Identification, Comparison, and Profiling of Selected Diarrhoeagenic Pathogens from Diverse Water Sources and Human and Animal Faeces Using Whole-Genome Sequencing
Consumption of contaminated drinking water is known to cause waterborne diseases such as diarrhoea, dysentery, typhoid, and hepatitis. This study applied whole-genome sequencing (WGS) to detect, identify, compare, and profile diarrhoeagenic pathogens (<i>Vibrio cholerae</i>, Shiga toxin-...
Saved in:
| Main Authors: | , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2025-06-01
|
| Series: | Microorganisms |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2076-2607/13/6/1373 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849704968627421184 |
|---|---|
| author | Arinao Murei Maggy Ndombo Benteke Momba |
| author_facet | Arinao Murei Maggy Ndombo Benteke Momba |
| author_sort | Arinao Murei |
| collection | DOAJ |
| description | Consumption of contaminated drinking water is known to cause waterborne diseases such as diarrhoea, dysentery, typhoid, and hepatitis. This study applied whole-genome sequencing (WGS) to detect, identify, compare, and profile diarrhoeagenic pathogens (<i>Vibrio cholerae</i>, Shiga toxin-producing <i>Escherichia coli</i>, and <i>Escherichia coli</i> O157:H7) from 3168 water samples and 135 faecal samples (human and animal). Culture-based methods, MALDI-TOF mass spectrometry, and PCR were employed prior to WGS for identification of pathogens. Culture-based results revealed high presumptive prevalence of STEC (40.2%), <i>V. cholerae</i> (37.1%), and <i>E. coli</i> O157:H7 (22.7%). The MALDI-TOF confirmed 555 isolates with <i>V. cholerae</i> identified as <i>Vibrio albensis</i>. Shiga toxin-producing <i>Escherichia coli</i> (STEC) was more prevalent in wastewater (60%), treated water (54.1%), and groundwater (36.8%). PCR detected 46.4% of virulence genes from the water isolates and 66% of virulence genes from the STEC stool isolates. WGS also revealed STEC (92.9%) as the most prevalent species and found common virulence (e.g., <i>hcp1/tssD1</i> and <i>hlyE</i>) and resistance (e.g., <i>acrA</i> and <i>baeR</i>) genes in all three types of samples. Five resistance and thirteen virulence genes overlapped among treated water and stool isolates. These findings highlight the diarrhoeagenic pathogens’ public health risk in water sources and underscore the need for better water quality monitoring and treatment standards. |
| format | Article |
| id | doaj-art-3afc7f43dcec4f2e81b424827012c76c |
| institution | DOAJ |
| issn | 2076-2607 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj-art-3afc7f43dcec4f2e81b424827012c76c2025-08-20T03:16:35ZengMDPI AGMicroorganisms2076-26072025-06-01136137310.3390/microorganisms13061373Identification, Comparison, and Profiling of Selected Diarrhoeagenic Pathogens from Diverse Water Sources and Human and Animal Faeces Using Whole-Genome SequencingArinao Murei0Maggy Ndombo Benteke Momba1Department of Environmental, Water and Earth Sciences, Arcadia Campus, Tshwane University of Technology, 175 Nelson Mandela Avenue, Arcadia, Pretoria 0001, South AfricaDepartment of Environmental, Water and Earth Sciences, Arcadia Campus, Tshwane University of Technology, 175 Nelson Mandela Avenue, Arcadia, Pretoria 0001, South AfricaConsumption of contaminated drinking water is known to cause waterborne diseases such as diarrhoea, dysentery, typhoid, and hepatitis. This study applied whole-genome sequencing (WGS) to detect, identify, compare, and profile diarrhoeagenic pathogens (<i>Vibrio cholerae</i>, Shiga toxin-producing <i>Escherichia coli</i>, and <i>Escherichia coli</i> O157:H7) from 3168 water samples and 135 faecal samples (human and animal). Culture-based methods, MALDI-TOF mass spectrometry, and PCR were employed prior to WGS for identification of pathogens. Culture-based results revealed high presumptive prevalence of STEC (40.2%), <i>V. cholerae</i> (37.1%), and <i>E. coli</i> O157:H7 (22.7%). The MALDI-TOF confirmed 555 isolates with <i>V. cholerae</i> identified as <i>Vibrio albensis</i>. Shiga toxin-producing <i>Escherichia coli</i> (STEC) was more prevalent in wastewater (60%), treated water (54.1%), and groundwater (36.8%). PCR detected 46.4% of virulence genes from the water isolates and 66% of virulence genes from the STEC stool isolates. WGS also revealed STEC (92.9%) as the most prevalent species and found common virulence (e.g., <i>hcp1/tssD1</i> and <i>hlyE</i>) and resistance (e.g., <i>acrA</i> and <i>baeR</i>) genes in all three types of samples. Five resistance and thirteen virulence genes overlapped among treated water and stool isolates. These findings highlight the diarrhoeagenic pathogens’ public health risk in water sources and underscore the need for better water quality monitoring and treatment standards.https://www.mdpi.com/2076-2607/13/6/1373whole-genome sequencing (WGS)conventional PCRMALDI-TOF MSwater sourcesrural communities |
| spellingShingle | Arinao Murei Maggy Ndombo Benteke Momba Identification, Comparison, and Profiling of Selected Diarrhoeagenic Pathogens from Diverse Water Sources and Human and Animal Faeces Using Whole-Genome Sequencing Microorganisms whole-genome sequencing (WGS) conventional PCR MALDI-TOF MS water sources rural communities |
| title | Identification, Comparison, and Profiling of Selected Diarrhoeagenic Pathogens from Diverse Water Sources and Human and Animal Faeces Using Whole-Genome Sequencing |
| title_full | Identification, Comparison, and Profiling of Selected Diarrhoeagenic Pathogens from Diverse Water Sources and Human and Animal Faeces Using Whole-Genome Sequencing |
| title_fullStr | Identification, Comparison, and Profiling of Selected Diarrhoeagenic Pathogens from Diverse Water Sources and Human and Animal Faeces Using Whole-Genome Sequencing |
| title_full_unstemmed | Identification, Comparison, and Profiling of Selected Diarrhoeagenic Pathogens from Diverse Water Sources and Human and Animal Faeces Using Whole-Genome Sequencing |
| title_short | Identification, Comparison, and Profiling of Selected Diarrhoeagenic Pathogens from Diverse Water Sources and Human and Animal Faeces Using Whole-Genome Sequencing |
| title_sort | identification comparison and profiling of selected diarrhoeagenic pathogens from diverse water sources and human and animal faeces using whole genome sequencing |
| topic | whole-genome sequencing (WGS) conventional PCR MALDI-TOF MS water sources rural communities |
| url | https://www.mdpi.com/2076-2607/13/6/1373 |
| work_keys_str_mv | AT arinaomurei identificationcomparisonandprofilingofselecteddiarrhoeagenicpathogensfromdiversewatersourcesandhumanandanimalfaecesusingwholegenomesequencing AT maggyndombobentekemomba identificationcomparisonandprofilingofselecteddiarrhoeagenicpathogensfromdiversewatersourcesandhumanandanimalfaecesusingwholegenomesequencing |