-IIa and aadA5], a sulfonamide resistance gene (sul1), a trimethoprim resistance gene (dfrA17), a tetracycline resistance gene [tet(A)], beta-lactam resistance genes (bla_CTX-M-15, bla_TEM-1B, and bla_OXA-1), and a phenicol resistance gene (catB4). Additionally, three more antimicrobial resistance genes were found in isolates H45 and H43iii, which were aminoglycoside resistance genes (strA and strB) and a sulfonamide resistance gene (sul2).

Whole-genome sequencing is an effective tool for the identification and characterization of bacterial pathogens. The genomic data will be useful for understanding the dissemination and pathogenicity of E. coli ST131, as well as for facilitating the development of novel antimicrobial therapies.

Data availability.

This whole-genome shotgun project has been deposited in DDBJ/ENA/GenBank under the accession and BioProject numbers listed in Table 1. The versions described here are the first versions.