TY - JOUR
T1 - A Novel 7-single nucleotide polymorphism-based clonotyping test allows rapid prediction of antimicrobial susceptibility of extraintestinal Escherichia coli directly from urine specimens
AU - Tchesnokova, Veronika
AU - Avagyan, Hovhannes
AU - Billig, Mariya
AU - Chattopadhyay, Sujay
AU - Aprikian, Pavel
AU - Chan, Diana
AU - Pseunova, Julietta
AU - Rechkina, Elena
AU - Riddell, Kim
AU - Scholes, Delia
AU - Fang, Ferric C.
AU - Johnson, James R.
AU - Sokurenko, Evgeni V.
N1 - Publisher Copyright:
© The Author 2016. Published by Oxford University Press on behalf of the Infectious Diseases Society of America.
PY - 2016/1/1
Y1 - 2016/1/1
N2 - Background. Escherichia coli is a highly clonal pathogen. Extraintestinal isolates belong to a limited number of genetically related groups, which often exhibit characteristic antimicrobial resistance profiles. Methods. We developed a rapid clonotyping method for extraintestinal E coli based on detection of the presence or absence of 7 single nucleotide polymorphisms (SNPs) within 2 genes (fumC and fimH). A reference set of 2559 E coli isolates, primarily of urinary origin, was used to predict the resolving power of the 7-SNP-based typing method, and 582 representative strains from this set were used to evaluate test robustness. Results. Fifty-four unique SNP combinations ("septatypes") were identified in the reference strains. These septatypes yielded a clonal group resolution power on par with that of traditional multilocus sequence typing. In 72% of isolates, septatype identity predicted sequence type identity with at least 90% (mean, 97%) accuracy. Most septatypes exhibited highly distinctive antimicrobial susceptibility profiles. The 7-SNP-based test could be performed with high specificity and sensitivity using single or multiplex conventional polymerase chain reaction (PCR) and quantitative PCR. In the latter format, E coli presence and septatype identity were determined directly in urine specimens within 45 minutes with bacterial loads as low as 102 colony-forming units/mL and, at clinically significant bacterial loads, with 100% sensitivity and specificity. Conclusion. 7-SNP-based typing of E coli can be used for both epidemiological studies and clinical diagnostics, which could greatly improve the empirical selection of antimicrobial therapy.
AB - Background. Escherichia coli is a highly clonal pathogen. Extraintestinal isolates belong to a limited number of genetically related groups, which often exhibit characteristic antimicrobial resistance profiles. Methods. We developed a rapid clonotyping method for extraintestinal E coli based on detection of the presence or absence of 7 single nucleotide polymorphisms (SNPs) within 2 genes (fumC and fimH). A reference set of 2559 E coli isolates, primarily of urinary origin, was used to predict the resolving power of the 7-SNP-based typing method, and 582 representative strains from this set were used to evaluate test robustness. Results. Fifty-four unique SNP combinations ("septatypes") were identified in the reference strains. These septatypes yielded a clonal group resolution power on par with that of traditional multilocus sequence typing. In 72% of isolates, septatype identity predicted sequence type identity with at least 90% (mean, 97%) accuracy. Most septatypes exhibited highly distinctive antimicrobial susceptibility profiles. The 7-SNP-based test could be performed with high specificity and sensitivity using single or multiplex conventional polymerase chain reaction (PCR) and quantitative PCR. In the latter format, E coli presence and septatype identity were determined directly in urine specimens within 45 minutes with bacterial loads as low as 102 colony-forming units/mL and, at clinically significant bacterial loads, with 100% sensitivity and specificity. Conclusion. 7-SNP-based typing of E coli can be used for both epidemiological studies and clinical diagnostics, which could greatly improve the empirical selection of antimicrobial therapy.
KW - Antibiotic resistance
KW - Clonal typing
KW - Escherichia coli
KW - Personal therapy
KW - Point-of-care testing
UR - http://www.scopus.com/inward/record.url?scp=85000788322&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85000788322&partnerID=8YFLogxK
U2 - 10.1093/ofid/ofw002
DO - 10.1093/ofid/ofw002
M3 - Article
C2 - 26925427
AN - SCOPUS:85000788322
SN - 2328-8957
VL - 3
JO - Open Forum Infectious Diseases
JF - Open Forum Infectious Diseases
IS - 1
M1 - ofw002
ER -