TY - JOUR
T1 - Predictive diagnostics for Escherichia coli infections based on the clonal association of antimicrobial resistance and clinical outcome
AU - Tchesnokova, Veronika
AU - Billig, Mariya
AU - Chattopadhyay, Sujay
AU - Linardopoulou, Elena
AU - Aprikian, Pavel
AU - Roberts, Pacita L.
AU - Skrivankova, Veronika
AU - Johnston, Brian
AU - Gileva, Alena
AU - Igusheva, Irina
AU - Toland, Angus
AU - Riddell, Kim
AU - Rogers, Peggy
AU - Qin, Xuan
AU - Butler-Wu, Susan
AU - Cookson, Brad T.
AU - Fang, Ferric C.
AU - Kahl, Barbara
AU - Price, Lance B.
AU - Weissman, Scott J.
AU - Limaye, Ajit
AU - Scholes, Delia
AU - Johnson, James R.
AU - Sokurenko, Evgeni V.
PY - 2013/9
Y1 - 2013/9
N2 - The ability to identify bacterial pathogens at the subspecies level in clinical diagnostics is currently limited. We investigated whether splitting Escherichia coli species into clonal groups (clonotypes) predicts antimicrobial susceptibility or clinical outcome. A total of 1,679 extraintestinal E. coli isolates (collected from 2010 to 2012) were collected from one German and 5 U.S. clinical microbiology laboratories. Clonotype identity was determined by fumC and fimH (CH) sequencing. The associations of clonotype with antimicrobial susceptibility and clinical variables were evaluated. CH typing divided the isolates into>200 CH clonotypes, with 93% of the isolates belonging to clonotypes with≥2 isolates. Antimicrobial susceptibility varied substantially among clonotypes but was consistent across different locations. Clonotype-guided antimicrobial selection significantly reduced "drug-bug" mismatch compared to that which occurs with the use of conventional empirical therapy. With trimethoprim-sulfamethoxazole and fluoroquinolones, the drug-bug mismatch was predicted to decrease 62% and 78%, respectively. Recurrent or persistent urinary tract infection and clinical sepsis were significantly correlated with specific clonotypes, especially with CH40-30 (also known as H30), a recently described clonotype within sequence type 131 (ST131). We were able to clonotype directly from patient urine samples within 1 to 3 h of obtaining the specimen. In E. coli, subspecies-level identification by clonotyping can be used to significantly improve empirical predictions of antimicrobial susceptibility and clinical outcomes in a timely manner.
AB - The ability to identify bacterial pathogens at the subspecies level in clinical diagnostics is currently limited. We investigated whether splitting Escherichia coli species into clonal groups (clonotypes) predicts antimicrobial susceptibility or clinical outcome. A total of 1,679 extraintestinal E. coli isolates (collected from 2010 to 2012) were collected from one German and 5 U.S. clinical microbiology laboratories. Clonotype identity was determined by fumC and fimH (CH) sequencing. The associations of clonotype with antimicrobial susceptibility and clinical variables were evaluated. CH typing divided the isolates into>200 CH clonotypes, with 93% of the isolates belonging to clonotypes with≥2 isolates. Antimicrobial susceptibility varied substantially among clonotypes but was consistent across different locations. Clonotype-guided antimicrobial selection significantly reduced "drug-bug" mismatch compared to that which occurs with the use of conventional empirical therapy. With trimethoprim-sulfamethoxazole and fluoroquinolones, the drug-bug mismatch was predicted to decrease 62% and 78%, respectively. Recurrent or persistent urinary tract infection and clinical sepsis were significantly correlated with specific clonotypes, especially with CH40-30 (also known as H30), a recently described clonotype within sequence type 131 (ST131). We were able to clonotype directly from patient urine samples within 1 to 3 h of obtaining the specimen. In E. coli, subspecies-level identification by clonotyping can be used to significantly improve empirical predictions of antimicrobial susceptibility and clinical outcomes in a timely manner.
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U2 - 10.1128/JCM.00984-13
DO - 10.1128/JCM.00984-13
M3 - Article
C2 - 23843485
AN - SCOPUS:84882767926
SN - 0095-1137
VL - 51
SP - 2991
EP - 2999
JO - Journal of Clinical Microbiology
JF - Journal of Clinical Microbiology
IS - 9
ER -