Genomics Analysis to Identify Multiple Genetic Determinants That Drive the Global Transmission of the Pandemic ST95 Lineage of Extraintestinal Pathogenic <i>Escherichia coli</i> (ExPEC)
Extraintestinal pathogenic <i>Escherichia coli</i> (ExPEC) is a pathogen that causes host extraintestinal diseases. The ST95 <i>E. coli</i> lineage is one of the dominant ExPEC lineages in humans and poultry. In this study, we took advantage of extensive <i>E. coli</...
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MDPI AG
2022-12-01
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| Series: | Pathogens |
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| Online Access: | https://www.mdpi.com/2076-0817/11/12/1489 |
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| author | Fufang Xia Jinlong Cheng Min Jiang Zhongxing Wang Zhe Wen Min Wang Jianluan Ren Xiangkai Zhuge |
| author_facet | Fufang Xia Jinlong Cheng Min Jiang Zhongxing Wang Zhe Wen Min Wang Jianluan Ren Xiangkai Zhuge |
| author_sort | Fufang Xia |
| collection | DOAJ |
| description | Extraintestinal pathogenic <i>Escherichia coli</i> (ExPEC) is a pathogen that causes host extraintestinal diseases. The ST95 <i>E. coli</i> lineage is one of the dominant ExPEC lineages in humans and poultry. In this study, we took advantage of extensive <i>E. coli</i> genomes available through public open-access databases to construct a detailed understanding of the phylogeny and evolution of ST95. We used a high variability of accessory genomes to highlight the diversity and dynamic traits of ST95. Isolates from diverse hosts and geographic sources were randomly located on the phylogenetic tree, which suggested that there is no host specificity for ST95. The time-scaled phylogeny showed that ST95 is an ancient and long-lasting lineage. The virulence genes, resistance genes, and pathogenicity islands (PAIs) were characterized in ST95 pan-genomes to provide novel insights into the pathogenicity and multidrug resistance (MDR) genotypes. We found that a pool of large plasmids drives virulence and MDR. Based on the unique genes in the ST95 pan-genome, we designed a novel multiplex PCR reaction to rapidly detect ST95. Overall, our study addressed a gap in the current understanding of ST95 ExPEC genomes, with significant implications for recognizing the success and spread of ST95. |
| first_indexed | 2024-03-09T15:59:53Z |
| format | Article |
| id | doaj.art-fa9f24d38a6b4c1bb56a4dbfe316dee8 |
| institution | Directory Open Access Journal |
| issn | 2076-0817 |
| language | English |
| last_indexed | 2024-03-09T15:59:53Z |
| publishDate | 2022-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Pathogens |
| spelling | doaj.art-fa9f24d38a6b4c1bb56a4dbfe316dee82023-11-24T17:13:37ZengMDPI AGPathogens2076-08172022-12-011112148910.3390/pathogens11121489Genomics Analysis to Identify Multiple Genetic Determinants That Drive the Global Transmission of the Pandemic ST95 Lineage of Extraintestinal Pathogenic <i>Escherichia coli</i> (ExPEC)Fufang Xia0Jinlong Cheng1Min Jiang2Zhongxing Wang3Zhe Wen4Min Wang5Jianluan Ren6Xiangkai Zhuge7MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, ChinaMOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, ChinaMOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, ChinaMOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, ChinaMOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, ChinaDepartment of Nutrition and Food Hygiene, School of Public Health, Nantong University, Nantong 226019, ChinaMOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, ChinaMOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, ChinaExtraintestinal pathogenic <i>Escherichia coli</i> (ExPEC) is a pathogen that causes host extraintestinal diseases. The ST95 <i>E. coli</i> lineage is one of the dominant ExPEC lineages in humans and poultry. In this study, we took advantage of extensive <i>E. coli</i> genomes available through public open-access databases to construct a detailed understanding of the phylogeny and evolution of ST95. We used a high variability of accessory genomes to highlight the diversity and dynamic traits of ST95. Isolates from diverse hosts and geographic sources were randomly located on the phylogenetic tree, which suggested that there is no host specificity for ST95. The time-scaled phylogeny showed that ST95 is an ancient and long-lasting lineage. The virulence genes, resistance genes, and pathogenicity islands (PAIs) were characterized in ST95 pan-genomes to provide novel insights into the pathogenicity and multidrug resistance (MDR) genotypes. We found that a pool of large plasmids drives virulence and MDR. Based on the unique genes in the ST95 pan-genome, we designed a novel multiplex PCR reaction to rapidly detect ST95. Overall, our study addressed a gap in the current understanding of ST95 ExPEC genomes, with significant implications for recognizing the success and spread of ST95.https://www.mdpi.com/2076-0817/11/12/1489ST95 ExPECcomparative genome analysisgenetic determinantsglobal transmissionzoonotic potentialrapid/specific detection |
| spellingShingle | Fufang Xia Jinlong Cheng Min Jiang Zhongxing Wang Zhe Wen Min Wang Jianluan Ren Xiangkai Zhuge Genomics Analysis to Identify Multiple Genetic Determinants That Drive the Global Transmission of the Pandemic ST95 Lineage of Extraintestinal Pathogenic <i>Escherichia coli</i> (ExPEC) Pathogens ST95 ExPEC comparative genome analysis genetic determinants global transmission zoonotic potential rapid/specific detection |
| title | Genomics Analysis to Identify Multiple Genetic Determinants That Drive the Global Transmission of the Pandemic ST95 Lineage of Extraintestinal Pathogenic <i>Escherichia coli</i> (ExPEC) |
| title_full | Genomics Analysis to Identify Multiple Genetic Determinants That Drive the Global Transmission of the Pandemic ST95 Lineage of Extraintestinal Pathogenic <i>Escherichia coli</i> (ExPEC) |
| title_fullStr | Genomics Analysis to Identify Multiple Genetic Determinants That Drive the Global Transmission of the Pandemic ST95 Lineage of Extraintestinal Pathogenic <i>Escherichia coli</i> (ExPEC) |
| title_full_unstemmed | Genomics Analysis to Identify Multiple Genetic Determinants That Drive the Global Transmission of the Pandemic ST95 Lineage of Extraintestinal Pathogenic <i>Escherichia coli</i> (ExPEC) |
| title_short | Genomics Analysis to Identify Multiple Genetic Determinants That Drive the Global Transmission of the Pandemic ST95 Lineage of Extraintestinal Pathogenic <i>Escherichia coli</i> (ExPEC) |
| title_sort | genomics analysis to identify multiple genetic determinants that drive the global transmission of the pandemic st95 lineage of extraintestinal pathogenic i escherichia coli i expec |
| topic | ST95 ExPEC comparative genome analysis genetic determinants global transmission zoonotic potential rapid/specific detection |
| url | https://www.mdpi.com/2076-0817/11/12/1489 |
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