A Novel 7-single nucleotide polymorphism-based clonotyping test allows rapid prediction of antimicrobial susceptibility of extraintestinal Escherichia coli directly from urine specimens

Open Forum Infectious Diseases

Volumn 3, Issue 1, 2016, Pages

  Tchesnokova, Veronika ^a   Avagyan, Hovhannes ^a   Billig, Mariya ^a   Chattopadhyay, Sujay ^a   Aprikian, Pavel ^b   Chan, Diana ^a   Pseunova, Julietta ^c   Rechkina, Elena ^b   Riddell, Kim ^d   Scholes, Delia ^d   Fang, Ferric C ^a   Johnson, James R ^e   Sokurenko, Evgeni V ^a  

^a UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^b ID Genomics Inc Inc   (United States)

^c Gemotest   (Russian Federation)

^d CENTER FOR HEALTH STUDIES   (United States)

^e UNIVERSITY OF MINNESOTA   (United States)

Author keywords

Antibiotic resistance; Clonal typing; Escherichia coli; Personal therapy; Point of care testing

Indexed keywords

AMOXICILLIN PLUS CLAVULANIC ACID; CEFAZOLIN; CEFTRIAXONE; CIPROFLOXACIN; COTRIMOXAZOLE; NITROFURANTOIN;

ALLELE; ANTIBIOTIC RESISTANCE; ANTIBIOTIC SENSITIVITY; ARTICLE; CONTROLLED STUDY; EXTRAINTESTINAL PATHOGENIC ESCHERICHIA COLI; FECES ANALYSIS; HUMAN; MULTILOCUS SEQUENCE TYPING; NONHUMAN; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; SINGLE NUCLEOTIDE POLYMORPHISM; URINALYSIS;

EID: 85000788322     PISSN: None     EISSN: 23288957     Source Type: Journal    
DOI: 10.1093/ofid/ofw002     Document Type: Article

References (21)

1. Foxman B. The epidemiology of urinary tract infection. Nat Rev Urol 2010; 7:653-60.
2. Kaper JB, Nataro JP, Mobley HL. Pathogenic Escherichia coli. Nat Rev Microbiol 2004; 2:123-40.
3. Tchesnokova V, Billig M, Chattopadhyay S, et al. Predictive diagnostics for Escherichia coli infections based on the clonal association of antimicrobial resistance and clinical outcome. J Clin Microbiol 2013; 51:2991-9.
4. Wirth T, Falush D, Lan R, et al. Sex and virulence in Escherichia coli: an evolutionary perspective. Mol Microbiol 2006; 60:1136-51.
5. Johnson JR, Murray AC, Kuskowski MA, et al. Distribution and characteristics of Escherichia coli clonal group A. Emerg Infect Dis 2005; 11:141-5.
6. Tartof SY, Solberg OD, Manges AR, Riley LW. Analysis of a uropathogenic Escherichia coli clonal group by multilocus sequence typing. J Clin Microbiol 2005; 43:5860-4.
7. Maiden MC, Bygraves JA, Feil E, et al. Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci U S A 1998; 95:3140-5.
8. Weissman SJ, Johnson JR, Tchesnokova V, et al. High-resolution two-locus clonal typing of extraintestinal pathogenic Escherichia coli. Appl Environ Microbiol 2012; 78:1353-60.
9. Feil EJ, Li BC, Aanensen DM, et al. eBURST: inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data. J Bacteriol 2004; 186:1518-30.
10. Willcox WR, Lapage SP, Holmes B. A review of numerical methods in bacterial identification. Antonie Van Leeuwenhoek 1980; 46:233-99.
11. CLSI. Performance Standards for Antimicrobial Susceptibility Testing; Twentieth Informational Supplement. Wayne, PA; Clinical and Laboratory Standards Institute; 2010; 30:M100-S20.
12. Johnson JR, Tchesnokova V, Johnston B, et al. Abrupt emergence of a single dominant multidrug-resistant strain of Escherichia coli. J Infect Dis 2013; 207:919-28.
13. Weissman SJ, Beskhlebnaya V, Chesnokova V, et al. Differential stability and trade-off effects of pathoadaptive mutations in the Escherichia coli FimH adhesin. Infect Immun 2007; 75:3548-55.
14. Perez-Losada M, Cabezas P, Castro-Nallar E, Crandall KA. Pathogen typing in the genomics era: MLST and the future of molecular epidemiology. Infect Genet Evol 2013; 16:38-53.
15. Clermont O, Christenson JK, Denamur E, Gordon DM. The Clermont Escherichia coli phylo-typing method revisited: improvement of specificity and detection of new phylo-groups. Environ Microbiol Rep 2013; 5:58-65.
16. Clermont O, Bonacorsi S, Bingen E. Rapid and simple determination of the Escherichia coli phylogenetic group. Appl Environ Microbiol 2000; 66:4555-8.
17. Hommais F, Pereira S, Acquaviva C, et al. Single-nucleotide polymorphism phylotyping of Escherichia coli. Appl Environ Microbiol 2005; 71:4784-92.
18. Sheludchenko MS, Huygens F, Hargreaves MH. Highly discriminatory single-nucleotide polymorphism interrogation of Escherichia coli by use of allele- specific real-time PCR and eBURST analysis. Appl Environ Microbiol 2010; 76:4337-45.
19. Mobley HL, Green DM, Trifillis AL, et al. Pyelonephritogenic Escherichia coli and killing of cultured human renal proximal tubular epithelial cells: role of hemolysin in some strains. Infect Immun 1990; 58:1281-9.
20. Grozdanov L, Raasch C, Schulze J, et al. Analysis of the genome structure of the nonpathogenic probiotic Escherichia coli strain Nissle 1917. J Bacteriol 2004; 186:5432-41.
21. IDSA. Principles and Strategies Intended to Limit the Impact of Antimicrobial Resistance, 2006. Available at: http://www.idsociety.org/View_All_Statements_on_Antimicrobial_Stewardship/. Accessed 24 April 2006.