Validation of β-lactam minimum inhibitory concentration predictions for pneumococcal isolates with newly encountered penicillin binding protein (PBP) sequences

BMC Genomics

Volumn 18, Issue 1, 2017, Pages

  Li, Yuan ^a   Metcalf, Benjamin J ^a   Chochua, Sopio ^a   Li, Zhongya ^a   Gertz, Robert E ^a   Walker, Hollis ^a   Hawkins, Paulina A ^a   Tran, Theresa ^a   McGee, Lesley ^a   Beall, Bernard W ^a  

^a NATIONAL CENTER FOR IMMUNIZATION AND RESPIRATORY DISEASES   (United States)

Author keywords

Minimum inhibitory concentration (MIC); Penicillin binding protein typing (PBP typing); Predictive modeling; Streptococcus Pneumoniae; lactam antibiotics

Indexed keywords

AMOXICILLIN; BETA LACTAM ANTIBIOTIC; CEFOTAXIME; CEFTRIAXONE; CEFUROXIME; MEROPENEM; PENICILLIN BINDING PROTEIN; PENICILLIN DERIVATIVE; BETA LACTAM;

AMINO ACID SEQUENCE; ARTICLE; BACTERIUM ISOLATE; BINOMIAL DISTRIBUTION; BROTH DILUTION; CONFIDENCE INTERVAL; CONTROLLED STUDY; CORRELATION COEFFICIENT; DNA SEQUENCE; MEASUREMENT ACCURACY; MINIMUM INHIBITORY CONCENTRATION; NONHUMAN; PREDICTIVE VALUE; PROBABILITY; PROTEIN SECONDARY STRUCTURE; RANDOM FOREST; STREPTOCOCCUS PNEUMONIAE; VALIDATION PROCESS; BIOLOGY; DRUG EFFECTS; GENETICS; MICROBIAL SENSITIVITY TEST; PHENOTYPE; VALIDATION STUDY;

BETA-LACTAMS; COMPUTATIONAL BIOLOGY; MICROBIAL SENSITIVITY TESTS; PENICILLIN-BINDING PROTEINS; PHENOTYPE; STREPTOCOCCUS PNEUMONIAE;

EID: 85027489571     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-017-4017-7     Document Type: Article

References (26)

1. Koser CU, Ellington MJ, Cartwright EJ, Gillespie SH, Brown NM, Farrington M, Holden MT, Dougan G, Bentley SD, Parkhill J, et al. Routine use of microbial whole genome sequencing in diagnostic and public health microbiology. PLoS Pathog. 2012;8(8):e1002824.
2. Koser CU, Bryant JM, Becq J, Torok ME, Ellington MJ, Marti-Renom MA, Carmichael AJ, Parkhill J, Smith GP, Peacock SJ. Whole-genome sequencing for rapid susceptibility testing of M. Tuberculosis. N Engl J Med. 2013;369(3):290-2.
3. Dowson CG, Johnson AP, Cercenado E, George RC. Genetics of oxacillin resistance in clinical isolates of Streptococcus Pneumoniae that are oxacillin resistant and penicillin susceptible. Antimicrob Agents Chemother. 1994;38(1):49-53.
4. Barcus VA, Ghanekar K, Yeo M, Coffey TJ, Dowson CG. Genetics of high level penicillin resistance in clinical isolates of Streptococcus Pneumoniae. FEMS Microbiol Lett. 1995;126(3):299-303.
5. Grebe T, Hakenbeck R. Penicillin-binding proteins 2b and 2x of Streptococcus Pneumoniae are primary resistance determinants for different classes of beta-lactam antibiotics. Antimicrob Agents Chemother. 1996;40(4):829-34.
6. Smith AM, Klugman KP. Alterations in PBP 1A essential-for high-level penicillin resistance in Streptococcus Pneumoniae. Antimicrob Agents Chemother. 1998;42(6):1329-33.
7. Hakenbeck R, Bruckner R, Denapaite D, Maurer P. Molecular mechanisms of beta-lactam resistance in Streptococcus Pneumoniae. Future Microbiol. 2012;7(3):395-410.
8. Metcalf BJ, Chochua S, Gertz RE Jr, Li Z, Walker H, Tran T, Hawkins PA, Glennen A, Lynfield R, Li Y, et al. Using whole genome sequencing to identify resistance determinants and predict antimicrobial resistance phenotypes for year 2015 invasive pneumococcal disease isolates recovered in the United States. Clin Microbiol Infect. 2016;22(12):1002.e1001-8.
9. Li Y, Metcalf BJ, Chochua S, Li Z, Gertz RE Jr, Walker H, Hawkins PA, Tran T, Whitney CG, McGee L, et al. Penicillin-Binding Protein Transpeptidase Signatures for Tracking and Predicting beta-Lactam Resistance Levels in Streptococcus pneumoniae. MBio. 2016;7(3). doi: 10.1128/mBio.00756-16.
10. Metcalf BJ, Gertz RE Jr, Gladstone RA, Walker H, Sherwood LK, Jackson D, Li Z, Law C, Hawkins PA, Chochua S, et al. Strain features and distributions in pneumococci from children with invasive disease before and after 13-valent conjugate vaccine implementation in the USA. Clin Microbiol Infect. 2016;22(1):60 e69-29.
11. Chewapreecha C, Harris SR, Croucher NJ, Turner C, Marttinen P, Cheng L, Pessia A, Aanensen DM, Mather AE, Page AJ, et al. Dense genomic sampling identifies highways of pneumococcal recombination. Nat Genet. 2014;46(3):305-9.
12. Chewapreecha C, Marttinen P, Croucher NJ, Salter SJ, Harris SR, Mather AE, Hanage WP, Goldblatt D, Nosten FH, Turner C, et al. Comprehensive identification of single nucleotide polymorphisms associated with beta-lactam resistance within pneumococcal mosaic genes. PLoS Genet. 2014;10(8):e1004547.
13. Coffey TJ, Dowson CG, Daniels M, Spratt BG. Horizontal spread of an altered penicillin-binding protein 2B gene between Streptococcus Pneumoniae and Streptococcus Oralis. FEMS Microbiol Lett. 1993;110(3):335-9.
14. Dowson CG, Coffey TJ, Kell C, Whiley RA. Evolution of penicillin resistance in Streptococcus Pneumoniae; the role of Streptococcus Mitis in the formation of a low affinity PBP2B in S. Pneumoniae. Mol Microbiol. 1993;9(3):635-43.
15. Dowson CG, Coffey TJ, Spratt BG. Origin and molecular epidemiology of penicillin-binding-protein-mediated resistance to beta-lactam antibiotics. Trends Microbiol. 1994;2(10):361-6.
16. Beall BW, Gertz RE, Hulkower RL, Whitney CG, Moore MR, Brueggemann AB. Shifting genetic structure of invasive serotype 19A pneumococci in the United States. J Infect Dis. 2011;203(10):1360-8.
17. Henikoff S, Henikoff JG. Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci U S A. 1992;89(22):10915-9.
18. FDA: Guidance for Industry and FDA Class II Special Controls Guidance Document: Antimicrobial Susceptibility Test (AST) Systems. In.; 2009.
19. Institute CaLS: Performance standards for antimicrobial susceptibility testing; twenty-third informational supplement M100-S23. 2013.
20. Donati C, Hiller NL, Tettelin H, Muzzi A, Croucher NJ, Angiuoli SV, Oggioni M, Dunning Hotopp JC, Hu FZ, Riley DR, et al. Structure and dynamics of the pan-genome of Streptococcus Pneumoniae and closely related species. Genome Biol. 2010;11(10):R107.
21. Tettelin H, Riley D, Cattuto C, Medini D. Comparative genomics: the bacterial pan-genome. Curr Opin Microbiol. 2008;11(5):472-7.
22. Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL, Angiuoli SV, Crabtree J, Jones AL, Durkin AS, et al. Genome analysis of multiple pathogenic isolates of Streptococcus Agalactiae: implications for the microbial "pan-genome". Proc Natl Acad Sci U S A. 2005;102(39):13950-5.
23. Team RC: R: A Language and Environment for Statistical Computing. In. https://www.R-project.org ; 2015.
24. Clauset A, Shalizi CR, Newman MEJ. Power-law Distrubtions in empirical data. SIAM Rev. 2009;51(4):661-703.
25. Virkar Y, Clauset A. Power-law distributions in binned empirical data. Ann Appl Stat. 2014;8(1):89-119.
26. Stumpf MP, Porter MA. Mathematics. Critical truths about power laws. Science. 2012;335(6069):665-6.