Shotgun metagenomics for microbiome and resistome detection in septic patients with urinary tract infection

International Journal of Antimicrobial Agents - Tập 54 - Trang 803-808 - 2019
Olivier Barraud1, Céline Ravry1,2, Bruno François1,2,3, Thomas Daix1,2, Marie-Cécile Ploy1, Philippe Vignon1,2,3
1Université Limoges, INSERM, CHU Limoges, UMR 1092, Limoges, France
2CHU Limoges, Service de Réanimation polyvalente, Limoges, France
3INSERM, CIC1435, Limoges, France

Tài liệu tham khảo

Cecconi, 2018, Sepsis and septic shock, Lancet, 392, 75, 10.1016/S0140-6736(18)30696-2 Kumar, 2006, The duration of hypotension before the initiation of antibiotic treatment is a critical determinant of survival in a murine model of Escherichia coli septic shock: association with serum lactate and inflammatory cytokine levels, J. Infect. Dis., 193, 251, 10.1086/498909 Roca, 2015, The global threat of antimicrobial resistance: science for intervention, New Microbes New Infect., 6, 22, 10.1016/j.nmni.2015.02.007 Mancini, 2010, The era of molecular and other non-culture-based methods in diagnosis of sepsis, Clin. Microbiol. Rev., 23, 235, 10.1128/CMR.00043-09 Mencacci, 2011, Comparison of conventional culture with SeptiFast real-time PCR for microbial pathogen detection in clinical specimens other than blood, J. Med. Microbiol., 60, 1774, 10.1099/jmm.0.034280-0 Forbes, 2018, Highlighting clinical metagenomics for enhanced diagnostic decision-making: a step towards wider implementation, Comput. Struct. Biotechnol. J., 16, 108, 10.1016/j.csbj.2018.02.006 Hasman, 2014, Rapid whole-genome sequencing for detection and characterization of microorganisms directly from clinical samples, J. Clin. Microbiol., 52, 139, 10.1128/JCM.02452-13 Schmidt, 2017, Identification of bacterial pathogens and antimicrobial resistance directly from clinical urines by nanopore-based metagenomic sequencing, J. Antimicrob. Chemother., 72, 104, 10.1093/jac/dkw397 Foxman, 2010, The epidemiology of urinary tract infection, Nat. Rev. Urol., 7, 653, 10.1038/nrurol.2010.190 Levy, 2003, 2001 SCCM/ESICM/ACCP/ATS/SIS International Sepsis Definitions Conference, Crit. Care Med., 31, 1250, 10.1097/01.CCM.0000050454.01978.3B Zankari, 2012, Identification of acquired antimicrobial resistance genes, J. Antimicrob. Chemother., 67, 2640, 10.1093/jac/dks261 Vanni, 2014, Fluoroquinolone resistance and molecular characterization of gyrA and parC quinolone resistance-determining regions in Escherichia coli isolated from poultry, Poult. Sci., 93, 856, 10.3382/ps.2013-03627 Ruppe, 2017, Clinical metagenomics of bone and joint infections: a proof of concept study, Sci. Rep., 7, 7718, 10.1038/s41598-017-07546-5 Joensen, 2017, Evaluating next-generation sequencing for direct clinical diagnostics in diarrhoeal disease, Eur. J. Clin. Microbiol. Infect. Dis., 36, 1325, 10.1007/s10096-017-2947-2 Majeed, 2017, An update on emerging therapies for urinary tract infections, Expert. Opin. Emerg. Drugs, 22, 53, 10.1080/14728214.2017.1293650 Cattoir, 2012, Actinobaculum schaalii: review of an emerging uropathogen, J. Infect., 64, 260, 10.1016/j.jinf.2011.12.009 Siddiqui, 2014, Pathogens in urine from a female patient with overactive bladder syndrome detected by culture-independent high throughput sequencing: a case report, Open. Microbiol. J., 8, 148, 10.2174/1874285801408010148 Sherry, 2013, Outbreak investigation using high-throughput genome sequencing within a diagnostic microbiology laboratory, J. Clin. Microbiol., 51, 1396, 10.1128/JCM.03332-12 Didelot, 2012, Transforming clinical microbiology with bacterial genome sequencing, Nat. Rev. Genet., 13, 601, 10.1038/nrg3226 Angers-Loustau, 2018, The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies, F1000Res., 7