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-␤-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.

Genomic Diversity within the Genus Pediococcus as Revealed by Randomly Amplified Polymorphic DNA PCR and Pulsed-Field Gel Electrophoresis

“…Indeed, in another study, two of the four isolates were considered to be identical after ribotyping and genomic restriction followed by conventional gel electrophoresis (18). Although pediococci remain uncommon as etiological agents of disease, their natural vancomycin resistance makes them a growing concern as opportunistic agents associated with human infections (3,36). In a previous study, proposed pediococci isolated from fermented cereals were assigned at the species level by using RAPD PCR and a primer identical to P1 (32).…”

“…The use of PFGE to discriminate among pediococci appears to have been limited to P. acidilactici and P. pentosaceus strains (3,12,24), and in only one case was a large number of isolates examined (3). For these two species, PFGE discriminated between both strains and species, with the latter discrimination being based on a difference in cutting frequency with the restriction enzyme SmaI (3).…”

“…These include the use of specific DNA target probes (23,27,28,29,37), ribotyping (2,18,38), total DNA-DNA hybridization (1,13), 16S rRNA gene sequencing (2,10,21,33), randomly amplified polymorphic DNA (RAPD) PCR (21,29,30,32) and pulsed-field gel electrophoresis (PFGE) (3,12,24).…”

Taxonomic Status of Lactic Acid Bacteria in Wine and Key Characteristics to Differentiate Species

“…1). Identification to species level is best obtained by 16S rDNA gene sequencing Kurzak et al, 1998;Omar et al, 2000;Barney et al, 2001), species-specific DNA probes (Lonvaud-Funel et al, 1993;Mora et al, 1997;Rodrigues et al, 1997), ribotyping (Jager & Harlander, 1992;Satokari et al, 2000;Barney et al, 2001;Santos et al, 2005), randomly amplified polymorphic DNA (RAPD) PCR (Kurzak et al, 1998;Nigatu et al, 1998;Mora et al, 2000;Simpson et al, 2002;Fujii et al, 2005;Tamang et al, 2005), and pulsed-field gel electrophoresis (PFGE) ( Dellaglio et al, 1981;Luchansky et al, 1992;Barros et al, 2001). Simpson et al (2006) developed a rapid PFGE protocol for species-and strain-level differentiation.…”

Pediococcus acidilactici Endocarditis Successfully Treated with Daptomycin

“…Most of the previous cases used a series of biochemical tests to provide a species identification. However, atypical biochemical reactions have been seen within the Pediococcus species which did not allow for phenotypic characterization to identify all Pediococcus strains isolated from human clinical specimens (2). To overcome this, molecular sequencing has been considered (6).…”