Respiratory pathogens across rural populations: general practice patients with community-acquired pneumonia, residents, and goat farmers

BACKGROUND: Residents living near goat farms (< 2000 m) in the Netherlands have consistently shown an elevated risk of pneumonia, yet the pathogens underlying this association remain unknown. This study assessed the presence of 33 respiratory pathogens, including bacteria, viruses, and fungi, across rural populations with different goat farm exposures. METHODS: This cross-sectional study included general practitioner (GP)-diagnosed pneumonia patients (PP; n = 108), non-farming rural residents without pneumonia (NFR; n = 200), and goat farm workers (GFW; n = 91). Oropharyngeal and nasopharyngeal swabs were collected and analyzed by a multiplex and two additional PCR test targeting in total 12 bacteria, 20 viruses and 1 fungus. Between-group differences in detection were assessed by Fisher's exact tests. Logistic regression analyses were performed to assess associations between pathogen detection and residential proximity to goat farming and other covariates. RESULTS: Presence of any of the examined pathogens was highest in the PP group (94.5%), followed by GFW (88.8%), and NFR (70%). The most frequently detected pathogens overall were Haemophilus influenzae, Staphylococcus aureus, Streptococcus pneumoniae, Moraxella catarrhalis, and rhinovirus. Of these, M. catarrhalis and S. pneumoniae were significantly more often detected in PP, whereas Salmonella spp. and S. aureus were more frequently detected in GFW. Eight pathogens, including Coxiella burnetii, were not detected. Age, season of sampling, smoking and other covariates were significantly associated with certain bacteria and viruses. However, no associations were identified between residential proximity to goat farming and detection of specific pathogens in NFR and PP. CONCLUSIONS: Respiratory pathogens were detected in nearly all PP, while substantial proportions of positives were also observed in GFW and NFR, likely reflecting (transient) colonization rather than active infection. Detection of the examined pathogens was not associated with residential proximity to goat farms, suggesting that these pathogens do not explain the observed increased pneumonia risk among nearby non-farming residents. As a substantial proportion of the Dutch population (~ 7%) lives within 2,000 m of a commercial goat farm, and goat farming is expanding globally, further research efforts, including microbiologic diagnostics and surveillance, are needed to elucidate the mechanisms underlying the increased pneumonia risk among nearby residents.