Human pathogen surveillance using a mobile and semi-autonomous environmental workflow Standard Operational Protocols, Pre--operation assessment and Best pracitices for Mobile Surveillance Laboratories (MLS)

To deliver efficient infectious disease surveillance, prevention, and control, as well as to enhance public health emergency preparedness, it is essential to implement a holistic One Health approach. This approach aims to sustainably balance and optimize the health of societies and the natural environment. Implementing the environmental and veterinary pillars within the One Health framework is particularly crucial in resource- and infrastructure-limited regions, such as slum settlements and small villages. These areas represent significant interfaces between humans, livestock, and the environment, leading to an elevated risk of human exposure to contaminated water, food and animal excrements carrying human pathogens.   Today, researchers and public health professionals today have access to improved and integrated research and surveillance infrastructure enabling the integration of genomic and epidemiology data. These capabilities facilitate a better understanding of infectious disease epidemiology and support the development of new, low-cost, and easy-to-implement solutions for public health interventions, particularly for vulnerable populations in low-resource settings. Mobile surveillance is especially suitable for detecting early signs of outbreaks in small villages that are not connected to a common wastewater treatment plant (WWTP) or for identifying localized outbreaks that may go undetected by broader community-wide environmental surveillance due to signal averaging and silencing.  The mobile lab protocols published herein are designed to facilitate the rapid detection of infectious agents while minimizing the need for extensive lab infrastructure for sample processing and analysis. These protocols have been specifically designed for use in field conditions and cover both untargeted analyses (high-throughput sequencing using the portable MinION Nanopore) and targeted analyses (using the portable Biomeme Franklin qPCR instrument). The guiding document details preparation for single mobile surveillance laboratory (MSL) deployment, pre-operational assessment, countermeasures for specific weather conditions, three situational scenarios related to workflows, and best practices. The Standard Operating Procedures (SOPs) are published in modular format:   Module A: Describes sample collection and filtration procedures for water samples (module A1) and the extraction of total Nucleic Acids (NA) from various sample types, including wastewater, clean (drinking) water, soil, and meat products (module A2).    Module B: Covers qPCR-based detection methods for emerging pathogens, including Mpox virus.    Module C: Includes protocols for library preparation for Nanopore sequencing on the MinION for metagenomic, metatranscriptomic, and amplicon sequencing analysis.  The published workflow represents a deliverable and milestone achievement (M3.1-ODIN, ODIN-mpox, D3.1-ODIN) from the following projects:   Strengthening Environmental Surveillance to Advance Public Health Action (ODIN): Financed by the Commission for the European Communities as part of Horizon Europe – the Framework Programme for Research and innovation (Grant Agreement Number 101103253) and Global Health EDCTP3.  Implementing wastewater and environmental surveillance for Mpox in Sub-Saharan Africa (ODIN-mpox): Financed by the Commission for the European Communities under EU call HORIZON-JU-GH-EDCTP3-2024-Mpox Mobilisation of Emergency funding for Mpox outbreak research response).  The published guiding document and SOPs contribute to Objective 3.1. in the ODIN project, which focuses on developing a mobile surveillance laboratory (MSL) (vehicle-based) for semi-automated molecular genetic tracking of human pathogens in environmental samples. Additionally, they contribute to the overall objective of the ODIN-Mpox project; developing a mobile wastewater and clean water surveillance system to efficiently detect, gather data on, and report outbreaks in remote areas of participating countries, thereby enabling a rapid response. These mobile protocols are part of the ongoing ODIN and ODIN-Mpox projects and may undergo minor adjustments based on feedback from African partners, informed by their field experiences.