Comparison of biochemical and genotypic speciation methods for vancomycin-resistant enterococci isolated from urban wastewater treatment plants

Haley Sanderson; Rodrigo Ortega-Polo; Kevin McDermott; Rahat Zaheer; R Stephen Brown; Anna Majury; Tim McAllister; Steven N Liss

doi:10.1016/j.mimet.2019.04.019

Comparison of biochemical and genotypic speciation methods for vancomycin-resistant enterococci isolated from urban wastewater treatment plants

J Microbiol Methods. 2019 Jun:161:102-110. doi: 10.1016/j.mimet.2019.04.019. Epub 2019 May 6.

Authors

Haley Sanderson¹, Rodrigo Ortega-Polo², Kevin McDermott³, Rahat Zaheer⁴, R Stephen Brown⁵, Anna Majury⁶, Tim McAllister⁷, Steven N Liss⁸

Affiliations

¹ School of Environmental Studies, Queen's University, Kingston, Ontario K7L 3N6, Canada; Agriculture and Agri-Food Canada, Lethbridge Research and Development Center, Lethbridge, Alberta T1J 4P4, Canada.
² Agriculture and Agri-Food Canada, Lethbridge Research and Development Center, Lethbridge, Alberta T1J 4P4, Canada; Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta T1K 6T5, Canada.
³ Public Health Ontario, Kingston, Ontario K7L 3K3, Canada.
⁴ Agriculture and Agri-Food Canada, Lethbridge Research and Development Center, Lethbridge, Alberta T1J 4P4, Canada.
⁵ School of Environmental Studies, Queen's University, Kingston, Ontario K7L 3N6, Canada; Department of Chemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada.
⁶ School of Environmental Studies, Queen's University, Kingston, Ontario K7L 3N6, Canada; Public Health Ontario, Kingston, Ontario K7L 3K3, Canada.
⁷ Agriculture and Agri-Food Canada, Lethbridge Research and Development Center, Lethbridge, Alberta T1J 4P4, Canada. Electronic address: [email protected].
⁸ School of Environmental Studies, Queen's University, Kingston, Ontario K7L 3N6, Canada; Department of Biology, Ryerson University, Toronto, Ontario M5B 2K3, Canada. Electronic address: [email protected].

PMID: 31071353
DOI: 10.1016/j.mimet.2019.04.019

Abstract

Enterococci species in wastewater including Enterococcus faecalis, Enterococcus faecium, Enterococcus casseliflavus and Enterococcus gallinarum isolates (n = 308) with low or high level vancomycin resistance were determined and compared using a phenotypic method (RapID™ STR system), 16S rRNA sequencing, and multi-locus (atpA, groESL, and pheS) sequence analysis (MLSA). Error rates for the RapID™ STR system were E. faecalis (15.9%), E. faecium (21.5%), and E. casseliflavus/E. gallinarum (56.9%) when referenced to the consensus of all methods tested. Comparison of single nucleotide polymorphism (SNP) distances and phylogenetic trees suggested that the groESL locus delineated species more effectively than other loci. The groESL locus was the most reliable loci for the correct identification of Enterococcus spp., including E. casseliflavus and E. gallinarum, with high congruence compared to the consensus (Adjusted Rand Index = 0.954; Adjusted Wallace Co-efficient = 0.941). All of the methods were compared to whole genome sequencing, which acted as a gold standard, for the isolates from this study and those downloaded from NCBI.

Keywords: 16S rRNA; ATP synthase subunit alpha (atpA); Chaperonin (groESL); Enterococcus; Phenylalanine—tRNA ligase alpha subunit (pheS); RapID STR system.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Bacterial Proteins / genetics
Genotype*
Genotyping Techniques / methods*
Multilocus Sequence Typing
Phylogeny
Polymerase Chain Reaction
Polymorphism, Single Nucleotide
RNA, Ribosomal, 16S / genetics
Vancomycin / pharmacology
Vancomycin-Resistant Enterococci / classification
Vancomycin-Resistant Enterococci / genetics*
Vancomycin-Resistant Enterococci / isolation & purification*
Wastewater / microbiology*
Water Purification*
Whole Genome Sequencing

Substances

Bacterial Proteins
RNA, Ribosomal, 16S
Waste Water
Vancomycin