Care-home pathogen and AMR surveillance

Overview

Shared buildings can amplify biological risk. In care homes, offices, hotels, factories, warehouses and other high-occupancy environments, respiratory viruses, gastrointestinal pathogens and antimicrobial-resistant organisms can move through people, air, surfaces and wastewater before an outbreak is obvious.

BioSeer's founding team helped develop and apply an integrated environmental surveillance model in live occupied buildings, including care-home and office settings. The programme combined air sampling, near-source wastewater monitoring, targeted qPCR, shotgun metagenomics, culturomics and antimicrobial resistance profiling to provide a fuller picture of pathogen and AMR risk across complex indoor environments.

The care-home component provided a particularly important proof point because residents are often older, clinically vulnerable and at increased risk from infection. The work demonstrated how routine environmental surveillance can move infection control and building-risk management from reactive response towards earlier warning, targeted intervention and better operational decision-making.

The Challenge

High-occupancy buildings face overlapping biological risks. Respiratory viruses such as SARS-CoV-2, influenza and RSV can spread quickly in shared air. Gastrointestinal pathogens such as norovirus can cause rapid outbreaks. Foodborne and opportunistic organisms can create additional risk in kitchens and care settings. At the same time, antimicrobial resistance can persist and circulate through people, surfaces, wastewater and the wider built environment.

Traditional surveillance often depends on clinical presentation or staff reporting: someone becomes symptomatic, cases are recognised, and control measures follow. The limitation is timing. By the time an outbreak is visible, transmission may already be underway. The programme asked a more proactive question: could air, wastewater and environmental microbiology provide earlier, broader and more actionable signals of risk across shared indoor environments?

What we did

We monitored a single nursing home intensively for more than a year, treating the building itself as the patient. Rather than testing individual residents, we sampled the environment they share — the air in the rooms they live and work in, the wastewater leaving the building, and the high-touch surfaces in between — and ran the full analytical stack on what we found.

The integrated approach

Air samples were collected from key indoor locations, including high-traffic and resident-facing areas, while composite wastewater samples captured pooled biological signals from the building. Samples were screened for norovirus, SARS-CoV-2, influenza A and RSV. In the care-home component, norovirus and SARS-CoV-2 were detected in wastewater up to seven days before the first symptomatic individuals were reported, with a similar lead time observed for SARS-CoV-2 in air samples.

• Extended pathogen surveillance. The programme extended beyond a narrow respiratory-virus panel to include viral, bacterial and fungal targets associated with gastrointestinal illness, opportunistic infection and built-environment risk — including sapovirus, astrovirus, Clostridioides difficile, Klebsiella oxytoca, Campylobacter, Listeria monocytogenes, Salmonella, Streptococcus pneumoniae, Candida auris and Aspergillus fumigatus.
• Genomics and microbiome analysis. Shotgun metagenomic sequencing investigated the taxonomic composition of air and wastewater microbiomes, providing a broader, less target-limited view including opportunistic and foodborne organisms that may not be fully captured by qPCR alone. Sequencing also supported variant-level interpretation: SARS-CoV-2-positive samples were linked to contemporaneous KP.3 and KP.3.1.1 variants.
• AMR surveillance and culturomics. The programme investigated antimicrobial resistance using qPCR screening for notifiable AMR genes, shotgun metagenomic analysis of resistance genes and culture-based isolation for phenotypic susceptibility testing. Genetic markers can indicate the presence of resistance potential, while cultured isolates and phenotypic testing help show whether organisms recovered from the environment express resistance to relevant drugs.

What the programme delivered

• Earlier warning: norovirus and SARS-CoV-2 were detected in wastewater up to seven days before the first symptomatic individuals were reported.
• Multi-route surveillance: air and wastewater monitoring provided complementary views of pathogen presence across the indoor environment.
• Broad pathogen coverage: the programme screened for respiratory viruses, gastrointestinal viruses, bacterial pathogens, fungal pathogens and opportunistic organisms.
• AMR intelligence: qPCR, metagenomics and culture-based methods were used to investigate antimicrobial resistance genes and resistant isolates.
• A scalable model: the work demonstrated a practical surveillance approach that can be adapted for care homes, offices, hotels, factories, distribution warehouses, healthcare facilities and other shared buildings.

Why it matters now

Organisations need better ways to understand biological risk in the buildings they operate. Environmental monitoring offers a privacy-preserving and practical way to detect pathogen and AMR signals across a whole facility without relying solely on individual testing or symptomatic reporting.

For BioSeer, this case study demonstrates the strength of an integrated model: microbiology, genomics, environmental surveillance and bioinformatics working together to generate evidence that infection-control, facilities, occupational-health and operational teams can use. Most laboratories specialise. BioSeer integrates.