ABSTRACT
We present the draft genome of a novel human-derived Escherichia coli strain isolated from a healthy control human microbiota that, when put into a mouse, spontaneously disseminated from the gut to the kidneys.
KEYWORDS: E. coli, gastrointestinal tract, genome, pathogen
ANNOUNCEMENT
Escherichia coli is a common gut commensal as well as a devastating and persistent pathogen. Pathogenic strains of E. coli can cause myriad types of infections, including diarrhea, urinary tract infections, bacteremia, and sepsis (1–3). Furthermore, E. coli strains that carry the pks+ gene cluster, encoding the secreted DNA-damaging toxin colibactin, can promote tumor development and are associated with colorectal cancer (4–6). Here, we present the draft genome of a novel human-derived strain isolated from a mouse after spontaneous dissemination from the gut.
This E. coli strain was recovered from the kidneys of an ex-germ-free Swiss Webster mouse, raised in house, which had undergone a human-to-mouse fecal microbial transplant in the Round lab at the University of Utah, IACUC protocol 00001562. The human sample was from the ColoCare study (7). The mouse was discovered near death, and upon necropsy, both kidneys were red and enlarged. Kidney homogenates were plated on LB agar and were incubated aerobically at 37°C overnight. The kidneys contained numerous bacteria, all seemingly the same type, which were then streaked to isolation. Plating on McConkey agar led to brilliant pink hues of the colonies, indicative of E. coli. We named the isolate AW001.
DNA was extracted from a pure culture of AW001 grown overnight in LB broth at 37°C in the Mulvey lab using the Qiagen DNeasy Blood & Tissue kit, and libraries were made using Tecan Ultralow V2, both according to the manufacturer protocols. Sequencing was performed by Illumina NovaSEQ6000 at the University of Colorado Anschutz with 151 bp paired-end reads. The total read count was 8,779,520, with an average depth of 257.79. Software default parameters were used, except where noted. Read preprocessing was performed using Trim Galore v0.6.5dev (8). Sequences were assembled de novo using Unicycler v.0.4.8 through BV-BRC v3.35.5 using -t 12 –min_fasta_length 300 –keep 2 –no_pilon (9–11). The assembled genome contains 109 contigs with an N50 value of 268,981. The genome was annotated using Genbank PGAP v6.6 (12). CheckM v1.0.5 revealed completeness of 99.97 (13).
The assembled AW001 genome contains 5,008,932 bps, comprising 4,952 genes, 4,868 CDS, and 50.7% GC content. AW001 was predicted to be E. coli phylogroup B2 using ClermonTyping (v23.06) (14). By MLST, it was ST “unknown,” closely related STs being 12998 and 2831 (MLST-2.0 Server). Using AMRFinderPlus v3.11.26 (15), putative antimicrobial resistance genes were identified including fosfomycin-resistant glpT variant (16), multidrug-resistance marR, colistin-resistant pmrB (17), efflux pump acrF (18), and beta-lactamase blaEC (19) (Table 1). This indicates that AW001 is likely resistant to multiple classes of clinically relevant antibiotics.
TABLE 1.
Key AMR and virulence factors identified in the AW001 E. coli genome
| Gene(s) | Protein ID | Type | Protein name and function |
|---|---|---|---|
| acrF | WP_001273251.1 | AMR | AcrF multidrug efflux RND transporter permease |
| blaEC | WP_001556381.1 | AMR | BlaEC family class C beta-lactamase |
| glpT | WP_000948732.1 | AMR | GlpT fosfomycin resistant |
| marR | WP_000799375.1 | AMR | MarR multidrug resistant |
| pmrB | WP_001052123.1 | AMR | PmrB colistin resistant |
| ariR | WP_000888771.1 | Stress | Biofilm/acid-resistance regulator AriR |
| emrE | WP_001070440.1 | Stress | EmrE multidrug efflux SMR transporter |
| astA | WP_000989438.1 | Virulence | EAST1 heat-stable enterotoxin |
| cbtA | WP_000854814.1 | Virulence | CbtA type IV toxin-antitoxin system |
| ccdA | WP_000125566.1 | Virulence | CcdA type II toxin-antitoxin system CcdA |
| chuA | WP_000089583.1 | Virulence | ChuA outer membrane hemin receptor |
| ClbA | WP_001217110.1 | Virulence | Colibactin synthesis proteins (pks) |
| entH | WP_000637953.1 | Virulence | EntH proofreading thioesterase |
| fdeC | WP_000092543.1 | Virulence | FdeC inverse autotransporter adhesin |
| fimH | WP_000832236.1 | Virulence | SfaH fimbrial protein subunit |
| fliP | WP_334615852.1 | Virulence | FliP flagellar type III secretion system |
| gspA | WP_000107592.1 | Virulence | GspA,C,D type II secretion system |
| gspG | WP_001087296.1 | Virulence | GspG type II secretion system major pseudopilin |
| hcp | WP_000458845.1 | Virulence | Hcp family type VI secretion system effector |
| hecB | WP_334616364.1 | Virulence | HecB family hemolysin secretion/activation protein |
| hhA | WP_001333231.1 | Virulence | Hha hemolysin expression modulator |
| ibsE | WP_001387082.1 | Virulence | Ibs family toxin type I toxin-antitoxin system |
| Irp1,2 | WP_000369530.1 | Virulence | Yersiniabactin siderophore |
| iss | WP_001298464.1 | Virulence | Iss increased serum survival lipoprotein |
| ldrD | WP_001295224.1 | Virulence | Ldr family protein type I toxin-antitoxin system |
| mchB | WP_001375214.1 | Virulence | H47 microcin |
| mchF | WP_001518504.1 | Virulence | MchF microcin H47 export transporter peptidase |
| neuC | WP_000723250.1 | Virulence | Polysialic acid biosynthesis protein P7 |
| ompA | WP_001518466.1 | Virulence | Outer membrane protein |
| paeA | WP_000935036.1 | Virulence | Hemolysin family protein |
| sitC | WP_001101732.1 | Virulence | MntB manganese transport membrane protein |
| sslE | WP_001034565.1 | Virulence | SslE lipoprotein metalloprotease |
| TssE | WP_000106967.1 | Virulence | TssE type VI secretion system baseplate subunit |
| tssJ | WP_000484008.1 | Virulence | TssJ type VI secretion system lipoprotein |
| vgrG | WP_001350146.1 | Virulence | VgrG type VI secretion system tip protein |
| ybtE | WP_001518699.1 | Virulence | 2,3-dihydroxybenzoate-AMP ligase |
| ybtP | WP_001327262.1 | Virulence | YbtP yersiniabactin ABC transporter |
| ybtQ | WP_001295637.1 | Virulence | YbtQ yersiniabactin ABC transporter |
| yqfA | WP_000250274.1 | Virulence | Hemolysin III family protein |
AW001 was analyzed for putative fitness and virulence factors using AMRFinderPlus, BLAST+ (v2.14.0+), and targeted searching (20). Like E. coli strain NC101 (21), AW001 carries the clb (pks) gene cluster that produces colibactin. AW001 contains genes involved in iron acquisition, adhesion, capsule biosynthesis, and mucin degradation (Table 1). AW001 also encodes toxin-antitoxin systems; enterotoxin AstA; antimicrobial microcin H47; type II, III, and VI secretion systems; and hemolysin biosynthesis genes (Table 1).
ACKNOWLEDGMENTS
Thanks to the Round and Mulvey labs for help with isolation, identification, and sequencing of this isolate.
This work was funded by R01AT011423-03, a W. M. Keck Award, by a Burrough’s Welcome grant to J.L.R., and by R01GM134331 and Department of Defense award W81XWH-22-1-0800 (SC210103) to M.A.M. A.M.W. was funded by NIH NCI NRSA F32CA243501, and O.J.M. was supported by NIH Genetics T32 training, grant no. GM007464.
Contributor Information
June L. Round, Email: June.round@path.utah.edu.
Vanja Klepac-Ceraj, Department of Biological Sciences, Wellesley College, Wellesley, Massachusetts, USA.
DATA AVAILABILITY
Data are in GenBank under accession JAYWIW000000000. Raw reads are under SRR28249370.
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Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Data Availability Statement
Data are in GenBank under accession JAYWIW000000000. Raw reads are under SRR28249370.