Urban Pigeons as Reservoirs of Critical Pathogens: Improved protocol for sequencing pigeon faeces in disease monitoring

The spread of pathogens by animals is a serious issue around the world that causes a severe threat to human health. Feral pigeons (Columba livia forma domestica) that live in urban areas are zoonotic carriers of various pathogens that can be transmitted to humans by faecal contamination. This study aimed to detect the presence of bacterial, viral, and specifically fungal pathogens in pigeon faeces based on the World Health Organization's (WHO) priority pathogen list published in 2022. Fresh faecal samples were collected at Uppsala, Central Station, and Svandammen, the pigeons' most relevant gathering spots and feeding sites. Genomic DNA was directly extracted from these samples, and ScilifeLab performed High throughput sequencing through Oxford Nanopore Technologies(ONT) (PromethION). Metagenomic analysis revealed that most of the critically prioritized viral and bacterial pathogens listed by WHO were present in pigeon faeces. Regarding fungal pathogens, which were the main objective of this study, samples from both studied locations contained all critical, high and, medium-important fungal pathogens published in the WHO list, such as Aspergillus fumigatus, Candida albicans, Candida auris, Cryptococcus neoformans, Nakaseomyces glabratus, Candida tropicalis, and Cryptococcus gattii. These fungal pathogens pose the risk of invasive fungal diseases and severe infections in low-immunity individuals and vulnerable populations. The findings indicate the importance of conducting further research to comprehensively understand potential exposure to feral pigeons. Furthermore, keeping pigeons away from sensitive areas, such as hospitals, and implementing measures to control pigeon populations can significantly decrease the spread of pathogens.