Ellström, P. | Search bioRxiv

bioRxiv2023

Urbanization spreads antimicrobial resistant enteric pathogens in wild bird microbiomes

Human behaviour is dramatically changing global ecology. Nowhere is this more apparent than in urbanization, where novel high human density habitats are disrupting long established ecotones. Resultant changes to the transitional areas between organisms, especially enhanced contact between humans and wild animals, provides new opportunities for the spread of zoonotic pathogens, posing a serious threat to global public health. Here, by studying the multi-host enteric pathogen Campylobacter jejuni isolated from the gut of 30 bird species in 8 countries, we investigated how proximity to urbanization influenced the spread of antimicrobial resistant (AMR) strains. Generalized linear models compared multiple behavioural and ecological traits and confirmed a positive correlation between proximity to urbanization and the number of C. jejuni genotypes and AMR genes in wild bird hosts. Wild birds from highly urban areas harboured up to four times more C. jejuni genotypes and six times more AMR genes. This is consistent with increased frequency of transition events. Quantifying zoonotic transmission and gene pool spread is essential for quantitative one health surveillance and control measures against future zoonosis emergences.

genomics↗

bioRxiv2021

A high-quality Genome and Comparison of Short versus Long Read Transcriptome of the Palaearctic duck Aythya fuligula (Tufted Duck)

BackgroundThe tufted duck is a non-model organism that suffers high mortality in highly pathogenic avian influenza out-breaks. It belongs to the same bird family (Anatidae) as the mallard, one of the best-studied natural hosts of low-pathogenic avian influenza viruses. Studies in non-model bird species are crucial to disentangle the role of the host response in avian influenza virus infection in the natural reservoir. Such endeavour requires a high-quality genome assembly and transcriptome. ResultsThis study presents the first high-quality, chromosome-level reference genome assembly of the tufted duck using the Vertebrate Genomes Project pipeline. We sequenced RNA (cDNA) from brain, ileum, lung, ovary, spleen and testis using Illumina short-read and PacBio long-read sequencing platforms, which was used for annotation. We found 34 autosomes plus Z and W sex chromosomes in the curated genome assembly, with 99.6% of the sequence assigned to chromosomes. Functional annotation revealed 14,099 protein-coding genes that generate 111,934 transcripts, which implies an average of 7.9 isoforms per gene. We also identified 246 small RNA families. ConclusionsThis annotated genome contributes to continuing research into the host response in avian influenza virus infections in a natural reservoir. Our findings from a comparison between short-read and long-read reference transcriptomics contribute to a deeper understanding of these competing options. In this study, both technologies complemented each other. We expect this annotation to be a foundation for further comparative and evolutionary genomic studies, including many waterfowl relatives with differing susceptibilities to the avian influenza virus.

genomics↗