TABLE 2.
Summary of the studies that constitute the stream dataset, including the methods of enumeration and/or detection of microbial targets
| Lab (citations) | Years | Months | States | No. of watersheds (sites) | No. of samples | Detection (method) a,b,c,d,e,f |
|||
|---|---|---|---|---|---|---|---|---|---|
| E. coli | FC | TC | Enterococcus | ||||||
| Community Science Institute (CSI) (37) | 2002 to 2020 | January to December | NY | 33 (250) | 5,696 | MF (5,411) | - | MF (4,066) | - |
| Food Safety Lab (FSL), Cornell University | |||||||||
| Survey studies (12, 38–40, 43, 77–79) | 2001 to 2015g | February to November | NY | 58 (228) | 424 | - | - | - | - |
| Predicting Agricultural Water Quality (PAWQ), Cornell University (32, 33, 36) | 2017 to 2018 | April to October | NY | 68 (74) | 377 | IDEXX (375) | - | IDEXX (375) | - |
| Green Lab, SUNY Environmental Science, and Forestry (34) | 2015 | July to August | NY | 2 (10) | 29 | - | - | - | - |
| Onondaga Environmental Institute (OEI) (35) | 2008 to 2015g | March to November | NY | 8 (224) | 2,816 | MF (281) | MF (2,658) | MF (96) | MF (288) |
| Richardson Lab, Cornell University (80, 81) | 2017 to 2018 | June to October | NJ and NY | 5 (27) | 157 | IDEXX (150) | - | - | IDEXX (153) |
| Watershed Watch, University of Rhode Island (URI) (82) | 1991 to 2018 | January to December | CT and RI | 97 (366) | 8,858 | MF (1,330) | MF (4,166) | - | IDEXX (6,724) |
Tables S1 to S3 in the supplemental material provide descriptive summaries of these data. Hyphens in this and other tables indicate that the column is not relevant for the given study (e.g., CSI did not collect fecal coliform data).
Listeria spp. testing was performed on 424 and 377 samples collected by the FSL as part of the survey and PAWQ studies, respectively. Listeria identification was performed to determine if L. monocytogenes was present for 801 of these 802 samples. While both studies used the same culture-based laboratory methods for Listeria isolation, the volume of water collected and the filtration method differed. The survey studies filtered 250 mL through a 0.45-μm filter, while the PAWQ study filtered 348 10-L samples through a modified Moore swab. The remaining 29 samples were separated into 9-L and 1-L aliquots, filtered through a modified Moore swab and a 0.45-μm filter, respectively. These 9-L and 1-L aliquots were treated as separate samples in this study; as a result, there were essentially 830 samples tested for Listeria spp., with identification being performed on 829.
Salmonella testing was performed on 191 and 377 samples (N = 568) collected by the FSL as part of the survey studies and PAWQ study, respectively, as well as 43 samples collected by the Richardson Lab. While both sets of studies conducted by the FSL used the same laboratory methods to isolate Salmonella, the Richardson lab used a culture-independent (i.e., molecular) method. Additionally, the PAWQ Salmonella isolation protocol incorporated a PCR screen, which was not part of the FSL survey protocol. For Salmonella detection, the PAWQ study collected and filtered 10 L through a modified Moore swab, while (i) the Richardson Lab collected and filtered 10 L using tangential flow ultrafiltration, and (ii) the FSL survey studies collected and filtered 250 mL of water through a 0.45-μm filter.
Pathogenic E. coli testing was performed on 191 and 377 samples (N = 568) collected by the FSL as part of the survey studies and PAWQ study, respectively, as well as 43 samples collected by the Richardson Lab. The FSL survey studies used a culture-based approach followed by PCR confirmation using a multiplex PCR, which included testing for the eaeA and stx. As a result, the FSL survey studies only reported if enterohemorrhagic E. coli (EHEC) was detected (i.e., if the isolate had both the eaeA and stx genes). However, the PAWQ study and Richardson Lab used culture-independent pathogenic E. coli detection methods. Both labs used methods that separately tested for the presence of the stx and eaeA genes, among others. Thus, unlike the FSL survey studies, the Richardson Lab and PAWQ studies were able to identify samples positive for Shiga toxin-producing E. coli (STEC; based on detection of the stx gene) and enteropathogenic E. coli (EPEC; based on detection of the eaeA genes) as well as for EHEC (based on detection of both the stx and eaeA genes). The sample volumes and filtration methods used for pathogenic E. coli detection were consistent with those used for Salmonella detection by the respective studies.
One hundred and ninety-six and 157 samples collected as part of the PAWQ study and by Richardson Lab, respectively, were tested for the presence of GFD, an avian microbial source tracking marker (MST) marker. Although all studies that performed avian MST detection used the same protocol, the PAWQ used a slightly modified version to improve host specificity (33). One hundred ninety-six, 29, and 157 samples collected as part of the PAWQ study and by the Green and Richardson Labs, respectively, were tested for HF183, a human MST marker. One hundred ninety-six, 29, and 144 samples collected as part of the PAWQ study and by the Green and Richardson Labs, respectively, were tested for Rum2Bac, a ruminant MST marker. Forty-three samples collected by the Richardson Lab were also tested for two additional human MST markers (HUMM2 and B. Theta), one additional ruminant MST marker (CowM3), and one additional avian MST marker (Brevibacterium spp. LA35 16S rRNA). The water volumes used for MST detection varied between studies. Specifically, 500 mL was used by the Green Lab, 100 mL was used during the PAWQ study, and either 250 mL (N = 48 samples) or 100 mL (N = 109 samples) was used by the Richardson Lab; all labs filtered samples through 0.45-μm filters.
IDEXX, a proprietary kit used for quantifying levels of specific fecal indicator bacteria as the most probable number of cells present in 100 mL; MF, membrane filtration that quantifies bacterial levels as colony-forming units (CFU)/per 100 mL. For E. coli, CSI and URI both used Environmental Protection Agency (EPA) Method 1603 and EPA Method 1604, respectively, while OEI used SM 9222B-2006/SM 9222G-2006 (ELAP 1049). For Enterococcus, OEI used SM 9230C-2007 (ELAP 1042), while URI used membrane filtration with m-Enterococcus (mE) agar before 2006 but shifted to IDEXX after 2006. For fecal coliforms, CSI used SM 9222D-2006, and OEI used SM 9222D-2006 (ELAP 1003). URI used a membrane filtration with membrane-thermotolerant Escherichia coli (mTEC) agar before 2005 but shifted to IDEXX after 2005. For total coliforms, CSI used EPA Method 1604, and OEI used SM 9222B-2006 (ELAP 1011).
Specifically, samples were collected by the FSL from 2001 to 2002, 2009 to 2011, and 2013 to 2014 and by OEI from 2008 to 2009 and 2012 to 2017. All other labs collected one or more samples annually during the period reported.