Nanopore R10.4 metagenomic detection of bla
Feces
/ microbiology
Escherichia coli
/ genetics
Humans
beta-Lactamases
/ genetics
Metagenomics
/ methods
Nanopores
Escherichia coli Proteins
/ genetics
Plasmids
/ genetics
Nanopore Sequencing
/ methods
Drug Resistance, Bacterial
/ genetics
Anti-Bacterial Agents
/ pharmacology
Gastrointestinal Microbiome
/ genetics
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
28 Aug 2024
28 Aug 2024
Historique:
received:
28
02
2024
accepted:
21
08
2024
medline:
31
8
2024
pubmed:
31
8
2024
entrez:
28
8
2024
Statut:
epublish
Résumé
The increasing prevalence of gut colonization with CTX-M extended-spectrum β-lactamase- and/or DHA plasmid-mediated AmpC-producing Escherichia coli is a concern. Here, we evaluate Nanopore-shotgun metagenomic sequencing (Nanopore-SMS) latest V14 chemistry to detect bla
Identifiants
pubmed: 39198442
doi: 10.1038/s41467-024-51929-y
pii: 10.1038/s41467-024-51929-y
doi:
Substances chimiques
beta-Lactamases
EC 3.5.2.6
Escherichia coli Proteins
0
Anti-Bacterial Agents
0
beta-lactamase CTX-M, E coli
EC 3.5.2.6
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
7450Subventions
Organisme : Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)
ID : 192514
Informations de copyright
© 2024. The Author(s).
Références
Campos-Madueno, E. I. et al. Intestinal colonization with multidrug-resistant Enterobacterales: screening, epidemiology, clinical impact, and strategies to decolonize carriers. Eur. J. Clin. Microbiol Infect. Dis. 42, 229–254 (2023).
pubmed: 36680641
pmcid: 9899200
doi: 10.1007/s10096-023-04548-2
Mathers, A. J., Peirano, G. & Pitout, J. D. The role of epidemic resistance plasmids and international high-risk clones in the spread of multidrug-resistant Enterobacteriaceae. Clin. Microbiol Rev. 28, 565–591 (2015).
pubmed: 25926236
pmcid: 4405625
doi: 10.1128/CMR.00116-14
Bezabih, Y. M. et al. Comparison of the global prevalence and trend of human intestinal carriage of ESBL-producing Escherichia coli between healthcare and community settings: a systematic review and meta-analysis. JAC Antimicrob. Resist. 4, dlac048 (2022).
pubmed: 35668909
pmcid: 9160884
doi: 10.1093/jacamr/dlac048
Rettedal, S. et al. Extended-spectrum β-lactamase-producing Enterobacteriaceae among pregnant women in Norway: prevalence and maternal-neonatal transmission. J. Perinatol. 35, 907–912 (2015).
pubmed: 26507147
doi: 10.1038/jp.2015.82
Ulstad, C. R. et al. Carriage of ESBL/AmpC-producing or ciprofloxacin non-susceptible Escherichia coli and Klebsiella spp. in healthy people in Norway. Antimicrob. Resist. Infect. Control 5, 57 (2016).
pubmed: 28018582
pmcid: 5159956
doi: 10.1186/s13756-016-0156-x
Ruh, E. et al. Extended-spectrum β-lactamase, plasmid-mediated AmpC β-lactamase, fluoroquinolone resistance, and decreased susceptibility to carbapenems in Enterobacteriaceae: fecal carriage rates and associated risk factors in the community of Northern Cyprus. Antimicrob. Resist. Infect. Control 8, 98 (2019).
pubmed: 31198531
pmcid: 6558775
doi: 10.1186/s13756-019-0548-9
Antimicrobial Resistance, C. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. Lancet 399, 629–655 (2022).
doi: 10.1016/S0140-6736(21)02724-0
Wheeler, N. E. et al. Innovations in genomic antimicrobial resistance surveillance. Lancet Microbe 4, e1063–e1070 (2023).
pubmed: 37977163
doi: 10.1016/S2666-5247(23)00285-9
Lim, C. et al. Surveillance strategies using routine microbiology for antimicrobial resistance in low- and middle-income countries. Clin. Microbiol. Infect. 27, 1391–1399 (2021).
pubmed: 34111583
pmcid: 7613529
doi: 10.1016/j.cmi.2021.05.037
Peterson, C. L. et al. Clinical metagenomics is increasingly accurate and affordable to detect enteric bacterial pathogens in stool. Microorganisms 10, 441 (2022).
pubmed: 35208895
pmcid: 8880012
doi: 10.3390/microorganisms10020441
Mu, A. et al. Reconstruction of the genomes of drug-resistant pathogens for outbreak investigation through metagenomic sequencing. mSphere 4, e00529–18 (2019).
pubmed: 30651402
pmcid: 6336080
doi: 10.1128/mSphere.00529-18
Gigliucci, F. et al. Metagenomic characterization of the human intestinal microbiota in fecal samples from STEC-infected patients. Front. Cell Infect. Microbiol. 8, 25 (2018).
pubmed: 29468143
pmcid: 5808120
doi: 10.3389/fcimb.2018.00025
Grall, N. et al. Unexpected persistence of extended-spectrum β-lactamase-producing Enterobacteriaceae in the faecal microbiota of hospitalised patients treated with imipenem. Int. J. Antimicrob. Agents 50, 81–87 (2017).
pubmed: 28499958
doi: 10.1016/j.ijantimicag.2017.02.018
Zhou, Y. et al. Metagenomic approach for identification of the pathogens associated with diarrhea in stool specimens. J. Clin. Microbiol. 54, 368–375 (2016).
pubmed: 26637379
pmcid: 4733167
doi: 10.1128/JCM.01965-15
Campos-Madueno, E. I. et al. Detection of bla
pubmed: 37720151
pmcid: 10501143
doi: 10.3389/fmicb.2023.1236208
Bertrand, D. et al. Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes. Nat. Biotechnol. 37, 937–944 (2019).
pubmed: 31359005
doi: 10.1038/s41587-019-0191-2
Viehweger, A. et al. Nanopore-based enrichment of antimicrobial resistance genes—a case-based study. GigaByte 2023, gigabyte75 (2023).
pubmed: 36949817
pmcid: 10027057
doi: 10.46471/gigabyte.75
Yee, R. et al. Metagenomic next-generation sequencing of rectal swabs for the surveillance of antimicrobial-resistant organisms on the Illumina Miseq and Oxford MinION platforms. Eur. J. Clin. Microbiol. Infect. Dis. 40, 95–102 (2021).
pubmed: 32783106
doi: 10.1007/s10096-020-03996-4
Leggett, R. M. et al. Rapid MinION profiling of preterm microbiota and antimicrobial-resistant pathogens. Nat. Microbiol. 5, 430–442 (2020).
pubmed: 31844297
doi: 10.1038/s41564-019-0626-z
Kumburu, H. H. et al. Nanopore sequencing technology for clinical diagnosis of infectious diseases where laboratory capacity is meager: A case report. Heliyon 9, e17439 (2023).
pubmed: 37539288
pmcid: 10395014
doi: 10.1016/j.heliyon.2023.e17439
Khan, M. A. A. et al. Feasibility of MinION nanopore rapid sequencing in the detection of common diarrhea pathogens in fecal specimen. Anal. Chem. 94, 16658–16666 (2022).
pubmed: 36413486
doi: 10.1021/acs.analchem.2c02771
Alili, R. et al. Exploring semi-quantitative metagenomic studies using oxford nanopore sequencing: A computational and experimental protocol. Genes 12, 1496 (2021).
pubmed: 34680891
pmcid: 8536095
doi: 10.3390/genes12101496
d’Humieres, C. et al. The potential role of clinical metagenomics in infectious diseases: therapeutic perspectives. Drugs 81, 1453–1466 (2021).
pubmed: 34328626
pmcid: 8323086
doi: 10.1007/s40265-021-01572-4
Sheka, D., Alabi, N. & Gordon, P. M. K. Oxford nanopore sequencing in clinical microbiology and infection diagnostics. Brief. Bioinform. 22, bbaa403 (2021).
pubmed: 33483726
doi: 10.1093/bib/bbaa403
Forbes, J. D., Knox, N. C., Ronholm, J., Pagotto, F. & Reimer, A. Metagenomics: The next culture-independent game changer. Front. Microbiol. 8, 1069 (2017).
pubmed: 28725217
pmcid: 5495826
doi: 10.3389/fmicb.2017.01069
Brochu, E. et al. Characterization of vancomycin-resistance vanD gene clusters in the human intestinal microbiota by metagenomics and culture-enriched metagenomics. JAC Antimicrob. Resist. 5, dlad026 (2023).
pubmed: 36968950
pmcid: 10036994
doi: 10.1093/jacamr/dlad026
Peto, L. et al. Selective culture enrichment and sequencing of feces to enhance detection of antimicrobial resistance genes in third-generation cephalosporin resistant Enterobacteriaceae. PLoS ONE 14, e0222831 (2019).
pubmed: 31703058
pmcid: 6839868
doi: 10.1371/journal.pone.0222831
Raymond, F. et al. Culture-enriched human gut microbiomes reveal core and accessory resistance genes. Microbiome 7, 56 (2019).
pubmed: 30953542
pmcid: 6451232
doi: 10.1186/s40168-019-0669-7
Maghini, D. G., Moss, E. L., Vance, S. E. & Bhatt, A. S. Improved high-molecular-weight DNA extraction, nanopore sequencing and metagenomic assembly from the human gut microbiome. Nat. Protoc. 16, 458–471 (2021).
pubmed: 33277629
doi: 10.1038/s41596-020-00424-x
Girlich, D., Bouihat, N., Poirel, L., Benouda, A. & Nordmann, P. High rate of faecal carriage of extended-spectrum β-lactamase and OXA-48 carbapenemase-producing Enterobacteriaceae at a university hospital in Morocco. Clin. Microbiol. Infect. 20, 350–354 (2014).
pubmed: 23927757
doi: 10.1111/1469-0691.12325
Nakayama, T., Kumeda, Y., Kawahara, R. & Yamamoto, Y. Quantification and long-term carriage study of human extended-spectrum/AmpC β-lactamase-producing Escherichia coli after international travel to Vietnam. J. Glob. Antimicrob. Resist. 21, 229–234 (2020).
pubmed: 31726236
doi: 10.1016/j.jgar.2019.11.001
Campos-Madueno, E. I. et al. Simultaneous gut colonization by Klebsiella grimontii and Escherichia coli co-possessing the bla
pubmed: 35643963
pmcid: 9250482
doi: 10.1007/s10096-022-04462-z
Campos-Madueno, E. I. et al. Carbapenemase-producing Klebsiella pneumoniae strains in Switzerland: human and non-human settings may share high-risk clones. J. Glob. Antimicrob. Resist. 28, 206–215 (2022).
pubmed: 35085791
doi: 10.1016/j.jgar.2022.01.016
Campos-Madueno, E. I., Aldeia, C., Sendi, P. & Endimiani, A. Escherichia ruysiae may serve as a reservoir of antibiotic resistance genes across multiple settings and regions. Microbiol. Spectr. 11, e0175323 (2023).
pubmed: 37318364
doi: 10.1128/spectrum.01753-23
Fagerstrom, A. et al. Comparative distribution of extended-spectrum β-lactamase-producing Escherichia coli from urine infections and environmental waters. PLoS ONE 14, e0224861 (2019).
pubmed: 31697734
pmcid: 6837386
doi: 10.1371/journal.pone.0224861
Huang, J. et al. Carbapenem-resistant Escherichia coli exhibit diverse spatiotemporal epidemiological characteristics across the globe. Commun. Biol. 7, 51 (2024).
pubmed: 38184739
pmcid: 10771496
doi: 10.1038/s42003-023-05745-7
Matamoros, S. et al. Global phylogenetic analysis of Escherichia coli and plasmids carrying the mcr-1 gene indicates bacterial diversity but plasmid restriction. Sci. Rep. 7, 15364 (2017).
pubmed: 29127343
pmcid: 5681592
doi: 10.1038/s41598-017-15539-7
Shaik, S. et al. Comparative genomic analysis of globally dominant ST131 clone with other epidemiologically successful extraintestinal pathogenic Escherichia coli (ExPEC) lineages. mBio 8, e01596–17 (2017).
pubmed: 29066550
pmcid: 5654935
doi: 10.1128/mBio.01596-17
Latorre-Perez, A., Villalba-Bermell, P., Pascual, J. & Vilanova, C. Assembly methods for nanopore-based metagenomic sequencing: a comparative study. Sci. Rep. 10, 13588 (2020).
pubmed: 32788623
pmcid: 7423617
doi: 10.1038/s41598-020-70491-3
Manni, M., Berkeley, M. R., Seppey, M., Simao, F. A. & Zdobnov, E. M. BUSCO Update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, Prokaryotic, and viral genomes. Mol. Biol. Evol. 38, 4647–4654 (2021).
pubmed: 34320186
pmcid: 8476166
doi: 10.1093/molbev/msab199
Ko, K. K. K., Chng, K. R. & Nagarajan, N. Metagenomics-enabled microbial surveillance. Nat. Microbiol. 7, 486–496 (2022).
pubmed: 35365786
doi: 10.1038/s41564-022-01089-w
Quince, C., Walker, A. W., Simpson, J. T., Loman, N. J. & Segata, N. Shotgun metagenomics, from sampling to analysis. Nat. Biotechnol. 35, 833–844 (2017).
pubmed: 28898207
doi: 10.1038/nbt.3935
Byrd, D. A. et al. Comparison of methods to collect fecal samples for microbiome studies using whole-genome shotgun metagenomic sequencing. mSphere 5, e00827–19 (2020).
pubmed: 32250964
pmcid: 7045388
doi: 10.1128/mSphere.00827-19
Guan, H. et al. Comparison of fecal collection methods on variation in gut metagenomics and untargeted metabolomics. mSphere 6, e0063621 (2021).
pubmed: 34523982
doi: 10.1128/mSphere.00636-21
Gand, M., Bloemen, B., Vanneste, K., Roosens, N. H. C. & De Keersmaecker, S. C. J. Comparison of 6 DNA extraction methods for isolation of high yield of high molecular weight DNA suitable for shotgun metagenomics Nanopore sequencing to detect bacteria. BMC Genomics 24, 438 (2023).
pubmed: 37537550
pmcid: 10401787
doi: 10.1186/s12864-023-09537-5
Govender, K. N., Street, T. L., Sanderson, N. D. & Eyre, D. W. Metagenomic sequencing as a pathogen-agnostic clinical diagnostic tool for infectious diseases: a systematic review and meta-analysis of diagnostic test accuracy studies. J. Clin. Microbiol 59, e0291620 (2021).
pubmed: 33910965
doi: 10.1128/JCM.02916-20
Ammer-Herrmenau, C. et al. Comprehensive wet-bench and bioinformatics workflow for complex microbiota using oxford nanopore technologies. mSystems 6, e0075021 (2021).
pubmed: 34427527
doi: 10.1128/msystems.00750-21
Chiu, C. Y. & Miller, S. A. Clinical metagenomics. Nat. Rev. Genet 20, 341–355 (2019).
pubmed: 30918369
pmcid: 6858796
doi: 10.1038/s41576-019-0113-7
Campos-Madueno, E. I., Moser, A. I., Risch, M., Bodmer, T. & Endimiani, A. Exploring the global spread of Klebsiella grimontii isolates possessing bla
pubmed: 34181480
doi: 10.1128/AAC.00724-21
Moser, A. I. et al. Travellers returning from the island of Zanzibar colonized with MDR Escherichia coli strains: assessing the impact of local people and other sources. J. Antimicrob. Chemother. 76, 330–337 (2021).
pubmed: 33257991
doi: 10.1093/jac/dkaa457
Budel, T. et al. Polyclonal gut colonization with extended-spectrum cephalosporin- and/or colistin-resistant Enterobacteriaceae: a normal status for hotel employees on the island of Zanzibar, Tanzania. J. Antimicrob. Chemother. 74, 2880–2890 (2019).
pubmed: 31361004
doi: 10.1093/jac/dkz296
Bernasconi, O. J. et al. Travelers can import colistin-resistant Enterobacteriaceae, including those possessing the plasmid-mediated mcr-1 gene. Antimicrob. Agents Chemother. 60, 5080–5084 (2016).
pubmed: 27297483
pmcid: 4958239
doi: 10.1128/AAC.00731-16
Kolmogorov, M. et al. metaFlye: scalable long-read metagenome assembly using repeat graphs. Nat. Methods 17, 1103–1110 (2020).
pubmed: 33020656
pmcid: 10699202
doi: 10.1038/s41592-020-00971-x
Vaser, R., Sovic, I., Nagarajan, N. & Sikic, M. Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res. 27, 737–746 (2017).
pubmed: 28100585
pmcid: 5411768
doi: 10.1101/gr.214270.116
Bortolaia, V. et al. ResFinder 4.0 for predictions of phenotypes from genotypes. J. Antimicrob. Chemother. 75, 3491–3500 (2020).
pubmed: 32780112
pmcid: 7662176
doi: 10.1093/jac/dkaa345
Clausen, P., Aarestrup, F. M. & Lund, O. Rapid and precise alignment of raw reads against redundant databases with KMA. BMC Bioinforma. 19, 307 (2018).
doi: 10.1186/s12859-018-2336-6
Carattoli, A. et al. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob. Agents Chemother. 58, 3895–3903 (2014).
pubmed: 24777092
pmcid: 4068535
doi: 10.1128/AAC.02412-14
Larsen, M. V. et al. Multilocus sequence typing of total-genome-sequenced bacteria. J. Clin. Microbiol. 50, 1355–1361 (2012).
pubmed: 22238442
pmcid: 3318499
doi: 10.1128/JCM.06094-11
Lu, J. et al. Metagenome analysis using the Kraken software suite. Nat. Protoc. 17, 2815–2839 (2022).
pubmed: 36171387
pmcid: 9725748
doi: 10.1038/s41596-022-00738-y