412
Views
1
CrossRef citations to date
0
Altmetric
Review

Strengths and caveats of identifying resistance genes from whole genome sequencing data

, , , &
Pages 533-547 | Received 04 Jul 2021, Accepted 30 Nov 2021, Published online: 16 Dec 2021

References

  • World Health Organization. The top 10 causes of death (Geneva: WHO). 2020.
  • Wellcome. The Global Response to AMR: momentum, success, and critical gaps. (London, 2020). [cited27 Sep 2021]. https://cms.wellcome.org/sites/default/files/2020-11/wellcome-global-response-amr-report.pdf
  • Dmp DO, Forde BM, Kidd TJ, et al. Antimicrobial Resistance in ESKAPE Pathogens. Clin Microbiol Rev. 2020;33(3):e00181–19.
  • Centers for Disease Control and Prevention. Antibiotic resistant threats in the United States. 2019. https://www.cdc.gov/drugresistance/pdf/threats-report/2019-ar-threats-report-508.pdf. ( Accessed. 2020 Jan 15th)
  • Cassini A, Hogberg LD, Plachouras D, et al. Attributable deaths and disability-adjusted life-years caused by infections with antibiotic-resistant bacteria in the EU and the European Economic Area in 2015: a population-level modelling analysis. Lancet Infect Dis. 2019;19(1):56–66.
  • Weist K, Hogberg LD. ECDC publishes 2015 surveillance data on antimicrobial resistance and antimicrobial consumption in Europe. Euro Surveill. 2016;21(46):30401.
  • Chiang HY, Perencevich EN, Nair R, et al. Incidence and Outcomes Associated With Infections Caused by Vancomycin-Resistant Enterococci in the United States: systematic Literature Review and Meta-Analysis. Infect Control Hosp Epidemiol. 2017;38(2):203–215.
  • Cosgrove SE, Sakoulas G, Perencevich EN, et al. Comparison of mortality associated with methicillin-resistant and methicillin-susceptible Staphylococcus aureus bacteremia: a meta-analysis. Clin Infect Dis. 2003;36(1):53–59.
  • Sk P, Ding Y, Ml L, et al. Economic and clinical impact of nosocomial meticillin-resistant Staphylococcus aureus infections in Singapore: a matched case-control study. J Hosp Infect. 2011;78(1):36–40.
  • Fleece ME, Pholwat S, Mathers AJ, et al. Molecular diagnosis of antimicrobial resistance in Escherichia coli. Expert Rev Mol Diagn. 2018;18(3):207–217.
  • Ferreira I, Beisken S, Lueftinger L, et al. Species Identification and Antibiotic Resistance Prediction by Analysis of Whole-Genome Sequence Data by Use of ARESdb: an Analysis of Isolates from the Unyvero Lower Respiratory Tract Infection Trial. J Clin Microbiol. 2020;58(7):e00273–00220.
  • McDermott PF, Tyson GH, Kabera C, et al. Whole-Genome Sequencing for Detecting Antimicrobial Resistance in Nontyphoidal Salmonella. Antimicrob Agents Chemother. 2016;60(9):5515–5520.
  • Argimon S, Masim MAL, Gayeta JM, et al. Integrating whole-genome sequencing within the National Antimicrobial Resistance Surveillance Program in the Philippines. Nat Commun. 2020;11(1):2719.
  • Kabra R, Chauhan N, Kumar A, et al. Efflux pumps and antimicrobial resistance: paradoxical components in systems genomics. Prog Biophys Mol Biol. 2019;141;15–24.
  • Li XZ, Plesiat P, Nikaido H. The challenge of efflux-mediated antibiotic resistance in Gram-negative bacteria. Clin Microbiol Rev. 2015;28(2):337–418.
  • Hassan KA, Liu Q, Henderson PJ, et al. Homologs of the Acinetobacter baumannii AceI transporter represent a new family of bacterial multidrug efflux systems. mBio. 2015;6(1).
  • Quinn JP, Dudek EJ, DiVincenzo CA, et al. Emergence of resistance to imipenem during therapy for Pseudomonas aeruginosa infections. J Infect Dis. 1986;154(2):289–294.
  • Hasdemir UO, Chevalier J, Nordmann P, et al. Detection and prevalence of active drug efflux mechanism in various multidrug-resistant Klebsiella pneumoniae strains from Turkey. J Clin Microbiol. 2004;42(6):2701–2706.
  • Laponogov I, Sohi MK, Veselkov DA, et al. Structural insight into the quinolone-DNA cleavage complex of type IIA topoisomerases. Nat Struct Mol Biol. 2009;16(6):667–669.
  • Morais Cabral JH, Jackson AP, Smith CV, et al. Crystal structure of the breakage-Reunion domain of DNA gyrase. Nature. 1997;388(6645):903–906.
  • Wohlkonig A, Chan PF, Fosberry AP, et al. Structural basis of quinolone inhibition of type IIA topoisomerases and target-mediated resistance. Nat Struct Mol Biol. 2010;17(9):1152–1153.
  • Horinouchi S, Weisblum B. Posttranscriptional modification of mRNA conformation: mechanism that regulates erythromycin-induced resistance. Proc Natl Acad Sci U S A. 1980;77(12):7079–7083.
  • Weisblum B. Erythromycin resistance by ribosome modification. Antimicrob Agents Chemother. 1995;39(3):577–585.
  • Arias CA, Murray BE. The rise of the Enterococcus: beyond vancomycin resistance. Nat Rev Microbiol. 2012;10(4):266–278.
  • Lakhundi S, Zhang K. Methicillin-Resistant Staphylococcus aureus: molecular Characterization, Evolution, and Epidemiology. Clin Microbiol Rev. 2018;31:4.
  • Cannatelli A, Santos-Lopez A, Giani T, et al. Polymyxin resistance caused by mgrB inactivation is not associated with significant biological cost in Klebsiella pneumoniae. Antimicrob Agents Chemother. 2015;59(5):2898–2900.
  • Leung LM, Cooper VS, Rasko DA, et al. Structural modification of LPS in colistin-resistant, KPC-producing Klebsiella pneumoniae. J Antimicrob Chemother. 2017;72(11):3035–3042.
  • Zowawi HM, Forde BM, Alfaresi M, et al. Stepwise evolution of pandrug-resistance in Klebsiella pneumoniae. Sci Rep. 2015;5(15082):e01982–14.
  • Keshri V, Diene SM, Estienne A, et al. An Integrative Database of beta-Lactamase Enzymes: sequences, Structures, Functions, and Phylogenetic Trees. Antimicrob Agents Chemother. 2019;63:5.
  • Naas T, Oueslati S, Bonnin RA, et al. Beta-lactamase database (BLDB) - structure and function. J Enzyme Inhib Med Chem. 2017;32(1):917–919.
  • Shaw KJ, Rather PN, Hare RS, et al. Molecular genetics of aminoglycoside resistance genes and familial relationships of the aminoglycoside-modifying enzymes. Microbiol Rev. 1993;57(1):138–163.
  • Bhatnagar K, Wong A. The mutational landscape of quinolone resistance in Escherichia coli. Plos One. 2019;14(11):e0224650.
  • Hamasuna R, Le PT, Kutsuna S, et al. Mutations in ParC and GyrA of moxifloxacin-resistant and susceptible Mycoplasma genitalium strains. Plos One. 2018;13(6):e0198355.
  • Buwembo W, Aery S, Rwenyonyi CM, et al. Point Mutations in the folP Gene Partly Explain Sulfonamide Resistance of Streptococcus mutans. Int J Microbiol. 2013;367021:2013.
  • Poirel L, Jayol A, Nordmann P. Polymyxins: antibacterial Activity, Susceptibility Testing, and Resistance Mechanisms Encoded by Plasmids or Chromosomes. Clin Microbiol Rev. 2017;30(2):557–596.
  • Partridge SR, Kwong SM, Firth N, et al. Mobile Genetic Elements Associated with Antimicrobial Resistance. Clin Microbiol Rev. 2018;31(4):e00088–17.
  • Koser CU, Ellington MJ, Peacock SJ. Whole-genome sequencing to control antimicrobial resistance. Trends Genet. 2014;30(9):401–407.
  • Chen TL, Wu RC, Shaio MF, et al. Acquisition of a plasmid-borne blaOXA-58 gene with an upstream IS1008 insertion conferring a high level of carbapenem resistance to Acinetobacter baumannii. Antimicrob Agents Chemother. 2008;52(7):2573–2580.
  • Vandecraen J, Chandler M, Aertsen A, et al. The impact of insertion sequences on bacterial genome plasticity and adaptability. Crit Rev Microbiol. 2017;43(6):709–730.
  • Rosenfeld N, Bouchier C, Courvalin P, et al. Expression of the resistance-nodulation-cell division pump AdeIJK in Acinetobacter baumannii is regulated by AdeN, a TetR-type regulator. Antimicrob Agents Chemother. 2012;56(5):2504–2510.
  • Lee CH, Chu C, Liu JW, et al. Collateral damage of flomoxef therapy: in vivo development of porin deficiency and acquisition of blaDHA-1 leading to ertapenem resistance in a clinical isolate of Klebsiella pneumoniae producing CTX-M-3 and SHV-5 beta-lactamases. J Antimicrob Chemother. 2007;60(2):410–413.
  • Quainoo S, Coolen JPM, van Hijum S, et al. Whole-Genome Sequencing of Bacterial Pathogens: the Future of Nosocomial Outbreak Analysis. Clin Microbiol Rev. 2017;30(4):1015–1063.
  • World Health Organization. Global Antimicrobial Resistance and Use Surveillance System (GLASS): whole-genome sequencing for surveillance of antimicrobial resistance. Geneva: WHO; 2020.
  • Gwinn M, MacCannell D, Armstrong GL. Next-Generation Sequencing of Infectious Pathogens. JAMA. 2019;321(9):893–894.
  • Loose M, Malla S, Stout M. Real-time selective sequencing using nanopore technology. Nat Methods. 2016;13(9):751–754.
  • Xie H, Yang C, Sun Y, et al. PacBio Long Reads Improve Metagenomic Assemblies, Gene Catalogs, and Genome Binning. Front Genet. 2020;11:516269.
  • Hendriksen RS, Bortolaia V, Tate H, et al. Using Genomics to Track Global Antimicrobial Resistance. Front Public Health. 2019;7(242).
  • Afgan E, Baker D, Batut B, et al. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucleic Acids Res. 2018;46(W1):W537–W544.
  • Doyle RM, O’Sullivan DM, Aller SD, et al. Discordant bioinformatic predictions of antimicrobial resistance from whole-genome sequencing data of bacterial isolates: an inter-laboratory study. Microb Genom. 2020;6(2):e000335.
  • Andrews S. FastQC: a quality control tool for high throughput sequence data. 2010. http://www.bioinformatics.babraham.ac.uk/projects/fastqc. ( Accessed. 2021 Jun 24)
  • Su M, Satola SW, Read TD. Genome-Based Prediction of Bacterial Antibiotic Resistance. J Clin Microbiol. 2019;57(3):e01405–18.
  • Van Camp PJ, Haslam DB, Porollo A. Bioinformatics Approaches to the Understanding of Molecular Mechanisms in Antimicrobial Resistance. Int J Mol Sci. 2020;21(4):1363.
  • Maryam L, Usmani SS, Raghava GPS. Computational resources in the management of antibiotic resistance: speeding up drug discovery. In Drug Discovery Today 26 9 . 2021 2138–2151 .
  • Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25(14):1754–1760.
  • Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357–359.
  • Li H. Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences. Bioinformatics. 2016;32(14):2103–2110.
  • Clausen P, Aarestrup FM, Lund O. Rapid and precise alignment of raw reads against redundant databases with KMA. BMC Bioinformatics. 2018;19(1):307.
  • Altschul SF, Gish W, Miller W, et al. Basic local alignment search tool. J Mol Biol. 1990;215(3):403–410.
  • Inouye M, Dashnow H, Raven LA, et al. SRST2: rapid genomic surveillance for public health and hospital microbiology labs. Genome Med. 2014;6(11):90.
  • Lakin SM, Dean C, Noyes NR, et al. MEGARes: an antimicrobial resistance database for high throughput sequencing. Nucleic Acids Res. 2017;45(D1):D574–D580.
  • Bortolaia V, Kaas RS, Ruppe E, et al. ResFinder 4.0 for predictions of phenotypes from genotypes. J Antimicrob Chemother. 2020;75(12):3491–3500.
  • Zankari E, Allesoe R, Joensen KG, et al. PointFinder: a novel web tool for WGS-based detection of antimicrobial resistance associated with chromosomal point mutations in bacterial pathogens. J Antimicrob Chemother. 2017;72(10):2764–2768.
  • Hunt M, Mather AE, Sanchez-Buso L, et al. ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads. Microb Genom. 2017;3(10):e000131.
  • Clausen PT, Zankari E, Aarestrup FM, et al. Benchmarking of methods for identification of antimicrobial resistance genes in bacterial whole genome data. J Antimicrob Chemother. 2016;71(9):2484–2488.
  • Cooper AL, Low AJ, Koziol AG, et al. Systematic Evaluation of Whole Genome Sequence-Based Predictions of Salmonella Serotype and Antimicrobial Resistance. Front Microbiol. 2020;11(549).
  • Schurch AC, van Schaik W. Challenges and opportunities for whole-genome sequencing-based surveillance of antibiotic resistance. Ann N Y Acad Sci. 2017;1388(1):108–120.
  • Ellington MJ, Ekelund O, Aarestrup FM, et al. The role of whole genome sequencing in antimicrobial susceptibility testing of bacteria: report from the EUCAST Subcommittee. Clin Microbiol Infect. 2017;23(1):2–22.
  • Berbers B, Ceyssens PJ, Bogaerts P, et al. Development of an NGS-Based Workflow for Improved Monitoring of Circulating Plasmids in Support of Risk Assessment of Antimicrobial Resistance Gene Dissemination. Antibiotics (Basel). 2020;9(8).
  • Mason A, Foster D, Bradley P, et al. Accuracy of Different Bioinformatics Methods in Detecting Antibiotic Resistance and Virulence Factors from Staphylococcus aureus Whole-Genome Sequences. J Clin Microbiol. 2018;56(9):e01815–17.
  • Feldgarden M, Brover V, Haft DH, et al. Validating the AMRFinder Tool and Resistance Gene Database by Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of Isolates. Antimicrob Agents Chemother. 2019;63(11): e00483–19.
  • Xavier BB, Das AJ, Cochrane G, et al. Consolidating and Exploring Antibiotic Resistance Gene Data Resources. J Clin Microbiol. 2016;54(4):851–859.
  • Madden DE, Webb JR, Steinig EJ, et al. Taking the next-gen step: comprehensive antimicrobial resistance detection from Burkholderia pseudomallei. EBioMedicine. 2021;63(103152).
  • Alcock BP, Raphenya AR, Lau TTY, et al. CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res. 2020;48(D1):D517–d525.
  • Doster E, Lakin SM, Dean CJ, et al. MEGARes 2.0: a database for classification of antimicrobial drug, biocide and metal resistance determinants in metagenomic sequence data. Nucleic Acids Res. 2019;48(D1):D561–D569.
  • National Center for Biotechnology Information. Bacterial Antimicrobial Resistance Reference Gene Database. 2016. https://www.ncbi.nlm.nih.gov/bioproject/PRJNA313047. ( Accessed. 2021 Jul 24)
  • Davis JJ, Wattam AR, Aziz RK, et al. The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities. Nucleic Acids Res. 2020;48(D1):D606–D612.
  • Evans BA, Amyes SG. OXA β-lactamases. Clin Microbiol Rev. 2014;27(2):241–263.
  • Tyson GH, McDermott PF, Li C, et al. WGS accurately predicts antimicrobial resistance in Escherichia coli. J Antimicrob Chemother. 2015;70(10):2763–2769.
  • Bradley P, Gordon NC, Walker TM, et al. Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis. Nat Commun. 2015;6(10063).
  • Depardieu F, Podglajen I, Leclercq R, et al. Modes and modulations of antibiotic resistance gene expression. Clin Microbiol Rev. 2007;20(1):79–114.
  • Ko ER, Philipson CW, Burke TW, et al. Direct-from-blood RNA sequencing identifies the cause of post-bronchoscopy fever. BMC Infect Dis. 2019;19(1):905.
  • Siguier P, Gourbeyre E, Varani A, et al. Everyman’s Guide to Bacterial Insertion Sequences. Microbiol Spectr. 2015;3:2. MDNA3-0030-2014
  • Bennett PM. Plasmid encoded antibiotic resistance: acquisition and transfer of antibiotic resistance genes in bacteria. Br J Pharmacol. 2008;153(Suppl 1):S347–357.
  • Haniford DB, Ellis MJ. Transposons Tn10 and Tn5. Microbiol Spectr. 2015;3:1. MDNA3-0002-2014
  • Liu YY, Wang Y, Walsh TR, et al. Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study. Lancet Infect Dis. 2016;16(2):161–168.
  • Weigel LM, Clewell DB, Gill SR, et al. Genetic analysis of a high-level vancomycin-resistant isolate of Staphylococcus aureus. Science. 2003;302(5650):1569–1571.
  • Peters JE. Tn7. Microbiol Spectr. 2014;2(5):MDNA3-0010-2014 .
  • Nicolas E, Lambin M, Dandoy D, et al. The Tn3-family of Replicative Transposons. Microbiol Spectr. 2015;3(4):MDNA3-0060-2014.
  • Partridge SR, Hall RM. Evolution of transposons containing blaTEM genes. Antimicrob Agents Chemother. 2005;49(3):1267–1268.
  • Lopez M, Saenz Y, Alvarez-Martinez MJ, et al. Tn1546 structures and multilocus sequence typing of vanA-containing enterococci of animal, human and food origin. J Antimicrob Chemother. 2010;65(8):1570–1575.
  • Zong Z, Ginn AN, Dobiasova H, et al. Different IncI1 plasmids from Escherichia coli carry ISEcp1-blaCTX-M-15 associated with different Tn2-derived elements. Plasmid. 2015;80(118–126).
  • Chen YG, Qu TT, Yu YS, et al. Insertion sequence ISEcp1-like element connected with a novel aph(2”) allele [aph(2”)-Ie] conferring high-level gentamicin resistance and a novel streptomycin adenylyltransferase gene in Enterococcus. J Med Microbiol. 2006;55(Pt 11):1521–1525.
  • Partridge SR. Mobilization of blaBKC-1 by ISKpn23? Antimicrob Agents Chemother. 2016;60(8):5102–5104.
  • Poirel L, Lartigue MF, Decousser JW, et al. ISEcp1B-mediated transposition of blaCTX-M in Escherichia coli. Antimicrob Agents Chemother. 2005;49(1):447–450.
  • Aubert D, Naas T, Nordmann P. IS1999 increases expression of the extended-spectrum beta-lactamase VEB-1 in Pseudomonas aeruginosa. J Bacteriol. 2003;185(17):5314–5319.
  • Naas T, Philippon L, Poirel L, et al. An SHV-derived extended-spectrum beta-lactamase in Pseudomonas aeruginosa. Antimicrob Agents Chemother. 1999;43(5):1281–1284.
  • Forde BM, Henderson A, Playford EG, et al. Fatal respiratory diphtheria caused by beta-lactam-resistant Corynebacterium diphtheriae. Clin Infect Dis. 2020.
  • Nicoloff H, Hjort K, Levin BR, et al. The high prevalence of antibiotic heteroresistance in pathogenic bacteria is mainly caused by gene amplification. Nat Microbiol. 2019;4(3):504–514.
  • Shintani M, Sanchez ZK, Kimbara K. Genomics of microbial plasmids: classification and identification based on replication and transfer systems and host taxonomy. Front Microbiol. 2015;6(242).
  • Carattoli A. Resistance plasmid families in Enterobacteriaceae. Antimicrob Agents Chemother. 2009;53(6):2227–2238.
  • Thomas CM, Nielsen KM. Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nat Rev Microbiol. 2005;3(9):711–721.
  • Couturier M, Bex F, Bergquist PL, et al. Identification and classification of bacterial plasmids. Microbiol Rev. 1988;52(3):375–395.
  • Carattoli A, Bertini A, Villa L, et al. Identification of plasmids by PCR-based replicon typing. J Microbiol Methods. 2005;63(3):219–228.
  • Carattoli A, Zankari E, Garcia-Fernandez A, et al. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother. 2014;58(7):3895–3903.
  • Rozwandowicz M, Brouwer MSM, Fischer J, et al. Plasmids carrying antimicrobial resistance genes in Enterobacteriaceae. J Antimicrob Chemother. 2018;73(5):1121–1137.
  • Petty NK, Ben Zakour NL, Stanton-Cook M, et al. Global dissemination of a multidrug resistant Escherichia coli clone. Proc Natl Acad Sci U S A. 2014;111(15):5694–5699.
  • Towner KJ, Evans B, Villa L, et al. Distribution of intrinsic plasmid replicase genes and their association with carbapenem-hydrolyzing class D beta-lactamase genes in European clinical isolates of Acinetobacter baumannii. Antimicrob Agents Chemother. 2011;55(5):2154–2159.
  • Walsh TR, Weeks J, Livermore DM, et al. Dissemination of NDM-1 positive bacteria in the New Delhi environment and its implications for human health: an environmental point prevalence study. Lancet Infect Dis. 2011;11(5):355–362.
  • Hennequin C, Chlilek A, Beyrouthy R, et al. Diversity of DHA-1-encoding plasmids in Klebsiella pneumoniae isolates from 16 French hospitals. J Antimicrob Chemother. 2018;73(11):2981–2989.
  • Philippon A, Arlet G, Jacoby GA. Plasmid-determined AmpC-type beta-lactamases. Antimicrob Agents Chemother. 2002;46(1):1–11.
  • Shearer JE, Wireman J, Hostetler J, et al. Major families of multiresistant plasmids from geographically and epidemiologically diverse staphylococci. G3 (Bethesda). 2011;1(7):581–591.
  • Malachowa N, DeLeo FR. Mobile genetic elements of Staphylococcus aureus. Cell Mol Life Sci. 2010;67(18):3057–3071.
  • Diep BA, Gill SR, Chang RF, et al. Complete genome sequence of USA300, an epidemic clone of community-acquired meticillin-resistant Staphylococcus aureus. Lancet. 2006;367(9512):731–739.
  • Archer GL, Johnston JL. Self-transmissible plasmids in staphylococci that encode resistance to aminoglycosides. Antimicrob Agents Chemother. 1983;24(1):70–77.
  • Turnidge J, Paterson DL. Setting and revising antibacterial susceptibility breakpoints. Clin Microbiol Rev. 2007;20(3):391–408.
  • Weinstein MP, Klugman KP, Jones RN. Rationale for Revised Penicillin Susceptibility Breakpoints versus Streptococcus pneumoniae: coping with Antimicrobial Susceptibility in an Era of Resistance. Clin Infect Dis. 2009;48(11):1596–1600.
  • Morrill HJ, Pogue JM, Kaye KS, et al. Treatment Options for Carbapenem-Resistant Enterobacteriaceae Infections. Open Forum Infect Dis. 2015;2:2. ofv050-ofv050
  • European Committee on Antimicrobial Susceptibility Testing (EUCAST). EUCAST general and public consultation. 2019. https://eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Consultation/2019/Agents_and_species_currently_categorised_as_SusceptibleHE_20190509.pdf. ( Accessed. Jun. 2021)
  • European Committee on Antimicrobial Susceptibility Testing (EUCAST). Data from the EUCAST MIC distribution website. https://mic.eucast.org. ( Accessed. 1 Jul. 2021)
  • Balloux F, Bronstad Brynildsrud O, van Dorp L, et al. From Theory to Practice: translating Whole-Genome Sequencing (WGS) into the Clinic. Trends Microbiol. 2018;26(12):1035–1048.
  • Jeukens J, Kukavica-Ibrulj I, Emond-Rheault JG, et al. Comparative genomics of a drug-resistant Pseudomonas aeruginosa panel and the challenges of antimicrobial resistance prediction from genomes. FEMS Microbiol Lett. 2017;364(18).
  • Tornheim JA, Starks AM, Rodwell TC, et al. Building the Framework for Standardized Clinical Laboratory Reporting of Next-generation Sequencing Data for Resistance-associated Mutations in Mycobacterium tuberculosis Complex. Clin Infect Dis. 2019;69(9):1631–1633.
  • Miotto P, Tessema B, Tagliani E, et al. A standardised method for interpreting the association between mutations and phenotypic drug resistance in Mycobacterium tuberculosis. Eur Respir J. 2017;50(6).
  • Ji H, Sandstrom P, Paredes R, et al. Are We Ready for NGS HIV Drug Resistance Testing? The Second ”Winnipeg Consensus” Symposium. Viruses, 12(6) (2020).
  • Kidd SE, Chen SC, Meyer W, et al. Age in Molecular Diagnostics for Invasive Fungal Disease: are We Ready? Front Microbiol. 2019;10(2903).
  • Rk S, Mh N, Eg P, et al. The presence of an FKS mutation rather than MIC is an independent risk factor for failure of echinocandin therapy among patients with invasive candidiasis due to Candida glabrata. Antimicrob Agents Chemother. 2012;56(9):4862–4869.
  • van der Pluijm RW, Imwong M, Chau NH, et al. Determinants of dihydroartemisinin-piperaquine treatment failure in Plasmodium falciparum malaria in Cambodia, Thailand, and Vietnam: a prospective clinical, pharmacological, and genetic study. Lancet Infect Dis. 2019;19(9):952–961.
  • Banerji S, Simon S, Tille A, et al. Genome-based Salmonella serotyping as the new gold standard. Sci Rep. 2020;10(1):4333.
  • Neuert S, Nair S, Mr D, et al. Prediction of Phenotypic Antimicrobial Resistance Profiles From Whole Genome Sequences of Non-typhoidal Salmonella enterica. Front Microbiol. 2018;9(592).
  • World Health Organization. GLASS whole-genome sequencing for surveillance of antimicrobial resistance. Geneva: WHO; 2020.
  • Wi T, Lahra MM, Ndowa F, et al. Antimicrobial resistance in Neisseria gonorrhoeae: global surveillance and a call for international collaborative action. PLoS Med. 2017;14(7):e1002344.
  • Roberts LW, Harris PNA, Forde BM, et al. Integrating multiple genomic technologies to investigate an outbreak of carbapenemase-producing Enterobacter hormaechei. Nat Commun. 2020;11(1):466.
  • Crisan A, McKee G, Munzner T, et al. Evidence-based design and evaluation of a whole genome sequencing clinical report for the reference microbiology laboratory. PeerJ. 2018;6(e4218).
  • American Society for Microbiology. American Academy of Microbiology Colloquia Reports. In: Applications of Clinical Microbial Next-Generation Sequencing: report on an American Academy of Microbiology Colloquium held in Washington, DC, in April 2015. Washington (DC): American Society for Microbiology; 2016.
  • International Organization for Standardization. ISO 15189 Medical laboratories - Requirements for quality and competence. 2012. https://www.iso.org/standard/56115.html. ( Accessed. 2021 Jun 24)
  • Bogaerts B, Delcourt T, Soetaert K, et al. A Bioinformatics Whole-Genome Sequencing Workflow for Clinical Mycobacterium tuberculosis Complex Isolate Analysis, Validated Using a Reference Collection Extensively Characterized with Conventional Methods and In Silico Approaches. J Clin Microbiol. 2021;59:6.
  • Goldberg B, Sichtig H, Geyer C, et al. Making the Leap from Research Laboratory to Clinic: challenges and Opportunities for Next-Generation Sequencing in Infectious Disease Diagnostics. mBio. 2015;6(6):e01888–01815.
  • Kozyreva VK, Truong CL, Greninger AL, et al. Validation and Implementation of Clinical Laboratory Improvements Act-Compliant Whole-Genome Sequencing in the Public Health Microbiology Laboratory. J Clin Microbiol. 2017;55(8):2502–2520.
  • Gargis AS, Kalman L, Lubin IM. Assuring the Quality of Next-Generation Sequencing in Clinical Microbiology and Public Health Laboratories. J Clin Microbiol. 2016;54(12):2857–2865.
  • Sichtig H, Minogue T, Yan Y, et al. FDA-ARGOS is a database with public quality-controlled reference genomes for diagnostic use and regulatory science. Nat Commun. 2019;10(1):3313.
  • Starks AM, Aviles E, Cirillo DM, et al. Collaborative Effort for a Centralized Worldwide Tuberculosis Relational Sequencing Data Platform. Clin Infect Dis. 2015;61(Suppl 3):S141–146.
  • Moran-Gilad J, Sintchenko V, Pedersen SK, et al. Proficiency testing for bacterial whole genome sequencing: an end-user survey of current capabilities, requirements and priorities. BMC Infect Dis. 2015;15:174.
  • Unemo M, Golparian D, Sanchez-Buso L, et al. The novel 2016 WHO Neisseria gonorrhoeae reference strains for global quality assurance of laboratory investigations: phenotypic, genetic and reference genome characterization. J Antimicrob Chemother. 2016;71(11):3096–3108.
  • Petrillo M, Fabbri M, Kagkli D, et al. A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing. F1000Res. 2021;10:80.
  • Kwong JC, McCallum N, Sintchenko V, et al. Whole genome sequencing in clinical and public health microbiology. Pathology. 2015;47(3):199–210.
  • Cameron A, Jl B, Taffner S, et al. Clinical Pathogen Genomics. Clin Lab Med. 2020;40(4):447–458.
  • Gu W, Deng X, Lee M, et al. Rapid pathogen detection by metagenomic next-generation sequencing of infected body fluids. Nat Med. 2021;27(1):115–124.
  • Gordon LG, Elliott TM, Forde B, et al. Budget impact analysis of routinely using whole-genomic sequencing of six multidrug-resistant bacterial pathogens in Queensland, Australia. BMJ Open. 2021;11(2):e041968.
  • Dymond A, Davies H, Mealing S, et al. Genomic Surveillance of Methicillin-resistant Staphylococcus aureus: a Mathematical Early Modeling Study of Cost-effectiveness. Clin Infect Dis. 2020;70(8):1613–1619.
  • Kumar P, Sundermann AJ, Martin EM, et al. Method for economic evaluation of bacterial whole genome sequencing surveillance compared to standard of care in detecting hospital outbreaks. Clin Infect Dis. 2020:1117–1122 .
  • Zhang X-D. Machine Learning. In: A Matrix Algebra Approach to Artificial Intelligence. Singapore: Springer Singapore; 2020. p. 223–440.
  • Donald M, Spiegelhalter DJ, Taylor CC, et al. Machine learning, neural and statistical classification. Ellis Horwood; 1995.
  • Kaprou GD, Bergspica I, Alexa EA, et al. Rapid Methods for Antimicrobial Resistance Diagnostics. Antibiotics (Basel). 2021;10(2).
  • Inglis TJJ, Paton TF, Kopczyk MK, et al. Same-day antimicrobial susceptibility test using acoustic-enhanced flow cytometry visualized with supervised machine learning. J Med Microbiol. 2020;69(5):657–669.
  • Lechowicz L, Urbaniak M, Adamus-Bialek W, et al. The use of infrared spectroscopy and artificial neural networks for detection of uropathogenic Escherichia coli strains’ susceptibility to cephalothin. Acta Biochim Pol. 2013;60(4):713–718.
  • Her HL, Wu YW. A pan-genome-based machine learning approach for predicting antimicrobial resistance activities of the Escherichia coli strains. Bioinformatics. 2018;34(13):i89–i95.
  • Anahtar MN, Yang JH, Kanjilal S. Applications of Machine Learning to the Problem of Antimicrobial Resistance: an Emerging Model for Translational Research. J Clin Microbiol. 2021;59(7):e0126020.
  • Hyun JC, Kavvas ES, Monk JM, et al. Machine learning with random subspace ensembles identifies antimicrobial resistance determinants from pan-genomes of three pathogens. PLoS Comput Biol. 2020;16(3):e1007608.
  • Eyre DW, De Silva D, Cole K, et al. WGS to predict antibiotic MICs for Neisseria gonorrhoeae. J Antimicrob Chemother. 2017;72(7):1937–1947.
  • Zhang C, Ju Y, Tang N, et al. Systematic analysis of supervised machine learning as an effective approach to predicate beta-lactam resistance phenotype in Streptococcus pneumoniae. Brief Bioinform. 2020;21(4):1347–1355.
  • Kavvas ES, Catoiu E, Mih N, et al. Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance. Nat Commun. 2018;9(1):4306.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.