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

Autor: Deborah Aragon, S. Brooks, Lesley McGee, L. McKnight, M. Schmidt, Suzanne McGuire, J. Benton, Nancy M. Bennett, C. Marquez, Zhongya Li, Kathy Angeles, Corinne Holtzman, Lee H. Harrison, R. Gierke, Lisa Miller, Bernard Beall, Megin Nichols, A. Riner, Gayle Fischer Langley, Olivia Almendares, S. Currenti, Richard Danila, Art Reingold, William Schaffner, K. Holmes, S. Zansky, R. Mansmann, Sopio Chochua, Rosemary Hollick, S. Khanlian, J. Hudson, Amy Tunali, T. Carter, Ben J. Metcalf, Ann Thomas, Hollis Walker, Jamie Thompson, K. Dyer, Robert E. Gertz, Sue Petit, L. Butler, J. Sadlowski, Stepy Thomas, L. McGlone, Anita Glennen, Meghan Barnes, M. Wilson, H. Randel, K. MacInnes, Paulina A. Hawkins, W. Baughman, B. White, Brenda Barnes, Y. Li, Joseph Bareta, Matthew L. Cartter, T. Tran, Ruth Lynfield, K. Leib, Tasha Poissant, Karen Scherzinger, Monica M. Farley
Jazyk: angličtina
Předmět:
0301 basic medicine
Microbiology (medical)
Penicillin binding proteins
Tetracycline
030106 microbiology
Core genome
Microbial Sensitivity Tests
Penicillins
Biology
medicine.disease_cause
Pneumococcal Infections
Microbiology
03 medical and health sciences
Antibiotic resistance
Ciprofloxacin
23S ribosomal RNA
Drug Resistance
Multiple
Bacterial
Trimethoprim
Sulfamethoxazole Drug Combination
Streptococcus pneumoniae
medicine
Humans
Penicillin-Binding Proteins
Whole genome
Genetics
Clindamycin
Accessory genome
Minimum inhibitory concentrations
General Medicine
biochemical phenomena
metabolism
and nutrition
medicine.disease
rpoB
United States
Anti-Bacterial Agents
Erythromycin
Penicillin
RNA
Ribosomal
23S
Pneumococcal infections
Chloramphenicol
Infectious Diseases
Genes
Bacterial
Mutation
Pneumococcal
medicine.drug
Zdroj: Clinical Microbiology and Infection. (12):1002.e1-1002.e8
ISSN: 1198-743X
DOI: 10.1016/j.cmi.2016.08.001
Popis: Our whole genome sequence (WGS) pipeline was assessed for accurate prediction of antimicrobial phenotypes. For 2316 invasive pneumococcal isolates recovered during 2015 we compared WGS pipeline data to broth dilution testing (BDT) for 18 antimicrobials. For 11 antimicrobials categorical discrepancies were assigned when WGS-predicted MICs and BDT MICs predicted different categorizations for susceptibility, intermediate resistance or resistance, ranging from 0.9% (tetracycline) to 2.9% (amoxicillin). For β-lactam antibiotics, the occurrence of at least four-fold differences in MIC ranged from 0.2% (meropenem) to 1.0% (penicillin), although phenotypic retesting resolved 25%–78% of these discrepancies. Non-susceptibility to penicillin, predicted by penicillin-binding protein types, was 2.7% (non-meningitis criteria) and 23.8% (meningitis criteria). Other common resistance determinants included mef (475 isolates), ermB (191 isolates), ermB + mef (48 isolates), tetM (261 isolates) and cat (51 isolates). Additional accessory resistance genes (tetS, tet32, aphA-3, sat4) were rarely detected (one to three isolates). Rare core genome mutations conferring erythromycin-resistance included a two-codon rplD insertion (rplD69-KG-70) and the 23S rRNA A2061G substitution (six isolates). Intermediate cotrimoxazole-resistance was associated with one or two codon insertions within folP (238 isolates) or the folA I100L substitution (38 isolates), whereas full cotrimoxazole-resistance was attributed to alterations in both genes (172 isolates). The two levofloxacin-resistant isolates contained parC and/or gyrA mutations. Of 11 remaining isolates with moderately elevated MICs to both ciprofloxacin and levofloxacin, seven contained parC or gyrA mutations. The two rifampin-resistant isolates contained rpoB mutations. WGS-based antimicrobial phenotype prediction was an informative alternative to BDT for invasive pneumococci.
Databáze: OpenAIRE
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