Bibliography

This bibliography page details selected recent papers to which Professor Sharon Peacock has contributed. Additional research can be found on her Google Scholar and ResearchGate profiles. Sharon has also recently been recognised by the Web of Science™ as one of the most highly cited individuals in her field with multiple highly-cited papers that rank in the top 1%. https://recognition.webofscience.com/awards/highly-cited/2020/ https://publons.com/researcher/4043075/sharon-j-peacock/

Gouliouris T, Coll F, Ludden C, Blane B, Raven KE, Naydenova P, Crawley C, Török ME, Enoch DA, Brown NM, Harrison EM, Parkhill J, Peacock SJ. Quantifying acquisition and transmission of Enterococcus faecium using genomic surveillance. Nat Microbiol. 2021;6(1):103-111. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7610418/pdf/EMS118380.pdf

Harvey WT, Carabelli AM, Jackson B, Gupta RK, Thomson EC, Harrison EM, Ludden C, Reeve R, Rambaut A; COVID-19 Genomics UK (COG-UK) Consortium, Peacock SJ, Robertson DL. SARS-CoV-2 variants, spike mutations and immune escape. Nat Rev Microbiol. 2021;19(7):409-424. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8167834/pdf/41579_2021_Article_573.pdf

Hamilton WL, Tonkin-Hill G, Smith E, Houldcroft C, Warne B, Meredith L, Hosmillo M, Jahun AS, Curran MD, Parmar S, Caller LG, Caddy SL, Khokhar FA, Yakovleva A, Hall G, Feltwell T, Brown N, Gonçalves S, Amato R, Harrison E, Beale M, Chapman MS, Jackson DK, Johnston I, Alderton A, Sillitoe J, Langford C, Dougan G, Peacock SJ, Kwiatkowski DP, Goodfellow I, Török ME. Wellcome Sanger Institute Covid-19 Surveillance Team, COVID-19 Genomics Consortium UK. COVID-19 infection dynamics in care homes in the East of England: a retrospective genomic epidemiology study. ELife.  2021;10:e64618.https://www.medrxiv.org/content/10.1101/2020.08.26.20182279v4.full.pdf

Meredith LW, Hamilton WL, Warne B, Houldcroft CJ, Hosmillo M, Jahun AS, Curran MD, Parmar S, Caller LG, Caddy SL, Khokhar FA, Yakovleva A, Hall G, Feltwell T, Forrest S, Sridhar S, Weekes MP, Baker S, Brown N, Moore E, Popay A, Roddick I, Reacher M, Gouliouris T, Peacock SJ, Dougan G, Török ME, Goodfellow I. Rapid implementation of real-time SARS-CoV-2 sequencing to investigate healthcare-associated COVID-19 infections. Lancet Infect Dis. 2020;20(11):1263-1272. https://www.thelancet.com/action/showPdf?pii=S1473-3099%2820%2930562-4

Coll F, Raven KE, Knight GM, Blane B, Harrison EM, Leek D, Enoch D, Brown NM, Parkhill J, Peacock SJ. Definition of a genetic relatedness cutoff to exclude recent transmission of meticillin-resistant Staphylococcus aureus: a genomic epidemiology analysis. Lancet Microbe. 2020;1(8):e328-e335. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7721685/pdf/main.pdf

Gaccioli F, Lager S, de Goffau MC, Sovio U, Dopierala J, Gong S, Cook E, Sharkey A, Moffett A, Lee WK, Delles C, Venturini C, Breuer J, Parkhill J, Peacock SJ, Charnock-Jones DS, Smith GCS. Fetal inheritance of chromosomally integrated human herpesvirus 6 predisposes the mother to pre-eclampsia. Nat Microbiol. 2020;5(7):901-908. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7610361/pdf/EMS118383.pdf

Dymond A, Davies H, Mealing S, Pollit V, Coll F, Brown NM, Peacock SJ. Genomic surveillance of methicillin-resistant Staphylococcus aureus: a mathematical early modelling study of cost effectiveness. Clin Infect Dis. 2020;70(8):1613-1619.  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145999/pdf/ciz480.pdf

de Goffau MC, Lager S, Sovio U Gaccioli F, Cook E, Peacock SJ, Parkhill J, Charnock-Jones DS, Smith GCS. Human placenta has no microbiome but can contain potential pathogens. Analysis of bacterial DNA in the human placenta of women with normal and adverse pregnancy outcome. Nature. 2019;572(7769):329-334. https://www.nature.com/articles/s41586-019-1451-5

Harrison EM, Ba X, Coll F, Blane B, Restif O, Carvell H, Köser CU, Jamrozy D, Reuter S, Lovering A, Gleadall N, Bellis KL, Uhlemann AC, Lowy FD, Massey RC, Grilo IR, Sobral R, Larsen J, Rhod Larsen A, Vingsbo Lundberg C, Parkhill J, Paterson GK, Holden MTG, Peacock SJ, Holmes MA. Genomic identification of cryptic susceptibility to penicillins and β-Lactamase inhibitors in methicillin resistant Staphylococcus aureus. Nature Microbiol. 2019;4(10):1680-1691. https://www.nature.com/articles/s41564-019-0471-0

Wagner J, Harrison EM, Martinez Del Pero M, Blane B, Mayer G, Leierer J, Gopaluni S, Holmes MA, Parkhill J, Peacock SJ, Jayne DRW, Kronbichler A. The composition and functional protein subsystems of the human nasal microbiome in granulomatosis with polyangiitis: a pilot study. Microbiome. 2019;7(1):137.https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-019-0753-z

Gouliouris T, Raven KE, Moradigaravand D, Ludden C, Coll F, Blane B, Naydenova P, Horner C, Brown NM, Corander J, Limmathurotsakul D, Parkhill J, Peacock SJ. Detection of vancomycin-resistant Enterococcus faecium hospital-adapted lineages in municipal wastewater treatment plants indicates widespread distribution and release into the environment. Genome Res. 2019;29:626-634. https://genome.cshlp.org/content/29/4/626.full.pdf+html

Ludden C, Raven KE, Jamrozy D, Gouliouris T, Blane B, Coll F, de Goffau M, Naydenova P, Horner C, Hernandez-Garcia J, Wood P, Hadjirin N, Radakovic M, Brown NM, Holmes M, Parkhill J, Peacock SJ. One Health genomic surveillance of Escherichia coli demonstrates distinct lineages and mobile genetic elements in isolates from humans versus livestock. mBio. 2019;10(1). https://mbio.asm.org/content/mbio/10/1/e02693-18.full.pdf

de Goffau MC, Lager S, Salter SJ, Wagner J, Kronbichler A, Charnock-Jones DS, Peacock SJ, Smith GCS, Parkhill J. Recognizing the reagent microbiome. Nature Microbiol. 2018;3:851-853. https://www.nature.com/articles/s41564-018-0202-y

Gouliouris T, Raven KE, Ludden C, Blane B, Corander J, Horner CS, Hernandez-Garcia J, Wood P, Hadjirin NF, Radakovic M, Holmes MA, de Goffau M, Brown NM, Parkhill J, Peacock SJ. Genomic surveillance of Enterococcus faecium reveals limited sharing of strains and resistance genes between livestock and humans. mBio. 2018;9(6). https://mbio.asm.org/content/mbio/9/6/e01780-18.full.pdf

Richardson EJ, Bacigalupe R, Harrison EM, Weinert LA, Lycett S, Vrieling M, Robb K, Hoskisson PA, Holden MTG, Feil EJ, Paterson GK, Tong SYC, Shittu A, van Wamel W, Aanensen DM, Parkhill J, Peacock SJ, Corander J, Holmes M, Fitzgerald JR. Gene exchange drives the ecological success of a multi-host bacterial pathogen. Nat Ecol Evol. 2018;2(9):1468-1478. https://www.nature.com/articles/s41559-018-0617-0

Coll F, Harrison EM, Toleman MS, Reuter S, Raven KE, Blane B, Palmer B, Kappeler ARM, Brown NM, Török ME, Parkhill J, Peacock SJ. Longitudinal genomic surveillance of MRSA in the UK reveals transmission patterns in hospitals and the community. Science Transl Med. 2017;9(413). https://stm.sciencemag.org/content/scitransmed/9/413/eaak9745.full.pdf

Chewapreecha C, Holden MT, Vehkala M, Välimäki N, Yang Z, Harris SR, Mather AE, Tuanyok A, De Smet B, Le Hello S, Bizet C, Mayo M, Wuthiekanun V, Limmathurotsakul D, Phetsouvanh R, Spratt BG, Corander J, Keim P, Dougan G, Dance DA, Currie BJ, Parkhill J, Peacock SJ. Global and regional dissemination and evolution of Burkholderia pseudomallei. Nature Microbiol. 2017;2:16263. https://www.nature.com/articles/nmicrobiol2016263

Recker M, Laabei M, Toleman MS, Reuter S, Saunderson RB, Blane B, Török ME, Ouadi K, Stevens E, Yokoyama M, Steventon J, Thompson L, Milne G, Bayliss S, Bacon L, Peacock SJ, Massey RC. Clonal differences in Staphylococcus aureus bacteraemia-associated mortality. Nature Microbiol. 2017;2(10):1381-1388. https://www.nature.com/articles/s41564-017-0001-x

Raven KE, Reuter S, Gouliouris T, Reynolds R, Russell JE, Brown NM, Török ME, Parkhill J, Peacock SJ. Whole-genome sequencing defines the population structure and evolution of vancomycin resistance in Enterococcus faecalis. Nature Microbiol. 2016;1:15033. https://www.nature.com/articles/nmicrobiol201533

Limmathurotsakul D, Golding N, Dance DA, Messina JP, Pigott DM, Moyes CL, Rolim DB, Bertherat E, Day NP, Peacock SJ, Hay SI. Predicted global distribution of Burkholderia pseudomallei and burden of melioidosis. Nature Microbiol. 2016;1(1):15008. https://www.nature.com/articles/nmicrobiol20158

Moradigaravand D, Reuter S, Martin V, Peacock SJ, Parkhill J. The dissemination of multidrug-resistant Enterobacter cloacae throughout the UK and Ireland. Nature Microbiol. 2016;1:16173. https://www.nature.com/articles/nmicrobiol2016173

Raven KE, Reuter S, Reynolds R, Brodrick HJ, Russell JE, Török ME, Parkhill J, Peacock SJ. A decade of genomic history for healthcare-associated Enterococcus faecium in the United Kingdom and Ireland. Genome Res. 2016;26:1388-1396. https://genome.cshlp.org/content/26/10/1388.full.pdf+html

Paterson GK, Harrison EM, Murray GGR, Welch JJ, Warland JH, Holden MTG, Morgan FJE, Ba X, Koop G, Harris SR, Maskell DJ, Peacock SJ, Herrtage ME, Parkhill J, Holmes MA. Capturing the cloud of diversity reveals complexity and heterogeneity of MRSA carriage, infection and transmission. Nature Comms. 2015;6:6560. https://www.nature.com/articles/ncomms7560

Chetchotisakd P, Chierakul W, Chaowagul W, Anunnatsiri S, Phimda K, Mootsikapun P, Chaisuksant S, Pilaikul J, Thinkhamrop B, Phiphitaporn S, Susaengrat W, Toondee C, Wongrattanacheewin S, Wuthiekanun V, Chantratita N, Thaipadungpanit J, Day NP, Limmathurotsakul D, Peacock SJ. Trimethoprim-sulphamethoxazole versus trimethoprim-sulphamethoxazole plus doxycycline as oral eradicative treatment for melioidosis (MERTH): a multicentre, double-blind, non-inferiority, randomised controlled trial. Lancet. 2014;383:807-814. https://www.thelancet.com/action/showPdf?pii=S0140-6736%2813%2961951-0

Uhlemann AC, Dordel J, Knox J, Raven KE, Parkhill J, Holden MT, Peacock SJ, Lowy FD. Molecular tracing of the emergence, diversification, and transmission of S. aureus sequence type 8 in a New York community. Proc Natl Acad Sci USA. 2014;111:6738-43. https://www.pnas.org/content/pnas/111/18/6738.full.pdf

Harris SR, Cartwright EJ, Török ME, Holden MT, Brown NM, Ogilvy-Stuart AL, Ellington MJ, Quail MA, Bentley SD, Parkhill J, Peacock SJ. Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study. Lancet Infect Dis. 2013;13:130-6. https://www.thelancet.com/action/showPdf?pii=S1473-3099%2812%2970268-2

Reuter S, Ellington MJ, Cartwright EJ, Köser CU, Török ME, Gouliouris T, Harris SR, Brown NM, Holden MT, Quail M, Parkhill J, Smith GP, Bentley SD, Peacock SJ. Rapid bacterial whole-genome sequencing to enhance diagnostic and public health microbiology. JAMA Intern Med. 2013;173:1397-404. https://jamanetwork.com/journals/jamainternalmedicine/fullarticle/1726980

Köser CU, Bryant JM, Becq J, Török ME, Ellington MJ, Marti-Renom MA, Carmichael AJ, Parkhill J, Smith GP, Peacock SJ. Whole-genome sequencing for rapid susceptibility testing of M. tuberculosis. New Engl J Med. 2013;369:290-292. https://www.nejm.org/doi/10.1056/NEJMc1215305?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%20%200pubmed

Harris SR, Török ME, Cartwright, EJ, Quail M, Peacock SJ, Parkhill J. Read and assembly metrics inconsequential for clinical utility of rapid whole genome sequencing in mapping outbreaks.  Nature Biotechnol. 2013;31:592-594. https://www.nature.com/articles/nbt.2616

Bryant J, Grogono DM, Greaves D, Foweraker J, Roddick I, Inns T, Reachers M, Haworth CS, Curran MD, Harris SR, Peacock SJ, Parkhill J, Floto RA. Whole-genome sequencing to identify transmission of Mycobacterium abscessus between patients with cystic fibrosis: a retrospective cohort study. Lancet. 2013;381:1551-60. https://www.thelancet.com/action/showPdf?pii=S0140-6736%2813%2960632-7

He M, Miyajima F, Roberts P, Ellison L, Pickard DJ, Martin MJ, Connor TR, Harris SR, Fairley D, Bamford KB, D’Arc S, Brazier J, Brown D, Coia JE, Douce G, Gerding D, Kim HJ, Koh TH, Kato H, Senoh M, Louie T, Michell S, Butt E, Peacock SJ, Brown NM, Riley T, Songer G, Wilcox M, Pirmohamed M, Kuijper E, Hawkey P, Wren BW, Dougan G, Parkhill J, Lawley TD. Emergence and global spread of epidemic healthcare-associated Clostridium difficile. Nature Genet. 2013;45:109-13. https://www.nature.com/articles/ng.2478

Köser CU, Holden MT, Ellington MJ, Cartwright EJ, Brown NM, Ogilvy-Stuart AL, Hsu LY, Chewapreecha C, Croucher NJ, Harris SR, Sanders M, Enright MC, Dougan G, Bentley SD, Parkhill J, Fraser LJ, Betley JR, Schulz-Trieglaff OB, Smith GP, Peacock SJ. Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak. New Engl J Med. 2012;363:2267-2275. https://www.nejm.org/doi/10.1056/NEJMoa1109910?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%20%200pubmed

Chantratita N, Rholl DA, Sim B, Wuthiekanun V, Limmathurotsakul D, Amornchai P, Thanwisai A, Chua HH, Ooi WF, Holden MT, Day NP, Tan P, Schweizer HP, Peacock SJ. Antimicrobial resistance to ceftazidime involving loss of penicillin-binding protein 3 in Burkholderia pseudomallei. Proc Natl Acad Sci USA. 2011;108:17165-70. https://www.pnas.org/content/108/41/17165.long

GarcÍa-Álvarez L, Holden MT, Lindsay H, Webb CR, Brown DF, Curran MD, Walpole E, Brooks K, Pickard DJ, Teale C, Parkhill J, Bentley SD, Edwards GF, Girvan EK, Kearns AM, Pichon B, Hill RL, Larsen AR, Skov RL, Peacock SJ, Maskell DJ, Holmes MA. Meticillin-resistant Staphylococcus aureus with a novel mecA homologue in human and bovine populations in the UK and Denmark: a descriptive study. Lancet Infect Dis. 2011; 11:595-603. https://www.thelancet.com/action/showPdf?pii=S1473-3099%2811%2970126-8

Koh GCKW, Maude RR, Schreiber MF, Limmathurotsakul D, Wiersinga WJ, Wuthiekanun V, Lee SJ, Mahavanakul W, Chaowagul W, Chierakul W, White NJ, van der Poll T, Day NPJ, Dougan G, Peacock SJ. Glyburide is anti-inflammatory and associated with reduced mortality in melioidosis. Clin Infect Dis. 2011;52:717-25. https://academic.oup.com/cid/article/52/6/717/361220

Harris SR, Feil EJ, Holden MT, Quail MA, Nickerson EK, Chantratita N, Gardete S, Tavares A, Day N, Lindsay JA, Edgeworth JD, de Lencastre H, Parkhill J, Peacock SJ, Bentley SD. Evolution of MRSA during hospital transmission and intercontinental spread. Science. 2010;327(5964):469-74.

Felgner PL, Kayala MA, Vigil A, Burk C, Nakajima-Sasaki R, Pablo J, Molina DM, Hirst S, Chew JSW, Wang D, Tan G, Duffield M, Yang R, Neel J, Chantratita N, Bancroft G, Lertmemongkolchai G, Davies DW, Vigil A, Baldi P, Peacock SJ, Titball RW. A Burkholderia pseudomallei protein microarray reveals serodiagnostic and cross-reactive antigens. Proc Natl Acad Sci USA 2009;106:13499-504.  https://www.pnas.org/content/106/32/13499.long

Cheng AC, Limmathurotsakul D, Chierakul W, Getchalarat N, Wuthiekanun V, Stephens DP, Day NPJ, White NJ, Chaowagul W, Currie BJ, Peacock SJ. A randomized controlled trial of granulocyte colony-stimulating factor for the treatment of severe sepsis due to melioidosis in Thailand. Clin Infect Dis. 2007; 45:308-314. https://academic.oup.com/cid/article/45/3/308/358466

Holden MT, Feil EJ, Lindsay JA, Peacock SJ, Day NP, Enright MC, Foster TJ, Moore CE, Hurst L, Atkin R, Barron A, Bason N, Bentley SD, Chillingworth C, Chillingworth T, Churcher C, Clark L, Corton C, Cronin A, Doggett J, Dowd L, Feltwell T, Hance Z, Harris B, Hauser H, Holroyd S, Jagels K, James KD, Lennard N, Line A, Mayes R, Moule S, Mungall K, Ormond D, Quail MA, Rabbinowitsch E, Rutherford K, Sanders M, Sharp S, Simmonds M, Stevens K, Whitehead S, Barrell BG, Spratt BG, Parkhill J. Complete genomes of two clinical Staphylococcus aureus strains: evidence for the rapid evolution of virulence and drug resistance. Proc Natl Acad Sci USA. 2004; 101:9786-9791. https://www.pnas.org/content/101/26/9786.long

Holden MT, Titball RW, Peacock SJ, Cerdeño-Tárraga AM, Atkins T, Crossman LC, Pitt T, Churcher C, Mungall K, Bentley SD, Sebahia M, Thomson NR, Bason N, Beacham IR, Brooks K, Brown KA, Brown NF, Challis GL, Cherevach I, Chillingworth T, Cronin A, Crossett B, Davis P, DeShazer D, Feltwell T, Fraser A, Hance Z, Hauser H, Holroyd S, Jagels K, Keith KE, Maddison M, Moule S, Price C, Quail MA, Rabbinowitsch E, Rutherford K, Sanders M. Simmonds M, Songsivilai S, Stevens K, Tumapa S, Vesaratchavest M, Whitehead S, Yeats C, Barrell BG, Oyston PCF, Parkhill J. Genomic plasticity of the causative agent of melioidosis, Burkholderia pseudomallei. Proc Natl Acad Sci USA.  2004; 101:14240-14245. https://www.pnas.org/content/101/39/14240.long

Post N, Eddy D, Huntley C, van Schalkwyk MCI, Shrotri M, Leeman D, Rigby S, Williams SV, Bermingham WH, Kellam P, Maher J, Shields AM, Amirthalingam G, Peacock SJ, Ismail SA. Antibody response to SARS-CoV-2 infection in humans: a systematic review. medRxiv preprint doi: https://doi.org/10.1101/2020.08.25.20178806

Shrotri M, van Schalkwyk MCI, Post N, Eddy D, Huntley C, Leeman D, Rigby S, Williams SV, Bermingham WH, Kellam P, Maher J, Shields AM, Amirthalingam G, Peacock SJ, Ismail SA. Cellular immune response to SARS-CoV-2 infection in humans: a systematic review. medRxiv preprint doi: https://doi.org/10.1101/2020.08.24.20180679

Wiersinga WJ, Rhodes A, Cheng AC, Peacock SJ, Prescott HC. Pathophysiology, Transmission, Diagnosis, and Treatment of Coronavirus Disease 2019 (COVID-19): A Review. JAMA. 2020;324(8):782-793. https://jamanetwork.com/journals/jama/fullarticle/2768391

The COVID-19 Genomics UK (COG-UK) consortium. An integrated national scale SARS-CoV-2 genomic surveillance network. Lancet Microbe. 2020. https://doi.org/10.1016/S2666-5247(20)30054-9.

Turner P, Rupal P, Opintan JA, Jaoko W, Feasey NA, Peacock SJ, Ashley EA. Laboratory informatics capacity is a neglected component of effective antimicrobial resistance surveillance in resource-limited settings. Lancet Infect Dis. Accepted.

Okeke IN, Feasey N, Parkhill J, Turner P, Limmathurosakul D, Georgiou P, Holmes A, Peacock SJ, Surveillance and Epidemiology of Drug Resistant Infections Consortium (SEDRIC) Leapfrogging laboratories? The promise and pitfalls of high-tech solutions for antimicrobial resistance surveillance in low income settings. BMJ Global Health. Accepted.

Laxminarayan R, Van Boeckel T, Frost I, Kariuki S, Khan E, Limmathurotsakul D, Larrson DGJ, Levy-Hara G, Mendelson M, Outterson K, Peacock SJ, Zhu YG. The Lancet Infectious Diseases Commission on antimicrobial resistance: 6 years Later. Lancet Infect Dis. 2020; pii: S1473-3099(20)30003-7.

Limmathurotsakul D, Dunachie S, Fukuda K, Feasey NA, Okeke IN, Holmes AH, Moore CE, Dolocek C, van Doorn HR, Shetty N, Lopez AD, Peacock SJ, Surveillance and Epidemiology of Drug Resistant Infections Consortium (SEDRIC). Improving the estimation of the global burden of antimicrobial resistant infections. Lancet Infect Dis. 2019;19:e392-e398.

Ashley EA, Shetty N, Patel J, van Doorn R, Limmathurotsakul D, Feasey NA, Okeke IN, Peacock SJ; Surveillance and Epidemiology of Drug Resistant Infections Consortium (SEDRIC). Harnessing alternative sources of antimicrobial resistance data to support surveillance in low-resource settings. J Antimicrob Chemother. 2019;74:541-546. https://academic.oup.com/jac/article/74/3/541/5245301

Wiersinga WJ, Virk HS, Torres AG, Currie BJ, Peacock SJ, Dance DAB, Limmathurotsakul D. Melioidosis. Nature Reviews Disease Primers. 2018;4:17107. https://www.nature.com/articles/nrdp2017107

Seale AC, Gordon NC, Islam J, Peacock SJ, Scott JAG.AMR Surveillance in low and middle-income settings – A roadmap for participation in the Global Antimicrobial Surveillance System (GLASS). Wellcome Open Res. 2017;2:92. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5645727/pdf/wellcomeopenres-2-13565.pdf

Limmathurotsakul D, Funnell SG, Torres AG, Morici LA, Brett PJ, Dunachie S, Atkins T, Altmann DM, Bancroft G, Peacock SJ, for the Steering Group on Melioidosis Vaccine Development. Consensus on the development of vaccines against naturally acquired melioidosis. Emerg Infect Dis. 2015;21(6). https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4451926/

Köser CU, Ellington M, Peacock SJ. Whole-genome sequencing to control antimicrobial resistance. Trends Genetics. 2014;30:401-407. https://www.cell.com/action/showPdf?pii=S0168-9525%2814%2900114-0