{"id":177227,"date":"2025-11-12T20:49:16","date_gmt":"2025-11-12T20:49:16","guid":{"rendered":"https:\/\/www.europesays.com\/ie\/177227\/"},"modified":"2025-11-12T20:49:16","modified_gmt":"2025-11-12T20:49:16","slug":"circulation-of-salmonella-spp-between-humans-animals-and-the-environment-in-animal-owning-households-in-malawi","status":"publish","type":"post","link":"https:\/\/www.europesays.com\/ie\/177227\/","title":{"rendered":"Circulation of Salmonella spp. between humans, animals and the environment in animal-owning households in Malawi"},"content":{"rendered":"
  • \n

    Blancou, J., Chomel, B. B., Belotto, A. & Meslin, F. X. Emerging or re-emerging bacterial zoonoses: factors of emergence, surveillance and control. Vet. Res. 36<\/b>, 507\u2013522 (2005).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Jones, K. E. et al. Global trends in emerging infectious diseases. Nature 451<\/b>, 990\u2013993 (2008).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Shaheen, M. N. F. The concept of one health applied to the problem of zoonotic diseases. Rev. Med. Virol. 32<\/b>, e2326 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Nandi, A. & Allen, L. J. S. Probability of a zoonotic spillover with seasonal variation. Infect. Dis. Model. 6<\/b>, 514\u2013531 (2021).<\/p>\n

    PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    One Health High-Level Expert Panel (OHHLEP) One health: a new definition for a sustainable and healthy future. PLOS Pathog. 18<\/b>, e1010537 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Nava, A., Shimabukuro, J. S., Chmura, A. A. & Luz, S. L. B. The impact of global environmental changes on infectious disease emergence with a focus on risks for Brazil. ILAR J. 58<\/b>, 393\u2013400 (2017).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    LaDeau, S. L., Calder, C. A., Doran, P. J. & Marra, P. P. West Nile virus impacts in American crow populations are associated with human land use and climate. Ecol. Res. 26<\/b>, 909 (2011).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Kruger, S. E., Lorah, P. A. & Okamoto, K. W. Mapping climate change\u2019s impact on cholera infection risk in Bangladesh. PLOS Glob. Public Health 2<\/b>, e0000711 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Hassell, J. M., Begon, M., Ward, M. J. & F\u00e8vre, E. M. Urbanization and disease emergence: dynamics at the wildlife\u2013livestock\u2013human interface. Trends Ecol. Evol. 32<\/b>, 55\u201367 (2017).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Carlson, C. J. et al. Climate change increases cross-species viral transmission risk. Nature 607<\/b>, 555\u2013562 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Mora, C. et al. Over half of known human pathogenic diseases can be aggravated by climate change. Nat. Clim. Change 12<\/b>, 869\u2013875 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Murray, C. J. et al. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. Lancet 399<\/b>, 629\u2013655 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Kariuki, S., Kering, K., Wairimu, C., Onsare, R. & Mbae, C. Antimicrobial resistance rates and surveillance in sub-Saharan Africa: where are we now?. Infect. Drug Resist. 15<\/b>, 3589\u20133609 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Fatica, M. K. & Schneider, K. R. Salmonella and produce: survival in the plant environment and implications in food safety. Virulence 2<\/b>, 573\u2013579 (2011).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Liu, H., Whitehouse, C. A. & Li, B. Presence and persistence of Salmonella in water: the impact on microbial quality of water and food safety. Front. Public Health 6<\/b>, 159 (2018).<\/p>\n<\/li>\n

  • \n

    Majowicz, S. E. et al. The global burden of nontyphoidal Salmonella gastroenteritis. Clin. Infect. Dis. Publ. Infect. Dis. Soc. Am. 50<\/b>, 882\u2013889 (2010).<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Hald, T. et al. World Health Organization estimates of the relative contributions of food to the burden of disease due to selected foodborne hazards: a structured expert elicitation. PLoS ONE 11<\/b>, e0145839 (2016).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Reddy, E. A., Shaw, A. V. & Crump, J. A. Community-acquired bloodstream infections in Africa: a systematic review and meta-analysis. Lancet Infect. Dis. 10<\/b>, 417\u2013432 (2010).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Feasey, N. A. et al. Three epidemics of invasive multidrug-resistant salmonella bloodstream infection in Blantyre, Malawi, 1998\u20132014. Clin. Infect. Dis. Publ. Infect. Dis. Soc. Am. 61<\/b>, S363\u2013S371 (2015).<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Uche, I. V., MacLennan, C. A. & Saul, A. A systematic review of the incidence, risk factors and case fatality rates of invasive nontyphoidal Salmonella (iNTS) disease in Africa (1966 to 2014). PLoS Negl. Trop. Dis. 11<\/b>, e0005118 (2017).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Marchello, C. S., Dale, A. P., Pisharody, S., Rubach, M. P. & Crump, J. A. A systematic review and meta-analysis of the prevalence of community-onset bloodstream infections among hospitalized patients in Africa and Asia. Antimicrob. Agents Chemother. 64<\/b>, https:\/\/doi.org\/10.1128\/aac.01974-19<\/a> (2019).<\/p>\n<\/li>\n

  • \n

    Balasubramanian, R. et al. The global burden and epidemiology of invasive non-typhoidal Salmonella infections. Hum. Vaccines Immunother. 15<\/b>, 1421\u20131426 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Park, S. E. et al. The genomic epidemiology of multi-drug resistant invasive non-typhoidal Salmonella in selected sub-Saharan African countries. BMJ Glob. Health 6<\/b>, e005659 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Akullian, A. et al. Multi-drug resistant non-typhoidal Salmonella associated with invasive disease in western Kenya. PLoS Negl. Trop. Dis. 12<\/b>, e0006156 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Feasey, N. A. et al. Distinct Salmonella Enteritidis lineages associated with enterocolitis in high-income settings and invasive disease in low-income settings. Nat. Genet. 48<\/b>, 1211\u20131217 (2016).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Kingsley, R. A. et al. Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype. Genome Res. 19<\/b>, 2279\u20132287 (2009).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Pulford, C. V. et al. Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa. Nat. Microbiol. 6<\/b>, 327\u2013338 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Van Puyvelde, S. et al. An African Salmonella Typhimurium ST313 sublineage with extensive drug-resistance and signatures of host adaptation. Nat. Commun. 10<\/b>, 4280 (2019).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    LEI International Policy et al. Dynamics of Food Systems in Sub-Saharan Africa: Implications for Consumption Patterns and Farmers\u2019 Position in Food Supply Chains. https:\/\/research.wur.nl\/en\/publications\/973b48c2-2933-4e13-825e-3815fe9be428<\/a>; https:\/\/doi.org\/10.18174\/417176<\/a> (2017).<\/p>\n<\/li>\n

  • \n

    Nyokabi, S. et al. Informal value chain actors\u2019 knowledge and perceptions about zoonotic diseases and biosecurity in Kenya and the importance for food safety and public health. Trop. Anim. Health Prod. 50<\/b>, 509\u2013518 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Cocker, D. et al. Investigating One Health risks for human colonisation with extended spectrum \u03b2-lactamase-producing Escherichia coli and Klebsiella pneumoniae in Malawian households: a longitudinal cohort study. Lancet Microbe S2666524723000629 https:\/\/doi.org\/10.1016\/S2666-5247(23)00062-9<\/a> (2023).<\/p>\n<\/li>\n

  • \n

    Hassell, J. M. et al. Clinically relevant antimicrobial resistance at the wildlife\u2013livestock\u2013human interface in Nairobi: an epidemiological study. Lancet Planet. Health 3<\/b>, e259\u2013e269 (2019).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Pathogenwatch | A Global Platform for Genomic Surveillance. https:\/\/pathogen.watch\/<\/a>.<\/p>\n<\/li>\n

  • \n

    Kariuki, S., Gordon, M. A., Feasey, N. & Parry, C. M. Antimicrobial resistance and management of invasive Salmonella disease. Vaccine 33<\/b>, C21\u2013C29 (2015).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Parisi, A. et al. The role of animals as a source of antimicrobial resistant nontyphoidal Salmonella causing invasive and non-invasive human disease in Vietnam. Infect. Genet. Evol. 85<\/b>, 104534 (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Musicha, P. et al. Trends in antimicrobial resistance in bloodstream infection isolates at a large urban hospital in Malawi (1998\u20132016): a surveillance study. Lancet Infect. Dis. 17<\/b>, 1042\u20131052 (2017).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Robertson, J. & Nash, J. H. E. MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies. Microb. Genomics 4<\/b>, e000206 (2018).<\/p>\n<\/li>\n

  • \n

    Seemann, T. ABRicate. Github https:\/\/github.com\/tseemann\/abricate<\/a>. (2021).<\/p>\n<\/li>\n

  • \n

    Tonkin-Hill, G. et al. Producing polished prokaryotic pangenomes with the Panaroo pipeline. Genome Biol. 21<\/b>, 180 (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Thorpe, H. A. et al. A large-scale genomic snapshot of Klebsiella spp. isolates in Northern Italy reveals limited transmission between clinical and non-clinical settings. Nat. Microbiol. 7<\/b>, 2054\u20132067 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Day, M. J. et al. Extended-spectrum \u03b2-lactamase-producing Escherichia coli in human-derived and foodchain-derived samples from England, Wales, and Scotland: an epidemiological surveillance and typing study. Lancet Infect. Dis. 19<\/b>, 1325\u20131335 (2019).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Ludden, C. et al. One health genomic surveillance of Escherichia coli demonstrates distinct lineages and mobile genetic elements in isolates from humans versus livestock. mBio 10<\/b>, https:\/\/doi.org\/10.1128\/mbio.02693-18<\/a> (2019).<\/p>\n<\/li>\n

  • \n

    Gouliouris, T. et al. Genomic surveillance of enterococcus faecium reveals limited sharing of strains and resistance genes between livestock and humans in the United Kingdom. mBio 9<\/b>, e01780-18 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Muloi, D. M. et al. Population genomics of Escherichia coli in livestock-keeping households across a rapidly developing urban landscape. Nat. Microbiol. 7<\/b>, 581\u2013589 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Fukushima, K., Yanagisawa, N., Sekiya, N. & Izumiya, H. Bacteremia caused by Salmonella Poona in a healthy adult in Tokyo, Japan. Intern. Med. 59<\/b>, 289\u2013292 (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Lang, B. Y., Varman, M., Reindel, R. & Hasley, B. P. Salmonella Gaminara osteomyelitis and septic arthritis in an infant with exposure to bearded dragon. Infect. Dis. Clin. Pract. 15<\/b>, 348\u2013350 (2007).<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Makendi, C. et al. A phylogenetic and phenotypic analysis of Salmonella enterica serovar Weltevreden, an emerging agent of diarrheal disease in tropical regions. PLoS Negl. Trop. Dis. 10<\/b>, e0004446 (2016).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Beyene, G. et al. Multidrug resistant Salmonella Concord is a major cause of salmonellosis in children in Ethiopia. J. Infect. Dev. Ctries. 5<\/b>, 023\u2013033 (2011).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Nutrition, C. for F. S. & A. Outbreak Investigation of Salmonella Oranienburg: Whole, Fresh Onions (October 2021). FDA (2022).<\/p>\n<\/li>\n

  • \n

    Mankhomwa, J. et al. A qualitative study of antibiotic use practices in intensive small-scale farming in urban and peri-urban Blantyre, Malawi: implications for antimicrobial resistance. Front. Vet. Sci. 9<\/b>, 876513 (2022).<\/p>\n<\/li>\n

  • \n

    Post, A. S. et al. Supporting evidence for a human reservoir of invasive non-Typhoidal Salmonella from household samples in Burkina Faso. PLoS Negl. Trop. Dis. 13<\/b>, e0007782 (2019).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Koolman, L. et al. Case-control investigation of invasive Salmonella disease in Malawi reveals no evidence of environmental or animal transmission of invasive strains, and supports human to human transmission. PLoS Negl. Trop. Dis. 16<\/b>, e0010982 (2022).<\/p>\n<\/li>\n

  • \n

    Crump, J. A. et al. Investigating the meat pathway as a source of human nontyphoidal Salmonella bloodstream infections and diarrhea in East Africa. Clin. Infect. Dis. 73<\/b>, e1570\u2013e1578 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Hassell, J. M. et al. Epidemiological connectivity between humans and animals across an urban landscape. Proc. Natl Acad. Sci. USA 120<\/b>, e2218860120 (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Octavia, S., Wang, Q., Tanaka, M. M., Sintchenko, V. & Lan, R. Genomic variability of serial human isolates of Salmonella enterica serovar Typhimurium associated with prolonged carriage. J. Clin. Microbiol. 53<\/b>, 3507\u20133514 (2015).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Chidziwisano, K., Slekiene, J., Kumwenda, S., Mosler, H.-J. & Morse, T. Toward complementary food hygiene practices among child caregivers in rural Malawi. Am. J. Trop. Med. Hyg. 101<\/b>, 294\u2013303 (2019).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Musoke, D. et al. The role of Environmental Health in preventing antimicrobial resistance in low- and middle-income countries. Environ. Health Prev. Med. 26<\/b>, 100 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Now 8 billion and counting: Where the world\u2019s population has grown most and why that matters |. UNCTAD https:\/\/unctad.org\/data-visualization\/now-8-billion-and-counting-where-worlds-population-has-grown-most-and-why<\/a> (2022).<\/p>\n<\/li>\n

  • \n

    FAO\u2014News Article: Small family farmers produce a third of the world\u2019s food. https:\/\/www.fao.org\/news\/story\/en\/item\/1395127\/icode\/<\/a>.<\/p>\n<\/li>\n

  • \n

    Paediatrics, R. C., Committee, C. H. & HULL, P. S. Guidelines for the ethical conduct of medical research involving children. Arch. Dis. Child. 82<\/b>, 177\u2013182 (2000).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Welcome to the QGIS project! https:\/\/www.qgis.org\/en\/site\/<\/a>.<\/p>\n<\/li>\n

  • \n

    Chipeta, M., Terlouw, D., Phiri, K. & Diggle, P. Inhibitory geostatistical designs for spatial prediction taking account of uncertain covariance structure. Environmetrics 28<\/b>, e2425 (2017).<\/p>\n

    Article<\/a>\u00a0
    \n     MathSciNet<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Hartung, C. et al. Open data kit: tools to build information services for developing regions. in Proceedings of the 4th ACM\/IEEE International Conference on Information and Communication Technologies and Development 1\u201312. https:\/\/doi.org\/10.1145\/2369220.2369236<\/a> (Association for Computing Machinery, 2010).<\/p>\n<\/li>\n

  • \n

    De Medici, D. et al. Evaluation of DNA extraction methods for use in combination with SYBR Green I real-time PCR To detect Salmonella enterica serotype enteritidis in poultry. Appl. Environ. Microbiol. 69<\/b>, 3456\u20133461 (2003).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Hensel, M., Hinsley, A. P., Nikolaus, T., Sawers, G. & Berks, B. C. The genetic basis of tetrathionate respiration in Salmonella typhimurium. Mol. Microbiol. 32<\/b>, 275\u2013287 (1999).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Custom DNA Oligos. https:\/\/www.sigmaaldrich.com\/GB\/en\/custom-pdp\/061ac088-00b9-47c0-8a48-faab9ca7f281<\/a>.<\/p>\n<\/li>\n

  • \n

    Babraham Bioinformatics\u2014FastQC A Quality Control tool for High Throughput Sequence Data. https:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/<\/a>.<\/p>\n<\/li>\n

  • \n

    Kraken: ultrafast metagenomic sequence classification using exact alignments | Genome Biology | Full Text. https:\/\/genomebiology.biomedcentral.com\/articles\/10.1186\/gb-2014-15-3-r46<\/a>.<\/p>\n<\/li>\n

  • \n

    Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P. & Tyson, G. W. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25<\/b>, 1043\u20131055 (2015).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    assembly-stats. Pathogen Informatics, Wellcome Sanger Institute. Github https:\/\/github.com\/sanger-pathogens\/assembly-stats<\/a>. (2022).<\/p>\n<\/li>\n

  • \n

    Gurevich, A., Saveliev, V., Vyahhi, N. & Tesler, G. QUAST: quality assessment tool for genome assemblies. Bioinforma. Oxf. Engl. 29<\/b>, 1072\u20131075 (2013).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Yoshida, C. E. et al. The Salmonella In Silico Typing Resource (SISTR): an open web-accessible tool for rapidly typing and subtyping draft Salmonella genome assemblies. PLoS ONE. 11<\/b>, e0147101 (2016).<\/p>\n<\/li>\n

  • \n

    Bankevich, A. et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19<\/b>, 455\u2013477 (2012).<\/p>\n

    Article<\/a>\u00a0
    \n     MathSciNet<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Seemann, T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30<\/b>, 2068\u20132069 (2014).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Page, A. J. et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 31<\/b>, 3691\u20133693 (2015).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments | Microbiology Society. https:\/\/www.microbiologyresearch.org\/content\/journal\/mgen\/10.1099\/mgen.0.000056<\/a>.<\/p>\n<\/li>\n

  • \n

    Minh, B. Q. et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 37<\/b>, 1530\u20131534 (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Hadfield, J. et al. Phandango: an interactive viewer for bacterial population genomics. Bioinformatics 34<\/b>, 292\u2013293 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Letunic, I. & Bork, P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res 49<\/b>, W293\u2013W296 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Yu, G. Using ggtree to visualize data on tree-like structures. Curr. Protoc. Bioinforma. 69<\/b>, e96 (2020).<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    AMRFinderPlus\u2014Pathogen Detection\u2014NCBI. https:\/\/www.ncbi.nlm.nih.gov\/pathogens\/antimicrobial-resistance\/AMRFinder\/<\/a>.<\/p>\n<\/li>\n

  • \n

    Feldgarden, M. et al. AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence. Sci. Rep. 11<\/b>, 12728 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Harris, S. Pairwise Difference Count. https:\/\/github.com\/simonrharris\/pairwise_difference_count<\/a>. (2020).<\/p>\n<\/li>\n

  • \n

    Seemann, T. snp-dists. https:\/\/github.com\/tseemann\/snp-dists<\/a> (2021).<\/p>\n<\/li>\n

  • \n

    igraph\u2014Network analysis software. https:\/\/igraph.org\/<\/a>.<\/p>\n<\/li>\n

  • \n

    Yu, D., Zhao, Y., Yin, C., Liang, F. & Chen, W. A network analysis of the association between intergroup contact and intergroup relations. Psychol. Res. Behav. Manag. 15<\/b>, 51\u201369 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    R Core Team. R: a language and environment for statistical computing. https:\/\/www.r-project.org\/<\/a> (2021).<\/p>\n<\/li>\n

  • \n

    Wilson, C. Circulation of Salmonella spp. between humans, animals and the environment in animal-owning households in Malawi. (2025).<\/p>\n<\/li>\n

  • \n

    NIAID Visual & Medical Arts. (10\/7\/2024). Lizard Outline. NIAID NIH BIOART Source. Bioart.Niaid.Nih.Gov\/Bioart\/302.<\/p>\n<\/li>\n

  • \n

    NIAID Visual & Medical Arts. (3\/27\/2025). Sunflower. NIAID NIH BIOART Source. Bioart.Niaid.Nih.Gov\/Bioart\/620.<\/p>\n<\/li>\n

  • \n

    NIAID Visual & Medical Arts. (4\/24\/2025). Goat. NIAID NIH BIOART Source. Bioart.Niaid.Nih.Gov\/Bioart\/636.<\/p>\n<\/li>\n

  • \n

    NIAID Visual & Medical Arts. (10\/7\/2024). Duck Silhouette. NIAID NIH BIOART Source. Bioart.Niaid.Nih.Gov\/Bioart\/135.<\/p>\n<\/li>\n

  • \n

    NIAID Visual & Medical Arts. (10\/7\/2024). Domestic Chicken. NIAID NIH BIOART Source. Bioart.Niaid.Nih.Gov\/Bioart\/131.<\/p>\n<\/li>\n

  • \n

    NIAID Visual & Medical Arts. (3\/12\/2025). Domestic Dog. NIAID NIH BIOART Source. Bioart.Niaid.Nih.Gov\/Bioart\/594.<\/p>\n<\/li>\n

  • \n

    NIAID Visual & Medical Arts. (10\/7\/2024). Lab Mouse. NIAID NIH BIOART Source. Bioart.Niaid.Nih.Gov\/Bioart\/279.<\/p>\n<\/li>\n

  • \n

    NIAID Visual & Medical Arts. (10\/7\/2024). Unisex Icon. NIAID NIH BIOART Source. Bioart.Niaid.Nih.Gov\/Bioart\/13.<\/p>\n<\/li>\n","protected":false},"excerpt":{"rendered":"Blancou, J., Chomel, B. B., Belotto, A. & Meslin, F. X. Emerging or re-emerging bacterial zoonoses: factors of…\n","protected":false},"author":2,"featured_media":177228,"comment_status":"","ping_status":"","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[269],"tags":[100527,100528,18,440,1099,19,17,1100,133],"class_list":{"0":"post-177227","1":"post","2":"type-post","3":"status-publish","4":"format-standard","5":"has-post-thumbnail","7":"category-environment","8":"tag-bacterial-genetics","9":"tag-bacterial-genomics","10":"tag-eire","11":"tag-environment","12":"tag-humanities-and-social-sciences","13":"tag-ie","14":"tag-ireland","15":"tag-multidisciplinary","16":"tag-science"},"share_on_mastodon":{"url":"https:\/\/pubeurope.com\/@ie\/115538704661342702","error":""},"_links":{"self":[{"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/posts\/177227","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/comments?post=177227"}],"version-history":[{"count":0,"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/posts\/177227\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/media\/177228"}],"wp:attachment":[{"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/media?parent=177227"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/categories?post=177227"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/tags?post=177227"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}