We report the draft genome sequence of Escherichia coli ASBT-1, a representative of E. coli sequence type 155 (ST155), obtained from India. Considering the known wide variety of pathogenic and antibiotic resistance potentials, this strain should be of great interest for detailed comparative genomic analysis.
ABSTRACT
We report the draft genome sequence of Escherichia coli ASBT-1, a representative of E. coli sequence type 155 (ST155), obtained from India. Considering the known wide variety of pathogenic and antibiotic resistance potentials, this strain should be of great interest for detailed comparative genomic analysis.
ANNOUNCEMENT
Escherichia coli sequence type 155 (ST155) represents important strains responsible for zoonotic transmission of extended-spectrum β-lactamase genes to humans (1–8). We announce an assembled draft genome of an E. coli ST155 strain obtained from wastewater in Kerala, India, and explore the diversity of different antibiotic resistance profiles in the region.
The organism was isolated from sewage in eosin-methylene blue agar, biochemically characterized as E. coli, and confirmed by 16S rRNA gene ribotyping (9). Genomic DNA was extracted using the phenol-chloroform method (10). The paired-end sequencing library was prepared using the TruSeq Nano DNA library prep kit. The Illumina HiSeq platform was used for sequencing the paired-end library, with a read length of 2 × 150 bp and coverage of 850×. Both quantity and quality checks of the amplified library were performed in a Bioanalyzer 2100 (Agilent Technologies) using a high-sensitivity DNA chip per the manufacturer’s instructions. The reads generated were filtered using Trimmomatic (v0.30) with a quality value (QV) of >20, and adapters were also removed. Subsequently, the high-quality (4.15 Gb) data were used for assembly. De novo assembly of paired-end reads was performed using Velvet v1.2.10. The total number of reads was 28,029,838. The details of the assembled genome are listed in Table 1. An NCBI genome annotation tool was used to annotate the genome and detected a total of 4,393 protein-coding genes with an average size of 945 bp. This genome was found to harbor 75 tRNA and 8 rRNA genes, as predicted by tRNAscan-SE v2.0 (11) and DFAST v1.0.1 (12), respectively. A total of 5 intact prophage regions were identified using the PHAST tool (13) (last accessed date, 18 September 2018). Two CRISPR-Cas sequences were detected, one by CRISPRFinder (14) (last accessed date, 18 September 2018) and one by Prokka v1.12 (15), respectively. Altogether, as an Indian representative of an E. coli ST155 clone, ASBT-1 warrants additional in-depth research on its genomic features, pathotype, and antibiotic resistance profile.
TABLE 1.
Summary of the genome sequence of strain ASBT-1
| Assembly or annotation element | Data |
|---|---|
| Genome size (bp) | 4,696,000 |
| No. of contigs | 54 |
| No. of scaffolds | 50 |
| Scaffold N50 (bp) | 383,050 |
| Avg scaffold length (bp) | 93,920 |
| GC content (%) | 50.81 |
| No. of protein-coding genes | 4,393 |
| Coding ratio (%) | 88.1 |
| Avg protein length (amino acids) | 313.9 |
| No. of tRNAs | 75 |
| No. of rRNAs | 8 |
| No. of CRISPRs | 2 |
| No. of intact prophage regions | 5 |
Data availability.
This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number RWJY00000000 (BioProject number PRJNA509104). The version described in this paper is RWJY01000000, with SRA accession number SRR8480428.
ACKNOWLEDGMENTS
This work was supported by the Reinvent the Toilet Challenge (RTTC) award (2014) funded by the Bill & Melinda Gates Foundation–BIRAC (Government of India) (grant number BIRAC/GCI/0067/02/13-RTTC OPP1107707) and School of Biotechnology, Amrita Vishwa Vidyapeetham, Kerala, India. We acknowledge the University Grant Commission (UGC) and Council of Industrial and Scientific Research (CSIR), New Delhi, India, for providing fellowships for the authors.
We declare no conflicts of interest.
REFERENCES
- 1.Ben Sallem R, Ben Slama K, Rojo-Bezares B, Porres-Osante N, Jouini A, Klibi N, Boudabous A, Sáenz Y, Torres C. 2014. IncI1 plasmids carrying blaCTX-M-1 or blaCMY-2 genes in Escherichia coli from healthy humans and animals in Tunisia. Microb Drug Resist 20:495–500. doi: 10.1089/mdr.2013.0224. [DOI] [PubMed] [Google Scholar]
- 2.Wang J, Stephan R, Power K, Yan Q, Hächler H, Fanning S. 2014. Nucleotide sequences of 16 transmissible plasmids identified in nine multidrug-resistant Escherichia coli isolates expressing an ESBL phenotype isolated from food-producing animals and healthy humans. J Antimicrob Chemother 69:2658–2668. doi: 10.1093/jac/dku206. [DOI] [PubMed] [Google Scholar]
- 3.Leverstein-van Hall MA, Dierikx CM, Cohen Stuart J, Voets GM, van den Munckhof MP, van Essen-Zandbergen A, Platteel T, Fluit AC, van de Sande-Bruinsma N, Scharinga J, Bonten MJM, Mevius DJ, National ESBL Surveillance Group . 2011. Dutch patients, retail chicken meat and poultry share the same ESBL genes, plasmids and strains. Clin Microbiol Infect 17:873–880. doi: 10.1111/j.1469-0691.2011.03497.x. [DOI] [PubMed] [Google Scholar]
- 4.Castellanos LR, Donado-Godoy P, León M, Clavijo V, Arevalo A, Bernal JF, Timmerman AJ, Mevius DJ, Wagenaar JA, Hordijk J. 2017. High heterogeneity of Escherichia coli sequence types harbouring ESBL/AmpC genes on IncI1 plasmids in the Colombian poultry chain. PLoS One 12:e0170777. doi: 10.1371/journal.pone.0170777. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5.Matamoros S, van Hattem JM, Arcilla MS, Willemse N, Melles DC, Penders J, Vinh TN, Thi Hoa N, COMBAT Consortium , de Jong MD, Schultsz C. 2017. Global phylogenetic analysis of Escherichia coli and plasmids carrying the mcr-1 gene indicates bacterial diversity but plasmid restriction. Sci Rep 7:15364. doi: 10.1038/s41598-017-15539-7. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.Grall N, Barraud O, Wieder I, Hua A, Perrier M, Babosan A, Gaschet M, Clermont O, Denamur E, Catzeflis F, Decré D, Ploy M-C, Andremont A. 2015. Lack of dissemination of acquired resistance to β-lactams in small wild mammals around an isolated village in the Amazonian forest. Environ Microbiol Rep 7:698–708. doi: 10.1111/1758-2229.12289. [DOI] [PubMed] [Google Scholar]
- 7.Skurnik D, Clermont O, Guillard T, Launay A, Danilchanka O, Pons S, Diancourt L, Lebreton F, Kadlec K, Roux D, Jiang D, Dion S, Aschard H, Denamur M, Cywes-Bentley C, Schwarz S, Tenaillon O, Andremont A, Picard B, Mekalanos J, Brisse S, Denamur E. 2016. Emergence of antimicrobial-resistant Escherichia coli of animal origin spreading in humans. Mol Biol Evol 33:898–914. doi: 10.1093/molbev/msv280. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8.Gomi R, Matsuda T, Matsumura Y, Yamamoto M, Tanaka M, Ichiyama S, Yoneda M. 2017. Whole-genome analysis of antimicrobial-resistant and extraintestinal pathogenic Escherichia coli in river water. Appl Environ Microbiol 83:e02703-16. doi: 10.1128/AEM.02703-16. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9.Marín M, Garcia-Lechuz JM, Alonso P, Villanueva M, Alcalá L, Gimeno M, Cercenado E, Sánchez-Somolinos M, Radice C, Bouza E. 2012. Role of universal 16S rRNA gene PCR and sequencing in diagnosis of prosthetic joint infection. J Clin Microbiol 50:583–589. doi: 10.1128/JCM.00170-11. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10.Park D. 2007. Genomic DNA isolation from different biological materials. Methods Mol Biol 353:3–13. doi: 10.1385/1-59745-229-7:3. [DOI] [PubMed] [Google Scholar]
- 11.Lowe TM, Chan PP. 2016. tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Res 44:W54–W57. doi: 10.1093/nar/gkw413. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 12.Tanizawa Y, Fujisawa T, Nakamura Y. 2018. DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication. Bioinforma 34:1037–1039. doi: 10.1093/bioinformatics/btx713. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 13.Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS. 2011. PHAST: a fast phage search tool. Nucleic Acids Res 39:W347–W352. doi: 10.1093/nar/gkr485. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 14.Grissa I, Vergnaud G, Pourcel C. 2007. CRISPRFinder: a Web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res 35:W52–W57. doi: 10.1093/nar/gkm360. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 15.Seemann T. 2014. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068–2069. doi: 10.1093/bioinformatics/btu153. [DOI] [PubMed] [Google Scholar]
Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Data Availability Statement
This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number RWJY00000000 (BioProject number PRJNA509104). The version described in this paper is RWJY01000000, with SRA accession number SRR8480428.