Draft genome sequence of multidrug-resistant Escherichia coli F14E isolated from a captive common peacock with colisepticemia

TL;DR

This paper presents the draft genome of a drug-resistant Escherichia coli strain from a peacock with a severe infection.

Contribution

The study provides a new draft genome sequence of a multidrug-resistant E. coli strain from a non-human source.

Findings

The genome is approximately 4.7 Mb in size with 50.50% GC content.

The assembled genome has 99.27% completeness across 130 contigs.

Abstract

We report the draft genome sequence of Escherichia coli F14E, a multidrug-resistant strain isolated from the fecal sample of a captive common peacock (Pavo cristatus) diagnosed withcolisepticemia. The assembled genome comprises approximately 4.7 Mb distributed across 130 contigs, with 50.50% GC content and 99.27% genome completeness.

Tables

TABLE 1. General genomic features of the E. coli F14E isolated from the feces of a captive common peacock with colisepticemia

Genome features	E. coli strain F14E
Genome size (bp)	4,667,555
Genome coverage (×)	133 ×
Genome completeness (%)	99.27 (0.38% contamination)
No. of contigs	130
Contig N50 (bp)	106,961
GC content (%)	50.5
Coding sequences (CDSs)	4,544
Protein-coding genes	4,345
No. of subsystems	377
No. of VFGs	59
No. of ARGs	51
PathogenFinder2 score	0.976
Genome accessions	JBOEQB000000000
Sequence read archive (SRA) accessions	SRR33697068

Full text

ANNOUNCEMENT

Escherichia coli, a gram-negative facultative anaerobe, comprises both commensal strains and pathogenic variants causing diseases in multiple hosts (1, 2). The rise of multidrug-resistant (MDR) E. coli strains is a global public health concern (3). Wildlife, including peacocks, can act as a reservoir, spreading antimicrobial resistance genes (ARGs) via environmental pathways (4, 5). Colisepticaemia, caused by E. coli, is a pathogenic condition that can occur in various avian species, including peacocks (6, 7). E. coli strains causing colisepticemia remain challenging to control and present zoonotic risks (8). Investigating avian-derived E. coli isolates enhances understanding of resistance–virulence dynamics (6). We report the isolation and genomic characterization of an MDR, pathogenic E. coli strain (F14E) from a colisepticaemic peacock.

Twelve freshly voided fecal samples were aseptically collected from a 21-month-old common peacock diagnosed with colisepticemia at the Wildlife Reproduction and Conservation Field Laboratory, Gazipur Agricultural University (24.09°N, 90.41°E), Bangladesh. Samples were collected using sterile stool tubes, diluted with sterile distilled water, vortexed, and preserved for subsequent analysis. For E. coli isolation, samples were enriched overnight in nutrient broth (Oxoid, UK) at 37°C under aerobic conditions, serially diluted (10^−3^), and streaked onto Eosin-methylene blue agar (Oxoid, UK). Metallic green sheen colonies observed after 24 h were sub-cultured, and the isolate was identified as E. coli based on morphology, Gram staining, and biochemical tests (5, 9). Species-level identification of E. coli was confirmed using the VITEK-2 system v9.01 (10). Strain F14E exhibited resistance to ampicillin, azithromycin, oxacillin, sulfonamides, and tetracycline, as determined by Kirby-Bauer disk diffusion following CLSI M100 (2023) guidelines (11). For DNA isolation, strain F14E was grown in nutrient broth at 37°C for 18–24 h under aerobic conditions. Genomic DNA was extracted with the QIAamp DNA Mini Kit (QIAGEN, Germany) and quantified using NanoDrop 2000 (Thermo Fisher, USA) (12). Libraries were prepared from 1 ng DNA using the Nextera DNA Flex Kit (Illumina, USA) according to the manufacturer’s protocol, which includes enzymatic fragmentation and size selection, and sequenced (2×250 bp) on an Illumina MiSeq platform. Raw reads (N = 5,023,404) were trimmed with Trimmomatic v0.39 (13) and assessed with FastQC v0.12.1 (14). Genome assembly was performed with SPAdes v4.2.0 (15) and annotated using the NCBI Prokaryotic Genome Annotation Pipeline v6.10 (16). Genome completeness, virulence factor genes, ARGs, metabolic pathways, and human pathogenic potential were evaluated using CheckM v1.2.3 (17, 18, 18, 19, 19), RAST server (20), and PathogenFinder2 v0.5.0 (21), respectively. Default parameters were used for all software unless otherwise specified.

The key genomic characteristics of E. coli F14E are presented in Table 1. The draft genome was assembled into 130 contigs, totaling approximately 4.67 Mbps with 50.5% GC content, and 99.27% genome completeness (0.38% contamination). We predicted 51 ARGs and 59 virulence factor genes (VFGs), along with 377 functional subsystems. Additionally, the strain was linked to 105 pathogenic families and exhibited a predicted score of 0.976 (out of 1.0) for being a human pathogen. These results highlight the potential role of E. coli F14E in colisepticemia in peacock, emphasizing its relevance in veterinary and public health research.