Implementing Wastewater-Based Epidemiology for Long-Read Metagenomic Sequencing of Antimicrobial Resistance in Kampala, Uganda
Antimicrobial resistance (AMR) is an emerging global threat that is expanding in many areas of the world. Wastewater-based epidemiology (WBE) is uniquely suited for use in areas of the world where clinical surveillance is limited or logistically slow to identify emerging threats, such as in Sub-Saha...
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MDPI AG
2025-05-01
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| Seria: | Microorganisms |
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| author | William Strike Temitope O. C. Faleye Brian Lubega Alexus Rockward Soroosh Torabi Anni Noble Mohammad Dehghan Banadaki James Keck Henry Mugerwa Matthew Scotch Scott Berry |
| author_facet | William Strike Temitope O. C. Faleye Brian Lubega Alexus Rockward Soroosh Torabi Anni Noble Mohammad Dehghan Banadaki James Keck Henry Mugerwa Matthew Scotch Scott Berry |
| author_sort | William Strike |
| collection | DOAJ |
| description | Antimicrobial resistance (AMR) is an emerging global threat that is expanding in many areas of the world. Wastewater-based epidemiology (WBE) is uniquely suited for use in areas of the world where clinical surveillance is limited or logistically slow to identify emerging threats, such as in Sub-Saharan Africa (SSA). Wastewater was analyzed from three urban areas of Kampala, including a local HIV research clinic and two informal settlements. Wastewater extraction was performed using a low-cost, magnetic bead-based protocol that minimizes consumable plastic consumption followed by sequencing on the Oxford Nanopore Technology MinION platform. The majority of the analysis was performed using cloud-based services to identify AMR biomarkers and bacterial pathogens. Assemblies containing AMR pathogens were isolated from all locations. As one example, clinically relevant AMR biomarkers for multiple drug classes were found within <i>Acinetobacter baumannii</i> genomic fragments. This work presents a metagenomic WBE workflow that is compatible with areas of the world without robust water treatment infrastructure. This study was able to identify various bacterial pathogens and AMR biomarkers without shipping water samples internationally or relying on complex concentration methods. Due to the time-dependent nature of wastewater surveillance data, this work involved cross-training researchers in Uganda to collect and analyze wastewater for future efforts in public health development. |
| format | Article |
| id | doaj-art-e112e84211fb4e128d40002cbe0aecbb |
| institution | Matheson Library |
| issn | 2076-2607 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj-art-e112e84211fb4e128d40002cbe0aecbb2025-06-25T14:12:10ZengMDPI AGMicroorganisms2076-26072025-05-01136124010.3390/microorganisms13061240Implementing Wastewater-Based Epidemiology for Long-Read Metagenomic Sequencing of Antimicrobial Resistance in Kampala, UgandaWilliam Strike0Temitope O. C. Faleye1Brian Lubega2Alexus Rockward3Soroosh Torabi4Anni Noble5Mohammad Dehghan Banadaki6James Keck7Henry Mugerwa8Matthew Scotch9Scott Berry10Department of Biomedical Engineering, University of Kentucky, 522 Robotics and Manufacturing Building, Lexington, KY 40506, USABiodesign Center for Environmental Health Engineering, Arizona State University, 1001 S McAllister Ave, Tempe, AZ 85281, USAJoint Clinical Research Centre, Lubowa Estates, Kampala 759125, UgandaDepartment of Biomedical Engineering, University of Kentucky, 522 Robotics and Manufacturing Building, Lexington, KY 40506, USADepartment of Mechanical and Aerospace Engineering, University of Kentucky, 151 Ralph G. Anderson Building, Lexington, KY 40506, USADepartment of Mechanical and Aerospace Engineering, University of Kentucky, 151 Ralph G. Anderson Building, Lexington, KY 40506, USADepartment of Mechanical and Aerospace Engineering, University of Kentucky, 151 Ralph G. Anderson Building, Lexington, KY 40506, USAWWAMI School of Medicine, University of Alaska Anchorage, 3211 Providence Dr, Anchorage, AK 99508, USAJoint Clinical Research Centre, Lubowa Estates, Kampala 759125, UgandaBiodesign Center for Environmental Health Engineering, Arizona State University, 1001 S McAllister Ave, Tempe, AZ 85281, USADepartment of Biomedical Engineering, University of Kentucky, 522 Robotics and Manufacturing Building, Lexington, KY 40506, USAAntimicrobial resistance (AMR) is an emerging global threat that is expanding in many areas of the world. Wastewater-based epidemiology (WBE) is uniquely suited for use in areas of the world where clinical surveillance is limited or logistically slow to identify emerging threats, such as in Sub-Saharan Africa (SSA). Wastewater was analyzed from three urban areas of Kampala, including a local HIV research clinic and two informal settlements. Wastewater extraction was performed using a low-cost, magnetic bead-based protocol that minimizes consumable plastic consumption followed by sequencing on the Oxford Nanopore Technology MinION platform. The majority of the analysis was performed using cloud-based services to identify AMR biomarkers and bacterial pathogens. Assemblies containing AMR pathogens were isolated from all locations. As one example, clinically relevant AMR biomarkers for multiple drug classes were found within <i>Acinetobacter baumannii</i> genomic fragments. This work presents a metagenomic WBE workflow that is compatible with areas of the world without robust water treatment infrastructure. This study was able to identify various bacterial pathogens and AMR biomarkers without shipping water samples internationally or relying on complex concentration methods. Due to the time-dependent nature of wastewater surveillance data, this work involved cross-training researchers in Uganda to collect and analyze wastewater for future efforts in public health development.https://www.mdpi.com/2076-2607/13/6/1240wastewatermetagenomic environmental surveillancedrug-resistant pathogens |
| spellingShingle | William Strike Temitope O. C. Faleye Brian Lubega Alexus Rockward Soroosh Torabi Anni Noble Mohammad Dehghan Banadaki James Keck Henry Mugerwa Matthew Scotch Scott Berry Implementing Wastewater-Based Epidemiology for Long-Read Metagenomic Sequencing of Antimicrobial Resistance in Kampala, Uganda Microorganisms wastewater metagenomic environmental surveillance drug-resistant pathogens |
| title | Implementing Wastewater-Based Epidemiology for Long-Read Metagenomic Sequencing of Antimicrobial Resistance in Kampala, Uganda |
| title_full | Implementing Wastewater-Based Epidemiology for Long-Read Metagenomic Sequencing of Antimicrobial Resistance in Kampala, Uganda |
| title_fullStr | Implementing Wastewater-Based Epidemiology for Long-Read Metagenomic Sequencing of Antimicrobial Resistance in Kampala, Uganda |
| title_full_unstemmed | Implementing Wastewater-Based Epidemiology for Long-Read Metagenomic Sequencing of Antimicrobial Resistance in Kampala, Uganda |
| title_short | Implementing Wastewater-Based Epidemiology for Long-Read Metagenomic Sequencing of Antimicrobial Resistance in Kampala, Uganda |
| title_sort | implementing wastewater based epidemiology for long read metagenomic sequencing of antimicrobial resistance in kampala uganda |
| topic | wastewater metagenomic environmental surveillance drug-resistant pathogens |
| url | https://www.mdpi.com/2076-2607/13/6/1240 |
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