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Staphylococcus aureus lineages associated with a free-ranging population of the fruit bat Pteropus livingstonii retained over 25 years in captivity

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  • Fischer, C. P. & Romero, L. M. Chronic captivity stress in wild animals is highly species-specific. Conserv. Physiol. 7, coz093 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • McGill, I. et al. Isosporoid coccidiosis in translocated cirl buntings (Emberiza cirlus). Vet. Rec. 167, 656–660 (2010).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Mohajeri, M. H. et al. The role of the microbiome for human health: from basic science to clinical applications. Eur. J. Nutr. 57, 1–14 (2018).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Song, S. J. et al. Engineering the microbiome for animal health and conservation. Exp. Biol. Med. 244, 494–504 (2019).

    Article 
    CAS 

    Google Scholar 

  • Peters, A., Meredith, A., Skerratt, L., Carver, S. & Raidal, S. Infectious disease and emergency conservation interventions. Conserv. Biol. 34, 784–785 (2020).

    PubMed 
    Article 

    Google Scholar 

  • Northover, A. S. et al. Altered parasite community structure in an endangered marsupial following translocation. Int. J. Parasitol. Parasites Wildl. 10, 13–22 (2019).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Daniel, B. M. et al. A bat on the brink? A range-wide survey of the Critically Endangered Livingstone’s fruit bat Pteropus livingstonii. Oryx 51, 742–751 (2017).

    Article 

    Google Scholar 

  • IUCN. Pteropus livingstonii: Sewall, B.J., Young, R., Trewhella, W.J. & Rodríguez-Clark, K.M. and Granek, E.F. IUCN Red List of Threatened Species (2016) https://doi.org/10.2305/iucn.uk.2016-2.rlts.t18732a22081502.en.

  • IUCN Species Survival Commission. Species action plan for Livingstone’s fruit bat ‘Pteropus livingstonii’. https://portals.iucn.org/library/node/7368 (1995).

  • Haag, A. F., Ross Fitzgerald, J. & Penadés, J. R. Staphylococcus aureus in animals. Gram-Positive Pathog. https://doi.org/10.1128/9781683670131.ch46 (2019).

    Article 

    Google Scholar 

  • Pirolo, M. et al. Unidirectional animal-to-human transmission of methicillin-resistant Staphylococcus aureus ST398 in pig farming; evidence from a surveillance study in southern Italy. Antimicrob. Resist. Infect. Control 8, 1–10 (2019).

    Article 

    Google Scholar 

  • Young, B. C. et al. Severe infections emerge from commensal bacteria by adaptive evolution. Elife 6, e30637 (2017).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Heaton, C. J., Gerbig, G. R., Sensius, L. D., Patel, V. & Smith, T. C. Staphylococcus aureus epidemiology in wildlife: A systematic review. Antibiotics 9, 89 (2020).

    PubMed Central 
    Article 

    Google Scholar 

  • Sheppard, S. K., Guttman, D. S. & Fitzgerald, J. R. Population genomics of bacterial host adaptation. Nat. Rev. Genet. 19, 549–565 (2018).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Richardson, E. J. et al. Gene exchange drives the ecological success of a multi-host bacterial pathogen. Nat. Ecol. Evol. 2, 1468–1478 (2018).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Bacigalupe, R., Tormo-Mas, M. Á., Penadés, J. R. & Ross Fitzgerald, J. A multihost bacterial pathogen overcomes continuous population bottlenecks to adapt to new host species. Sci. Adv. 5, eaax0063 (2019).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Spoor, L. E. et al. Recombination-mediated remodelling of host–pathogen interactions during Staphylococcus aureus niche adaptation. Microb. Genomics 1(4), e000036. https://doi.org/10.1099/mgen.0.000036 (2015).

    Article 

    Google Scholar 

  • Tong, S. Y. C., Davis, J. S., Eichenberger, E., Holland, T. L. & Fowler, V. G. Jr. Staphylococcus aureus infections: Epidemiology, pathophysiology, clinical manifestations, and management. Clin. Microbiol. Rev. 28, 603–661 (2015).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Fountain, K. et al. Diversity of staphylococcal species cultured from captive Livingstone’s fruit bats (Pteropus livingstonii) and their environment. J. Zoo Wildl. Med. 50, 266–269 (2019).

    PubMed 
    Article 

    Google Scholar 

  • Fountain, K. et al. Fatal exudative dermatitis in island populations of red squirrels (Sciurus vulgaris): spillover of a virulent clone (ST49) from reservoir hosts. Microb. Genom. 7(5), 000565. https://doi.org/10.1099/mgen.0.000565 (2021).

    CAS 
    Article 
    PubMed Central 

    Google Scholar 

  • Rohmer, C. & Wolz, C. The role of hlb-converting bacteriophages in Staphylococcus aureus host adaption. Microb. Physiol. 31 109–122. https://doi.org/10.1159/000516645 (2021).

    PubMed 
    Article 

    Google Scholar 

  • Senghore, M. et al. Transmission of Staphylococcus aureus from humans to green monkeys in The Gambia as revealed by whole-genome sequencing. Appl. Environ. Microbiol. 82, 5910–5917 (2016).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Xue, H., Lu, H. & Zhao, X. Sequence diversities of serine-aspartate repeat genes among Staphylococcus aureus isolates from different hosts presumably by horizontal gene transfer. PLoS ONE 6, e20332 (2011).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Paharik, A. E. et al. The Spl serine proteases modulate protein production and virulence in a rabbit model of pneumonia. mSphere 1, e00208-16 (2016).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Wein, T., Hülter, N. F., Mizrahi, I. & Dagan, T. Emergence of plasmid stability under non-selective conditions maintains antibiotic resistance. Nat. Commun. 10, 2595 (2019).

    ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Cheng, A. G., Missiakas, D. & Schneewind, O. The giant protein Ebh is a determinant of Staphylococcus aureus cell size and complement resistance. J. Bacteriol. 196, 971–981 (2014).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Lin, Y.-C. et al. Staphylococcal phosphatidylinositol-specific phospholipase C potentiates lung injury via complement sensitisation. Cell. Microbiol. 21, e13085 (2019).

    PubMed 

    Google Scholar 

  • Siboo, I. R., Chambers, H. F. & Sullam, P. M. Role of SraP, a serine-rich surface protein of Staphylococcus aureus, in binding to human platelets. Infect. Immun. 73, 2273–2280 (2005).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Nakamura, Y. et al. Phosphatidylinositol-specific phospholipase C enhances epidermal penetration by Staphylococcus aureus. Sci. Rep. 10, 17845 (2020).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Peng, X. et al. Flight is the key to postprandial blood glucose balance in the fruit bats Eonycteris spelaea and Cynopterus sphinx. Ecol. Evol. 7, 8804–8811 (2017).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Partridge, S. R., Kwong, S. M., Firth, N. & Jensen, S. O. Mobile genetic elements associated with antimicrobial resistance. Clin. Microbiol. Rev. 31, e00088-17 (2018).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Pence, M. A. et al. Beta-lactamase repressor BlaI modulates Staphylococcus aureus cathelicidin antimicrobial peptide resistance and virulence. PLoS ONE 10, e0136605 (2015).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Raafat, D. et al. Molecular epidemiology of methicillin-susceptible and methicillin-resistant Staphylococcus aureus in wild, captive and laboratory rats: Effect of habitat on the nasal S. aureus population. Toxins 12, 80 (2020).

    CAS 
    PubMed Central 
    Article 

    Google Scholar 

  • National Library of Medicine (US), National Center for Biotechnology Information. Genbank. (1982).

  • PubMLST—Public databases for molecular typing and microbial genome diversity. https://pubmlst.org/.

  • Wick, R. R., Judd, L. M. & Holt, K. E. Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks. PLoS Comput. Biol. 14, e1006583 (2018).

    ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Wick, R. R., Judd, L. M., Gorrie, C. L. & Holt, K. E. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput. Biol. 13, e1005595 (2017).

    ADS 
    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Andrews, S. FastQC: A Quality Control Tool for High Throughput Sequence Data (2010).

  • Bankevich, A. et al. SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455–477 (2012).

    MathSciNet 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Seemann, T. Prokka: Rapid prokaryotic genome annotation. Bioinformatics 30, 2068–2069 (2014).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Seeman, T. MLST. Github https://github.com/tseemann/mlst.

  • Page, A. J. et al. Roary: Rapid large-scale prokaryote pan genome analysis. Bioinformatics 31, 3691–3693 (2015).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Kozlov, A. M., Darriba, D., Flouri, T., Morel, B. & Stamatakis, A. RAxML-NG: A fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics 35, 4453–4455 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Seeman, T. Snippy: Fast Bacterial Variant Calling from NGS Reads (2015).

  • Carver, T., Harris, S. R., Berriman, M., Parkhill, J. & McQuillan, J. A. Artemis: An integrated platform for visualization and analysis of high-throughput sequence-based experimental data. Bioinformatics 28, 464–469 (2012).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Sievers, F. & Higgins, D. G. Clustal Omega for making accurate alignments of many protein sequences. Protein Sci. 27, 135–145 (2018).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Waterhouse, A. M., Procter, J. B., Martin, D. M. A., Clamp, M. & Barton, G. J. Jalview Version 2—A multiple sequence alignment editor and analysis workbench. Bioinformatics 25, 1189–1191 (2009).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Seeman, T. Abricate; Mass screening of contigs for antimicrobial resistance or virulence genes. Github https://github.com/tseemann/abricate.

  • Feldgarden, M. et al. Validating the AMRFinder tool and resistance gene database by using antimicrobial resistance genotype-phenotype correlations in a collection of isolates. Antimicrob. Agents Chemother. 63, e00483-19 (2019).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Zankari, E. et al. Identification of acquired antimicrobial resistance genes. J. Antimicrob. Chemother. 67, 2640–2644 (2012).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Chen, L., Zheng, D., Liu, B., Yang, J. & Jin, Q. VFDB 2016: Hierarchical and refined dataset for big data analysis–10 years on. Nucleic Acids Res. 44, D694–D697 (2016).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Carattoli, A. et al. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob. Agents Chemother. 58, 3895–3903 (2014).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Gupta, S. K. et al. ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes. Antimicrob. Agents Chemother. 58, 212–220 (2014).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Arndt, D., Marcu, A., Liang, Y. & Wishart, D. S. PHAST, PHASTER and PHASTEST: Tools for finding prophage in bacterial genomes. Brief. Bioinform. 20, 1560–1567 (2019).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Antipov, D. et al. plasmidSPAdes: Assembling plasmids from whole genome sequencing data. Bioinformatics https://doi.org/10.1093/bioinformatics/btw493 (2016).

    Article 
    PubMed 

    Google Scholar 

  • Robertson, J. & Nash, J. H. E. MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies. Microb. Genom. 4(8), e000206. https://doi.org/10.1099/mgen.0.000206 (2018).

    CAS 
    Article 

    Google Scholar 

  • Jaillard, M. et al. A fast and agnostic method for bacterial genome-wide association studies: Bridging the gap between k-mers and genetic events. PLoS Genet. 14, e1007758 (2018).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 


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