{"corpus_id":146113289,"paper_sha":"13b15b20b39cc79a4915186954b90bd7440d398c","doi":"10.1098/rsif.2019.0260","arxiv_id":null,"pmid":31409239,"pmcid":"PMC6731517","mag_id":2939697982,"dblp_id":null,"acl_id":null,"title":"Mathematical modelling to study the horizontal transfer of antimicrobial resistance genes in bacteria: current state of the field and recommendations","year":2019,"publication_date":"2019-04-15","venue":"Journal of the Royal Society Interface","journal":{"name":"Journal of the Royal Society Interface","pages":null,"volume":"16"},"journal_issn":null,"journal_title":null,"publication_types":["JournalArticle","Review"],"pubmed_pub_types":["Journal Article","Research Support, Non-U.S. Gov't"],"s2_fields_of_study":["Biology","Mathematics","Medicine","Environmental Science"],"reference_count":82,"citation_count":54,"influential_citation_count":2,"is_open_access":true,"arxiv_categories":null,"arxiv_license":null,"arxiv_journal_ref":null,"mesh_headings":[{"d":"Anti-Bacterial Agents","mj":false,"qs":[{"q":"pharmacology","mj":true,"ui":"Q000494"}],"ui":"D000900"},{"d":"Bacteria","mj":false,"qs":[{"q":"drug effects","mj":true,"ui":"Q000187"},{"q":"genetics","mj":true,"ui":"Q000235"}],"ui":"D001419"},{"d":"Drug Resistance, Bacterial","mj":false,"qs":[{"q":"genetics","mj":true,"ui":"Q000235"}],"ui":"D024881"},{"d":"Gene Transfer, Horizontal","mj":true,"ui":"D022761"},{"d":"Models, Biological","mj":true,"ui":"D008954"}],"chemicals":[{"n":"Anti-Bacterial Agents","ui":"D000900","reg":"0"}],"comments_corrections":null,"source_flags":5,"s2_open_access_pdf_url":"https://royalsocietypublishing.org/doi/pdf/10.1098/rsif.2019.0260","s2_open_access_landing_url":"https://www.semanticscholar.org/paper/13b15b20b39cc79a4915186954b90bd7440d398c","s2_open_access_license":null,"s2_open_access_status":"BRONZE","pmc_open_access_pdf_url":null,"pmc_open_access_landing_url":null,"pmc_open_access_license":null,"pmc_open_access_status":null,"unpaywall_open_access_pdf_url":null,"unpaywall_open_access_landing_url":null,"unpaywall_open_access_license":null,"unpaywall_open_access_status":null,"abstract":"Antimicrobial resistance (AMR) is one of the greatest public health challenges we are currently facing. To develop effective interventions against this, it is essential to understand the processes behind the spread of AMR. These are partly dependent on the dynamics of horizontal transfer of resistance genes between bacteria, which can occur by conjugation (direct contact), transformation (uptake from the environment) or transduction (mediated by bacteriophages). Mathematical modelling is a powerful tool to investigate the dynamics of AMR; however, the extent of its use to study the horizontal transfer of AMR genes is currently unclear. In this systematic review, we searched for mathematical modelling studies that focused on horizontal transfer of AMR genes. We compared their aims and methods using a list of predetermined criteria and used our results to assess the current state of this research field. Of the 43 studies we identified, most focused on the transfer of single genes by conjugation in Escherichia coli in culture and its impact on the bacterial evolutionary dynamics. Our findings highlight the existence of an important research gap in the dynamics of transformation and transduction and the overall public health implications of horizontal transfer of AMR genes. To further develop this field and improve our ability to control AMR, it is essential that we clarify the structural complexity required to study the dynamics of horizontal gene transfer, which will require cooperation between microbiologists and modellers.","claims":[{"public_id":"cl_44cb35421d2b604ac84afb60bc1c6ef2","status":"active","text":"A significant research gap exists in modelling the dynamics of transformation and transduction and the overall public health implications of horizontal transfer of antimicrobial resistance genes.","confidence":0.9,"contributors":[{"id":171,"public_id":"b9tnx83g25","public_label":"eunsjani (b9tnx83g25)","roles":["extraction"],"url":"https://sah.borca.ai/u/b9tnx83g25"},{"id":2,"public_id":"4715169a40","public_label":"AK (4715169a40)","roles":["review"],"url":"https://sah.borca.ai/u/4715169a40"},{"id":17,"public_id":"322360f1c1","public_label":"Killer Whale (322360f1c1)","roles":["review"],"url":"https://sah.borca.ai/u/322360f1c1"}],"url":"https://sah.borca.ai/claims/cl_44cb35421d2b604ac84afb60bc1c6ef2"},{"public_id":"cl_bdcc68e0f995af7dfcf5caf4efe80666","status":"active","text":"Of the 43 mathematical modelling studies identified, most focused on the transfer of single genes by conjugation in Escherichia coli in culture and its impact on bacterial evolutionary dynamics.","confidence":0.95,"contributors":[{"id":171,"public_id":"b9tnx83g25","public_label":"eunsjani (b9tnx83g25)","roles":["extraction"],"url":"https://sah.borca.ai/u/b9tnx83g25"},{"id":2,"public_id":"4715169a40","public_label":"AK (4715169a40)","roles":["review"],"url":"https://sah.borca.ai/u/4715169a40"},{"id":17,"public_id":"322360f1c1","public_label":"Killer Whale (322360f1c1)","roles":["review"],"url":"https://sah.borca.ai/u/322360f1c1"}],"url":"https://sah.borca.ai/claims/cl_bdcc68e0f995af7dfcf5caf4efe80666"}],"concepts":[{"public_id":"co_1ec73cfbfe9e15dd2bcbcedda6a68bd6","status":"active","name":"horizontal transfer of antimicrobial resistance genes","description":"The lateral movement of resistance genes between bacterial cells via conjugation, transformation, or transduction.","types":["biological process"],"aliases":["horizontal gene transfer","HGT"],"contributors":[{"id":171,"public_id":"b9tnx83g25","public_label":"eunsjani (b9tnx83g25)","roles":["extraction"],"url":"https://sah.borca.ai/u/b9tnx83g25"},{"id":2,"public_id":"4715169a40","public_label":"AK (4715169a40)","roles":["review"],"url":"https://sah.borca.ai/u/4715169a40"},{"id":17,"public_id":"322360f1c1","public_label":"Killer Whale (322360f1c1)","roles":["review"],"url":"https://sah.borca.ai/u/322360f1c1"}],"url":"https://sah.borca.ai/concepts/co_1ec73cfbfe9e15dd2bcbcedda6a68bd6"},{"public_id":"co_71ecdfacbda1660177d776293ebba8a5","status":"active","name":"systematic review","description":"The structured literature search methodology used to identify and compare 43 mathematical modelling studies on horizontal AMR gene transfer.","types":["study design"],"aliases":[],"contributors":[{"id":171,"public_id":"b9tnx83g25","public_label":"eunsjani (b9tnx83g25)","roles":["extraction"],"url":"https://sah.borca.ai/u/b9tnx83g25"},{"id":2,"public_id":"4715169a40","public_label":"AK (4715169a40)","roles":["review"],"url":"https://sah.borca.ai/u/4715169a40"},{"id":17,"public_id":"322360f1c1","public_label":"Killer Whale (322360f1c1)","roles":["review"],"url":"https://sah.borca.ai/u/322360f1c1"}],"url":"https://sah.borca.ai/concepts/co_71ecdfacbda1660177d776293ebba8a5"},{"public_id":"co_743cb0115aacd7831caec511dab866ca","status":"active","name":"bacteriophages","description":"Viruses that infect bacteria and serve as vectors for transduction-mediated horizontal gene transfer.","types":["organism"],"aliases":["phages"],"contributors":[{"id":171,"public_id":"b9tnx83g25","public_label":"eunsjani (b9tnx83g25)","roles":["extraction"],"url":"https://sah.borca.ai/u/b9tnx83g25"},{"id":2,"public_id":"4715169a40","public_label":"AK (4715169a40)","roles":["review"],"url":"https://sah.borca.ai/u/4715169a40"},{"id":17,"public_id":"322360f1c1","public_label":"Killer Whale (322360f1c1)","roles":["review"],"url":"https://sah.borca.ai/u/322360f1c1"}],"url":"https://sah.borca.ai/concepts/co_743cb0115aacd7831caec511dab866ca"},{"public_id":"co_83642e0cd1c36b828d9de9b1f6454041","status":"active","name":"Escherichia coli","description":"The bacterial species most commonly studied in the mathematical modelling literature on horizontal AMR gene transfer.","types":["organism"],"aliases":["E. coli"],"contributors":[{"id":171,"public_id":"b9tnx83g25","public_label":"eunsjani (b9tnx83g25)","roles":["extraction"],"url":"https://sah.borca.ai/u/b9tnx83g25"},{"id":2,"public_id":"4715169a40","public_label":"AK (4715169a40)","roles":["review"],"url":"https://sah.borca.ai/u/4715169a40"},{"id":17,"public_id":"322360f1c1","public_label":"Killer Whale (322360f1c1)","roles":["review"],"url":"https://sah.borca.ai/u/322360f1c1"}],"url":"https://sah.borca.ai/concepts/co_83642e0cd1c36b828d9de9b1f6454041"},{"public_id":"co_960064517dd2f019ecbec3dbaebf1f08","status":"active","name":"mathematical modelling","description":"Mathematical frameworks used to simulate and analyze the dynamics of AMR gene spread in bacterial populations.","types":["method"],"aliases":[],"contributors":[{"id":171,"public_id":"b9tnx83g25","public_label":"eunsjani (b9tnx83g25)","roles":["extraction"],"url":"https://sah.borca.ai/u/b9tnx83g25"},{"id":2,"public_id":"4715169a40","public_label":"AK (4715169a40)","roles":["review"],"url":"https://sah.borca.ai/u/4715169a40"},{"id":17,"public_id":"322360f1c1","public_label":"Killer Whale (322360f1c1)","roles":["review"],"url":"https://sah.borca.ai/u/322360f1c1"}],"url":"https://sah.borca.ai/concepts/co_960064517dd2f019ecbec3dbaebf1f08"},{"public_id":"co_9fd8931874a48f0c9cefd03ac1111a41","status":"active","name":"antimicrobial resistance","description":"The ability of bacteria to resist antimicrobial drugs, identified here as a major public health challenge driving the need for mathematical modelling.","types":["phenomenon"],"aliases":["AMR"],"contributors":[{"id":171,"public_id":"b9tnx83g25","public_label":"eunsjani (b9tnx83g25)","roles":["extraction"],"url":"https://sah.borca.ai/u/b9tnx83g25"},{"id":2,"public_id":"4715169a40","public_label":"AK (4715169a40)","roles":["review"],"url":"https://sah.borca.ai/u/4715169a40"},{"id":17,"public_id":"322360f1c1","public_label":"Killer Whale (322360f1c1)","roles":["review"],"url":"https://sah.borca.ai/u/322360f1c1"}],"url":"https://sah.borca.ai/concepts/co_9fd8931874a48f0c9cefd03ac1111a41"},{"public_id":"co_ba9db2b310e7eb81a6d921ee9dbc4e56","status":"active","name":"transformation","description":"Uptake of free DNA from the environment by bacteria as a mode of horizontal gene transfer.","types":["mechanism"],"aliases":[],"contributors":[{"id":171,"public_id":"b9tnx83g25","public_label":"eunsjani (b9tnx83g25)","roles":["extraction"],"url":"https://sah.borca.ai/u/b9tnx83g25"},{"id":2,"public_id":"4715169a40","public_label":"AK (4715169a40)","roles":["review"],"url":"https://sah.borca.ai/u/4715169a40"},{"id":17,"public_id":"322360f1c1","public_label":"Killer Whale (322360f1c1)","roles":["review"],"url":"https://sah.borca.ai/u/322360f1c1"}],"url":"https://sah.borca.ai/concepts/co_ba9db2b310e7eb81a6d921ee9dbc4e56"},{"public_id":"co_bac19d022512089a68a7bef910455a53","status":"active","name":"conjugation","description":"Direct cell-to-cell contact mechanism by which bacteria transfer resistance genes, the most studied transfer mode in the reviewed literature.","types":["mechanism"],"aliases":[],"contributors":[{"id":171,"public_id":"b9tnx83g25","public_label":"eunsjani (b9tnx83g25)","roles":["extraction"],"url":"https://sah.borca.ai/u/b9tnx83g25"},{"id":2,"public_id":"4715169a40","public_label":"AK (4715169a40)","roles":["review"],"url":"https://sah.borca.ai/u/4715169a40"},{"id":17,"public_id":"322360f1c1","public_label":"Killer Whale (322360f1c1)","roles":["review"],"url":"https://sah.borca.ai/u/322360f1c1"}],"url":"https://sah.borca.ai/concepts/co_bac19d022512089a68a7bef910455a53"},{"public_id":"co_ef91adfb7b5aaccd85ddcad960b22404","status":"active","name":"transduction","description":"Bacteriophage-mediated horizontal transfer of resistance genes between bacteria.","types":["mechanism"],"aliases":[],"contributors":[{"id":171,"public_id":"b9tnx83g25","public_label":"eunsjani (b9tnx83g25)","roles":["extraction"],"url":"https://sah.borca.ai/u/b9tnx83g25"},{"id":2,"public_id":"4715169a40","public_label":"AK (4715169a40)","roles":["review"],"url":"https://sah.borca.ai/u/4715169a40"},{"id":17,"public_id":"322360f1c1","public_label":"Killer Whale (322360f1c1)","roles":["review"],"url":"https://sah.borca.ai/u/322360f1c1"}],"url":"https://sah.borca.ai/concepts/co_ef91adfb7b5aaccd85ddcad960b22404"},{"public_id":"co_fdde776508dbc48650cf5d613bccd25c","status":"active","name":"bacterial evolutionary dynamics","description":"The processes governing how bacterial populations change over time, particularly under selective pressure from resistance gene transfer.","types":["phenomenon"],"aliases":[],"contributors":[{"id":171,"public_id":"b9tnx83g25","public_label":"eunsjani (b9tnx83g25)","roles":["extraction"],"url":"https://sah.borca.ai/u/b9tnx83g25"},{"id":2,"public_id":"4715169a40","public_label":"AK (4715169a40)","roles":["review"],"url":"https://sah.borca.ai/u/4715169a40"},{"id":17,"public_id":"322360f1c1","public_label":"Killer Whale (322360f1c1)","roles":["review"],"url":"https://sah.borca.ai/u/322360f1c1"}],"url":"https://sah.borca.ai/concepts/co_fdde776508dbc48650cf5d613bccd25c"}],"external_ids":{"DOI":"10.1098/rsif.2019.0260","ArXiv":null,"PubMed":31409239,"PubMedCentral":"PMC6731517","MAG":2939697982,"DBLP":null,"ACL":null},"open_access":{"is_open_access":true,"pdf_url":"https://royalsocietypublishing.org/doi/pdf/10.1098/rsif.2019.0260","landing_url":"https://www.semanticscholar.org/paper/13b15b20b39cc79a4915186954b90bd7440d398c","source":"semantic_scholar","pdf_url_source":"semantic_scholar_open_access_pdf","license":null,"status":"BRONZE","reason":null},"reference_availability":{"status":"available","references_indexed":true,"full_text_available":false,"full_text_source":null,"count_basis":"semantic_scholar_metadata","extraction_status":"not_applicable","reason":null},"source":{"provider":"episteme2","base_corpus":"semantic_scholar_dump","freshness_mode":"unknown","basis":["semantic_scholar_metadata","postgres_metadata"],"limits":["paper metadata is based on indexed upstream scholarly datasets","claims and concepts are available only for extracted papers","absence of claims or concepts means no extracted graph data is available in this response"],"status":"available","degraded":false,"degraded_reasons":[],"diagnostics":{"status":"available","degraded":false,"degraded_reasons":[],"metadata_status":"available","graph_status":"available","abstract_status":"available"},"source_flags":5},"paper_id":630656,"paper_uid":"798f9c05-869c-4e9f-9252-90a03ace81ae","canonical_identity":{"paper_id":630656,"paper_uid":"798f9c05-869c-4e9f-9252-90a03ace81ae","identity_status":"available","lookup_basis":"semantic_scholar_external_id","compatibility_path":"corpus_id"},"url":"https://sah.borca.ai/papers/146113289"}