Phenotypic and genotypic characterization of Pediococcus strains isolated from human clinical sources

Abstract

Seventy-two strains of pediococci isolated from human clinical sources were characterized by conventional physiological tests, chromogenic enzymatic tests, analysis of whole-cell protein profiles (WCPP) by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and analysis of chromosomal DNA restriction profiles by pulsed-field gel electrophoresis (PFGE). Conventional tests allowed identification of 67 isolates: 52 strains were identified as Pediococcus acidilactici, 15 strains were identified as Pediococcus pentosaceus, and 5 strains were not identified because of atypical reactions. Analysis of WCPP identified all isolates since each species had a unique WCPP. By the WCPP method, the atypical strains were identified as P. acidilactici (two strains) and P. pentosaceus (three strains). The chromogenic substrate test with o-nitrophenyl-beta-D-glucopyranoside differentiated all 54 strains of P. acidilactici (negative reactions) and 13 (72%) of 18 strains of P. pentosaceus (positive reactions). Isolates of both species were shown to be nonclonal as revealed by the genetic diversity when chromosomal DNA was analyzed by PFGE. Using WCPP as the definitive identification procedure, P. acidilactici (28 of 54 strains; 51.8%) was more likely than P. pentosaceus (4 of 18 strains; 22.3%) to be isolated from blood cultures.

FIG. 1

(A) SDS-PAGE profiles of whole-cell protein extracts of Pediococcus and related species. Lanes 1 and 11, molecular mass markers; lane 2, P. pentosaceus ATCC 33316; lane 3, P. pentosaceus ATCC 33314 (previously considered the type strain for P. acidilactici); lane 4, P. acidilactici DSM 20284 (recently designated the type strain for P. acidilactici); lane 5, P. dextrinicus ATCC 33087; lane 6, P. damnosus, ATCC 29358; lane 7, P. parvulus ATCC 19371; lane 8, A. viridans ATCC 29273; lane 9, T. halophilus ATCC 33315; lane 10, E. solitarius ATCC 49428. (B) Dendrogram resulting from computer-assisted analysis of the protein profiles shown in panel A. The scale represents the average percentage of similarity.

FIG. 2

(A) PFGE profiles of chromosomal DNA of P. pentosaceus strains after digestion with SmaI. Lanes 1 and 19, molecular size markers (in kilobases, lambda DNA concatemers ranging from 48.5 to 1,018.5 kb); lanes 2 to 19, clinical isolates of P. pentosaceus. Lane 2, 1728-86; lane 3, 2140-86; lane 4, 2160-86; lane 5, 3143-90; lane 6, 2215-91; lane 7, 866-91; lane 8, 2890-90; lane 2891-90; lane 10, 3049-90; lane 11, 46-92; lane 12, 150-88; lane 13, 14-89; lane 14, 1959-88; lane 15, 2364-91; lane 16, 1235-92; lane 17, 322-94; lane 18, 1874-89. (B) Dendrogram resulting from computer-assisted analysis of the PFGE profiles shown in panel A. The scale represents the average percentage of similarity.

FIG. 3

(A) PFGE profiles of chromosomal DNA of P. acidilactici strains after digestion with NotI. Lane 1, molecular size markers; lanes 2 to 19, clinical isolates of P. acidilactici. Lane 2, 3141-90; lane 3, 3142-90; lane 4, 3144-90; lane 5, 3146-90; lane 6, 874-92; lane 7, 989-92; lane 8, 1701-93; lane 9, 2165-93; lane 10, 194-94; lane 11, 768-95; lane 12, 155-89; lane 13, 562-89; lane 14, 2893-90; lane 15, 578-91; lane 16, 579-91; lane 17, 1616-91; lane 18, 1934-94; lane 19, 4140-96. (B) Dendrogram resulting from computer-assisted analysis of the PFGE profiles shown in panel A. The scale represents the average percentage of similarity.