Phylogenetic Analysis of <i>Escherichia coli</i> Isolated from Australian Feedlot Cattle in Comparison to Pig Faecal and Poultry/Human Extraintestinal Isolates
The similarity of commensal <i>Escherichia coli</i> isolated from healthy cattle to antimicrobial-resistant bacteria causing extraintestinal infections in humans is not fully understood. In this study, we used a bioinformatics approach based on whole genome sequencing data to determine t...
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MDPI AG
2023-05-01
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| Series: | Antibiotics |
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| Online Access: | https://www.mdpi.com/2079-6382/12/5/895 |
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| author | Yohannes E. Messele Darren J. Trott Mauida F. Hasoon Tania Veltman Joe P. McMeniman Stephen P. Kidd Steven P. Djordjevic Kiro R. Petrovski Wai Y. Low |
| author_facet | Yohannes E. Messele Darren J. Trott Mauida F. Hasoon Tania Veltman Joe P. McMeniman Stephen P. Kidd Steven P. Djordjevic Kiro R. Petrovski Wai Y. Low |
| author_sort | Yohannes E. Messele |
| collection | DOAJ |
| description | The similarity of commensal <i>Escherichia coli</i> isolated from healthy cattle to antimicrobial-resistant bacteria causing extraintestinal infections in humans is not fully understood. In this study, we used a bioinformatics approach based on whole genome sequencing data to determine the genetic characteristics and phylogenetic relationships among faecal <i>Escherichia coli</i> isolates from beef cattle (n = 37) from a single feedlot in comparison to previously analysed pig faecal (n = 45), poultry extraintestinal (n = 19), and human extraintestinal <i>E. coli</i> isolates (n = 40) from three previous Australian studies. Most beef cattle and pig isolates belonged to <i>E. coli</i> phylogroups A and B1, whereas most avian and human isolates belonged to B2 and D, although a single human extraintestinal isolate belonged to phylogenetic group A and sequence type (ST) 10. The most common <i>E. coli</i> sequence types (STs) included ST10 for beef cattle, ST361 for pig, ST117 for poultry, and ST73 for human isolates. Extended-spectrum and AmpC β-lactamase genes were identified in seven out of thirty-seven (18.9%) beef cattle isolates. The most common plasmid replicons identified were IncFIB (AP001918), followed by IncFII, Col156, and IncX1. The results confirm that feedlot cattle isolates examined in this study represent a reduced risk to human and environmental health with regard to being a source of antimicrobial-resistant <i>E. coli</i> of clinical importance. |
| first_indexed | 2024-03-11T04:00:10Z |
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| language | English |
| last_indexed | 2024-03-11T04:00:10Z |
| publishDate | 2023-05-01 |
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| series | Antibiotics |
| spelling | doaj.art-c62e32418c1c4d2286487be08140afb02023-11-18T00:12:52ZengMDPI AGAntibiotics2079-63822023-05-0112589510.3390/antibiotics12050895Phylogenetic Analysis of <i>Escherichia coli</i> Isolated from Australian Feedlot Cattle in Comparison to Pig Faecal and Poultry/Human Extraintestinal IsolatesYohannes E. Messele0Darren J. Trott1Mauida F. Hasoon2Tania Veltman3Joe P. McMeniman4Stephen P. Kidd5Steven P. Djordjevic6Kiro R. Petrovski7Wai Y. Low8The Davies Livestock Research Centre, The University of Adelaide, Adelaide, SA 5371, AustraliaThe Australian Centre for Antimicrobial Resistance Ecology, The University of Adelaide, Adelaide, SA 5005, AustraliaThe Australian Centre for Antimicrobial Resistance Ecology, The University of Adelaide, Adelaide, SA 5005, AustraliaThe Australian Centre for Antimicrobial Resistance Ecology, The University of Adelaide, Adelaide, SA 5005, AustraliaMeat & Livestock Australia, Level 1, 40 Mount Street, North Sydney, NSW 2060, AustraliaThe Australian Centre for Antimicrobial Resistance Ecology, The University of Adelaide, Adelaide, SA 5005, AustraliaAustralian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, NSW 2007, AustraliaThe Davies Livestock Research Centre, The University of Adelaide, Adelaide, SA 5371, AustraliaThe Davies Livestock Research Centre, The University of Adelaide, Adelaide, SA 5371, AustraliaThe similarity of commensal <i>Escherichia coli</i> isolated from healthy cattle to antimicrobial-resistant bacteria causing extraintestinal infections in humans is not fully understood. In this study, we used a bioinformatics approach based on whole genome sequencing data to determine the genetic characteristics and phylogenetic relationships among faecal <i>Escherichia coli</i> isolates from beef cattle (n = 37) from a single feedlot in comparison to previously analysed pig faecal (n = 45), poultry extraintestinal (n = 19), and human extraintestinal <i>E. coli</i> isolates (n = 40) from three previous Australian studies. Most beef cattle and pig isolates belonged to <i>E. coli</i> phylogroups A and B1, whereas most avian and human isolates belonged to B2 and D, although a single human extraintestinal isolate belonged to phylogenetic group A and sequence type (ST) 10. The most common <i>E. coli</i> sequence types (STs) included ST10 for beef cattle, ST361 for pig, ST117 for poultry, and ST73 for human isolates. Extended-spectrum and AmpC β-lactamase genes were identified in seven out of thirty-seven (18.9%) beef cattle isolates. The most common plasmid replicons identified were IncFIB (AP001918), followed by IncFII, Col156, and IncX1. The results confirm that feedlot cattle isolates examined in this study represent a reduced risk to human and environmental health with regard to being a source of antimicrobial-resistant <i>E. coli</i> of clinical importance.https://www.mdpi.com/2079-6382/12/5/895<i>Escherichia coli</i>genotypeepidemiologyphylogeny |
| spellingShingle | Yohannes E. Messele Darren J. Trott Mauida F. Hasoon Tania Veltman Joe P. McMeniman Stephen P. Kidd Steven P. Djordjevic Kiro R. Petrovski Wai Y. Low Phylogenetic Analysis of <i>Escherichia coli</i> Isolated from Australian Feedlot Cattle in Comparison to Pig Faecal and Poultry/Human Extraintestinal Isolates Antibiotics <i>Escherichia coli</i> genotype epidemiology phylogeny |
| title | Phylogenetic Analysis of <i>Escherichia coli</i> Isolated from Australian Feedlot Cattle in Comparison to Pig Faecal and Poultry/Human Extraintestinal Isolates |
| title_full | Phylogenetic Analysis of <i>Escherichia coli</i> Isolated from Australian Feedlot Cattle in Comparison to Pig Faecal and Poultry/Human Extraintestinal Isolates |
| title_fullStr | Phylogenetic Analysis of <i>Escherichia coli</i> Isolated from Australian Feedlot Cattle in Comparison to Pig Faecal and Poultry/Human Extraintestinal Isolates |
| title_full_unstemmed | Phylogenetic Analysis of <i>Escherichia coli</i> Isolated from Australian Feedlot Cattle in Comparison to Pig Faecal and Poultry/Human Extraintestinal Isolates |
| title_short | Phylogenetic Analysis of <i>Escherichia coli</i> Isolated from Australian Feedlot Cattle in Comparison to Pig Faecal and Poultry/Human Extraintestinal Isolates |
| title_sort | phylogenetic analysis of i escherichia coli i isolated from australian feedlot cattle in comparison to pig faecal and poultry human extraintestinal isolates |
| topic | <i>Escherichia coli</i> genotype epidemiology phylogeny |
| url | https://www.mdpi.com/2079-6382/12/5/895 |
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