title: Comparison of arbitrarily primed PCR with restriction endonuclease and immunoblot analyses for typing Clostridium difficile isolates.
abstract: Arbitrarily primed PCR (AP-PCR) was used to genotype 26 clinical isolates of Clostridium difficile previously analyzed by immunoblotting (IB) and 20 isolates typed by restriction endonuclease analysis (REA) with HindIII. Two levels of differentiation were achieved with the AP-PCR approach by use of two different arbitrary primers. With the 19-mer arbitrary primer T-7 (first level of differentiation), a good correlation was found between IB and AP-PCR typing. Twenty isolates grouped into six IB types were separated into seven major AP-PCR types. These seven AP-PCR groups were further discriminated into 12 subtypes after genotyping with the arbitrary primer PG-05 (second level of differentiation). The remaining six isolates, all of different IB types, showed a unique and distinct DNA banding pattern with both of the arbitrary primers, T-7 and PG-05. Twenty isolates representing 20 REA types from 15 REA groups were resolved into 13 AP-PCR DNA profiles with the arbitrary primer T-7. A good correlation was found at this level of differentiation between the major REA groups, Y and M, and AP-PCR typing. While AP-PCR with this primer failed to differentiate isolates in REA groups J, G, R, and B, AP-PCR with PG-05 resolved these four isolates into four distinct AP-PCR types. In addition, one of three M strains and one of four Y strains displayed a slightly different DNA banding pattern by AP-PCR (with PG-05) from that of the other strains in the group. We conclude that AP-PCR is a rapid and sensitive method which not only complements other typing schemes but also may be a substitute and prove to be especially suited for immediate epidemiological tracking of nosocomial infections due to C. difficile.
authors.affiliation: Department of Internal Medicine, University of California, Davis Medical Center, Sacramento, USA.
authors.forename: Y J
authors.initials: YJ
authors.lastname: Tang
authors.forename: S T
authors.initials: ST
authors.lastname: Houston
authors.forename: P H
authors.initials: PH
authors.lastname: Gumerlock
authors.forename: M E
authors.initials: ME
authors.lastname: Mulligan
authors.forename: D N
authors.initials: DN
authors.lastname: Gerding
authors.forename: S
authors.initials: S
authors.lastname: Johnson
authors.forename: F R
authors.initials: FR
authors.lastname: Fekety
authors.forename: J
authors.initials: J
authors.lastname: Silva
mesh_terms: D015373:Bacterial Typing Techniques / Q000706:statistics & numerical data; D001483:Base Sequence; D016360:Clostridioides difficile / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D017931:DNA Primers / Q000235:genetics; D004262:DNA Restriction Enzymes; D004269:DNA, Bacterial / Q000235:genetics; D015247:Deoxyribonuclease HindIII; D005069:Evaluation Studies as Topic; D005838:Genotype; D006801:Humans; D015151:Immunoblotting / Q000379:methods* / Q000706:statistics & numerical data; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction / Q000379:methods* / Q000706:statistics & numerical data; D000091402:Prohibitins; D012680:Sensitivity and Specificity
chemical_list: D017931:DNA Primers; D004269:DNA, Bacterial; C000717331:PHB2 protein, human; D000091402:Prohibitins; D004262:DNA Restriction Enzymes; D015247:Deoxyribonuclease HindIII