Genomic characteristics and phylogenetic analyses of enteroaggregative Escherichia coli infection in diarrhea outpatients in Pudong New Area， Shanghai
ObjectiveTo investigate the whole genomic characteristics and phylogenetic relationships of clinical isolates of enteroaggregative Escherichia coli (EAEC) in diarrhea outpatients in Pudong New Area, Shanghai.MethodsBased on the diarrheal disease surveillance network in Pudong New Area, Shanghai, who...
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Shanghai Preventive Medicine Association
2025-04-01
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| Series: | Shanghai yufang yixue |
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| Online Access: | http://www.sjpm.org.cn/article/doi/10.19428/j.cnki.sjpm.2025.24576 |
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| author | CUI Qiqi LU Yuchen WU Suping ZHANG Yinwen ZHAO Bing PAN Lifeng ZHENG Yingjie HAO Lipeng |
| author_facet | CUI Qiqi LU Yuchen WU Suping ZHANG Yinwen ZHAO Bing PAN Lifeng ZHENG Yingjie HAO Lipeng |
| author_sort | CUI Qiqi |
| collection | DOAJ |
| description | ObjectiveTo investigate the whole genomic characteristics and phylogenetic relationships of clinical isolates of enteroaggregative Escherichia coli (EAEC) in diarrhea outpatients in Pudong New Area, Shanghai.MethodsBased on the diarrheal disease surveillance network in Pudong New Area, Shanghai, whole-genome sequencing was performed on a total of 55 EAEC strains isolated from fecal samples of the diarrhea outpatients from January 2015 to December 2019. The genome analyses based on raw sequencing data encompassed genome size, coding genes, dispersed repeat sequences, genomic islands, and protein coding regions, and pan-genome analyses were conducted simultaneously. Contigs sequences assays were performed to analyze molecular characteristics including serotypes, antibiotic resistance genes, and virulence factors. The phylogenetic clusters and multilocus sequence typing (MLST) were identified, and a phylogenetic tree was constructed.ResultsEAEC exhibited an open pan-genome. The predominant serotype of EAEC in diarrhea outpatients in Pudong New Area was O130:H27, and the carriage rate of β-lactam resistance genes was the highest (67.27%, 37/55). A total of 29 virulence factors and 106 virulence genes were identified, phylogenic group B1 was the predominant group, and clonal group CC31 was the dominant clonal group. The strain distribution was highly heterogeneous.ConclusionThe genomic characteristics of EAEC displayed significant strain polymorphism. It is necessary to develop effective strategies for differential diagnosis and improve detection capabilities for infection with EAEC of different serotypes and genotypes. |
| format | Article |
| id | doaj-art-cb8bc33a7345463cb0dd6579ff12db1f |
| institution | DOAJ |
| issn | 1004-9231 |
| language | zho |
| publishDate | 2025-04-01 |
| publisher | Shanghai Preventive Medicine Association |
| record_format | Article |
| series | Shanghai yufang yixue |
| spelling | doaj-art-cb8bc33a7345463cb0dd6579ff12db1f2025-08-20T02:44:43ZzhoShanghai Preventive Medicine AssociationShanghai yufang yixue1004-92312025-04-0137434234910.19428/j.cnki.sjpm.2025.245761004-9231（2025）04-0342-08Genomic characteristics and phylogenetic analyses of enteroaggregative Escherichia coli infection in diarrhea outpatients in Pudong New Area， ShanghaiCUI Qiqi0LU Yuchen1WU Suping2ZHANG Yinwen3ZHAO Bing4PAN Lifeng5ZHENG Yingjie6HAO Lipeng7Pudong New District Center for Disease Control and Prevention, Pudong Institute of Preventive Medicine, Fudan University, Shanghai 200136, ChinaPudong New District Center for Disease Control and Prevention, Pudong Institute of Preventive Medicine, Fudan University, Shanghai 200136, ChinaUnit 94969 of the Chinese People’s Liberation Army, Shanghai 200137, ChinaPudong New District Center for Disease Control and Prevention, Pudong Institute of Preventive Medicine, Fudan University, Shanghai 200136, ChinaPudong New District Center for Disease Control and Prevention, Pudong Institute of Preventive Medicine, Fudan University, Shanghai 200136, ChinaPudong New District Center for Disease Control and Prevention, Pudong Institute of Preventive Medicine, Fudan University, Shanghai 200136, ChinaSchool of Public Health, Fudan University, Shanghai 200032, ChinaPudong New District Center for Disease Control and Prevention, Pudong Institute of Preventive Medicine, Fudan University, Shanghai 200136, ChinaObjectiveTo investigate the whole genomic characteristics and phylogenetic relationships of clinical isolates of enteroaggregative Escherichia coli (EAEC) in diarrhea outpatients in Pudong New Area, Shanghai.MethodsBased on the diarrheal disease surveillance network in Pudong New Area, Shanghai, whole-genome sequencing was performed on a total of 55 EAEC strains isolated from fecal samples of the diarrhea outpatients from January 2015 to December 2019. The genome analyses based on raw sequencing data encompassed genome size, coding genes, dispersed repeat sequences, genomic islands, and protein coding regions, and pan-genome analyses were conducted simultaneously. Contigs sequences assays were performed to analyze molecular characteristics including serotypes, antibiotic resistance genes, and virulence factors. The phylogenetic clusters and multilocus sequence typing (MLST) were identified, and a phylogenetic tree was constructed.ResultsEAEC exhibited an open pan-genome. The predominant serotype of EAEC in diarrhea outpatients in Pudong New Area was O130:H27, and the carriage rate of β-lactam resistance genes was the highest (67.27%, 37/55). A total of 29 virulence factors and 106 virulence genes were identified, phylogenic group B1 was the predominant group, and clonal group CC31 was the dominant clonal group. The strain distribution was highly heterogeneous.ConclusionThe genomic characteristics of EAEC displayed significant strain polymorphism. It is necessary to develop effective strategies for differential diagnosis and improve detection capabilities for infection with EAEC of different serotypes and genotypes.http://www.sjpm.org.cn/article/doi/10.19428/j.cnki.sjpm.2025.24576enteroaggregative escherichia coliwhole genome sequencingpan-genomemolecular characteristicphylogenetic evolution |
| spellingShingle | CUI Qiqi LU Yuchen WU Suping ZHANG Yinwen ZHAO Bing PAN Lifeng ZHENG Yingjie HAO Lipeng Genomic characteristics and phylogenetic analyses of enteroaggregative Escherichia coli infection in diarrhea outpatients in Pudong New Area， Shanghai Shanghai yufang yixue enteroaggregative escherichia coli whole genome sequencing pan-genome molecular characteristic phylogenetic evolution |
| title | Genomic characteristics and phylogenetic analyses of enteroaggregative Escherichia coli infection in diarrhea outpatients in Pudong New Area， Shanghai |
| title_full | Genomic characteristics and phylogenetic analyses of enteroaggregative Escherichia coli infection in diarrhea outpatients in Pudong New Area， Shanghai |
| title_fullStr | Genomic characteristics and phylogenetic analyses of enteroaggregative Escherichia coli infection in diarrhea outpatients in Pudong New Area， Shanghai |
| title_full_unstemmed | Genomic characteristics and phylogenetic analyses of enteroaggregative Escherichia coli infection in diarrhea outpatients in Pudong New Area， Shanghai |
| title_short | Genomic characteristics and phylogenetic analyses of enteroaggregative Escherichia coli infection in diarrhea outpatients in Pudong New Area， Shanghai |
| title_sort | genomic characteristics and phylogenetic analyses of enteroaggregative escherichia coli infection in diarrhea outpatients in pudong new area shanghai |
| topic | enteroaggregative escherichia coli whole genome sequencing pan-genome molecular characteristic phylogenetic evolution |
| url | http://www.sjpm.org.cn/article/doi/10.19428/j.cnki.sjpm.2025.24576 |
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