Real-Time PCR Typing of Escherichia coli Based on Multiple Single Nucleotide Polymorphisms--a Convenient and Rapid Method.
| Title: | Real-Time PCR Typing of Escherichia coli Based on Multiple Single Nucleotide Polymorphisms--a Convenient and Rapid Method. |
|---|---|
| Authors: | Lager M; Mernelius S; Löfgren S; Söderman J |
| Source: | Clinical laboratory [Clin Lab] 2016; Vol. 62 (3), pp. 349-55. |
| Publication Type: | Journal Article; Research Support, Non-U.S. Gov't |
| Language: | English |
| Journal Info: | Publisher: Clinical Laboratory Publications Country of Publication: Germany NLM ID: 9705611 Publication Model: Print Cited Medium: Print ISSN: 1433-6510 (Print) Linking ISSN: 14336510 NLM ISO Abbreviation: Clin Lab Subsets: MEDLINE |
| Imprint Name(s): | Publication: 2010- : Mainz : Clinical Laboratory Publications; Original Publication: Heidelberg : Verlag Klinisches Labor, [1997- |
| MeSH Terms: | Polymorphism, Single Nucleotide*; Escherichia coli/*classification ; Real-Time Polymerase Chain Reaction/*methods; Escherichia coli/genetics ; Bacterial Typing Techniques |
| Abstract: | Background: Healthcare-associated infections caused by Escherichia coli and antibiotic resistance due to extended-spectrum beta-lactamase (ESBL) production constitute a threat against patient safety. To identify, track, and control outbreaks and to detect emerging virulent clones, typing tools of sufficient discriminatory power that generate reproducible and unambiguous data are needed.; Methods: A probe based real-time PCR method targeting multiple single nucleotide polymorphisms (SNP) was developed. The method was based on the multi locus sequence typing scheme of Institute Pasteur and by adaptation of previously described typing assays.; Results: An 8 SNP-panel that reached a Simpson's diversity index of 0.95 was established, based on analysis of sporadic E. coli cases (ESBL n = 27 and non-ESBL n = 53). This multi-SNP assay was used to identify the sequence type 131 (ST131) complex according to the Achtman's multi locus sequence typing scheme. However, it did not fully discriminate within the complex but provided a diagnostic signature that outperformed a previously described detection assay. Pulsed-field gel electrophoresis typing of isolates from a presumed outbreak (n = 22) identified two outbreaks (ST127 and ST131) and three different non-outbreak-related isolates. Multi-SNP typing generated congruent data except for one non-outbreak-related ST131 isolate.; Conclusions: We consider multi-SNP real-time PCR typing an accessible primary generic E. coli typing tool for rapid and uniform type identification. |
| Entry Date(s): | Date Created: 20160510 Date Completed: 20160602 Latest Revision: 20160509 |
| Update Code: | 20260130 |
| PMID: | 27156323 |
| Database: | MEDLINE |
Journal Article; Research Support, Non-U.S. Gov't