Peleg AY, Seifert H, Paterson DL. Acinetobacter baumannii: emergence of a successful pathogen. Clin Microbiol Rev. 2008;21:538–82.
Article
CAS
Google Scholar
Mataseje LF, Bryce E, Roscoe D, Boyd DA, Embree J, Gravel D, Katz K, Kibsey P, Kuhn M, Mounchili A, et al. Carbapenem-resistant gram-negative bacilli in Canada 2009-10: results from the Canadian nosocomial infection surveillance program (CNISP). J Antimicrob Chemother. 2012;67:1359–67.
Article
CAS
Google Scholar
Simor AE, Lee M, Vearncombe M, Jones-Paul L, Barry C, Gomez M, Fish JS, Cartotto RC, Palmer R, Louie M. An outbreak due to multiresistant Acinetobacter baumannii in a burn unit: risk factors for acquisition and management. Infect Control Hosp Epidemiol. 2002;23:261–7.
Article
Google Scholar
Gray AP, Allard R, Pare R, Tannenbaum T, Lefebvre B, Levesque S, Mulvey M, Maalouf L, Perna S, Longtin Y. Management of a hospital outbreak of extensively drug-resistant Acinetobacter baumannii using a multimodal intervention including daily chlorhexidine baths. J Hosp Infect. 2016;93:29–34.
Article
CAS
Google Scholar
Singh A, Goering RV, Simjee S, Foley SL, Zervos MJ. Application of molecular techniques to the study of hospital infection. Clin Microbiol Rev. 2006;19:512–30.
Article
CAS
Google Scholar
Koser CU, Ellington MJ, Cartwright EJ, Gillespie SH, Brown NM, Farrington M, Holden MT, Dougan G, Bentley SD, Parkhill J, Peacock SJ. Routine use of microbial whole genome sequencing in diagnostic and public health microbiology. PLoS Pathog. 2012;8:e1002824.
Article
CAS
Google Scholar
Salipante SJ, SenGupta DJ, Cummings LA, Land TA, Hoogestraat DR, Cookson BT. Application of whole-genome sequencing for bacterial strain typing in molecular epidemiology. J Clin Microbiol. 2015;53:1072–9.
Article
CAS
Google Scholar
Robinson ER, Walker TM, Pallen MJ. Genomics and outbreak investigation: from sequence to consequence. Genome Med. 2013;5:36.
Article
Google Scholar
Reuter S, Harrison TG, Koser CU, Ellington MJ, Smith GP, Parkhill J, Peacock SJ, Bentley SD, Torok ME. A pilot study of rapid whole-genome sequencing for the investigation of a legionella outbreak. BMJ Open. 2013;3:e002175.
Article
Google Scholar
Butcher H, Elson R, Chattaway MA, Featherstone CA, Willis C, Jorgensen F, Dallman TJ, Jenkins C, Mc LJ, Beck CR, Harrison S. Whole genome sequencing improved case ascertainment in an outbreak of Shiga toxin-producing Escherichia coli O157 associated with raw drinking milk. Epidemiol Infect. 2016;144:2812–23.
Article
CAS
Google Scholar
Eyre DW, Golubchik T, Gordon NC, Bowden R, Piazza P, Batty EM, Ip CL, Wilson DJ, Didelot X, O'Connor L, et al. A pilot study of rapid benchtop sequencing of Staphylococcus aureus and Clostridium difficile for outbreak detection and surveillance. BMJ Open. 2012;2:e001124.
Article
Google Scholar
Otter JA, Doumith M, Davies F, Mookerjee S, Dyakova E, Gilchrist M, Brannigan ET, Bamford K, Galletly T, Donaldson H, et al. Emergence and clonal spread of colistin resistance due to multiple mutational mechanisms in carbapenemase-producing Klebsiella pneumoniae in London. Sci Rep. 2017;7:12711.
Article
Google Scholar
Kanamori H, Parobek CM, Juliano JJ, van Duin D, Cairns BA, Weber DJ, Rutala WA. A prolonged outbreak of KPC-3-producing Enterobacter cloacae and Klebsiella pneumoniae driven by multiple mechanisms of resistance transmission at a large academic burn center. Antimicrob Agents Chemother. 2017;61:e01516.
Article
CAS
Google Scholar
Snitkin ES, Zelazny AM, Thomas PJ, Stock F, Group NCSP, Henderson DK, Palmore TN, Segre JA. Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing. Sci Transl Med. 2012;4:148ra116.
Article
Google Scholar
Tenover FC, Arbeit RD, Goering RV, Mickelsen PA, Murray BE, Persing DH, Swaminathan B. Interpreting chromosomal DNA restriction patterns produced by pulsed-field gel electrophoresis: criteria for bacterial strain typing. J Clin Microbiol. 1995;33:2233–9.
CAS
PubMed
PubMed Central
Google Scholar
Woodford N, Ellington MJ, Coelho JM, Turton JF, Ward ME, Brown S, Amyes SG, Livermore DM. Multiplex PCR for genes encoding prevalent OXA carbapenemases in Acinetobacter spp. Int J Antimicrob Agents. 2006;27:351–3.
Article
CAS
Google Scholar
Petkau A, Mabon P, Sieffert C, Knox NC, Cabral J, Iskander M, Iskander M, Weedmark K, Zaheer R, Katz LS, et al. SNVPhyl: a single nucleotide variant phylogenomics pipeline for microbial genomic epidemiology. Microb Genom. 2017;3:e000116.
PubMed
PubMed Central
Google Scholar
Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 2010;59:307–21.
Article
CAS
Google Scholar
Vila J, Ruiz J, Goni P, Marcos A, Jimenez de Anta T. Mutation in the gyrA gene of quinolone-resistant clinical isolates of Acinetobacter baumannii. Antimicrob Agents Chemother. 1995;39:1201–3.
Article
CAS
Google Scholar
Vila J, Ruiz J, Goni P, Jimenez de Anta T. Quinolone-resistance mutations in the topoisomerase IV parC gene of Acinetobacter baumannii. J Antimicrob Chemother. 1997;39:757–62.
Article
CAS
Google Scholar
Lesson 6: Investigating an outbreak. In: Principles of Epidemiology in Public Health Practice, Third edition: an introduction to applied epidemiology and biostatistics; 2012.
Inns T, Ashton PM, Herrera-Leon S, Lighthill J, Foulkes S, Jombart T, Rehman Y, Fox A, Dallman T, E DEP, et al. Prospective use of whole genome sequencing (WGS) detected a multi-country outbreak of Salmonella Enteritidis. Epidemiol Infect. 2016;145:1–10.
Google Scholar
Joensen KG, Scheutz F, Lund O, Hasman H, Kaas RS, Nielsen EM, Aarestrup FM. Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli. J Clin Microbiol. 2014;52:1501–10.
Article
Google Scholar
Agren EC, Wahlstrom H, Vesterlund-Carlson C, Lahti E, Melin L, Soderlund R. Comparison of whole genome sequencing typing results and epidemiological contact information from outbreaks of Salmonella Dublin in Swedish cattle herds. Infect Ecol Epidemiol. 2016;6:31782.
Article
Google Scholar
Mellmann A, Harmsen D, Cummings CA, Zentz EB, Leopold SR, Rico A, Prior K, Szczepanowski R, Ji Y, Zhang W, et al. Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology. PLoS One. 2011;6:e22751.
Article
CAS
Google Scholar
Koser CU, Holden MT, Ellington MJ, Cartwright EJ, Brown NM, Ogilvy-Stuart AL, Hsu LY, Chewapreecha C, Croucher NJ, Harris SR, et al. Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak. N Engl J Med. 2012;366:2267–75.
Article
CAS
Google Scholar
Kanamori H, Parobek CM, Weber DJ, van Duin D, Rutala WA, Cairns BA, Juliano JJ. Next-generation sequencing and comparative analysis of sequential outbreaks caused by multidrug-resistant Acinetobacter baumannii at a large academic burn center. Antimicrob Agents Chemother. 2015;60:1249–57.
Article
Google Scholar
Didelot X, Bowden R, Wilson DJ, Peto TEA, Crook DW. Transforming clinical microbiology with bacterial genome sequencing. Nat Rev Genet. 2012;13:601–12.
Article
CAS
Google Scholar
Kwong JC, McCallum N, Sintchenko V, Howden BP. Whole genome sequencing in clinical and public health microbiology. Pathology. 2015;47:199–210.
Article
CAS
Google Scholar
Leekitcharoenphon P, Nielsen EM, Kaas RS, Lund O, Aarestrup FM. Evaluation of whole genome sequencing for outbreak detection of Salmonella enterica. PLoS One. 2014;9:e87991.
Article
Google Scholar
Foley SL, Zhao S, Walker RD. Comparison of molecular typing methods for the differentiation of Salmonella foodborne pathogens. Foodborne Pathog Dis. 2007;4:253–76.
Article
CAS
Google Scholar
Valenzuela JK, Thomas L, Partridge SR, van der Reijden T, Dijkshoorn L, Iredell J. Horizontal gene transfer in a polyclonal outbreak of carbapenem-resistant Acinetobacter baumannii. J Clin Microbiol. 2007;45:453–60.
Article
CAS
Google Scholar
Fitzpatrick MA, Ozer EA, Hauser AR. Utility of whole-genome sequencing in characterizing Acinetobacter epidemiology and analyzing hospital outbreaks. J Clin Microbiol. 2016;54:593–612.
Article
Google Scholar
Higgins PG, Perez-Llarena FJ, Zander E, Fernandez A, Bou G, Seifert H. OXA-235, a novel class D beta-lactamase involved in resistance to carbapenems in Acinetobacter baumannii. Antimicrob Agents Chemother. 2013;57:2121–6.
Article
CAS
Google Scholar
Buser GL, Cassidy PM, Cunningham MC, Rudin S, Hujer AM, Vega R, Furuno JP, Marshall SH, Higgins PG, Jacobs MR, et al. Failure to communicate: transmission of extensively drug-resistant Bla OXA-237-containing Acinetobacter baumannii-multiple facilities in Oregon, 2012-2014. Infect Control Hosp Epidemiol. 2017;38:1–7.
Article
Google Scholar
Hujer AM, Higgins PG, Rudin SD, Buser GL, Marshall SH, Xanthopoulou K, Seifert H, Rojas LJ, Domitrovic TN, Cassidy PM, et al. Nosocomial outbreak of extensively drug-resistant Acinetobacter baumannii isolates containing blaOXA-237 carried on a plasmid. Antimicrob Agents Chemother. 2017;61:e00797.
Article
CAS
Google Scholar
Sheppard AE, Stoesser N, Wilson DJ, Sebra R, Kasarskis A, Anson LW, Giess A, Pankhurst LJ, Vaughan A, Grim CJ, et al. Nested Russian doll-like genetic mobility drives rapid dissemination of the Carbapenem resistance gene blaKPC. Antimicrob Agents Chemother. 2016;60:3767–78.
Article
CAS
Google Scholar
Willems S, Kampmeier S, Bletz S, Kossow A, Kock R, Kipp F, Mellmann A. Whole-genome sequencing elucidates epidemiology of nosocomial clusters of Acinetobacter baumannii. J Clin Microbiol. 2016;54:2391–4.
Article
Google Scholar
Halachev MR, Chan JZ, Constantinidou CI, Cumley N, Bradley C, Smith-Banks M, Oppenheim B, Pallen MJ. Genomic epidemiology of a protracted hospital outbreak caused by multidrug-resistant Acinetobacter baumannii in Birmingham, England. Genome Med. 2014;6:70.
Article
Google Scholar
Lewis T, Loman NJ, Bingle L, Jumaa P, Weinstock GM, Mortiboy D, Pallen MJ. High-throughput whole-genome sequencing to dissect the epidemiology of Acinetobacter baumannii isolates from a hospital outbreak. J Hosp Infect. 2010;75:37–41.
Article
CAS
Google Scholar