Multilocus Sequence Typing versus Pulsed-Field Gel Electrophoresis for Characterization of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli Isolates

Abstract

Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli strains are emerging pathogens. Molecular typing of ESBL-producing E. coli is useful for surveillance purposes, to monitor outbreaks and track nosocomial spread. Although pulsed-field gel electrophoresis (PFGE) is the current "gold standard" for bacterial molecular typing, multilocus sequence typing (MLST) may offer advantages. Forty ESBL-producing E. coli isolates were selected at random from a cohort of intensive care unit patients who had active surveillance perirectal cultures done. PFGE identified 19 unique PFGE types (PT) among the 40 isolates; MLST identified 22 unique sequence types. MLST had greater discriminatory ability than PFGE for ESBL-producing E. coli. Simpson's indices of diversity for PFGE and MLST were 0.895 and 0.956, respectively. There were five clonal complexes (CCs) (isolates with differences of no more than two loci) that each contained multiple PT, but each PT was found in only one CC, indicating genetic consistency within a CC. MLST has clear utility in studies of ESBL-producing E. coli, based on a greater discriminatory ability and reproducibility than PFGE and the ability to a priori define genetically related bacterial strains.Pulsed-field gel electrophoresis (PFGE) is the most widely used tool for molecular typing of bacterial strains (1), but new DNA fingerprinting techniques, including multilocus sequence typing (MLST), are emerging as alternatives, particularly when information regarding evolutionary history is needed (30). MLST is a relatively new technique where multiple genes (loci) are sequenced to measure genetic relatedness and analyze sequence variation between alleles from many strains (20). MLST has already been used to characterize a number of pathogenic bacteria, including Neisseria meningitidis, Enterococcus spp., Staphylococcus aureus, and Campylobacter spp. (3,4,7,21). In studies comparing MLST to PFGE among Salmonella spp., Vibrio cholerae, Enterococcus faecalis, and S. aureus isolates, MLST has been found to have similar or greater discriminatory ability than PFGE (17,18,21,27). However, these results may not be generalizable to all species, since a study comparing MLST to PFGE in Escherichia coli O157:H7 found that PFGE had a greater discriminatory ability than MLST did (26).MLST has not yet been used to characterize extended-spectrum beta-lactamase (ESBL)-producing E. coli isolates. ESBL production, which confers resistance to all penicillins and cephalosporins, is found in E. coli and other members of the family Enterobacteriaceae. In the United States, the prevalence of ESBL carriage ranges between 0 and 25%, with a national average of approximately 6%, and these numbers are increasing (2, 24). ESBL-producing E. coli bacteria cause nosocomial infections, including bloodstream infections, urinary tract infections, and pneumonias, and are associated with increased patient morbidity and mortality (29). Molecular typing of ESBL-producing E. coli is useful as a framework for hospital epidemiologist...

Analysis of a Uropathogenic Escherichia coli Clonal Group by Multilocus Sequence Typing

“…A similar observation was made by Noller et al, who compared PFGE and MLST for their discriminatory ability using a collection of diarrheagenic E. coli serotype O157:H7 (16). In one study, MLST was found to be more discriminatory than PFGE only if gene templates in addition to the 7 housekeeping genes were included (15).…”

Characterization of Epidemiologically Unrelated Acinetobacter baumannii Isolates from Four Continents by Use of Multilocus Sequence Typing, Pulsed-Field Gel Electrophoresis, and Sequence-Based Typing of bla OXA-51-like Genes

“…Increasing antimicrobial resistance (42) and the ability of A. baumannii to survive on inanimate and dry surfaces (19) have been linked to the occurrence of outbreaks observed in various hospitals (5). MLST has emerged as the technique of choice for studying the population structure of many bacterial species (15,17,20,30,40), including A. baumannii (1,10,24,29,37,38). However, profiles for only 93 isolates of A. baumannii are available in the current MLST database (http://pubmlst.org/abaumannii/), which is considerably less than the numbers deposited in databases for other bacteria (http://pubmlst.org/databases.shtml).…”

Genotypes of Klebsiella oxytoca Isolates from Patients with Nosocomial Pneumonia Are Distinct from Those of Isolates from Patients with Antibiotic-Associated Hemorrhagic Colitis

“…MLST schemes for Enterobacteriaceae (27,28) and thus is appropriate for evolutionary population genetics. Additionally, wholegenome comparison of the eight publicly available K. oxytoca genome sequences was done using genomic BLAST, followed by dendrogram construction based on genetic distance.…”