Facilitated molecular typing of Shigella isolates using ERIC-PCR

Abstract

To evaluate the performance of enterobacterial repetitive intergenic sequence-based polymerase chain reaction (ERIC-PCR) typing versus the current standard for the typing of Shigella pulsed gel electrophoresis (PFGE), we typed 116 Shigella isolates from a village in an endemic setting over a 20-month period using both methods. PFGE identified 37 pulse types and had a discrimination index of 0.925 (95% confidence interval = 0.830-1.00), whereas ERIC-PCR identified 42 types and had a discrimination index of 0.961 (95% confidence interval = 0.886-1.00). PFGE and ERIC-PCR showed a 90.4% correlation in the designation of isolates as clonal or non-clonal in pairwise comparisons. Both systems were highly reproducible and provided highly similar and supplementary data compared with serotyping regarding the transmission dynamics of shigellosis in this community. ERIC-PCR is considerably more rapid and inexpensive than PFGE and may have a complementary role to PFGE for initial investigations of hypothesized outbreaks in resource-limited settings.

Figure 1.

(A) UPMGA dendrogram of ERIC types. (B) UPMGA dendrogram of PFGE patterns.

Figure 2.

(A) Frequency distribution of ERIC types. (B) Frequency distribution of PFGE types. Dotted areas refer to isolates from asymptomatic cases, and striped areas represent isolates from patients with diarrhea.

Figure 3.

(A) ERIC patterns over the study period grouped by serotype (S. flexneri only; the rest appear in a single graphic). (B) PFGE pulse types over the study period grouped by serotype (S. flexneri only; the rest appear in a single graphic).

Figure 3.

(A) ERIC patterns over the study period grouped by serotype (S. flexneri only; the rest appear in a single graphic). (B) PFGE pulse types over the study period grouped by serotype (S. flexneri only; the rest appear in a single graphic).