DOI: 10.5061/dryad.xpnvx0ktx
title: Establishing a wastewater environmental surveillance network for enteropathogens in low-and middle-income countries – experience from Pakistan

description: 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.
description: # Establishing a wastewater environmental surveillance network for
 enteropathogens in low-and middle-income countries – experience from
 Pakistan ## 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