Bio-Math Mapping: Water Quality Analysis of Hudson River and Gowanus Canal: A SENCER-based Summer Project
The Summer 2010 Bio-Math Mapping project, based on SENCER (Science Education for New Civic Engagements and Responsibilities) ideals, provided nine undergraduate students from New York City College of Technology of the City University of New York with the opportunity to study and perform interdisciplinary research, combining mathematics with epidemiology, microbiology and environmental studies. It met the SENCER ideal to connect science and civic engagement by teaching through complex, contested current and unresolved public issues to basic science.
A significant and unresolved environmental problem is the cleanliness of waterways. Human presence frequently causes adversarial impact in natural aquatic ecosystems. Preservation of natural biodiversity of recreational waters is important for preventing the growth and survival of pathogenic microorganisms. All waterways, in particular, recreational water bodies should be continuously monitored and, whenever necessary, preventive measures should be taken to avoid adversarial effects (Lobova 2008; Mallin 2000; Nevers 2007). One of the most widely used methods of monitoring environmental water quality is to measure the levels of enteric bacteria, most commonly and naturally occurring in human and animal intestines. The presence of enteric bacteria in aquatic environments indicates fecal contamination induced by human activities. The level of fecal coliforms present in water, including E. coli, is one of the most common measures of this type of bacteria (Coulliette 2009; Eaton 2005; Morgan 2003; Nevers 2007; Tortora 2010). Contamination by fecal coliforms is a major concern since their higher levels indicate the existence of human and warm-blooded animals' pollution and the presence of pathogens in the water (bacteria, viruses, etc.) (Alali 2009; Bergman 2009; Eaton 2005; Mallin 2000; Nevers 2007; Smith 2006; Watkinson 2007). Over time bacteria may adapt to the environment and acquire characteristics needed for survival, such as resistance to antibiotics (Drlica 2011; Lobova 2008; Tortora 2010). Antibiotic resistance is the capability of particular microorganisms to grow in the presence of a given antibiotic. There are several types of antibiotic resistance. One is called acquired resistance. Mutant cells arise either spontaneously (about one in a million cells) or from the transfer of resistance genes from other microbes (Drlica 2011). The resistance genes can be transferred via plasmid exchange (horizontal gene transfer by conjugation, transformation or transduction) and/or by reproduction (vertical transfer) (Drlica 2011; Tortora 2010). If a bacterium carries several resistance genes, relating to more than just one antibiotic, it is termed multidrug resistant (MDR).
Antibiotics are now frequently used in public health for the treatment and prevention of bacterial infections. A considerable amount of these antibiotics end up in the environmental waters by excretion, un-metabolized when consumed by humans or animals (Diwan 2010). Moreover, pharmaceutical plants also use the waterways as dumping grounds for unused antibiotics. As a result, bacterial populations are acquiring resistance to more and more antibiotics. Increasingly there is growing concern about antibiotic usage and the effects on resistance development and, consequently, on public health (Alali 2009; Drlica 2011; Fogarty 2007).
The Gowanus canal in Brooklyn, New York, once served as a major cargo transportation waterway. It is currently extremely polluted and poses a major threat to communal health. The proximity of several industrial sites, such as chemical plants, tanneries, concrete mixing facilities, and oil refineries pollutes the canal with various industrial wastes including coal tar and heavy metals like lead and mercury. The Environmental Protection Agency (EPA) recently added the canal to the National Priorities List of its Superfundprogram for further investigation (Navarro 2010).
In contrast, the water quality of the Hudson River, a major recreation water source, is "generally acceptable."(Associated Press 2008). However, many of the wastewater facilities built in the 1970s are crumbling now and unable to withstand extreme weather conditions. Sewage overflow or polluted storm water discharge into nearby waterways occurs after heavy rainfall either through cracks in treatment facilities, overflow valves or infrastructure failures. The release of pathogens, toxins, and other pollutants leads to a potential risk for safe recreational use of the Hudson River water body during this type of weather (Coulliette 2009; Michaels, 2008).
The pathogenic bacteria in the waterways can cause infections via the fecal/oral route of transmission or by direct contact. Treatment of these types of infections becomes more complicated when the microorganisms develop resistance to commonly used antibiotics. At present, the widespread use of antibiotics, both inside and outside of medicine, is playing a significant role in the emergence of resistant bacteria. Tetracycline is an antibiotic, commonly used to treat various types of infections in humans, such as Lyme disease, periodontal disease, chlamydial or rickettsial infections, acne etc. Moreover, it is used to promote the growth of livestock and fisheries. Contamination of water bodies by tetracycline resistant bacteria mostly occurs through human feces (Dotson 2008). Virginiamycin is an antibiotic primarily used in industrial farms not only to treat sick animals but also to offset the impact of crowding and poor sanitation, as well as to spur animal growth (Human Health and Industrial Firming). In fact, up to 70 percent of all antibiotics sold in the U.S. are given to healthy food animals (Clark 2000). Virginiamycin is one of the antibiotics, commonly used in livestock (poultry, swine and cattle) to prevent infectious diseases caused by bacteria, to decrease the amount of feed needed or to increase the rate of weight gain. Environmental contamination can occur either directly via livestock or when antibiotics are washed away from the feed following a heavy rainfall. Such consistent overuse of antibiotics may contribute to drug resistance development of intestinal bacteria. There are several recent reports on the effect of antibiotic resistance to Virginiamycin in the Hudson River (Benotti 2006; Furtula 2010; Palmer 2008; Wilson 2006).
The main goal of the present study was to perform comparative water quality analyses of two major waterways of New York City. The microbiologic research aims were as follows:
- To collect data on the total number of cultivable bacteria (TCB).
- To determine the number of fecal coliforms and E. coli for the Hudson River and the Gowanus Canal.
- To determine the antibiotic resistant bacteria (ARB) from the coliforms.
The mathematical objectives are presented below:
- To compare the water quality of the Hudson River and the Gowanus canal using basic statistical tools such as measures of central tendency and standard deviations.
- To perform regression analyses for finding possible associations between E. coli and ARB.
- To analyze variations of E. coli and ARB obtained from coliforms among various locations of the Hudson River and the Gowanus canal, using chi-square test. Note that the samples are collected from six different locations for each waterway. The null hypothesis for each waterway is given below.
HE.coli–0: E-coli counts independent of locations
where E-coli counts obtained from coliforms
HARB–0: ARB counts independent of locations
where ARB counts obtained from coliforms
At the end of the project term, the students had to prepare a complete written report with the microbiology results, statistical analysis and discussion on the environmental issues associated with the two waterways. Particularly, students were informed and provided literature on drinking water and recreational water testing guidelines. Our aim was to engage our students in solving multidisciplinary problems and answering civic questions by connecting knowledge in microbiology, epidemiology and mathematics, motivating students to pursue higher studies in an interdisciplinary field, particularly bio-math connected fields.
The project lasted four weeks and the participating students were all from the Applied Mathematics major except one from Computer Engineering. All nine students had taken two sequences of calculus, four students had linear algebra, four of them took differential equation, five students had an introductory statistics course and five students had at least one General Biology course. None of these students had prior knowledge in Microbiology (Figure 1).
Figure 1. In front of Hudson, June 2010. From left: Philip Ajisogun, Prof. Urmi Ghosh-Dastidar; Prof. Liana Tsenova; Renne Clarke; YaPing Zhang; Tisha Brookes; Jodi-Ann Youn (back); Steven Lora (back); Karmen T. Yu, YiMing Yu; and Jorge Paucar.
Project Design and Methods
The project started with an introductory lecture describing the research goals, students' responsibilities, academic integrity, punctuality, and team work. Due to the interdisciplinary nature of this project, students were introduced to several topics of Microbiology and Statistics in lectures. The topics were:
- The Microbial World and You
- Aquatic Microbiology and Sewage Treatment
- Introduction to Genetics and Antibiotic Resistance
- in Bacteria
- Water Purity tests and Lab Methods
- Safety Rules and Regulations for work in the
- Microbiology Lab.
- Measures of Central Tendency
- Data Presentation for Ungrouped and Multiple Data sets in Particular Medical Literature
- Probability of Counting
- Diagnostic Checking, Discrete and Continuous random
- variable, expected value
- Binomial distribution
- Hypothesis testing
- Chi-square goodness of fit test and test of independence
- Correlation and linear regression
- Evaluating the strength of the linear relationship.
Throughout these lectures, the bio-math connection was strongly reinforced by providing numerous applied example problems. Students were also introduced to Excel for efficient calculations and visual representations. Since the project lasted only four weeks, roughly the first two weeks were spent on orientation, introducing microbiology concepts, reviewing literature, collecting samples, and lab analysis. The second half of the project term was spent on teaching various statistical techniques, reviewing literature, data analysis, and writing technical reports.
On June 16, 2010, students collected water samples (200ml) from six different sites along the Hudson River in Manhattan (Table 1 and Figure 2).
Figure 2. Hudson River Sampling Locations
Figure 3. Gowanus Canal Sampling Locations
Figure 4. Sample Collection from Gowanus Canal with Prof. Tsenova and Prof. Ghosh-Dastidar.
Each water sample was poured into two sterile 100ml bottles (IDEXX Labs Inc., Maine, USA), which were then placed on ice to prevent the growth of bacteria. The samples were transported to the Microbiology Lab at the NYC College of Technology for testing. To determine the total number of bacteria in the water, the SimPlate Test® (IDEXX Labs Inc. Maine, USA) was performed. Ten-fold dilutions were used and the test was done according to the manufacturer's instructions. The samples were incubated at 350C for 48 hours. Then the plates were removed from the incubator and a UV light lamp was used to illuminate them. The number of fluorescent wells was counted and recorded (Figure 5).
Figure 5. SimPlates under UV Light, for measuring Total Cultivable bacteria (TCB)
The Most Probable Number (MPN) (Maier 2009) of total bacteria was determined using a table provided by the manufacturer (IDEXX). The dilution factor was considered for the final calculation. QuantiTray Test® (IDEXX Labs Inc. Maine, USA) was used to determine the numbers of coliforms and E. coli (a main indicator for fecal contamination of the water). Ten-fold dilutions were prepared and the procedures were done according to the manufacturer's instructions. The QuantiTrays were sealed using a special sealer (IDEXX Labs Inc. Maine, USA), and placed in the incubator at 350C for 24 hours. After the appropriate time had elapsed, the trays were removed from the incubator and the number of yellow large and small wells was counted and recorded (Figure 6).
Figure 6. QuantiTray with large and small wells for measuring the number of coliforms; In the Microbiology Lab with Prof. Tsenova and Prof. Ghosh-Dastidar.
The number of coliforms was determined using the manufacturer's table for MPN (IDEXX Quanti-Tray®/2000 MPN Table). Next, a UV light lamp was used to illuminate the tray, and the number of fluorescent wells counted and recorded as an indication of E. coli. The two selected antibiotics, Tetracycline and Virginiamicin were added to the medium to estimate the number of antibiotic resistant bacteria (ARB) (from coliforms and E. coli). The same method (QuantiTray Test®) was used. The obtained results for MPN of E. coli were compared to the guidelines and standards for recreational water.
Results and Analyses
A strong correlation was observed between the ARB population and E. coli counts (R2 ≈ 0.93, F-ratio = 51.72) (Figure 7) obtained from the Hudson River samples. Both of these estimates were obtained from coliforms. The presence of E. coli possibly influences the presence of ARB. Approximately 13.4% E. coli were ARB (median 9.4%) whereas about 2.6% coliforms were ARB (median 2.3%).
Figure 7. Regression line: both estimates of ARB and E. coli are obtained from coliforms.
A chi-squared analysis (Milton 1999; Evans 2004; Nelson 2007) performed for both E. coli and ARB counts estimated from coliforms revealed that these counts are highly dependent on sampling locations of Hudson River (X2E-coli = 263.135; X2arb= 1849.91; PE-coli < 0.001; Parb < 0.001) i.e. the variations in E. coli and ARB counts were too large to have occurred by chance alone. This fact probably can be justified by the various levels of human activities along the Hudson River shoreline.
Note that the regression analysis and chi-square test were not performed for the Gowanus Canal because of the relatively low numbers for E. coli and ARB obtained from the samples.
Our data set for the Gowanus Canal, showed lower average of coliforms in comparison with the data set for the Hudson River (Figure 8A and B). However, larger counts of TCB were observed in the Gowanus Canal compared to the Hudson River (Figure 9). The highest number of E. colifrom the Hudson River was obtained from 79th Street (269 MPN/100ml). Comparatively lower counts were obtained from Pier 62, Pier 45 and Battery Park City North, indicating better water quality downstream.
Figure 8. Box Plots for coliforms/100mL (A) Gowanus Canal (B) Hudson River.
Figure 9. Box Plots for TCB/ml for Gowanus Canal and Hudson River.
The presence of higher numbers of coliforms in the Hudson River could be due to sanitation businesses, the many residential buildings along the shore line and the boats along the river or on the waterfront (Figure 10A). Another factor that could contribute to the higher numbers of coliforms is an overflow, usually occurring after a heavy rainfall, which introduces new bacteria from the mainland into the water (Coulliette 2009). In contrast, for the past several years the Gowanus canal has encountered a lot of industrial pollutants such as cement, oil, sulfur and heavy metals (lead and mercury) (Figures 10B and C). The increase in industrial waste and toxic materials present in the canal has decreased the oxygen levels and henceforth makes it difficult for any organism that requires oxygen to live and reproduce. This could explain the lower counts of coliforms found in the Gowanus Canal. In addition flushing tunnel and tide effects may bring fresh water in the canal. Although our one day sampling provided fewer coliforms in the Gowanus, other data suggests that the water quality of Gowanus Canal is often poor (Durkin, 2009). On the other hand, TCB are primarily environmental and more adaptable microorganisms, which may explain higher counts of TCB in the canal in spite of heavy pollution.
In our study, all water samples along the Hudson River had E.coli less than 235 MPN/100 mL based on the standards set for recreational water (Recreational Water Testing guideline), meaning that the water was good enough for recreational purposes (swimming, boating and fishing) at most places. Only the 79th Street sample provided E. colicounts of 269/100 ml, indicating further analysis required and possibly an advisory needed to be issued. It might be of interest to mention that one of the boat basins in Manhattan is located at this site.
Figure 10 A-C: A. Hudson Site 1, 79th St.; B. Gowanus Site 2, Nearby a Cement Plant; C. Gowanus Site 6, Debris.
Towards the end of the project, students were provided with a presentation, "What Next?" indicating different career opportunities available to them during or after their undergraduate studies. Students were informed about SENCER goals and ideals and various opportunities available in Environmental Protection Agency (EPA). The presentation also included information on different career paths, internships, and summer research opportunities in the mathematical-biology field, applied physical field, and graduate record examination. As indicated above, all participants were from an Applied Mathematics major except one, and all of them showed interest in pursuing higher-level studies.
Assessment and Students' Reflections
At the end of the project term an exit survey (IRB-approved) in a form of a questionnaire was administered to monitor and measure students' learning outcomes and their levels of satisfaction. Typical survey questions, relevant to this project, are presented below.
Six out of nine students responded to the following question: List anything you feel you have learned or gained.Responses:
- I learned a lot about statistics and how they relate to the project. I also know more information about Microbiology.
- T-test, Chi-square Test, Statistical Analysis
- A better understanding of interpreting data
- I have learned statistics, such as simple linear regression, box plot, chi-square, T-test, SD and correlation. I have learned Excel for all the math calculations; I have learnt much biology such as E. coli and coliforms. I have the experience of a research project.
- During this research project, I've learned the important topics in probability, which we used to analyze data. I've learned the overall knowledge about microbiology. I've learned how to write a report based on the results of our research.
Seven responses came in answer to the question: Which aspects of the project did you like the most? You can write more than one.
- The lab part and the math part.
- Aspects of this project I like the most are to obtain results and interpret the results from both scientific way and mathematical ways.
- Field Trips to collect data – Lab work (experiments, Sim Plate Test, Quanti Tray Test)
- Collection - Math analysis
- I like the statistics math part.
- The Collection (water samples)
- I like the fact that everyone interacted with each other and worked together.
Figure 11 A-D: (A), (B) and (C) - Scale: 5 = learned a substantial amount; 4 = learned quite a bit; 3 = learned to a moderate degree; 2 = learned a little; 1 = did not learn anything; NA = not applicable. (D) Scale: 5 = very satisfied; 4 = somewhat satisfied; 3 = neither satisfied or dissatisfied; 2 = somewhat dissatisfied; 1 = very dissatisfied.
To assess learning outcomes students were also encouraged to rate their experience on using laboratory techniques, data analysis, and understanding how scientists think. These three were administered with the following question.
Tell us what you have learned as a result of your research experience. Please rate the extent to which you feel you learned each of the following items as a result of conducting your research project.For each item, the scale ranged from (1) did not learn anything at all to (5) learned a substantial amount.
Four of the nine reported they learned quite a bit (4) and four reported they learned a substantial amount (5) on using a microbiology lab. Three mentioned they learned quite a bit (4) and four informed they learned a substantial amount (5) on data analysis. Seven students reported they learned quite a bit (4) and two reported they gained substantially (5) on understanding how scientists think (Figures 11A, B, and C).
Students' overall satisfaction with this research is measured with the following question: Please rate your overall satisfaction with your research experience. The scale ranged from very dissatisfied to very satisfied.
Seven reported they were very satisfied with their overall research experience when two students were somewhat satisfied. A summary of these responses is presented below (Figure 11D).
The success of the research project is best conveyed by the students' reflections on their overall impression of the summer research. Three are presented below:
My research experience this summer was fun! This was my first math based research and I like the whole interdisciplinary thing. I wish we had more time and resources to do more. I got to see the stuff learned in the classroom, applied in real life. It was actually really cool seeing these practical uses. It made the concepts clearer, solidifying their meaning. We had two passionate mentors, whose enthusiasm rubbed off on me. And my colleagues were fun to be around and eager to get their work done.
The summer research program was a wonderful experience, one that I enjoyed very much. I very much appreciated the field experience, going out to collect data. Also, I enjoyed the lab analysis and microbiology aspects of our project. Prior to our research project, I was not aware of the pollution in the Hudson River and the Gowanus Canal. I was aware only that they were not safe to swim in. Hence the program has offered me insight in my environment, particularly the water bodies of NYC. During the program I also learned statistical analyses Chi-Square Test, Correlation (Regression) Analysis and how to do Box Plots.
This summer research provided me a chance to learn and to touch upon topics in statistics in advance since I haven't taken that class yet. In this summer research I learned how to effectively use statistics equations and the box and whisker plot to analyze data. This research also provided me a chance to learn about microbiology. This research helped to introduce me to new knowledge of math and microbiology. My overall impression of this summer research is that participating in a research project not only means to perform experiments or to analyze data, but is also to learn and to explore new knowledge. In order to accomplish a goal within a short amount of time during summer research requires a lot of teamwork and communication between everyone in the research group. This is the first research that I've participated in my college life. This experiment taught me a lot.
Conclusion and Future Direction
The strong correlation found between ARB and E. coli suggests that the antibiotic resistance is probably influenced by E. coli in the water. A single sample analysis of the Hudson River indicated good quality of the water in most of the sampling locations except at 79th Street, where the E. coli counts exceeded the acceptable 235 MPN/100 mL, meaning further analysis should be performed. A statistically significant difference was observed for E. coli and ARB counts among the various Hudson River locations most likely due to different levels of human activities along the Hudson River. Our one day sampling of the Gowanus Canal did not indicate higher coliform counts than that of the Hudson River. However, it showed higher counts of TCB than the ones found in the Hudson River. Due to inadequate oxygen supply and pollution, the conditions of the Gowanus Canal may not be favorable for the growth and survival of coliforms. Compared to them, TCB are mainly environmental bacteria, more adaptable to various conditions.
Figure 12. City Tech students at MathFest with Prof. Ghost-Dastidar. Pittsburgh, August 2010.
As a whole, we consider the summer project very successful. Our aim was to combine different subject areas, such as epidemiology, microbiological tests for water quality and statistical analyses, to address serious environmental questions such as standards and monitoring of drinking and recreational water, potential sources of pollution of the Hudson River and the Gowanus Canal, and to motivate the students to pursue research and more advanced studies. Over all, we found that the students were very enthusiastic and eager to learn. The interaction with them was easy and pleasant. They worked very well as a team while collecting the water samples, while working in the microbiology lab and in the computer lab. They also assisted each other during mathematical problem solving sessions, writing reports and prior to the conference presentation. At the end of the project term, students submitted their individual reports, showing great creativity and accuracy in interpretation. Students presented their work in August 2010, at the MathFest in Pittsburgh, an event organized by the Mathematical Society of America (MAA) (Figure 12). In September 2010 Jodi-Ann Young made a presentation at the Peach State LSAMP 5th Annual Fall Symposium & Research Conference at the University of Georgia in Athens, GA and received the second prize. During the summer of 2011 four out of these nine students applied for summer research opportunities for undergraduates and all four were accepted as REU (Research Experience for Undergraduates) students in the Center for Discrete Mathematics and Theoretical Computer Science (DIMACS) at Rutgers University, NJ. Two students already graduated with Applied Math majors and one of them is pursuing graduate studies.
In conclusion, we consider the Summer project of 2010 very sustainable and we plan to offer similar research opportunities to student majoring in Applied Mathematics but also to students interested in pursuing a degree in Biological and Environmental sciences.
We wish to express our gratitude to Prof. Aaron Barlow and Prof. A.E. Dreyfuss for their valuable comments. We thank Dr. Pamela Brown, Dean of School of Arts and Sciences, NYCCT, CUNY for funding this project through NSF DUE grant #0622493 and for her continuous support; Dr. Janet Liou-Mark for assisting with student selection; William Dungey, Senior Environmental Account Manager, and Sharon Muhilly, Technical Support from IDEXX Laboratories for their assistance with the equipment and valuable suggestions; Mr. Christos Tsiamis, Project Manager, Central New York, USEPA for his consultation. We also thank the New York City Louis Stokes Alliance for Minority Participation (NYCLSAMP) for providing support. Finally, we acknowledge all of the student participants for their enthusiasm and eagerness to learn and for their excellent performance. Alphabetically these students are Philip Ajisogun, Tisha Brookes, Renee Clarke, Steven Lora, Jorge Paucar, Jodi-Ann Young, Yi Ming Yu, Karmen T. Yu, and Ya Ping Zhang.
About the Authors
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