16S-ARDRA and MALDI-TOF mass spectrometry as tools for identification of Lactobacillus bacteria isolated from poultry. Issue 1 (December 2016)

• Record Type: Journal Article
• Authors: Dec, Marta; Puchalski, Andrzej; Urban-Chmiel, Renata; Wernicki, Andrzej
• Is Part Of: BMC microbiology. Volume 16:Issue 1(2016)
• Page Start: 1
• Page End: 16
• Publication Date: 2016-12
• Subjects: Lactobacillus -- Lactic acid bacteria -- Identification -- Poultry -- MALDI-TOF MS -- ARDRA -- 16S rDNA; Microbiology -- Periodicals; 579.05
• DOI: 10.1186/s12866-016-0732-5
• Languages: English
• ISSNs: 1471-2180

Abstract

Abstract Background The objective of our study is to evaluate the potential use of Amplified 16S Ribosomal DNA Restriction Analysis (16S-ARDRA) and MALDI-TOF mass spectrometry (MS) as methods for species identification ofLactobacillus strains in poultry. Results A total of 80Lactobacillus strains isolated from the cloaca of chicken, geese and turkeys were identified to the species level by MALDI-TOF MS (on-plate extraction method) and 16S-ARDRA. The two techniques produced comparable classification results, some of which were additionally confirmed by sequencing of 16S rDNA. MALDI-TOF MS enabled rapid species identification but produced more than one reliable identification result for 16.25 % of examined strains (mainly of the speciesL. johnsonii ). For 30 % of isolates intermediate log(scores) of 1.70–1.99 were obtained, indicating correct genus identification but only presumptive species identification. The 16S-ARDRA protocol was based on digestion of 16S rDNA with the restriction enzymesMse I, Hinf I, Mbo I andAlu I. This technique was able to distinguish 17 of the 19Lactobacillus reference species tested and enabled identification of all 80 wild isolates.L. salivarius dominated among the 15 recognized species, followed byL. johnsonii andL. ingluviei . Conclusions The MALDI-TOF MS and 16S-ARDRA assays are valuable tools for the identification of avian lactobacilli to the species level. MALDI-TOF MS is a fast, simple and cost-effective technique, and despite generating a high percentage of results with a log(score) <2.00, the on-plate extraction method is characterized by high-performance. For samples for which Biotyper produces more than one reliable result, MALDI-TOF MS must be used in combination with genotypic techniques to achieve unambiguous results. 16S-ARDRA is simple, repetitive method with high power of discrimination, whose sole limitation is its inability to discriminate between species with very high 16S rDNA sequence homology, such asL. casei andL. zeae . The assays can be used for discrimination ofLactobacillus bacteria from different habitats.