Wastewater based genomic surveillance key to population level monitoring of AmpC/ESBL producing Escherichia coli
Abstract Antimicrobial resistance (AMR) is a serious threat to global public health, but obtaining representative data on AMR for healthy human populations is difficult. Here, we leverage the power of whole genome sequencing (WGS) to screen AmpC- and extended-spectrum beta-lactamase (ESBL)-producing...
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Nature Portfolio
2025-03-01
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| Online Access: | https://doi.org/10.1038/s41598-025-91516-9 |
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| author | Ahmad Ibrahim Al-Mustapha Ananda Tiwari Riikka Laukkanen-Ninios Kirsi-Maarit Lehto Sami Oikarinen Anssi Lipponen Tarja Pitkänen Annamari Heikinheimo WastPan Study Group |
| author_facet | Ahmad Ibrahim Al-Mustapha Ananda Tiwari Riikka Laukkanen-Ninios Kirsi-Maarit Lehto Sami Oikarinen Anssi Lipponen Tarja Pitkänen Annamari Heikinheimo WastPan Study Group |
| author_sort | Ahmad Ibrahim Al-Mustapha |
| collection | DOAJ |
| description | Abstract Antimicrobial resistance (AMR) is a serious threat to global public health, but obtaining representative data on AMR for healthy human populations is difficult. Here, we leverage the power of whole genome sequencing (WGS) to screen AmpC- and extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli from 77 composite samples obtained from 10 wastewater treatment plants across Finland. We found a high abundance of multidrug-resistant AmpC/ESBL-producing E. coli and significant differences in the diversity of AMR genes between the sampled cities. The in silico analysis of 73 short-read genome sequences shows the clonally diverse isolates consisting of 30 sequence types (STs), including the globally distributed pandemic ST131 clone. The CTX-M ESBL genes were detected in 86.3% (63/73) of the isolates concurrently with the blaTEM-1 (31.5%, 23/73) and blaOXA-1 (9.6%, 7/73) genes. The most prevalent ESBL genes were blaCTX-M-15 (46.6%, 34/73), blaCTX-M-27 (16.4%, 12/73), blaCTX-M-14 (4.1%, 3/73), and blaCTX-M-55 (4.1%, 3/73). Two isolates harboured the carbapenemase resistance gene, blaKPC-2 and blaNDM-1, respectively. In addition, WGS predicted phenotypic resistance against aminoglycosides, beta-lactams, cephalosporins, quinolones, sulfonamides, carbapenems, and polymyxins. The diversity of antibiotic- and stress-resistance genes correlated with the clinical incidence reported in the Finnish AMR report. Core-genome MLST revealed two wastewater genomic clusters but no genomic clusters among human and wastewater ST131 isolates. Our findings suggest the circulation of distinct clonal lineages of AmpC/ESBL-producing E. coli across Finland, with variations in AMR gene diversity and abundance by wellbeing service county. Also, our findings underscore the fact that wastewater surveillance could be key to population-level monitoring of AmpC/ESBL-producing Escherichia coli and can serve as complementary data to guide public health decisions. We propose longitudinal WGS-based epidemiology as an economically feasible approach for global AMR surveillance, pathogen evolution, and prediction of AMR. |
| format | Article |
| id | doaj-art-e2f30544f1d44f70b294b04cd3416843 |
| institution | DOAJ |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | Nature Portfolio |
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| spelling | doaj-art-e2f30544f1d44f70b294b04cd34168432025-08-20T03:05:53ZengNature PortfolioScientific Reports2045-23222025-03-0115111210.1038/s41598-025-91516-9Wastewater based genomic surveillance key to population level monitoring of AmpC/ESBL producing Escherichia coliAhmad Ibrahim Al-Mustapha0Ananda Tiwari1Riikka Laukkanen-Ninios2Kirsi-Maarit Lehto3Sami Oikarinen4Anssi Lipponen5Tarja Pitkänen6Annamari Heikinheimo7WastPan Study GroupDepartment of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of HelsinkiDepartment of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of HelsinkiDepartment of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of HelsinkiDepartment of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of HelsinkiFaculty of Medicine and Health Technology, Tampere UniversityDepartment of Public Health, Microbiology Unit, Finnish Institute for Health and WelfareDepartment of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of HelsinkiDepartment of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of HelsinkiAbstract Antimicrobial resistance (AMR) is a serious threat to global public health, but obtaining representative data on AMR for healthy human populations is difficult. Here, we leverage the power of whole genome sequencing (WGS) to screen AmpC- and extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli from 77 composite samples obtained from 10 wastewater treatment plants across Finland. We found a high abundance of multidrug-resistant AmpC/ESBL-producing E. coli and significant differences in the diversity of AMR genes between the sampled cities. The in silico analysis of 73 short-read genome sequences shows the clonally diverse isolates consisting of 30 sequence types (STs), including the globally distributed pandemic ST131 clone. The CTX-M ESBL genes were detected in 86.3% (63/73) of the isolates concurrently with the blaTEM-1 (31.5%, 23/73) and blaOXA-1 (9.6%, 7/73) genes. The most prevalent ESBL genes were blaCTX-M-15 (46.6%, 34/73), blaCTX-M-27 (16.4%, 12/73), blaCTX-M-14 (4.1%, 3/73), and blaCTX-M-55 (4.1%, 3/73). Two isolates harboured the carbapenemase resistance gene, blaKPC-2 and blaNDM-1, respectively. In addition, WGS predicted phenotypic resistance against aminoglycosides, beta-lactams, cephalosporins, quinolones, sulfonamides, carbapenems, and polymyxins. The diversity of antibiotic- and stress-resistance genes correlated with the clinical incidence reported in the Finnish AMR report. Core-genome MLST revealed two wastewater genomic clusters but no genomic clusters among human and wastewater ST131 isolates. Our findings suggest the circulation of distinct clonal lineages of AmpC/ESBL-producing E. coli across Finland, with variations in AMR gene diversity and abundance by wellbeing service county. Also, our findings underscore the fact that wastewater surveillance could be key to population-level monitoring of AmpC/ESBL-producing Escherichia coli and can serve as complementary data to guide public health decisions. We propose longitudinal WGS-based epidemiology as an economically feasible approach for global AMR surveillance, pathogen evolution, and prediction of AMR.https://doi.org/10.1038/s41598-025-91516-9Antimicrobial resistanceAntibiotic resistance genesExtended spectrum beta lactamaseEscherichia coliOne HealthPopulation surveillance |
| spellingShingle | Ahmad Ibrahim Al-Mustapha Ananda Tiwari Riikka Laukkanen-Ninios Kirsi-Maarit Lehto Sami Oikarinen Anssi Lipponen Tarja Pitkänen Annamari Heikinheimo WastPan Study Group Wastewater based genomic surveillance key to population level monitoring of AmpC/ESBL producing Escherichia coli Scientific Reports Antimicrobial resistance Antibiotic resistance genes Extended spectrum beta lactamase Escherichia coli One Health Population surveillance |
| title | Wastewater based genomic surveillance key to population level monitoring of AmpC/ESBL producing Escherichia coli |
| title_full | Wastewater based genomic surveillance key to population level monitoring of AmpC/ESBL producing Escherichia coli |
| title_fullStr | Wastewater based genomic surveillance key to population level monitoring of AmpC/ESBL producing Escherichia coli |
| title_full_unstemmed | Wastewater based genomic surveillance key to population level monitoring of AmpC/ESBL producing Escherichia coli |
| title_short | Wastewater based genomic surveillance key to population level monitoring of AmpC/ESBL producing Escherichia coli |
| title_sort | wastewater based genomic surveillance key to population level monitoring of ampc esbl producing escherichia coli |
| topic | Antimicrobial resistance Antibiotic resistance genes Extended spectrum beta lactamase Escherichia coli One Health Population surveillance |
| url | https://doi.org/10.1038/s41598-025-91516-9 |
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