Choice of indicator organism and library size considerations for phenotypic microbial source tracking by FAME profiling

2009 ◽  
Vol 60 (10) ◽  
pp. 2659-2668 ◽  
Author(s):  
Metin Duran ◽  
Deniz Yurtsever ◽  
Timur Dunaev
Keyword(s):  
Average Rate ◽  
Acid Methyl Ester ◽  
Primary Objective ◽  
Source Tracking ◽  
Indicator Organism ◽  
Indicator Organisms ◽  
Library Size ◽  
Level Indicator ◽  
E Coli

The primary objective of this study was to investigate the effects of choice of the indicator organisms on the accuracy of classifying the fatty acid methyl ester (FAME) profiles of the known-source library isolates. First, a known-source library containing the FAME profiles of Enterococcus isolates cultured from six different possible sources of microbial pollution was developed. A total of 511 Enterococcus isolates were profiled: 120 isolates from sewage samples representing humans; 69 from dairy and cattle cow; 74 from chicken; 76 from swine; 94 from deer; and 78 from waterfowl. Classification of known-source Enterococcus isolates into their respective host categories resulted with a 66% average rate of correct classification (ARCC) in a six-way discriminant analysis (DA). The ARCC increased to 75% when the individual hosts were pooled into larger categories of human, livestock, and wildlife. The accuracy was 80% when isolates of human origin were discriminated against those of non-human origins. Recently, several studies reported the ARCCs for various classification schemes associated with total coliform (TC), fecal coliform (FC), and Escherichia coli of the known-source isolates. When the accuracy of classification of Enterococcus isolates was compared to those reported for TC, FC, and E. coli isolates, the lowest ARCCs were associated with classification of E. coli isolates, the only species level indicator organism among the four compared. It was found that the degree of discrimination increases as the indicator becomes more inclusive of bacteria from different genus. In addition, random cluster formation analysis indicates that known-source libraries with isolate numbers between 300 and 500 might be sufficient for MST by FAME.

Occurrence of antibiotic resistance inEscherichia colifrom surface waters and fecal pollution sources near Hamilton, Ontario

2005 ◽  
Vol 51 (6) ◽  
pp. 501-505 ◽  
Author(s):  
Thomas A Edge ◽  
Stephen Hill
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Surface Waters ◽  
Municipal Wastewater ◽  
Average Rate ◽  
Fecal Pollution ◽  
Pollution Sources ◽  
Source Tracking ◽  
E Coli ◽  
Bird Feces

Antibiotic resistance was examined in 462 Escherichia coli isolates from surface waters and fecal pollution sources around Hamilton, Ontario. Escherichia coli were resistant to the highest concentrations of each of the 14 antibiotics studied, although the prevalence of high resistance was mostly low. Two of 12 E. coli isolates from sewage in a CSO tank had multiple resistance to ampicillin, ciprofloxacin, gentamicin, and tetracycline above their clinical breakpoints. Antibiotic resistance was less prevalent in E. coli from bird feces than from municipal wastewater sources. A discriminant function calculated from antibiotic resistance data provided an average rate of correct classification of 68% for discriminating E. coli from bird and wastewater fecal pollution sources. The preliminary microbial source tracking results suggest that, at times, bird feces might be a more prominent contributor of E. coli to Bayfront Park beach waters than municipal wastewater sources.Key words: antibiotic resistance, Escherichia coli, surface water, fecal pollution.

scholarly journals Selecting rep-PCR markers to source track fecal contamination in Laguna Lake, Philippines

2019 ◽  
Vol 18 (1) ◽  
pp. 19-29 ◽  
Author(s):  
Kevin L. Labrador ◽  
Mae Ashley G. Nacario ◽  
Gicelle T. Malajacan ◽  
Joseth Jermaine M. Abello ◽  
Luiza H. Galarion ◽  
...  
Keyword(s):  
Average Rate ◽  
Fecal Contamination ◽  
Total Coliform ◽  
Source Tracking ◽  
Library Size ◽  
Significant Difference ◽  
Host Origin ◽  
Polymerase Chain ◽  
Element Sequence ◽  
Laguna Lake

Abstract Fecal contamination is one of the factors causing deterioration of Laguna Lake. Although total coliform levels are constantly monitored, no protocol is in place to identify their origin. This can be addressed using the library-dependent microbial source tracking (MST) method, repetitive element sequence-based polymerase chain reaction (rep-PCR) fingerprinting. Serving as a prerequisite in developing the host-origin library, we assessed the discriminatory power of three fingerprinting primers, namely BOX-A1R, (GTG)5, and REP1R-1/2-1. Fingerprint profiles were obtained from 290 thermotolerant Escherichia coli isolated from sewage waters and fecal samples of cows, chickens, and pigs from regions surrounding the lake. Band patterns were converted into binary profiles and were classified using the discriminant analysis of principal components. Results show that: (1) REP1R-1/2-1 has a low genotyping success rate and information content; (2) increasing the library size led to more precise estimates of library accuracy; and (3) combining fingerprint profiles from BOX-A1R and (GTG)5 revealed the best discrimination (average rate of correct classification (ARCC) = 0.82 ± 0.06) in a two-way categorical split; while (4) no significant difference was found between the combined profiles (0.74 ± 0.15) and using solely BOX-A1R (0.76 ± 0.09) in a four-way split. Testing the library by identifying known isolates from a separate dataset has shown that a two-way classification performed better (ARCC = 0.66) than a four-way split (ARCC = 0.29). The library can be developed further by adding more representative isolates per host source. Nevertheless, our results have shown that combining profiles from BOX-A1R and (GTG)5 is recommended in developing the MST library for Laguna Lake.

Identification of Inadequately Cleaned Equipment Used in a Sheep Carcass-Breaking Process†

1999 ◽  
Vol 62 (6) ◽  
pp. 637-643 ◽  
Author(s):  
C. O. GILL ◽  
L. P. BAKER ◽  
T. JONES
Keyword(s):  
Aeromonas Hydrophila ◽  
Membrane Filtration ◽  
Current Practice ◽  
Conveyor Belt ◽  
Indicator Organism ◽  
Indicator Organisms ◽  
Detection Level ◽  
E Coli ◽  
Membrane Filters ◽  
Large Numbers

Aeromonads deposited on pork during a carcass-breaking process were recovered on hydrophobic grid membrane filters placed on ampicillin-dextrin-ethanol agar. Isolates from 85 honey-yellow colonies from filters on that medium were Aeromonas hydrophila (95%) or Vibrio sp. (5%). Presumptive aeromonads, coliforms, and Escherichia coli in swab samples from product passing through a sheep carcass-breaking process were enumerated by hydrophobic grid membrane filtration techniques with a detection level of 1 CFU/100 cm2. Total aerobic counts were determined by a spread plate procedure with a detection level of 1 CFU/cm2. The numbers of aerobes, coliforms, and E. coli in the product were apparently unaffected by the carcass-breaking process, although coliforms and E. coli appeared to be redistributed from shoulder to loin and leg portions. However, the numbers of aeromonads on product increased by about two orders of magnitude as a result of the process. Few bacteria were recovered from most cleaned, large items of equipment, but aerobes, coliforms, and aeromonads were recovered at log total numbers of 5.25, 3.96, and 3.26, respectively, from most of 25 samples from bars supporting a conveyor belt. Also, aerobes, coliforms, E. coli, and aeromonads were recovered from 25 supposedly cleaned steel mesh gloves at log total numbers of 10.14, 5.54, 4.73, and 8.30, respectively. Those findings indicate that inspection of cleaned equipment and microbiological sampling of only food-contacting surfaces, as is the current practice at meat plants, cannot provide assurance that the cleaning of carcass-breaking equipment is adequate. Instead, enumeration of indicator organisms on product passing through a process seems to be required as well, with subsequent sampling of equipment to identify sources of contaminants if increases in numbers during processing are observed. For surety of adequate cleaning, enumeration of several types of indicator organism may be necessary, as increases during processing in the numbers of organisms that are present in relatively large numbers on product entering a process may be difficult to detect.

scholarly journals Diversity and Distribution of Escherichia coli Genotypes and Antibiotic Resistance Phenotypes in Feces of Humans, Cattle, and Horses

2006 ◽  
Vol 72 (11) ◽  
pp. 6914-6922 ◽  
Author(s):  
Matthew A. Anderson ◽  
John E. Whitlock ◽  
Valerie J. Harwood
Keyword(s):  
Escherichia Coli ◽  
Water Quality ◽  
Antibiotic Resistance ◽  
Host Species ◽  
Model Organism ◽  
Source Tracking ◽  
Sampling Effort ◽  
Indicator Organisms ◽  
High Genetic Diversity ◽  
E Coli

ABSTRACT Escherichia coli is the most completely characterized prokaryotic model organism and one of the dominant indicator organisms for food and water quality testing, yet comparatively little is known about the structure of E. coli populations in their various hosts. The diversities of E. coli populations isolated from the feces of three host species (human, cow, and horse) were compared by two subtyping methods: ribotyping (using HindIII) and antibiotic resistance analysis (ARA). The sampling effort required to obtain a representative sample differed by host species, as E. coli diversity was consistently greatest in horses, followed by cattle, and was lowest in humans. The diversity of antibiotic resistance patterns isolated from individuals was consistently greater than the diversity of ribotypes. E. coli populations in individuals sampled monthly, over a 7- to 8-month period, were highly variable in terms of both ribotypes and ARA phenotypes. In contrast, E. coli populations in cattle and humans were stable over an 8-h period. Following the cessation of antibiotic therapy, the E. coli population in the feces of one human experienced a rapid and substantial shift, from a multiply antibiotic-resistant phenotype associated with a particular ribotype to a relatively antibiotic-susceptible phenotype associated with a different ribotype. The high genetic diversity of E. coli populations, differences in diversity among hosts, and temporal variability all indicate complex population dynamics that influence the usefulness of E. coli as a water quality indicator and its use in microbial source tracking studies.

scholarly journals Spatial variation of waterborne Escherichia coli – implications for routine water quality monitoring

2011 ◽  
Vol 9 (4) ◽  
pp. 734-737 ◽  
Author(s):  
Richard S. Quilliam ◽  
Katie Clements ◽  
Caroline Duce ◽  
Simon B. Cottrill ◽  
Shelagh K. Malham ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Water Quality ◽  
Spatial Variation ◽  
Water Quality Monitoring ◽  
Source Tracking ◽  
Microbial Water Quality ◽  
Physiochemical Properties ◽  
E Coli ◽  
Significant Difference

Escherichia coli are often used as faecal indicator bacteria (FIB) to provide a measure of microbial pollution in recreational and shellfish harvesting waters. However, although model forecasts for predicting the concentrations of FIB in surface waters are becoming more robust, they suffer from an inconsistency in quantification methods and an understanding of the spatial variation of FIB within a water course. The aim of this study was to investigate the transverse spatial variation in E. coli numbers (as an indicator of faecal pollution) across the estuary of the River Conwy, UK. Water samples were collected from four transverse transects across the estuary. Spatial variation of E. coli was significantly different from one side of the river to the other, although was not correlated with depth or the physiochemical properties of the water. Subsequently, microbial water quality classifications on the two opposite banks suggested very different levels of pollution coming down the river. This work has shown that the side of the river that routine water monitoring samples are taken from can make a significant difference to the classification of microbial water quality. This has important implications for sampling strategies and the use of microbial source tracking (MST) techniques.

Campylobacter in waterborne epidemics in Finland

2004 ◽  
Vol 4 (2) ◽  
pp. 39-45 ◽  
Author(s):  
M.-L. Hänninen ◽  
R. Kärenlampi
Keyword(s):  
Campylobacter Jejuni ◽  
Causative Agent ◽  
Water Samples ◽  
Fecal Coliforms ◽  
Risk Level ◽  
Source Water ◽  
Indicator Organisms ◽  
Faecal Contamination ◽  
E Coli ◽  
July August September

The sources for drinking water in Finland are surface water, groundwater or artificially recharged groundwater. There are approximately 1400 groundwater plants in Finland that are microbiologically at a high risk level because in most cases they do not use any disinfection treatment. Campylobacter jejuni has caused waterborne epidemics in several countries. Since the middle of the 1980s, C. jejuni has been identified as the causative agent in several waterborne outbreaks in Finland. Between 1998 and 2001, C. jejuni or C. upsaliensis caused seven reported waterborne epidemics. In these epidemics approximately 4000 people acquired the illness. Most of the outbreaks occurred in July, August , September or October. In four of them source water and net water samples were analysed for total coliforms or fecal coliforms, E. coli and campylobacters. We showed that large volumes of water samples in studies of indicator organisms (up to 5000 ml) and campylobacters (4000–20,000 ml) increased the possibility to identify faecal contamination and to detect the causative agent from suspected sources.

Comparison of decay rates of faecal indicator organisms in recreational coastal water and sediment

2002 ◽  
Vol 2 (3) ◽  
pp. 131-138 ◽  
Author(s):  
D.L. Craig ◽  
H.J. Fallowfield ◽  
N.J. Cromar
Keyword(s):  
Water Column ◽  
Coastal Water ◽  
Decay Rates ◽  
Organic Carbon Content ◽  
Indicator Organisms ◽  
Filtration Method ◽  
E Coli ◽  
Water And Sediment ◽  
Increased Risk ◽  
High Organic Carbon Content

A laboratory based microcosm study utilising intact non-sterile sediment cores was undertaken to determine the survival of the faecal indicator organisms Escherichia coli, Enterococcus faecium and somatic coliphage in both recreational coastal water and sediment. Overlying water was inoculated with the test organisms and incubated at 10°C, 20°C or 30°C. E. coli, enterococcus and coliphage were enumerated from the water column and sediment by the membrane filtration method, Enterolert (IDEXX Laboratories) and the double-agar overlay methods respectively on days 0, 1, 2, 7, 14 and 28 following inoculation. It was demonstrated that for all organisms, greater decay (k; d-1) occurred in the water column compared to sediment. Sediment characteristics were found to influence decay, with lowest decay rates observed in sediment consisting of high organic carbon content and small particle size. Decay of E. coli was significantly greater in both the water column and sediment compared with enterococcus and coliphage under all conditions. Decay of enterococcus was found to closely resemble that of coliphage decay. Survival of all organisms was inversely related to temperature, with greatest decay at 30°C. However, increased temperature had a less significant impact on survival of enterococcus and coliphage compared with E. coli. The importance of this study for estimating risk from recreational exposure is great if some pathogenic microorganisms behave similarly to the organisms tested in this study. In particular if survival rates of pathogens are similar to enterococcus and coliphage, then their ability to accumulate in coastal sediment may lead to an increased risk of exposure if these organisms are resuspended into the water column due to natural turbulence or human recreational activity.

Water Quality of Swimming Pools in Jerusalem

1993 ◽  
Vol 27 (7-8) ◽  
pp. 287-294 ◽  
Author(s):  
S. Lerman ◽  
O. Lev ◽  
A. Adin ◽  
E. Katzenelson
Keyword(s):  
Water Quality ◽  
Fecal Coliforms ◽  
Pathogenic Microorganisms ◽  
Swimming Pools ◽  
Indicator Organisms ◽  
Indicator Microorganisms ◽  
E Coli ◽  
Safe Water ◽  
Indirect Information

The Israel Ministry of Health is now revising its regulations for the assurance of safe water quality in public swimming pools. Since it is not possible to monitor each of the pathogenic microorganisms, it is often recommended to monitor indicator bacteria which provide indirect information on the water quality in the swimming pool. Three indicator microorganisms are often recommended: coliform counts (total coliforms, fecal coliforms or E. Coli), staphylococcus aureus and pseudomonas aeruginosa. A four year survey of the water quality of swimming pools in the Jerusalem District was conducted in order to determine whether the monitoring of all three indicators is necessary to assure safe water quality or is it sufficient to monitor only a single microorganism. A statistical analysis, conducted by using several different statistical techniques, reveals that the populations of the three indicator organisms are significantly interdependent but the correlations between each pair of these indicators are not sufficient to base a prediction of any of the organisms based on the measurements of the others. Therefore, it is concluded that monitoring of all three indicators should be recommended in order to provide an adequate picture of the water quality in swimming pools.

A simplified low-cost approach to antibiotic resistance profiling for faecal source tracking

2004 ◽  
Vol 50 (1) ◽  
pp. 185-191 ◽  
Author(s):  
J.E. Ebdon ◽  
J.L. Wallis ◽  
H.D. Taylor
Keyword(s):  
Antibiotic Resistance ◽  
Binary Data ◽  
Human Error ◽  
Function Analysis ◽  
Average Rate ◽  
Low Cost ◽  
Source Tracking ◽  
Source Discrimination ◽  
Cost Approach ◽  
Faecal Bacteria

Antibiotic resistance profiling (ARP) is a potentially useful method for distinguishing faecal bacteria according to host source. This phenotypic approach has cost benefits over genotypic methods, but existing protocols are time-consuming and manual data handling is open to human error. A simplified, low-cost approach to the ARP technique was developed that used automated data recording techniques combined with simple statistical analyses to compare isolates of the genus Enterococcus from various faecal sources. An initial battery of 21 antibiotics (at up to four concentrations) was chosen for source discrimination. Images of growth or non-growth in microplate wells were stored as bitmaps and converted to binary data to form a database of known antibiotic resistance profiles. Discriminant function analysis (DFA) showed that the average rate of isolates correctly classified by the database (wastewater vs non-wastewater) was 86%. Once the more discriminating antibiotics and their concentrations had been identified, it was possible to reduce the number of tests from 80 to 18 whilst increasing the number of correctly classified human isolates. ARP could offer a low-cost and rapid means of identifying sources of faecal pollution. As such, the technique may be of particular benefit to developing countries, where water quality may have a significant impact on health and where cost is a major factor when choosing environmental management technology.

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