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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.

bmc microbiology

SNP diversity of Enterococcus faecalis and Enterococcus faecium in a South East Queensland waterway, Australia, and associated antibiotic resistance gene profiles