{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,2]],"date-time":"2026-11-02T11:29:00Z","timestamp":1793618940375,"version":"4.5.0"},"reference-count":18,"publisher":"SAGE Publications","issue":"11","license":[{"start":{"date-parts":[[2023,11,1]],"date-time":"2023-11-01T00:00:00Z","timestamp":1698796800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.sagepub.com\/page\/policies\/text-and-data-mining-license"}],"content-domain":{"domain":["journals.sagepub.com"],"crossmark-restriction":true},"short-container-title":["Microbial Drug Resistance"],"published-print":{"date-parts":[[2023,11]]},"abstract":"<jats:p>\n                    Metagenomic sequencing (mDNA-seq) is one of the best approaches to address antimicrobial resistance (AMR) issues and characterize AMR genes (ARGs) and their host bacteria (ARB); however, the sensitivity provided is insufficient for the overall detection in wastewater treatment plant (WWTP) effluents because the effluent is well treated. This study investigated the multiplex hybrid capture (xHYB) method (QIAseq\u2009\u00d7\u2009HYB AMR Panel) and its potential to increase AMR assessment sensitivity. The mDNA-Seq analysis suggested that the WWTP effluents had an average of 104 reads per kilobase of gene per million (RPKM) for the detection of all targeted ARGs, whereas xHYB significantly improved detection at 601,576 RPKM, indicating an average 5,805-fold increase in sensitivity. For instance,\n                    <jats:italic toggle=\"yes\">sul1<\/jats:italic>\n                    was detected at 15 and 114,229 RPKM using mDNA-seq and xHYB, respectively. The\n                    <jats:italic toggle=\"yes\">bla<\/jats:italic>\n                    <jats:sub>CTX-M<\/jats:sub>\n                    ,\n                    <jats:italic toggle=\"yes\">bla<\/jats:italic>\n                    <jats:sub>KPC<\/jats:sub>\n                    , and\n                    <jats:italic toggle=\"yes\">mcr<\/jats:italic>\n                    gene variants were not detected by mDNA-Seq but were detected by xHYB at 67, 20, and 1,010 RPKM, respectively. This study demonstrates that the multiplex xHYB method could be a suitable evaluation standard with high sensitivity and specificity for deep-dive detection, highlighting a broader illustration of ongoing dissemination in the entire community.\n                  <\/jats:p>","DOI":"10.1089\/mdr.2023.0016","type":"journal-article","created":{"date-parts":[[2023,7,11]],"date-time":"2023-07-11T17:05:49Z","timestamp":1689095149000},"page":"510-515","update-policy":"https:\/\/doi.org\/10.1177\/sage-journals-update-policy","source":"Crossref","is-referenced-by-count":7,"title":["Multiplex Hybrid Capture Improves the Deep Detection of Antimicrobial Resistance Genes from Wastewater Treatment Plant Effluents to Assess Environmental Issues"],"prefix":"10.1177","volume":"29","author":[{"given":"Tsuyoshi","family":"Sekizuka","sequence":"first","affiliation":[{"name":"Pathogen Genomics Center, National Institute of Infectious Diseases, Shinjyuku, Tokyo, Japan."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nobuyasu","family":"Yamaguchi","sequence":"additional","affiliation":[{"name":"Department of Environmental Health, Osaka Institute of Public Health, Osaka, Japan."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hajime","family":"Kanamori","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases, Internal Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Makoto","family":"Kuroda","sequence":"additional","affiliation":[{"name":"Pathogen Genomics Center, National Institute of Infectious Diseases, Shinjyuku, Tokyo, Japan."}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"179","published-online":{"date-parts":[[2023,11,7]]},"reference":[{"issue":"7","key":"e_1_3_7_2_2","doi-asserted-by":"crossref","first-page":"1785","DOI":"10.1093\/jac\/dku079","article-title":"Waste water effluent contributes to the dissemination of CTX-M-15 in the natural environment","volume":"69","author":"Amos GC","year":"2014","unstructured":"Amos GC, , Hawkey PM, , Gaze WH, et al. Waste water effluent contributes to the dissemination of CTX-M-15 in the natural environment. J Antimicrob Chemother, 2014; 69(7):1785\u20131791; doi: 10.1093\/jac\/dku079","journal-title":"J Antimicrob Chemother"},{"key":"e_1_3_7_3_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0078906"},{"key":"e_1_3_7_4_2","doi-asserted-by":"crossref","first-page":"657353","DOI":"10.3389\/fmicb.2021.657353","article-title":"Increased antimicrobial and multidrug resistance downstream of wastewater treatment plants in an urban watershed","volume":"12","author":"Mukherjee M","year":"2021","unstructured":"Mukherjee M, , Laird E, , Gentry TJ, et al. Increased antimicrobial and multidrug resistance downstream of wastewater treatment plants in an urban watershed. Front Microbiol, 2021; 12:657353; doi: 10.3389\/fmicb.2021.657353","journal-title":"Front Microbiol"},{"issue":"1","key":"e_1_3_7_5_2","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1186\/s40168-021-01192-w","article-title":"High-resolution genomic surveillance elucidates a multilayered hierarchical transfer of resistance between WWTP- and human\/animal-associated bacteria","volume":"10","author":"Che Y","year":"2022","unstructured":"Che Y, , Xu X, , Yang Y, et al. High-resolution genomic surveillance elucidates a multilayered hierarchical transfer of resistance between WWTP- and human\/animal-associated bacteria. Microbiome, 2022; 10(1):16; doi: 10.1186\/s40168-021-01192-w","journal-title":"Microbiome"},{"key":"e_1_3_7_6_2","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dks261"},{"key":"e_1_3_7_7_2","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.2584"},{"key":"e_1_3_7_8_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp616"},{"issue":"11","key":"e_1_3_7_9_2","doi-asserted-by":"crossref","DOI":"10.3390\/microorganisms9112212","article-title":"The natural history of integrons","volume":"9","author":"Ghaly TM","year":"2021","unstructured":"Ghaly TM, , Gillings MR, , Penesyan A, et al. The natural history of integrons. Microorganisms, 2021; 9(11); doi: 10.3390\/microorganisms9112212","journal-title":"Microorganisms"},{"issue":"8","key":"e_1_3_7_10_2","doi-asserted-by":"crossref","first-page":"2145","DOI":"10.1093\/jac\/dkx146","article-title":"Global epidemiology of CTX-M beta-lactamases: Temporal and geographical shifts in genotype","volume":"72","author":"Bevan ER","year":"2017","unstructured":"Bevan ER, , Jones AM, , Hawkey PM. Global epidemiology of CTX-M beta-lactamases: Temporal and geographical shifts in genotype. J Antimicrob Chemother, 2017; 72(8):2145\u20132155; doi: 10.1093\/jac\/dkx146","journal-title":"J Antimicrob Chemother"},{"key":"e_1_3_7_11_2","doi-asserted-by":"crossref","DOI":"10.1128\/AAC.02729-16","article-title":"Global molecular epidemiology of IMP-producing Enterobacteriaceae","volume":"61","author":"Matsumura Y","year":"2017","unstructured":"Matsumura Y, , Peirano G, , Motyl MR, et al. Global molecular epidemiology of IMP-producing Enterobacteriaceae. Antimicrob Agents Chemother, 2017; 61(4); doi: 10.1128\/AAC.02729-16","journal-title":"Antimicrob Agents Chemother"},{"issue":"8","key":"e_1_3_7_12_2","doi-asserted-by":"crossref","first-page":"1290","DOI":"10.1093\/cid\/cix893","article-title":"Carbapenemase-producing organisms: A global scourge","volume":"66","author":"Bonomo RA","year":"2018","unstructured":"Bonomo RA, , Burd EM, , Conly J, et al. Carbapenemase-producing organisms: A global scourge. Clin Infect Dis, 2018; 66(8):1290\u20131297; doi: 10.1093\/cid\/cix893","journal-title":"Clin Infect Dis"},{"key":"e_1_3_7_13_2","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1016\/j.jgar.2021.07.021","article-title":"Epidemiology of mobile colistin resistance (mcr) genes in aquatic environments","volume":"27","author":"Cherak Z","year":"2021","unstructured":"Cherak Z, , Loucif L, , Moussi A, et al. Epidemiology of mobile colistin resistance (mcr) genes in aquatic environments. J Glob Antimicrob Resist, 2021; 27:51\u201362; doi: 10.1016\/j.jgar.2021.07.021","journal-title":"J Glob Antimicrob Resist"},{"key":"e_1_3_7_14_2","doi-asserted-by":"crossref","DOI":"10.1128\/mSphere.00314-18","article-title":"Complete genome sequence of a blaKPC-2-positive Klebsiella pneumoniae strain isolated from the effluent of an urban sewage treatment plant in Japan","volume":"3","author":"Sekizuka T","year":"2018","unstructured":"Sekizuka T, , Yatsu K, , Inamine Y, et al. Complete genome sequence of a blaKPC-2-positive Klebsiella pneumoniae strain isolated from the effluent of an urban sewage treatment plant in Japan. mSphere, 2018; 3(5); doi: 10.1128\/mSphere.00314-18","journal-title":"mSphere"},{"issue":"4","key":"e_1_3_7_15_2","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1111\/1758-2229.12772","article-title":"Potential KPC-2 carbapenemase reservoir of environmental Aeromonas hydrophila and Aeromonas caviae isolates from the effluent of an urban wastewater treatment plant in Japan","volume":"11","author":"Sekizuka T","year":"2019","unstructured":"Sekizuka T, , Inamine Y, , Segawa T, et al. Potential KPC-2 carbapenemase reservoir of environmental Aeromonas hydrophila and Aeromonas caviae isolates from the effluent of an urban wastewater treatment plant in Japan. Environ Microbiol Rep, 2019; 11(4):589\u2013597; doi: 10.1111\/1758-2229.12772","journal-title":"Environ Microbiol Rep"},{"key":"e_1_3_7_16_2","doi-asserted-by":"crossref","first-page":"2243","DOI":"10.2147\/IDR.S215273","article-title":"Characterization of NDM-5- and CTX-M-55-coproducing Escherichia coli GSH8M-2 isolated from the effluent of a wastewater treatment plant in Tokyo Bay","volume":"12","author":"Sekizuka T","year":"2019","unstructured":"Sekizuka T, , Inamine Y, , Segawa T, et al. Characterization of NDM-5- and CTX-M-55-coproducing Escherichia coli GSH8M-2 isolated from the effluent of a wastewater treatment plant in Tokyo Bay. Infect Drug Resist, 2019; 12:2243\u20132249; doi: 10.2147\/IDR.S215273","journal-title":"Infect Drug Resist"},{"key":"e_1_3_7_17_2","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1016\/j.jgar.2016.01.008","article-title":"Emergence of ciprofloxacin-resistant extended-spectrum beta-lactamase-producing enteric bacteria in hospital wastewater and clinical sources","volume":"5","author":"Maheshwari M","year":"2016","unstructured":"Maheshwari M, , Yaser NH, , Naz S, et al. Emergence of ciprofloxacin-resistant extended-spectrum beta-lactamase-producing enteric bacteria in hospital wastewater and clinical sources. J Glob Antimicrob Resist, 2016; 5:22\u201325; doi: 10.1016\/j.jgar.2016.01.008","journal-title":"J Glob Antimicrob Resist"},{"issue":"6","key":"e_1_3_7_18_2","doi-asserted-by":"crossref","first-page":"1818","DOI":"10.1128\/AEM.02929-15","article-title":"Long-term colonization by bla(CTX-M)-harboring Escherichia coli in healthy Japanese people engaged in food handling","volume":"82","author":"Nakane K","year":"2016","unstructured":"Nakane K, , Kawamura K, , Goto K, et al. Long-term colonization by bla(CTX-M)-harboring Escherichia coli in healthy Japanese people engaged in food handling. Appl Environ Microbiol, 2016; 82(6):1818\u20131827; doi: 10.1128\/aem.02929-15","journal-title":"Appl Environ Microbiol"},{"key":"e_1_3_7_19_2","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1016\/j.mib.2021.09.013","article-title":"Seizing the moment: Now is the time for integrated global surveillance of antimicrobial resistance in wastewater environments","volume":"64","author":"Pruden A","year":"2021","unstructured":"Pruden A, , Vikesland PJ, , Davis BC, et al. Seizing the moment: Now is the time for integrated global surveillance of antimicrobial resistance in wastewater environments. Curr Opin Microbiol, 2021; 64:91\u201399; doi: 10.1016\/j.mib.2021.09.013","journal-title":"Curr Opin Microbiol"}],"container-title":["Microbial Drug Resistance"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.sagepub.com\/doi\/full-xml\/10.1089\/mdr.2023.0016","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.sagepub.com\/doi\/pdf\/10.1089\/mdr.2023.0016","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.sagepub.com\/doi\/pdf\/10.1089\/mdr.2023.0016","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,5,1]],"date-time":"2026-05-01T20:40:58Z","timestamp":1777668058000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.sagepub.com\/doi\/full\/10.1089\/mdr.2023.0016"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,11]]},"references-count":18,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2023,11]]}},"alternative-id":["10.1089\/mdr.2023.0016"],"URL":"https:\/\/doi.org\/10.1089\/mdr.2023.0016","relation":{},"ISSN":["1076-6294","1931-8448"],"issn-type":[{"value":"1076-6294","type":"print"},{"value":"1931-8448","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,11]]}}}