title: SNP diversity of Enterococcus faecalis and Enterococcus faecium in a South East Queensland waterway, Australia, and associated antibiotic resistance gene profiles.
abstract: BACKGROUND
  Enterococcus faecalis and Enterococcus faecium are associated with faecal pollution of water, linked to swimmer-associated gastroenteritis and demonstrate a wide range of antibiotic resistance. The Coomera River is a main water source for the Pimpama-Coomera watershed and is located in South East Queensland, Australia, which is used intensively for agriculture and recreational purposes. This study investigated the diversity of E. faecalis and E. faecium using Single Nucleotide Polymorphisms (SNPs) and associated antibiotic resistance profiles.
  
  
  RESULTS
  Total enterococcal counts (cfu/ml) for three/six sampling sites were above the United States Environmental Protection Agency (USEPA) recommended level during rainfall periods and fall into categories B and C of the Australian National Health and Medical Research Council (NHMRC) guidelines (with a 1-10% gastrointestinal illness risk). E. faecalis and E. faecium isolates were grouped into 29 and 23 SNP profiles (validated by MLST analysis) respectively. This study showed the high diversity of E. faecalis and E. faecium over a period of two years and both human-related and human-specific SNP profiles were identified. 81.8% of E. faecalis and 70.21% of E. faecium SNP profiles were associated with genotypic and phenotypic antibiotic resistance. Gentamicin resistance was higher in E. faecalis (47% resistant) and harboured the aac(6')-aph(2') gene. Ciprofloxacin resistance was more common in E. faecium (12.7% resistant) and gyrA gene mutations were detected in these isolates. Tetracycline resistance was less common in both species while tet(L) and tet(M) genes were more prevalent. Ampicillin resistance was only found in E. faecium isolates with mutations in the pbp5 gene. Vancomycin resistance was not detected in any of the isolates. We found that antibiotic resistance profiles further sub-divided the SNP profiles of both E. faecalis and E. faecium.
  
  
  CONCLUSIONS
  The distribution of E. faecalis and E. faecium genotypes is highly diverse in the Coomera River. The SNP genotyping method is rapid and robust and can be applied to study the diversity of E. faecalis and E. faecium in waterways. It can also be used to test for human-related and human-specific enterococci in water. The resolving power can be increased by including antibiotic-resistant profiles which can be used as a possible source tracking tool. This warrants further investigation.
authors.affiliation: Cell and Molecular Biosciences, Faculty of Science and Technology, Queensland University of Technology, 2 George Street, Brisbane, 4001, Australia.
authors.forename: Irani
authors.initials: I
authors.lastname: Rathnayake
authors.forename: Megan
authors.initials: M
authors.lastname: Hargreaves
authors.forename: Flavia
authors.initials: F
authors.lastname: Huygens
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology; D001426:Bacterial Proteins / Q000235:genetics; D024881:Drug Resistance, Bacterial; D013293:Enterococcus faecalis / Q000187:drug effects / Q000235:genetics* / Q000302:isolation & purification; D016984:Enterococcus faecium / Q000187:drug effects / Q000235:genetics* / Q000302:isolation & purification; D014644:Genetic Variation; D005838:Genotype; D006801:Humans; D008826:Microbial Sensitivity Tests; D020641:Polymorphism, Single Nucleotide; D011793:Queensland; D045483:Rivers / Q000382:microbiology*; D014481:United States
chemical_list: D000900:Anti-Bacterial Agents; D001426:Bacterial Proteins