Considerations When Using Discriminant Function Analysis of Antimicrobial Resistance Profiles To Identify Sources of Fecal Contamination of Surface Water in Michigan

Abstract

The goals of this study were to (i) identify issues that affect the ability of discriminant function analysis (DA) of antimicrobial resistance profiles to differentiate sources of fecal contamination, (ii) test the accuracy of DA from a known-source library of fecal Escherichia coli isolates with isolates from environmental samples, and (iii) apply this DA to classify E. coli from surface water. A repeated cross-sectional study was used to collect fecal and environmental samples from Michigan livestock, wild geese, and surface water for bacterial isolation, identification, and antimicrobial susceptibility testing using disk diffusion for 12 agents chosen for their importance in treating E. coli infections or for their use as animal feed additives. Nonparametric DA was used to classify E. coli by source species individually and by groups according to antimicrobial exposure. A modified backwards model-building approach was applied to create the best decision rules for isolate differentiation with the smallest number of antimicrobial agents. Decision rules were generated from fecal isolates and applied to environmental isolates to determine the effectiveness of DA for identifying sources of contamination. Principal component analysis was applied to describe differences in resistance patterns between species groups. The average rate of correct classification by DA was improved by reducing the numbers of species classifications and antimicrobial agents. DA was able to correctly classify environmental isolates when fewer than four classifications were used. Water sample isolates were classified by livestock type. An evaluation of the performance of DA must take into consideration relative contributions of random chance and the true discriminatory power of the decision rules.

Expression profiles of sex differentiation‐related genes during ontogenesis in the European sea bass acclimated to two different temperatures

“…CDA is used in many research fields, including numerical ecology applied to fisheries management to categorize the exploitation of a given ecosystem (Tudela et al, 2005); in microbiology, to discriminate between human and animal sources of contamination in surface waters (Kaneene et al, 2007); in forensics, to estimate the sex of unknown skeletal remains (Kemkes-Grottenthaler, 2005); and also in medical research, for instance to discriminate between different types of anemia (Ahluwalia et al,'95). However, to the best of our knowledge, this is the first time that it is used for the study of sex differentiation.…”

Occurrence and patterns of antibiotic resistance in vertebrates off the Northeastern United States coast

“…Escherichia coli is often used exclusively to determine occurrence of antibiotic resistance in an environment in general, and for source tracking of fecal pollution based on antibiotic resistance patterns (e.g. Krumperman, 1983; Parveen et al , 1997; Bass et al , 1999; Kelsey et al , 2003; Edge & Hill, 2005; Dolejska et al , 2007; Kaneene et al , 2007; Sjolund et al , 2008). Our results are consistent, however, with two studies examining antibiotic resistance across a variety of bacterial taxa.…”

Isolation and Characterization of Bacteria from Sewage and Pond Water, Malda, India

“…In the increasingly and injudiciously used ages of antibiotics A total of 14 wastewater bacteria isolated (10 isolates from the sample I: S1W1, S1W2, S1W3, S1W4, S1W5, S1W6, S1W7, S1W8, S1W9 and S1W10, and 4 isolates from sample II: S2W1, S2W2, S2W3 and S2W4), displayed varied morphological features of their colonies developed on nutrient agar plates (Figure 1). Among the isolated bacteria ( Figure 2), 3 were gram-negative rods (S1W6, S1W10 and S2W4), and the other 11 isolates were either gram-positive rods (n = 10; S1W1, S1W2, S1W3, S1W4, S1W5, S1W8, S1W9, S2W1, S2W2 and S2W3) or gram-positive cocci (n = 1; S1W7 As per the criteria reported earlier [11,24,25], the instant study,…”