Establishing a wastewater environmental surveillance network for enteropathogens in low-and middle-income countries – experience from Pakistan
Data files
Nov 18, 2025 version files 302.29 KB
Abstract
Background: Wastewater surveillance has emerged as a powerful public health tool for the early detection of pathogens and the monitoring of community-level disease trends. This study aimed to establish and validate the utility of an ES system in Karachi, Pakistan, for tracking diverse pathogens to inform targeted public health actions. This manuscript describes the methodology, process, and challenges encountered during the establishment of an environmental surveillance network in Karachi.
Methods: A wastewater environmental surveillance (WES) study was implemented in 3 towns in Karachi (Gadap, Lyari and Gulshan-e-Iqbal). Teams manually traced drainage pathways, flow direction, and georeferenced data. Sites were selected based on population catchment, absence of industrial effluent, and logistical feasibility. From 2021-2023, wastewater samples were collected using Bag Mediated Filtration System (BMFS). Thirty two sites were validated through sensitivity analyses comparing wastewater detection of pathogens like Sabin poliovirus, SARS-CoV-2, and S. typhi with clinical data.
Results: The mean ± SD duration of blue line tracing and mapping was 15.6 ± 4.0 days for each town. In the first round, conducted during and after the bOPV Supplemental Immunization Activity (SIA), 403 wastewater samples from 12 ES sites in Gadap town were analyzed, showing low detection of Sabin targets. Detection rates remained low in the second round during which 232 wastewater samples from 28 WES sites in the 3 towns were analyzed. In the third round, 32 287 wastewater samples from 32 WES sites showed improved results with enhanced pathogen detection including site-level SARS-CoV-2 and EV. We highlighted challenges that WES faces such as field, laboratory and analytical including, logistical barriers and environmental variability.
Conclusion: We identified and validated 32 WES sites for the detection of enteropathogens in wastewater across three towns in Karachi. The successful establishment of WES network was made possible by strong collaboration with key stakeholders and experts.
Data File Descriptions
Tac_data_20251001.xlsx
This dataset contains TaqMan Array Card (TAC) results from sewage water samples collected across three towns in Karachi. Samples were collected from multiple surveillance sites as part of environmental monitoring activities.
The data file includes four sheets: Codebook -- Contains variable names, labels, and coding information used across all data sheets. Round 1 Round 2 Round 3 (Each round represents a separate sampling phase, as also described in the published manuscript. To facilitate ease of use and clarity, TAC results for each round are maintained on separate sheets.)
Key Variables (Round Sheets) keps_site: KEPS site ID town: Selected towns for sewage surveillance uc: Union Council within the selected town date_sample: Date of sample collection keps_id: Unique sample identifier LAB_SAMPLE_ID: Unique laboratory sample ID sample_type: Sample type (BMFS / NanoTrap)
Remaining columns: TAC targets including bacterial, viral, protozoal markers, and assay controls
TAC Result Interpretation Positive Ct value ≤ 35.00\ Negative Ct value ≥ 35.01 or reported as "Und"\ Invalid / Excluded Value reported as NA (Post-QC)-Excluded
Clinical_cases_data_of_Enteric_Fever_Culture_Positive_from_(Aug_2022_to_Jul_2023).xlsx
This data file presents the monthly distribution of blood culture testing and culture-confirmed enteric fever cases (S. Typhi and S. Paratyphi) across three selected towns of Karachi. For each town, the table reports:
S. Typhi cases S. Paratyphi cases Total blood cultures tested from hospitals Total blood cultures tested from laboratories Overall total tests conducted
The final columns show the combined totals across all three towns, along with the overall grand total of blood cultures performed in Karachi for each month.
The dataset includes monthly counts from August 2022 to July 2023, with a final row summarizing cumulative totals for the period.
This table is intended to support monitoring trends in blood culture
testing and laboratory-confirmed enteric fever burden across priority
surveillance towns in Karachi.
This data set was used to access the correlation between clinical case burden and environmental surveillance abundance of Salmonella Typhi.
Clinical_cases_data_of_Rotavirus_from_Stool_Samples_TAC_Results_-_(Aug_2022_to_Jul_2023).xlsx
This dataset contains clinical case information related to rotavirus detection from stool samples collected as part of surveillance activities. Each record represents an individual participant enrolled through health facilities or from laboratory within the study area.
Key Variables: Study ID: Unique identifier assigned to each enrolled participant. LAB_SAMPLE_ID: Laboratory sample identifier corresponding to each stool specimen. Date of Collection: The date on which the stool sample was collected. Enrollment Site: The health facility or Laboratory where the participant was enrolled. Potential Participant Location: Geographic area/location of the participant. Enrollment_from: Source of enrollment (e.g., Health Facility or Laboratory). Rotavirus: TAC test result for rotavirus. Values include:] Ct value (less than equal to 35.00) --- indicates a positive detection greater than equal to 35.01 or written as "Und" --- undetected or negative result
This data set was used to access the correlation between clinical case burden and environmental surveillance abundance of rotavirus.
Sharing/Access information
Links to other publicly accessible locations of the data: - None
Data was derived from the following sources: - None