Draft genome sequence of an extended-spectrum β-lactamase-producing Escherichia coli ST58 isolate from cattle in Pakistan
Objectives: Food animals have been recognised as an important reservoir of extended-spectrum β-lactamase-producing Escherichia coli (ESBL-Ec). This study reports the draft genome sequence of a bovine ESBL-Ec from Pakistan. Methods: Genomic DNA from a bovine E. coli (PK-1421) was extracted and whole-...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2020-06-01
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| Series: | Journal of Global Antimicrobial Resistance |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2213716520301120 |
| _version_ | 1818572917756133376 |
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| author | Arslan Ali Qasim Ali Riasat Ali Mashkoor Mohsin |
| author_facet | Arslan Ali Qasim Ali Riasat Ali Mashkoor Mohsin |
| author_sort | Arslan Ali |
| collection | DOAJ |
| description | Objectives: Food animals have been recognised as an important reservoir of extended-spectrum β-lactamase-producing Escherichia coli (ESBL-Ec). This study reports the draft genome sequence of a bovine ESBL-Ec from Pakistan. Methods: Genomic DNA from a bovine E. coli (PK-1421) was extracted and whole-genome sequencing was performed using an Illumina HiSeq 2500 platform. De novo genome assembly was performed using SPAdes v.3.9 and annotation of the assembled genome was performed using the DDBJ Fast Annotation and Submission Tool (DFAST). In silico tools from the Center for Genomic Epidemiology were used to find out for analysis of antimicrobial resistance genes, sequence type (ST), plasmid replicon type, serotype and phylogenetics. Results: Escherichia coli strain PK-1421 showed multiple drug resistance. The draft genome was calculated at 4 869 610 bp, comprising a total of 131 contigs with a G + C content of 50.6% and 4487 protein-coding sequences. Escherichia coli PK-1412 belongs to ST58 and serotype O75:H9. A large number of antimicrobial resistance genes associated with resistance to β-lactams (blaCTX-M-15, blaTEM-1B), trimethoprim (dfrA14), aminoglycosides [aph(3ʹ)-lb, aph(6)-ld], sulfonamides (sul2), tetracycline (tetA), macrolides (mdfA) and quinolones (qnrS1) were detected. A conjugation experiment showed successful transfer of the blaCTX-M-15 gene to an E. coli J53 recipient strain. The phylogenetic tree indicated that ST58 E. coli PK-1421 was distant from other strains. Conclusion: This is the first draft genome of an E. coli of bovine origin in Pakistan. The genome sequence presented here may be helpful to understand the genomic diversity and antimicrobial resistance potential of E. coli from large ruminants. |
| first_indexed | 2024-12-15T00:04:03Z |
| format | Article |
| id | doaj.art-2799df0a68e44e00b59a85b219b0aef5 |
| institution | Directory Open Access Journal |
| issn | 2213-7165 |
| language | English |
| last_indexed | 2024-12-15T00:04:03Z |
| publishDate | 2020-06-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Global Antimicrobial Resistance |
| spelling | doaj.art-2799df0a68e44e00b59a85b219b0aef52022-12-21T22:42:47ZengElsevierJournal of Global Antimicrobial Resistance2213-71652020-06-0121303305Draft genome sequence of an extended-spectrum β-lactamase-producing Escherichia coli ST58 isolate from cattle in PakistanArslan Ali0Qasim Ali1Riasat Ali2Mashkoor Mohsin3Institute of Microbiology, University of Agriculture, Faisalabad 38000, PakistanInstitute of Microbiology, University of Agriculture, Faisalabad 38000, Pakistan; Public Health Laboratory Division, National Institute of Health, Islamabad, PakistanInstitute of Microbiology, University of Agriculture, Faisalabad 38000, PakistanInstitute of Microbiology, University of Agriculture, Faisalabad 38000, Pakistan; Corresponding author.Objectives: Food animals have been recognised as an important reservoir of extended-spectrum β-lactamase-producing Escherichia coli (ESBL-Ec). This study reports the draft genome sequence of a bovine ESBL-Ec from Pakistan. Methods: Genomic DNA from a bovine E. coli (PK-1421) was extracted and whole-genome sequencing was performed using an Illumina HiSeq 2500 platform. De novo genome assembly was performed using SPAdes v.3.9 and annotation of the assembled genome was performed using the DDBJ Fast Annotation and Submission Tool (DFAST). In silico tools from the Center for Genomic Epidemiology were used to find out for analysis of antimicrobial resistance genes, sequence type (ST), plasmid replicon type, serotype and phylogenetics. Results: Escherichia coli strain PK-1421 showed multiple drug resistance. The draft genome was calculated at 4 869 610 bp, comprising a total of 131 contigs with a G + C content of 50.6% and 4487 protein-coding sequences. Escherichia coli PK-1412 belongs to ST58 and serotype O75:H9. A large number of antimicrobial resistance genes associated with resistance to β-lactams (blaCTX-M-15, blaTEM-1B), trimethoprim (dfrA14), aminoglycosides [aph(3ʹ)-lb, aph(6)-ld], sulfonamides (sul2), tetracycline (tetA), macrolides (mdfA) and quinolones (qnrS1) were detected. A conjugation experiment showed successful transfer of the blaCTX-M-15 gene to an E. coli J53 recipient strain. The phylogenetic tree indicated that ST58 E. coli PK-1421 was distant from other strains. Conclusion: This is the first draft genome of an E. coli of bovine origin in Pakistan. The genome sequence presented here may be helpful to understand the genomic diversity and antimicrobial resistance potential of E. coli from large ruminants.http://www.sciencedirect.com/science/article/pii/S2213716520301120Antimicrobial resistanceFood animalsESBLEscherichia coliCattlePakistan |
| spellingShingle | Arslan Ali Qasim Ali Riasat Ali Mashkoor Mohsin Draft genome sequence of an extended-spectrum β-lactamase-producing Escherichia coli ST58 isolate from cattle in Pakistan Journal of Global Antimicrobial Resistance Antimicrobial resistance Food animals ESBL Escherichia coli Cattle Pakistan |
| title | Draft genome sequence of an extended-spectrum β-lactamase-producing Escherichia coli ST58 isolate from cattle in Pakistan |
| title_full | Draft genome sequence of an extended-spectrum β-lactamase-producing Escherichia coli ST58 isolate from cattle in Pakistan |
| title_fullStr | Draft genome sequence of an extended-spectrum β-lactamase-producing Escherichia coli ST58 isolate from cattle in Pakistan |
| title_full_unstemmed | Draft genome sequence of an extended-spectrum β-lactamase-producing Escherichia coli ST58 isolate from cattle in Pakistan |
| title_short | Draft genome sequence of an extended-spectrum β-lactamase-producing Escherichia coli ST58 isolate from cattle in Pakistan |
| title_sort | draft genome sequence of an extended spectrum β lactamase producing escherichia coli st58 isolate from cattle in pakistan |
| topic | Antimicrobial resistance Food animals ESBL Escherichia coli Cattle Pakistan |
| url | http://www.sciencedirect.com/science/article/pii/S2213716520301120 |
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