164
Views
7
CrossRef citations to date
0
Altmetric
Original Research

Comparative genomic analysis of multidrug-resistant Streptococcus pneumoniae isolates

, , , , , , & show all
Pages 659-670 | Published online: 03 May 2018

References

  • World Health Organization. Pneumococcal conjugate vaccine for childhood immunization: WHO position paper. Wkly Epidemiol Rec. 2007;82(12):93–104.
  • Kim SH, Song JH, Chung DR, et al; ANSORP Study Group. Changing trends in antimicrobial resistance and serotypes of Streptococcus pneumoniae isolates in Asian countries: an Asian Network for Surveillance of Resistant Pathogens (ANSORP) study. Antimicrob Agents Chemother. 2012;56(3):1418–1426.
  • Merker M, Kohl TA, Roetzer A, et al. Whole genome sequencing reveals complex evolution patterns of multidrug-resistant Mycobacterium tuberculosis Beijing strains in patients. PLoS One. 2013;8(12): e82551.
  • Cherazard R, Epstein M, Doan TL, Salim T, Bharti S, Smith MA. Antimicrobial resistant Streptococcus pneumoniae: prevalence, mechanisms, and clinical implications. Am J Ther. 2017;24(3):e361–e369.
  • Schweizer I, Blättner S, Maurer P, et al. New aspects of the interplay between penicillin binding proteins, murM, and the two-component system CiaRH of penicillin-resistant Streptococcus pneumoniae Serotype 19A isolates from Hungary. Antimicrob Agents Chemother. 2017;61(7):e00414–e00417.
  • Rayner RE, Savill J, Hafner LM, Huygens F. Genotyping Streptococcus pneumoniae. Future Microbiol. 2015;10(4):653–664.
  • Andam CP, Hanage WP. Mechanisms of genome evolution of Streptococcus. Infect Genet Evol. 2015;33:334–342.
  • Côrtes MF, Costa MO, Lima NC, et al. Complete genome sequence of community-associated methicillin-resistant Staphylococcus aureus (strain USA400-0051), a prototype of the USA400 clone. Mem Inst Oswaldo Cruz. 2017;112(11):790–792.
  • Jakobsson HE, Salvà-Serra F, Thorell K, et al. Draft genome sequences of six strains of Streptococcus pneumoniae from serotypes 5, 6A, 6B, 18C, 19A, and 23F. Genome Announc. 2017;5(14):e00125–e00117.
  • Gardner KAJA, Osawa M, Erickson HP. Whole genome re-sequencing to identify suppressor mutations of mutant and foreign Escherichia coli FtsZ. PLoS One. 2017;12(4):e0176643.
  • Loman NJ, Constantinidou C, Chan JZ, et al. High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity. Nat Rev Microbiol. 2012;10(9):599–606.
  • Wessels E, Schelfaut JJ, Bernards AT, Claas EC. Evaluation of several biochemical and molecular techniques for identification of Streptococcus pneumoniae and Streptococcus pseudopneumoniae and their detection in respiratory samples. J Clin Microbiol. 2012;50:1171–1177.
  • Clinical and Laboratory Standards Institute (CLSI). Performance Standards for Antimicrobial Susceptibility Testing; 26th Informational Supplement. CLSI document M100-26. Wayne, PA: Clinical and Laboratory Standards Institute; 2016.
  • Enright MC, Spratt BG. A multilocus sequence typing scheme for Streptococcus pneumoniae: identification of clones associated with serious invasive disease. Microbiology. 1998;144(Pt 11):3049–3060.
  • Schubert M, Lindgreen S, Orlando L. AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Res Notes. 2016;9:88.
  • Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25(14):1754–1760.
  • Darling AC, Mau B, Blattner FR, Perna NT. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 2004;14(7):1394–1403.
  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215(3):403–410.
  • Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Bio Evol. 2013;30(12):2725–2729.
  • Köser CU, Holden MT, Ellington MJ, et al. Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak. N Engl J Med. 2012;366(24):2267–2275.
  • Liu F, Hu Y, Wang Q, et al. Comparative genomic analysis of Mycobacterium tuberculosis clinical isolates. BMC Genomics. 2014;15:469.
  • Kwong JC, McCallum N, Sintchenko V, Howden BP. Whole genome sequencing in clinical and public health microbiology. Pathology. 2015;47(3):199–210.
  • Relman DA. Microbial genomics and infectious diseases. N Engl J Med. 2011;365(4):347–357.
  • Ding F, Tang P, Hsu MH, et al. Genome evolution driven by host adaptations results in a more virulent and antimicrobial-resistant Streptococcus pneumoniae serotype 14. BMC Genomics. 2009;10:158.
  • Korona-Glowniak I, Siwiec R, Malm A. Resistance determinants and their association with different transposons in the antibiotic-resistant Streptococcus pneumoniae. Biomed Res Int. 2015;2015:836496.
  • Iannelli F, Santoro F, Oggioni MR, Pozzi G. Nucleotide sequence analysis of integrative conjugative element Tn5253 of Streptococcus pneumoniae. Antimicrob Agents Chemother. 2014;58(2):1235–1239.
  • Miller WR, Munita JM, Arias CA. Mechanisms of antibiotic resistance in enterococci. Expert Rev Anti Infect Ther. 2014;12(10):1221–1236.
  • Blair JM, Richmond GE, Piddock LJ. Multidrug efflux pumps in Gram-negative bacteria and their role in antibiotic resistance. Future Microbiol. 2014;9(10):1165–1177.
  • Sanbongi Y, Ida T, Ishikawa M, et al. Complete sequences of six penicillin-binding protein genes from 40 Streptococcus pneumoniae clinical isolates collected in Japan. Antimicrob Agents Chemother. 2004;48(6):2244–2250.
  • Chaguza C, Cornick JE, Everett DB. Mechanisms and impact of genetic recombination in the evolution of Streptococcus pneumoniae. Comput Struct Biotechnol J. 2015;13:241–247.
  • Davey L, Halperin SA, Lee SF. Mutation of the Streptococcus gordonii thiol-disulfide oxidoreductase SdbA leads to enhanced biofilm formation mediated by the CiaRH two-component signaling system. PLoS One. 2016;11(11):e0166656.
  • Metcalf BJ, Chochua S, Gertz RE Jr, et al; Active Bacterial Core Surveillance Team. 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.e1–1002.e8.
  • Haasum Y, Ström K, Wehelie R, et al. Amino acid repetitions in the dihydropteroate synthase of Streptococcus pneumoniae lead to sulfonamide resistance with limited effects on substrate K(m). Antimicrob Agents Chemother. 2001;45(3):805–809.
  • Maskell JP, Sefton AM, Hall LM. Multiple mutations modulate the function of dihydrofolate reductase in trimethoprim-resistant Streptococcus pneumoniae. Antimicrob Agents Chemother. 2001;45(4):1104–1108.
  • Oz T, Guvenek A, Yildiz S, et al. Strength of selection pressure is an important parameter contributing to the complexity of antibiotic resistance evolution. Mol Biol Evol. 2014;31(9):2387–2401.