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Original Research

Profile of Bacteria with ARGs Among Real-World Samples from ICU Admission Patients with Pulmonary Infection Revealed by Metagenomic NGS

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Pages 4993-5004 | Published online: 27 Nov 2021

References

  • Mehta AB, Syeda SN, Wiener RS, et al. Epidemiological trends in invasive mechanical ventilation in the United States: a population-based study. J Crit Care. 2015;30(6):1217–1221. doi:10.1016/j.jcrc.2015.07.00726271686
  • Luyt CE, Hékimian G, Koulenti D, et al. Microbial cause of ICU-acquired pneumonia: hospital-acquired pneumonia versus ventilator-associated pneumonia. Curr Opin Crit Care. 2018;24(5):332–338. doi:10.1097/MCC.000000000000052630036192
  • Boucher HW, Talbot GH, Bradley JS, et al. Bad bugs, no drugs: no ESKAPE! An update from the infectious diseases society of America. Clin Infect Dis. 2009;48(1):1–12. doi:10.1086/59501119035777
  • Moore LS, Freeman R, Gilchrist MJ, et al. Homogeneity of antimicrobial policy, yet heterogeneity of antimicrobial resistance: antimicrobial non-susceptibility among 108,717 clinical isolates from primary, secondary and tertiary care patients in London. J Antimicrob Chemother. 2014;69(12):3409–3422. doi:10.1093/jac/dku30725118270
  • Kalil AC, Metersky ML, Klompas M, et al. Executive summary: management of adults with hospital-acquired and ventilator-associated pneumonia: 2016 clinical practice guidelines by the infectious diseases society of America and the American thoracic society. Clin Infect Dis. 2016;63(5):575–582. doi:10.1093/cid/ciw50427521441
  • Dananché C, Vanhems P, Machut A, et al. Trends of incidence and risk factors of ventilator-associated pneumonia in elderly patients admitted to French ICUs between 2007 and 2014. Crit Care Med. 2018;46(6):869–877. doi:10.1097/CCM.000000000000301929432348
  • Luna CM, Aruj P, Niederman MS, et al. Appropriateness and delay to initiate therapy in ventilator-associated pneumonia. Eur Respir J. 2006;27(1):158–164. doi:10.1183/09031936.06.0004910516387949
  • MacVane SH. Antimicrobial resistance in the intensive care unit: a focus on gram-negative bacterial infections. J Intensive Care Med. 2017;32(1):25–37. doi:10.1177/088506661561989526772199
  • Martins ST, Moreira M, Furtado GH, et al. Application of control measures for infections caused by multi-resistant gram-negative bacteria in intensive care unit patients. Mem Inst Oswaldo Cruz. 2004;99(3):331–334. doi:10.1590/S0074-0276200400030001715273810
  • Sader HS, Farrell DJ, Flamm RK, et al. Antimicrobial susceptibility of Gram-negative organisms isolated from patients hospitalised with pneumonia in US and European hospitals: results from the SENTRY Antimicrobial Surveillance Program, 2009–2012. Int J Antimicrob Agents. 2014;43(4):328–334. doi:10.1016/j.ijantimicag.2014.01.00724630306
  • Torres A, Zhong N, Pachl J, et al. Ceftazidime-avibactam versus meropenem in nosocomial pneumonia, including ventilator-associated pneumonia (REPROVE): a randomised, double-blind, Phase 3 non-inferiority trial. Lancet Infect Dis. 2018;18(3):285–295. doi:10.1016/S1473-3099(17)30747-829254862
  • Bowstead TT, Santiago SM. Pleuropulmonary infection due to Corynebacterium striatum. Br J Dis Chest. 1980;74(2):198–200. doi:10.1016/0007-0971(80)90035-27426360
  • Alibi S, Ferjani A, Boukadida J, et al. Occurrence of Corynebacterium striatum as an emerging antibiotic-resistant nosocomial pathogen in a Tunisian hospital. Sci Rep. 2017;7(1):9704. doi:10.1038/s41598-017-10081-y28848236
  • Wang X, Zhou H, Chen D, et al. Whole-genome sequencing reveals a prolonged and persistent intrahospital transmission of Corynebacterium striatum, an emerging multidrug-resistant pathogen. J Clin Microbiol. 2019;57(9):e00683–19. doi:10.1128/JCM.00683-1931315959
  • Shariff M, Aditi A, Beri K. Corynebacterium striatum: an emerging respiratory pathogen. J Infect Dev Ctries. 2018;12(7):581–586. doi:10.3855/jidc.1040631954008
  • McMullen AR, Anderson N, Wallace MA, et al. When good bugs go bad: epidemiology and antimicrobial resistance profiles of Corynebacterium striatum, an emerging multidrug-resistant, opportunistic pathogen. Antimicrob Agents Chemother. 2017;61(11):e01111–17. doi:10.1128/AAC.01111-1728848008
  • Verroken A, Bauraing C, Deplano A, et al. Epidemiological investigation of a nosocomial outbreak of multidrug-resistant Corynebacterium striatum at one Belgian university hospital. Clin Microbiol Infect. 2014;20(1):44–50. doi:10.1111/1469-0691.1219723586637
  • Wang J, Wang Y, Du X, et al. Rapid transmission of multidrug-resistant Corynebacterium striatum among susceptible patients in a tertiary hospital in China. J Infect Dev Ctries. 2016;10(12):1299–1305. doi:10.3855/jidc.757728036309
  • Ortiz-Pérez A, Martín-de-hijas NZ, Esteban J, et al. High frequency of macrolide resistance mechanisms in clinical isolates of Corynebacterium species. Microb Drug Resist. 2010;16(4):273–277. doi:10.1089/mdr.2010.003220624090
  • Otsuka Y, Ohkusu K, Kawamura Y, et al. Emergence of multidrug-resistant Corynebacterium striatum as a nosocomial pathogen in long-term hospitalized patients with underlying diseases. Diagn Microbiol Infect Dis. 2006;54(2):109–114. doi:10.1016/j.diagmicrobio.2005.08.00516406181
  • Ramos JN, Souza C, Faria YV, et al. Bloodstream and catheter-related infections due to different clones of multidrug-resistant and biofilm producer Corynebacterium striatum. BMC Infect Dis. 2019;19(1):672. doi:10.1186/s12879-019-4294-731357945
  • Asgin N, Otlu B. Antimicrobial resistance and molecular epidemiology of Corynebacterium striatum isolated in a tertiary hospital in Turkey. Pathogens. 2020;9(2):136. doi:10.3390/pathogens9020136
  • Schröder J, Maus I, Meyer K, et al. Complete genome sequence, lifestyle, and multi-drug resistance of the human pathogen Corynebacterium resistens DSM 45100 isolated from blood samples of a leukemia patient. BMC Genomics. 2012;13:141. doi:10.1186/1471-2164-13-14122524407
  • Eguchi H, Kuwahara T, Miyamoto T, et al. High-level fluoroquinolone resistance in ophthalmic clinical isolates belonging to the species Corynebacterium macginleyi. J Clin Microbiol. 2008;46(2):527–532. doi:10.1128/JCM.01741-0718077650
  • Campanile F, Carretto E, Barbarini D, et al. Clonal multidrug-resistant Corynebacterium striatum strains, Italy. Emerg Infect Dis. 2009;15(1):75–78. doi:10.3201/eid1501.08080419116057
  • Inchai J, Pothirat C, Liwsrisakun C, et al. Ventilator-associated pneumonia: epidemiology and prognostic indicators of 30-day mortality. Jpn J Infect Dis. 2015;68(3):181–186. doi:10.7883/yoken.JJID.2014.28225672347
  • Koulenti D, Tsigou E, Rello J. Nosocomial pneumonia in 27 ICUs in Europe: perspectives from the EU-VAP/CAP study. Eur J Clin Microbiol Infect Dis. 2017;36(11):1999–2006. doi:10.1007/s10096-016-2703-z27287765
  • Vincent JL, Rello J, Marshall J, et al. International study of the prevalence and outcomes of infection in intensive care units. JAMA. 2009;302(21):2323–2329. doi:10.1001/jama.2009.175419952319
  • Jia W, Li C, Zhang H, et al. Prevalence of genes of OXA-23 carbapenemase and AdeABC efflux pump associated with multidrug resistance of Acinetobacter baumannii isolates in the ICU of a comprehensive hospital of Northwestern China. Int J Environ Res Public Health. 2015;12(8):10079–10092. doi:10.3390/ijerph12081007926308027
  • Hollenbeck BL, Rice LB. Intrinsic and acquired resistance mechanisms in enterococcus. Virulence. 2012;3(5):421–433. doi:10.4161/viru.2128223076243
  • Cattoir V, Giard JC. Antibiotic resistance in Enterococcus faecium clinical isolates. Expert Rev Anti Infect Ther. 2014;12(2):239–248. doi:10.1586/14787210.2014.87088624392717
  • Fernández L, Hancock RE. Adaptive and mutational resistance: role of porins and efflux pumps in drug resistance. Clin Microbiol Rev. 2012;25(4):661–681. doi:10.1128/CMR.00043-1223034325
  • Palmeiro JK, de Souza RF, Schörner MA, et al. Molecular epidemiology of multidrug-resistant Klebsiella pneumonia isolates in a Brazilian tertiary hospital. Front Microbiol. 2019;10:1669. doi:10.3389/fmicb.2019.0166931396186
  • Pan YP, Xu YH, Wang ZX, et al. Overexpression of MexAB-OprM efflux pump in carbapenem-resistant Pseudomonas aeruginosa. Arch Microbiol. 2016;198(6):565–571. doi:10.1007/s00203-016-1215-727060003
  • Horna G, López M, Guerra H, et al. Interplay between MexAB-OprM and MexEF-OprN in clinical isolates of Pseudomonas aeruginosa. Sci Rep. 2018;8(1):16463. doi:10.1038/s41598-018-34694-z30405166
  • Mazzariol A, Zuliani J, Cornaglia G, et al. AcrAB efflux system: expression and contribution to fluoroquinolone resistance in Klebsiella spp. Antimicrob Agents Chemother. 2002;46(12):3984–3986. doi:10.1128/AAC.46.12.3984-3986.200212435706
  • Bernardini A, Cuesta T, Tomás A, et al. The intrinsic resistome of Klebsiella pneumoniae. Int J Antimicrob Agents. 2019;53(1):29–33. doi:10.1016/j.ijantimicag.2018.09.01230236960
  • Rizek CF, Jonas D, Garcia Paez JI, et al. Multidrug-resistant Stenotrophomonas maltophilia: description of new MLST profiles and resistance and virulence genes using whole-genome sequencing. J Glob Antimicrob Resist. 2018;15:212–214. doi:10.1016/j.jgar.2018.07.00930036694
  • Chang LL, Chen HF, Chang CY, et al. Contribution of integrons, and SmeABC and SmeDEF efflux pumps to multidrug resistance in clinical isolates of Stenotrophomonas maltophilia. J Antimicrob Chemother. 2004;53(3):518–521. doi:10.1093/jac/dkh09414749340
  • Fritz CQ, Edwards KM, Self WH, et al. Prevalence, risk factors, and outcomes of bacteremic pneumonia in children. Pediatrics. 2019;144(1):e20183090. doi:10.1542/peds.2018-309031217309
  • Beumer MC, Koch RM, van Beuningen D, et al. Influenza virus and factors that are associated with ICU admission, pulmonary co-infections and ICU mortality. J Crit Care. 2019;50:59–65. doi:10.1016/j.jcrc.2018.11.01330481669
  • Wierzbowski AK, Boyd D, Mulvey M, et al. Expression of the mef (E) gene encoding the macrolide efflux pump protein increases in Streptococcus pneumoniae with increasing resistance to macrolides. Antimicrob Agents Chemother. 2005;49(11):4635–4640. doi:10.1128/AAC.49.11.4635-4640.200516251306
  • Izumikawa K, Yamamoto Y, Yanagihara K, et al. Active surveillance of methicillin-resistant Staphylococcus aureus with the BD GeneOhm MRSA™ assay in a respiratory ward in Nagasaki, Japan. Jpn J Infect Dis. 2012;65(1):33–36.22274155
  • Veloso JO, Lamaro-Cardoso J, Neves LS, et al. Methicillin-resistant and vancomycin-intermediate Staphylococcus aureus colonizing patients and intensive care unit environment: virulence profile and genetic variability. APMIS. 2019;127(11):717–726. doi:10.1111/apm.1298931407405
  • Ziakas PD, Anagnostou T, Mylonakis E. The prevalence and significance of methicillin-resistant Staphylococcus aureus colonization at admission in the general ICU setting: a meta-analysis of published studies. Crit Care Med. 2014;42(2):433–444. doi:10.1097/CCM.0b013e3182a66bb824145849
  • Qiao F, Huang W, Cai L, et al. Methicillin-resistant Staphylococcus aureus nasal colonization and infection in an intensive care unit of a university hospital in China. J Int Med Res. 2018;46(9):3698–3708. doi:10.1177/030006051877781229911488
  • Wang Q, Wu B, Yang D, et al. Optimal specimen type for accurate diagnosis of infectious peripheral pulmonary lesions by mNGS. BMC Pulm Med. 2020;20(1):268. doi:10.1186/s12890-020-01298-133059646
  • Wang Q, Miao Q, Pan J, et al. The clinical value of metagenomic next-generation sequencing in the microbiological diagnosis of skin and soft tissue infections. Int J Infect Dis. 2020;100:414–420. doi:10.1016/j.ijid.2020.09.00732898669
  • Hu YY, Cao JM, Yang Q, et al. Risk factors for carbapenem-resistant pseudomonas aeruginosa, Zhejiang Province, China. Emerg Infect Dis. 2019;25(10):1861–1867. doi:10.3201/eid2510.18169931538558
  • Huang L, Zhang R, Hu Y, et al. Epidemiology and risk factors of methicillin-resistant Staphylococcus aureus and vancomycin-resistant enterococci infections in Zhejiang China from 2015 to 2017. Antimicrob Resist Infect Control. 2019;8:90. doi:10.1186/s13756-019-0539-x31164979
  • Simner PJ, Miller S, Carroll KC. Understanding the promises and hurdles of metagenomic next-generation sequencing as a diagnostic tool for infectious diseases. Clin Infect Dis. 2018;66(5):778–788. doi:10.1093/cid/cix88129040428
  • Li H, Gao H, Meng H, et al. Detection of pulmonary infectious pathogens from lung biopsy tissues by metagenomic next-generation sequencing. Front Cell Infect Microbiol. 2018;8:205. doi:10.3389/fcimb.2018.0020529988504
  • Yuan J, Li W, Qiu E, et al. Metagenomic NGS optimizes the use of antibiotics in appendicitis patients: bacterial culture is not suitable as the only guidance. Am J Transl Res. 2021;13(4):3010–3021.34017469
  • Yee R, Breitwieser FP, Hao S, 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. 2021;40(1):95–102. doi:10.1007/s10096-020-03996-432783106
  • Sukhum KV, Diorio-Toth L, Dantas G. Genomic and metagenomic approaches for predictive surveillance of emerging pathogens and antibiotic resistance. Clin Pharmacol Ther. 2019;106(3):512–524. doi:10.1002/cpt.153531172511
  • Langelier C, Kalantar KL, Moazed F, et al. Integrating host response and unbiased microbe detection for lower respiratory tract infection diagnosis in critically ill adults. Proc Natl Acad Sci U S A. 2018;115(52):E12353–E12362. doi:10.1073/pnas.180970011530482864
  • Zinter MS, Dvorak CC, Mayday MY, et al. Pulmonary metagenomic sequencing suggests missed infections in immunocompromised children. Clin Infect Dis. 2019;68(11):1847–1855. doi:10.1093/cid/ciy80230239621
  • Schlaberg R, Chiu CY, Miller S, et al. Validation of metagenomic next-generation sequencing tests for universal pathogen detection. Arch Pathol Lab Med. 2017;141(6):776–786. doi:10.5858/arpa.2016-0539-RA28169558
  • Liapikou A, Cillóniz C, Torres A. Emerging strategies for the noninvasive diagnosis of nosocomial pneumonia. Expert Rev Anti Infect Ther. 2019;17(7):523–533. doi:10.1080/14787210.2019.163501031237462
  • Nicolau DP, Dimopoulos G, Welte T, et al. Can we improve clinical outcomes in patients with pneumonia treated with antibiotics in the intensive care unit? Expert Rev Respir Med. 2016;10(8):907–918. doi:10.1080/17476348.2016.119027727181707
  • Jeukens J, Freschi L, Kukavica-Ibrulj I, et al. Genomics of antibiotic-resistance prediction in Pseudomonas aeruginosa. Ann N Y Acad Sci. 2019;1435(1):5–17. doi:10.1111/nyas.1335828574575
  • Angers-Loustau A, Petrillo M, Bengtsson-Palme J, et al. The challenges of designing a benchmark strategy for bioinformatics pipelines in the identification of antimicrobial resistance determinants using next generation sequencing technologies. F1000Res. 2018;7:459. doi:10.12688/f1000research.14509.2
  • Chen X, Ding S, Lei C, et al. Blood and bronchoalveolar lavage fluid metagenomic next-generation sequencing in pneumonia. Can J Infect Dis Med Microbiol. 2020;2020:6839103. doi:10.1155/2020/683910332879643
  • Murugesan K, Hogan CA, Palmer Z, et al. Investigation of preanalytical variables impacting pathogen cell-free DNA in blood and urine. J Clin Microbiol. 2019;57(11):e00782–19. doi:10.1128/JCM.00782-1931511335
  • Han D, Li R, Shi J, et al. Liquid biopsy for infectious diseases: a focus on microbial cell-free DNA sequencing. Theranostics. 2020;10(12):5501–5513. doi:10.7150/thno.4555432373224
  • Ho J, Marks GB, Fox GJ. The impact of sputum quality on tuberculosis diagnosis: a systematic review. Int J Tuberc Lung Dis. 2015;19(5):537–544. doi:10.5588/ijtld.14.079825868021
  • Carnevale GG, Vargas FS, Caiaffa-Filho HH, et al. Preanalytical conditions can interfere with M. tuberculosis detection by PCR in respiratory samples. Clinics. 2018;73:e410. doi:10.6061/clinics/2017/e41030517280
  • Hector A, Jonas F, Kappler M, et al. Novel method to process cystic fibrosis sputum for determination of oxidative state. Respiration. 2010;80(5):393–400. doi:10.1159/00027160720029169
  • Sandiumenge A, Lisboa T, Gomez F, et al. Effect of antibiotic diversity on ventilator-associated pneumonia caused by ESKAPE organisms. Chest. 2011;140(3):643–651. doi:10.1378/chest.11-046221659436
  • Patterson JE, Sweeney AH, Simms M, et al. An analysis of 110 serious enterococcal infections. Epidemiology, antibiotic susceptibility, and outcome. Medicine. 1995;74(4):191–200. doi:10.1097/00005792-199507000-000037623654
  • Li F, Wang Y, Sun L, Wang X. Vancomycin-resistant Enterococcus faecium pneumonia in a uremic patient on hemodialysis: a case report and review of the literature. BMC Infect Dis. 2020;20(1):167. doi:10.1186/s12879-020-4892-432087689