ABSTRACT
The whole genome sequence of Escherichia coli strain DP51 is reported here. DP51 was isolated in 2011 from a human rectal specimen in Breda, Netherlands. DP51 genome is 4.7 Mb with 50.68% GC content. DP51 possesses 34 extraintestinal virulence-related genes and is presumptive extraintestinal pathogenic E. coli (ExPEC).
KEYWORDS: extraintestinal diseases, Escherichia coli (ExPEC), human rectal specimen
ANNOUNCEMENT
Extraintestinal pathogenic Escherichia coli (ExPEC) is an E. coli subgroup that causes illness outside the gastrointestinal tract, including urinary tract infections and neonatal meningitis (1). A human fecal carriage survey was performed in Breda, Netherlands, to compare isolates from humans and chicken meat (2). DP51 was isolated from a human rectal swab by incubation for 16–18 h at 37°C in 15 mL of tryptic soy broth (TSB), then in TSB plus vancomycin and cefotaxime, followed by selection for the presence of extended-spectrum β-lactamase (ESBL).
Genomic DNA was isolated from overnight cultures (18 h) grown in LB broth at 37°C, with shaking at 180 rpm and sequenced as described previously (3) with >205× coverage. Briefly, genomic DNA was sheared and underwent size selection for 20 kb fragments. DNA sequencing was performed using a PacBio Sequel machine with Single Molecule Real-Time (SMRT) technology. Default parameters were used for all software analysis, unless otherwise specified. SMRT Link software v6.0.0 was used for quality control and filtering, which generated 21,697 reads, with 1,278,540,836 bases with a mean subread length of 9,732 and N50 value of 11,218.
A chromosome (4,764,301 bp; 50.68% GC content) and three plasmids (97,470 bp; 48.48% GC content, 69,739 bp, 54.41% GC content, and 42,753 bp, 51.47% GC content) were generated using Flye/2.9.1 software for genome assembly (4). Both chromosomes and plasmids were assembled as circular molecules. The chromosome was rotated with the dnaA gene as the origin of replication (circulator/v1.5.5) (5). The NCBI-Prokaryotic Genome Annotation Pipeline (PGAP, Software version: 6.7) (6) was used for genome annotation, which identified 4,911 genes and 117 RNA sequences, including 88 tRNA genes. Eleven intact phages were predicted on the chromosome using the PhageBoost software package (7) (accessed on 4/02/2025). SerotypeFinder-2.0 (https://cge.food.dtu.dk/services/SerotypeFinder/) (8) and MLST-2.0 databases (Software version: 2.0.9 [2022-05-11]; Database version [2023-06-19]; https://cge.food.dtu.dk/services/MLST/) (9) assigned DP51 to sequence type 93, and serotype O5:H4. ResFinder-4.3.3 (10) identified nine resistance genes (Table 1), all in plasmid sequences (10).
TABLE 1.
Antimicrobial resistance genes (AMRs) and virulence genes identified in DP51
| Gene category | Genes identified |
|---|---|
| AMRs | aph (6)-Id, aph(3'')-Ib, aadA4, blaCTX-M-1, blaTEM-1B, mph(A), sul2, tet(A), dfrA2. |
| Virulence genes | aslA, anr, capU, csgA, cvaC, etsC, fdeC, fyuA, gad, hlyE, hlyF, hra, iroN, irp2, iss, iucC, iutA, kpsE, kpsMII_K5, mchF, nlpI, ompT, papA_F13, papC, shiA, sitA, terC, traJ, traT, tsh, yehA, yehB, yehC, yehD. |
VirulenceFinder-2.0 identified a total of 34 chromosomal virulence genes (Table 1), using parameters of 90% minimum identity and 60% minimum length (11) (Software version: 2.0.5 [2024-01-31]; Database version [2022-12-02]). In addition, genes related to iron acquisition (chuA, fyuA, iucC, irp2, sitA, and iutA), adhesins/attachment (afaA, afaC, afaD, iha, nfaE, papA_F43, terC, and yfcV), protectins/serum resistance (iss, kpsE, kpsMII_K5, and ompT), and toxin production (sat and usp) were identified. PathogenFinder-1.1 (https://cge.cbs.dtu.dk/services/PathogenFinder/) estimated a 0.933 probability of DP51 being a human pathogen.
The presence of more than two out of the key virulence genes (pap, sfa/foc, afa/dra, iutA, and kpsMT II) qualifies a strain as ExPEC (12). DP51 was qualified presumptively as ExPEC based on its carriage of iutA, afaB/C, papAH, papC, and kpsE/MII (12). The sequence data could offer the possibility of determining the relatedness of strains from food and humans through comparative genomics (11).
ACKNOWLEDGMENTS
We thank Pina Fratamico for critical reading of the manuscript. This research used resources provided by the SCINet project and/or the AI Center of Excellence of the USDA Agricultural Research Service, ARS project numbers 0201-88888-003-000D and 0201-88888-002-000D. Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the U.S. Department of Agriculture.
Contributor Information
Yanhong Liu, Email: yanhong.liu@usda.gov.
David Rasko, University of Maryland School of Medicine, Baltimore, Maryland, USA.
DATA AVAILABILITY
The whole-genome project has been deposited in BioProject number PRJNA642167, Sequence
Read Archive (SRA) number SRR29021894 BioSample number SAMN41394341
with the GenBank accession number CP156034 for the DP51 chromosome and CP156035, CP156036 and CP156037 for the plasmids.
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Data Availability Statement
The whole-genome project has been deposited in BioProject number PRJNA642167, Sequence
Read Archive (SRA) number SRR29021894 BioSample number SAMN41394341
with the GenBank accession number CP156034 for the DP51 chromosome and CP156035, CP156036 and CP156037 for the plasmids.