{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T03:14:55Z","timestamp":1789960495506,"version":"4.0.1"},"reference-count":47,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,5,30]],"date-time":"2025-05-30T00:00:00Z","timestamp":1748563200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2025,5,30]],"date-time":"2025-05-30T00:00:00Z","timestamp":1748563200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BB\/X011011\/1"],"award-info":[{"award-number":["BB\/X011011\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BB\/X011011\/1"],"award-info":[{"award-number":["BB\/X011011\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BB\/X011011\/1"],"award-info":[{"award-number":["BB\/X011011\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BB\/X011011\/1"],"award-info":[{"award-number":["BB\/X011011\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BB\/X011011\/1"],"award-info":[{"award-number":["BB\/X011011\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["npj Antimicrob Resist"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    Piperacillin-Tazobactam is a \u03b2-lactam\/\u03b2-lactamase inhibitor combination that is amongst the most prescribed antimicrobials in hospital medicine. Piperacillin is inactivated by many common beta-lactamases, but tazobactam inhibits these, allowing successful treatment. The effect of piperacillin on Gram-negative bacteria has been widely studied, but less attention has been paid to the effects of tazobactam. We used a massive transposon mutagenesis approach (TraDIS-\n                    <jats:italic>Xpress<\/jats:italic>\n                    ) to identify genes in\n                    <jats:italic>Escherichia coli<\/jats:italic>\n                    that affect survival when exposed to piperacillin and tazobactam, separately and together. We found significant differences between the two drugs: a striking finding was that multiple efflux pump families and regulators were essential for survival in the presence of tazobactam, but only one efflux system was beneficial for piperacillin. Exposure of\n                    <jats:italic>Escherichia coli<\/jats:italic>\n                    and\n                    <jats:italic>Klebsiella pneumoniae<\/jats:italic>\n                    to piperacillin and\/or tazobactam selected for mutants with reduced susceptibility, and tazobactam selected for efflux and cell envelope mutants associated with multidrug resistance. We identified other pathways involved in tazobactam susceptibility, including the shikimate kinase AroK. Genes involved in DNA replication and repair reduced\n                    <jats:italic>E. coli<\/jats:italic>\n                    susceptibility to a combination of piperacillin and tazobactam but were not identified after exposure to either drug alone. Tazobactam can select for mutants with increased efflux activity, and the development of future \u03b2-lactamase inhibitors should consider potential selective impacts of both inhibitor and antibiotic.\n                  <\/jats:p>","DOI":"10.1038\/s44259-025-00122-2","type":"journal-article","created":{"date-parts":[[2025,5,30]],"date-time":"2025-05-30T08:11:43Z","timestamp":1748592703000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Tazobactam selects for multidrug resistance"],"prefix":"10.1038","volume":"3","author":[{"given":"Emma R.","family":"Holden","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muhammad","family":"Yasir","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"A. Keith","family":"Turner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ian G.","family":"Charles","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark A.","family":"Webber","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,5,30]]},"reference":[{"key":"122_CR1","doi-asserted-by":"publisher","first-page":"805","DOI":"10.2165\/00003495-199957050-00017","volume":"57","author":"CM Perry","year":"1999","unstructured":"Perry, C. M. & Markham, A. Piperacillin\/Tazobactam. Drugs 57, 805\u2013843 (1999).","journal-title":"Drugs"},{"key":"122_CR2","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1111\/j.1600-0463.2009.02563.x","volume":"118","author":"KF Kong","year":"2010","unstructured":"Kong, K. F., Schneper, L. & Mathee, K. Beta-lactam antibiotics: from antibiosis to resistance and bacteriology. APMIS 118, 1\u201336 (2010).","journal-title":"APMIS"},{"key":"122_CR3","doi-asserted-by":"publisher","first-page":"3472","DOI":"10.1016\/j.jmb.2019.04.002","volume":"431","author":"CL Tooke","year":"2019","unstructured":"Tooke, C. L. et al. \u03b2-lactamases and \u03b2-lactamase inhibitors in the 21st century. J. Mol. Biol. 431, 3472\u20133500 (2019).","journal-title":"J. Mol. Biol."},{"key":"122_CR4","doi-asserted-by":"publisher","DOI":"10.1038\/s41576-020-0244-x","author":"AK Cain","year":"2020","unstructured":"Cain, A. K. et al. A decade of advances in transposon-insertion sequencing. Nat. Rev. Genet. https:\/\/doi.org\/10.1038\/s41576-020-0244-x (2020).","journal-title":"Nat. Rev. Genet."},{"key":"122_CR5","doi-asserted-by":"publisher","DOI":"10.1101\/gr.254391.119","author":"M Yasir","year":"2020","unstructured":"Yasir, M. et al. TraDIS-Xpress: a high-resolution whole-genome assay identifies novel mechanisms of triclosan action and resistance. Genome Res. https:\/\/doi.org\/10.1101\/gr.254391.119 (2020).","journal-title":"Genome Res."},{"key":"122_CR6","doi-asserted-by":"publisher","first-page":"3144","DOI":"10.1093\/jac\/dkaa296","volume":"75","author":"AK Turner","year":"2020","unstructured":"Turner, A. K. et al. A genome-wide analysis of Escherichia coli responses to fosfomycin using TraDIS-Xpress reveals novel roles for phosphonate degradation and phosphate transport systems. J. Antimicrob. Chemother. 75, 3144\u20133151 (2020).","journal-title":"J. Antimicrob. Chemother."},{"key":"122_CR7","doi-asserted-by":"publisher","first-page":"2516","DOI":"10.1093\/jac\/dkaa204","volume":"75","author":"AK Turner","year":"2020","unstructured":"Turner, A. K. et al. A whole-genome screen identifies Salmonella enterica serovar Typhi genes involved in fluoroquinolone susceptibility. J. Antimicrob. Chemother. 75, 2516\u20132525 (2020).","journal-title":"J. Antimicrob. Chemother."},{"key":"122_CR8","doi-asserted-by":"publisher","unstructured":"Thomson, N. M. et al. A whole-genome assay identifies four principal gene functions that confer tolerance of meropenem stress upon Escherichia coli. Front. Antibiot. 1 https:\/\/doi.org\/10.3389\/frabi.2022.957942 (2022).","DOI":"10.3389\/frabi.2022.957942"},{"key":"122_CR9","doi-asserted-by":"publisher","unstructured":"Turner, A. K. et al. Chemical biology-whole genome engineering datasets predict new antibacterial combinations. Microb. Genom. 7 https:\/\/doi.org\/10.1099\/mgen.0.000718 (2021).","DOI":"10.1099\/mgen.0.000718"},{"key":"122_CR10","doi-asserted-by":"publisher","unstructured":"Holden, E. R. et al. Genome-wide analysis of genes involved in efflux function and regulation within Escherichia coli and Salmonella enterica serovar Typhimurium. Microbiology 169 https:\/\/doi.org\/10.1099\/mic.0.001296 (2023).","DOI":"10.1099\/mic.0.001296"},{"key":"122_CR11","doi-asserted-by":"publisher","unstructured":"Bontemps-Gallo, S., Bohin, J.-P., Lacroix, J.-M. & Slauch, J. M. Osmoregulated periplasmic glucans. EcoSal Plus 7 https:\/\/doi.org\/10.1128\/ecosalplus.ESP-0001-2017(2017).","DOI":"10.1128\/ecosalplus.ESP-0001-2017"},{"key":"122_CR12","doi-asserted-by":"publisher","first-page":"881","DOI":"10.1111\/1462-2920.12054","volume":"15","author":"S Bontemps-Gallo","year":"2013","unstructured":"Bontemps-Gallo, S. et al. Concentration of osmoregulated periplasmic glucans (OPGs) modulates the activation level of the RcsCD RcsB phosphorelay in the phytopathogen bacteria Dickeya dadantii. Environ. Microbiol. 15, 881\u2013894 (2013).","journal-title":"Environ. Microbiol."},{"key":"122_CR13","doi-asserted-by":"publisher","first-page":"e00743","DOI":"10.1128\/Spectrum.00743-21","volume":"9","author":"Y Song","year":"2021","unstructured":"Song, Y. et al. Reducing the periplasmic glutathione content makes Escherichia coli resistant to trimethoprim and other antimicrobial drugs. Microbiol. Spectrum 9, e00743\u201300721 (2021).","journal-title":"Microbiol. Spectrum"},{"key":"122_CR14","doi-asserted-by":"publisher","first-page":"24155","DOI":"10.1074\/jbc.M110715200","volume":"277","author":"SJ Cai","year":"2002","unstructured":"Cai, S. J. & Inouye, M. EnvZ-OmpR interaction and osmoregulation in Escherichia coli. J. Biol. Chem. 277, 24155\u201324161 (2002).","journal-title":"J. Biol. Chem."},{"key":"122_CR15","doi-asserted-by":"publisher","first-page":"1287","DOI":"10.1111\/j.1365-2958.1996.tb02473.x","volume":"19","author":"R Chen","year":"1996","unstructured":"Chen, R. & Henning, U. A. Periplasmic protein (Skp) of Escherichia coli selectively binds a class of outer membrane proteins. Mol. Microbiol. 19, 1287\u20131294 (1996).","journal-title":"Mol. Microbiol."},{"key":"122_CR16","doi-asserted-by":"publisher","first-page":"e90447","DOI":"10.1371\/journal.pone.0090447","volume":"9","author":"T Shimada","year":"2014","unstructured":"Shimada, T., Yamazaki, Y., Tanaka, K. & Ishihama, A. The whole set of constitutive promoters recognized by RNA polymerase RpoD holoenzyme of Escherichia coli. PLoS ONE 9, e90447 (2014).","journal-title":"PLoS ONE"},{"key":"122_CR17","doi-asserted-by":"publisher","first-page":"525","DOI":"10.1128\/jb.174.2.525-529.1992","volume":"174","author":"A L\u00f8bner-Olesen","year":"1992","unstructured":"L\u00f8bner-Olesen, A. & Marinus, M. G. Identification of the gene (aroK) encoding shikimic acid kinase I of Escherichia coli. J. Bacteriol. 174, 525\u2013529 (1992).","journal-title":"J. Bacteriol."},{"key":"122_CR18","doi-asserted-by":"publisher","first-page":"5723","DOI":"10.1128\/JB.187.16.5723-5731.2005","volume":"187","author":"E Batchelor","year":"2005","unstructured":"Batchelor, E., Walthers, D., Kenney, L. J. & Goulian, M. The Escherichia coli CpxA-CpxR envelope stress response system regulates expression of the porins OmpF and OmpC. J. Bacteriol. 187, 5723\u20135731 (2005).","journal-title":"J. Bacteriol."},{"key":"122_CR19","doi-asserted-by":"publisher","first-page":"655","DOI":"10.1128\/mr.57.3.655-682.1993","volume":"57","author":"CA Schnaitman","year":"1993","unstructured":"Schnaitman, C. A. & Klena, J. D. Genetics of lipopolysaccharide biosynthesis in enteric bacteria. Microbiol. Rev. 57, 655\u2013682 (1993).","journal-title":"Microbiol. Rev."},{"key":"122_CR20","doi-asserted-by":"publisher","first-page":"1394","DOI":"10.1016\/j.bbalip.2016.10.008","volume":"1862","author":"SD Liston","year":"2017","unstructured":"Liston, S. D., Mann, E. & Whitfield, C. Glycolipid substrates for ABC transporters required for the assembly of bacterial cell-envelope and cell-surface glycoconjugates. Biochim. Biophys. Acta 1862, 1394\u20131403 (2017).","journal-title":"Biochim. Biophys. Acta"},{"key":"122_CR21","doi-asserted-by":"publisher","unstructured":"Anzai, T. et al. Expanded roles of lactate-sensing LldR in transcription regulation of the Escherichia coli K-12 genome: lactate utilisation and acid resistance. Microb. Genomics 9 https:\/\/doi.org\/10.1099\/mgen.0.001015 (2023).","DOI":"10.1099\/mgen.0.001015"},{"key":"122_CR22","doi-asserted-by":"publisher","unstructured":"Cabezas, A., L\u00f3pez-Villamizar, I., Costas, M. J., Cameselle, J. C. & Ribeiro, J. M. Substrate specificity of chimeric enzymes formed by interchange of the catalytic and specificity domains of the 5(\u2018)-nucleotidase UshA and the 3(\u2018)-nucleotidase CpdB. Molecules 26 https:\/\/doi.org\/10.3390\/molecules26082307 (2021).","DOI":"10.3390\/molecules26082307"},{"key":"122_CR23","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-022-21396-w","volume":"12","author":"T Merciecca","year":"2022","unstructured":"Merciecca, T. et al. Role of Klebsiella pneumoniae Type VI secretion system (T6SS) in long-term gastrointestinal colonization. Sci. Rep. 12, 16968 (2022).","journal-title":"Sci. Rep."},{"key":"122_CR24","doi-asserted-by":"publisher","first-page":"664","DOI":"10.1073\/pnas.75.2.664","volume":"75","author":"H Suzuki","year":"1978","unstructured":"Suzuki, H., Nishimura, Y. & Hirota, Y. On the process of cellular division in Escherichia coli: a series of mutants of E. coli altered in the penicillin-binding proteins. Proc. Natl. Acad. Sci. USA. 75, 664\u2013668 (1978).","journal-title":"Proc. Natl. Acad. Sci. USA."},{"key":"122_CR25","doi-asserted-by":"publisher","first-page":"478","DOI":"10.1038\/318478a0","volume":"318","author":"PJ Hedge","year":"1985","unstructured":"Hedge, P. J. & Spratt, B. G. Resistance to beta-lactam antibiotics by re-modelling the active site of an E. coli penicillin-binding protein. Nature 318, 478\u2013480 (1985).","journal-title":"Nature"},{"key":"122_CR26","doi-asserted-by":"publisher","first-page":"333","DOI":"10.1128\/jb.145.1.333-340.1981","volume":"145","author":"GA Botta","year":"1981","unstructured":"Botta, G. A. & Park, J. T. Evidence for involvement of penicillin-binding protein 3 in murein synthesis during septation but not during cell elongation. J. Bacteriol. 145, 333\u2013340 (1981).","journal-title":"J. Bacteriol."},{"key":"122_CR27","doi-asserted-by":"publisher","first-page":"52","DOI":"10.1021\/ja410813j","volume":"136","author":"TJ Lupoli","year":"2014","unstructured":"Lupoli, T. J. et al. Lipoprotein activators stimulate Escherichia coli penicillin-binding proteins by different mechanisms. J. Am. Chem. Soc. 136, 52\u201355 (2014).","journal-title":"J. Am. Chem. Soc."},{"key":"122_CR28","doi-asserted-by":"publisher","first-page":"3818","DOI":"10.1128\/jb.178.13.3818-3828.1996","volume":"178","author":"D Vinella","year":"1996","unstructured":"Vinella, D., Gagny, B., Joseleau-Petit, D., D\u2019Ari, R. & Cashel, M. Mecillinam resistance in Escherichia coli is conferred by loss of a second activity of the AroK protein. J. Bacteriol. 178, 3818\u20133828 (1996).","journal-title":"J. Bacteriol."},{"key":"122_CR29","doi-asserted-by":"publisher","first-page":"2255","DOI":"10.1016\/S0021-9258(18)69199-9","volume":"263","author":"HO Kammen","year":"1988","unstructured":"Kammen, H. O., Marvel, C. C., Hardy, L. & Penhoet, E. E. Purification, structure, and properties of Escherichia coli tRNA pseudouridine synthase I. J. Biol. Chem. 263, 2255\u20132263 (1988).","journal-title":"J. Biol. Chem."},{"key":"122_CR30","doi-asserted-by":"publisher","first-page":"2295","DOI":"10.1101\/gad.207701","volume":"15","author":"D Br\u00e9geon","year":"2001","unstructured":"Br\u00e9geon, D., Colot, V., Radman, M. & Taddei, F. Translational misreading: a tRNA modification counteracts a +2 ribosomal frameshift. Genes Dev 15, 2295\u20132306 (2001).","journal-title":"Genes Dev"},{"key":"122_CR31","doi-asserted-by":"publisher","first-page":"1819","DOI":"10.1128\/JB.00023-15","volume":"197","author":"P Choudhury","year":"2015","unstructured":"Choudhury, P. & Flower, A. M. Efficient assembly of ribosomes is inhibited by deletion of bipA in Escherichia coli. J. Bacteriol. 197, 1819\u20131827 (2015).","journal-title":"J. Bacteriol."},{"key":"122_CR32","doi-asserted-by":"publisher","first-page":"199","DOI":"10.1111\/j.1365-2958.1994.tb01281.x","volume":"14","author":"JC Bardwell","year":"1994","unstructured":"Bardwell, J. C. Building bridges: disulphide bond formation in the cell. Mol. Microbiol. 14, 199\u2013205 (1994).","journal-title":"Mol. Microbiol."},{"key":"122_CR33","doi-asserted-by":"publisher","first-page":"3330","DOI":"10.1101\/gad.936701","volume":"15","author":"MV Sukhodolets","year":"2001","unstructured":"Sukhodolets, M. V., Cabrera, J. E., Zhi, H. & Jin, D. J. RapA, a bacterial homolog of SWI2\/SNF2, stimulates RNA polymerase recycling in transcription. Genes Dev. 15, 3330\u20133341 (2001).","journal-title":"Genes Dev."},{"key":"122_CR34","doi-asserted-by":"publisher","first-page":"320","DOI":"10.1038\/nrmicro.2016.34","volume":"14","author":"A Brauner","year":"2016","unstructured":"Brauner, A., Fridman, O., Gefen, O. & Balaban, N. Q. Distinguishing between resistance, tolerance and persistence to antibiotic treatment. Nat. Rev. Microbiol. 14, 320\u2013330 (2016).","journal-title":"Nat. Rev. Microbiol."},{"key":"122_CR35","doi-asserted-by":"publisher","first-page":"382","DOI":"10.1128\/CMR.19.2.382-402.2006","volume":"19","author":"LJ Piddock","year":"2006","unstructured":"Piddock, L. J. Clinically relevant chromosomally encoded multidrug resistance efflux pumps in bacteria. Clin. Microbiol. Rev. 19, 382\u2013402 (2006).","journal-title":"Clin. Microbiol. Rev."},{"key":"122_CR36","doi-asserted-by":"publisher","first-page":"814","DOI":"10.1128\/AAC.44.4.814-820.2000","volume":"44","author":"WV Kern","year":"2000","unstructured":"Kern, W. V., Oethinger, M., Jellen-Ritter, A. S. & Levy, S. B. Non-target gene mutations in the development of fluoroquinolone resistance in Escherichia coli. Antimicrob. Agents Chemother. 44, 814\u2013820 (2000).","journal-title":"Antimicrob. Agents Chemother."},{"key":"122_CR37","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1128\/AAC.44.1.10-13.2000","volume":"44","author":"M Oethinger","year":"2000","unstructured":"Oethinger, M., Kern, W. V., Jellen-Ritter, A. S., McMurry, L. M. & Levy, S. B. Ineffectiveness of Topoisomerase Mutations in Mediating Clinically Significant Fluoroquinolone Resistance in Escherichia coli in the Absence of the AcrAB Efflux Pump. Antimicrob. Agents Chemother. 44, 10\u201313 (2000).","journal-title":"Antimicrob. Agents Chemother."},{"key":"122_CR38","doi-asserted-by":"publisher","first-page":"1040","DOI":"10.1016\/j.arcped.2016.07.004","volume":"23","author":"C Cotteret","year":"2016","unstructured":"Cotteret, C. et al. Profil de consommation et de sensibilit\u00e9 aux antibiotiques utilis\u00e9s dans un centre hospitalier universitaire : \u00e9tude r\u00e9trospective sur cinq ans. Arch. Pediatr. 23, 1040\u20131049 (2016).","journal-title":"Arch. Pediatr."},{"key":"122_CR39","doi-asserted-by":"publisher","first-page":"160","DOI":"10.1128\/CMR.00037-09","volume":"23","author":"SM Drawz","year":"2010","unstructured":"Drawz, S. M. & Bonomo, R. A. Three decades of beta-lactamase inhibitors. Clin. Microbiol. Rev. 23, 160\u2013201 (2010).","journal-title":"Clin. Microbiol. Rev."},{"key":"122_CR40","unstructured":"O\u2019Neill, J. https:\/\/amr-review.org\/sites\/default\/files\/AMR%20Review%20Paper%20-%20Tackling%20a%20crisis%20for%20the%20health%20and%20wealth%20of%20nations_1.pdf (2014)."},{"key":"122_CR41","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1016\/j.resmic.2010.03.006","volume":"161","author":"K Val\u00e9ria dos Santos","year":"2010","unstructured":"Val\u00e9ria dos Santos, K. et al. Proteomic analysis of Escherichia coli with experimentally induced resistance to piperacillin\/tazobactam. Res. Microbiol. 161, 268\u2013275 (2010).","journal-title":"Res. Microbiol."},{"key":"122_CR42","doi-asserted-by":"publisher","first-page":"917","DOI":"10.1080\/14756366.2017.1344235","volume":"32","author":"T Naas","year":"2017","unstructured":"Naas, T. et al. Beta-lactamase database (BLDB)\u2014structure and function. J. Enzyme Inhibit. Med. Chem. 32, 917\u2013919 (2017).","journal-title":"J. Enzyme Inhibit. Med. Chem."},{"key":"122_CR43","doi-asserted-by":"publisher","first-page":"e00397","DOI":"10.1128\/AAC.00397-20","volume":"64","author":"SE Boyd","year":"2020","unstructured":"Boyd, S. E., Livermore, D. M., Hooper, D. C. & Hope, W. W. Metallo-\u03b2-lactamases: structure, function, epidemiology, treatment options, and the development pipeline. Antimicrob. Agents Chemother. 64, e00397\u201300320 (2020).","journal-title":"Antimicrob. Agents Chemother."},{"key":"122_CR44","doi-asserted-by":"publisher","DOI":"10.1038\/s41522-020-00178-0","volume":"7","author":"E Trampari","year":"2021","unstructured":"Trampari, E. et al. Exposure of Salmonella biofilms to antibiotic concentrations rapidly selects resistance with collateral tradeoffs. npj Biofilms Microbiomes 7, 3 (2021).","journal-title":"npj Biofilms Microbiomes"},{"key":"122_CR45","doi-asserted-by":"publisher","first-page":"1109","DOI":"10.1093\/bioinformatics\/btw022","volume":"32","author":"L Barquist","year":"2016","unstructured":"Barquist, L. et al. The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries. Bioinformatics 32, 1109\u20131111 (2016).","journal-title":"Bioinformatics"},{"key":"122_CR46","doi-asserted-by":"publisher","first-page":"464","DOI":"10.1093\/bioinformatics\/btr703","volume":"28","author":"T Carver","year":"2011","unstructured":"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\u2013469 (2011).","journal-title":"Bioinformatics"},{"key":"122_CR47","unstructured":"Seemann, T. Snippy: fast bacterial variant calling from NGS reads. https:\/\/github.com\/tseemann\/snippy (2015)."}],"container-title":["npj Antimicrobials and Resistance"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s44259-025-00122-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s44259-025-00122-2","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s44259-025-00122-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,5,30]],"date-time":"2025-05-30T08:11:44Z","timestamp":1748592704000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s44259-025-00122-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,5,30]]},"references-count":47,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["122"],"URL":"https:\/\/doi.org\/10.1038\/s44259-025-00122-2","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2023.08.15.553388","asserted-by":"object"}]},"ISSN":["2731-8745"],"issn-type":[{"value":"2731-8745","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,5,30]]},"assertion":[{"value":"19 February 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"19 May 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"30 May 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"48"}}