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Transcriptome studies are indispensable to comprehend the pathology and biology of these bacteria. Recently, we showed that nanoparticles loaded with Hesperidin are potential novel antibacterial agents against <jats:italic>E. coli<\/jats:italic> K1. Here, bacteria were treated with and without Hesperidin conjugated with silver nanoparticles, and silver alone, and 50% minimum inhibitory concentration was determined. Differential gene expression analysis using RNA-seq, was performed using Degust software and a set of genes involved in cell stress response and metabolism were selected for the study.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>50% minimum inhibitory concentration with silver-conjugated Hesperidin was achieved with 0.5\u2009\u03bcg\/ml of Hesperidin conjugated with silver nanoparticles at 1\u2009h. Differential genetic analysis revealed the expression of 122 genes (\u2265 2-log FC, <jats:italic>P<\/jats:italic>&lt;\u20090.01) in both <jats:italic>E. coli<\/jats:italic> K1 treated with Hesperidin conjugated silver nanoparticles and <jats:italic>E. coli<\/jats:italic> K1 treated with silver alone, compared to untreated <jats:italic>E. coli<\/jats:italic> K1. Of note, the expression levels of cation efflux genes (<jats:italic>cusA<\/jats:italic> and <jats:italic>copA<\/jats:italic>) and translocation of ions, across the membrane genes (<jats:italic>rsxB<\/jats:italic>) were found to increase 2.6, 3.1, and 3.3- log FC, respectively. Significant regulation was observed for metabolic genes and several genes involved in the coordination of flagella.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>The antibacterial mechanism of nanoparticles maybe due to disruption of the cell membrane, oxidative stress, and metabolism in <jats:italic>E. coli<\/jats:italic> K1. Further studies will lead to a better understanding of the genetic mechanisms underlying treatment with nanoparticles and identification of much needed novel antimicrobial drug candidates.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12866-021-02097-2","type":"journal-article","created":{"date-parts":[[2021,2,18]],"date-time":"2021-02-18T08:00:13Z","timestamp":1613635213000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":26,"title":["Transcriptome analysis of Escherichia coli K1 after therapy with hesperidin conjugated with silver nanoparticles"],"prefix":"10.1186","volume":"21","author":[{"given":"Abdulkader","family":"Masri","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Naveed Ahmed","family":"Khan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Muhammad Zarul Hanifah Md","family":"Zoqratt","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qasim","family":"Ayub","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ayaz","family":"Anwar","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Komal","family":"Rao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Muhammad Raza","family":"Shah","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ruqaiyyah","family":"Siddiqui","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2021,2,17]]},"reference":[{"key":"2097_CR1","doi-asserted-by":"publisher","first-page":"533","DOI":"10.1136\/bmj.323.7312.533","volume":"323","author":"H Bedford","year":"2001","unstructured":"Bedford H, de Louvois J, Halket S, Peckham C, Hurley R, Harvey D. 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