Use of Antibiotic Resistance Analysis for Representativeness Testing of Multiwatershed Libraries

Abstract

The use of antibiotic resistance analysis (ARA) for microbial source tracking requires the generation of a library of isolates collected from known sources in the watershed. The size and composition of the library are critical in determining if it represents the diversity of patterns found in the watershed. This study was performed to determine the size that an ARA library needs to be to be representative of the watersheds for which it will be used and to determine if libraries from different watersheds can be merged to create multiwatershed libraries. Fecal samples from known human, domesticated, and wild animal sources were collected from six Virginia watersheds. From these samples, enterococci were isolated and tested by ARA. Based on cross-validation discriminant analysis, only the largest of the libraries (2,931 isolates) were found to be able to classify nonlibrary isolates as well as library isolates (i.e., were representative). Small libraries tended to have higher average rates of correct classification, but were much less able to correctly classify nonlibrary isolates. A merged multiwatershed library (6,587 isolates) was created and was found to be large enough to be representative of the isolates from the contributing watersheds. When isolates that were collected from the contributing watersheds approximately 1 year later were analyzed with the multiwatershed library, they were classified as well as the isolates in the library, suggesting that the resistance patterns are temporally stable for at least 1 year. The ability to obtain a representative, temporally stable library demonstrates that ARA can be used to identify sources of fecal pollution in natural waters.

Antibiotic resistance in Escherichia coli isolates from roof-harvested rainwater tanks and urban pigeon faeces as the likely source of contamination

“…Despite the lack of reports on antimicrobial susceptibility patterns of E. coli from RHRW and their comparison to the likely sources of faecal origin, a number of researches have shown increasing resistance to tetracycline, ampicillin and gentamicin, with resistance at lower levels to cotrimoxazole, nalidixic acid chloramphenicol enrofloxacin cefoxitin and ciprofloxacin, similar to our findings (Harwood et al 2003;Wiggins et al 2003;Silva et al 2009). …”

“…have cited it as a useful tool in assessing contamination sources with average rates of correct classification ranging from 62 to 84%, (Harwood et al 2003;Wiggins et al 2003).…”

Microbial Source Tracking in a Watershed Dominated by Swine

“…All isolates below the 80% correct classification certainty (based on posterior probabilities from discriminant analysis) were excluded from the library. The second approach was to calculate the average frequency of misclassification (AFM) for each source category, and use this average to develop a minimum detectable percentage (MDP) to make decisions about the significance of hosts contributing minor sources E. coli in water samples [22,34].…”

“…The ARA approach is based on the premise that fecal indicator bacteria (FIB) from hosts exposed to antibiotics will develop resistance to those antibiotics, and on the hypothesis that this selective pressure would be a mechanism for discriminating among fecal indicator bacteria from a variety of hosts [30][31][32][33][34][35]. A library or database composed of antibiotic resistance profiles (ARP) of FIB from known host sources is developed and serves as a point of reference for identifying unknown source isolates from water sources.…”

Source tracking faecal contamination in an urbanised and a rural waterway in the Nelson-Tasman region, New Zealand

“…Library-dependent methods rely on the collection of FIB isolates from a known source for comparison of genetic or phenotypic patterns (fingerprints) of isolates from environmental samples. Such libraries are relatively location specific, and their utility is greatly hampered by the diversity and temporal variability of faecal organisms (Gordon 2001;Wiggins et al 2003;Anderson et al 2006).…”