Rapid qPCR-Based Water Quality Monitoring in New York State Recreational Waters

Public swimming beaches often rely on culture-based methods to determine if fecal indicator bacteria (FIB) levels are greater than health risk-based beach action values (BAV). The slow turnaround time of culture-based assays can prevent effective beach closure and reopening decisions. Faster testing methods that can be completed on-site are needed. Additionally, beach closures are currently based on high FIB levels, but at-present there are no tools to examine the health risks to bathers from myriad pathogens (e.g., bacteria, viruses, protozoa) that may be present in recreational waters. Twelve New York State beaches (n = 9 freshwater and n = 3 marine) were monitored over the course of summer 2018, and two of the freshwater beaches were monitored in fall 2017 as part of a preliminary study. A rapid, in-field workflow for detecting fecal enterococci in water samples was tested using four assays on two Biomeme handheld devices. All Biomeme-based workflows involved in-field DNA extractions and qPCR using portable devices. Beach water samples were also analyzed using EPA-approved or EPA-based qPCR methods: two culture-based methods, Enterolert (targeting enterococci at freshwater and marine beaches) and Colilert (targeting E. coli at freshwater beaches); and one qPCR method based on EPA 1611.1. For low abundance pathogen quantification, nanoscale-qPCR was conducted in 2018 using the Pathogen Panel which targeted 12 viral, bacterial, and protozoal pathogens. In fall 2017, the qPCR-based methods performed similarly to Enterolert (r2 from 0.537 to 0.687) and correctly classified 62.5–75.0% of water samples for a BAV of 104 MPN per 100 ml. In summer 2018, the correlation between Enterococcus levels based on Biomeme qPCR and Enterolert varied substantially between the 12 beaches. Inclusion of diverse regions and beach types may have confounded the Biomeme qPCR results. The EPA 1611.1-based method showed a weak, significant correlation (r2 = 0.317, p = 0.00012) with Enterolert. Nanoscale-qPCR showed low-levels of pathogens present at all beach sites; but only three showed up with any substantial frequency, E. coli eae (25% of samples), norovirus (31.4%), and Giardia lamblia (11.4%). Preliminary studies to establish beach-specific correlation curves between rapid qPCR and Enterolert methods are needed before any qPCR assay is used to inform beach decisions.

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Plant-Pathogenic Oomycetes, Escherichia coli Strains, and Salmonella spp. Frequently Found in Surface Water Used for Irrigation of Fruit and Vegetable Crops in New York State

Applied and Environmental Microbiology ◽

10.1128/aem.01012-14 ◽

2014 ◽

Vol 80 (16) ◽

pp. 4814-4820 ◽

Cited By ~ 24

Author(s):

Lisa A. Jones ◽

Randy W. Worobo ◽

Christine D. Smart

Keyword(s):

Escherichia Coli ◽

Water Quality ◽

New York ◽

Food Safety ◽

Surface Water ◽

New York State ◽

Quality Parameters ◽

Content Type ◽

York State ◽

E Coli

ABSTRACTIn the United States, surface water is commonly used to irrigate a variety of produce crops and can harbor pathogens responsible for food-borne illnesses and plant diseases. Understanding when pathogens infest water sources is valuable information for produce growers to improve the food safety and production of these crops. In this study, prevalence data along with regression tree analyses were used to correlate water quality parameters (pH, temperature, turbidity), irrigation site properties (source, the presence of livestock or fowl nearby), and precipitation data to the presence and concentrations ofEscherichia coli,Salmonellaspp., and hymexazol-insensitive (HIS) oomycetes (PhytophthoraandPythiumspp.) in New York State surface waters. A total of 123 samples from 18 sites across New York State were tested forE. coliandSalmonellaspp., of which 33% and 43% were positive, respectively. Additionally, 210 samples from 38 sites were tested for HIS oomycetes, and 88% were found to be positive, with 10 species ofPhytophthoraand 11 species ofPythiumbeing identified from the samples. Regression analysis found no strong correlations between water quality parameters, site factors, or precipitation to the presence or concentration ofE. coliin irrigation sources. ForSalmonella, precipitation (≤0.64 cm) 3 days before sampling was correlated to both presence and the highest counts. Analyses for oomycetes found creeks to have higher average counts than ponds, and higher turbidity levels were associated with higher oomycete counts. Overall, information gathered from this study can be used to better understand the food safety and plant pathogen risks of using surface water for irrigation.

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1237. New York State Outpatient Regional Antibiogram for Urinary Pathogens: Have We Reached a Post Antibiotic Era for the Treatment of UTIs?

Open Forum Infectious Diseases ◽

10.1093/ofid/ofy210.1070 ◽

2018 ◽

Vol 5 (suppl_1) ◽

pp. S376-S376

Author(s):

Elliot Rank ◽

Thomas P Lodise ◽

Lisa Avery ◽

Eve Bankert ◽

Erica Dobson ◽

...

Keyword(s):

New York ◽

New York State ◽

Empiric Therapy ◽

Outpatient Setting ◽

York State ◽

E Coli ◽

Enterococcus Spp ◽

Acute Uncomplicated Cystitis ◽

Uncomplicated Cystitis ◽

Outpatient Settings

Abstract Background Outpatient prescribing for acute uncomplicated cystitis is a significant driver of antimicrobial use. Empiric therapy should be based on local susceptibility data. However, there is limited guidance on regional susceptibility trends in outpatient settings. This study describes the epidemiology and prevalence of antimicrobial resistance in uropathogens in New York State outpatient settings to help inform empiric treatment decisions. Methods Retrospective analysis of positive urine cultures sent to Quest Diagnostics in 2016 from outpatient settings. Cultures that grew ≥105 CFU/mL were included from 17 NYS counties. Bacterial identification and antimicrobial sensitivities were determined on the Vitek-2 using CLSI M-100 S-25 breakpoints. Data were summarized as proportions and stratified by age (<17, 18–64, ≥65) and sex. Results Over 78,000 isolates were included (Table 1). The most prevalent isolates were Escherichia coli (65.2%), Enterococcus spp. (11.9%), and Klebsiella pneumoniae (9.9%). E. coli was highly susceptible to nitrofurantoin (NTF, 97.2%) and cefazolin (CFZ, 89.9%) and less susceptible to trimethoprim–sulfamethoxazole (TMP-SMX, 72.9%) and ciprofloxacin (CIP, 78.0%). Enterococcus spp. was highly susceptible to NTF (99.0%) and ampicillin (99.8%). K. pneumoniae was highly susceptible to TMP-SMX (90.0%) and CIP (95.2%) and markedly less susceptible to NTF (42.0%). E. coli was more prevalent in females (69.7% vs. 39.6%, P < 0.001). Enterococcus was more prevalent in males (39.6% vs. 10.1%, P < 0.001). The prevalence of K. pneumoniae was similar in men and women (9.6% vs. 10.1%, P = 0.08). Resistance was more prevalent in males (NTF: 6.3% vs. 4.2%; TMP-SMX: 26.3% vs. 22.7%; CIP: 35% vs. 17.3%) and for adults ≥65 (NTF: 6.2% vs. 3.6%; TMP-SMX: 25.1% vs. 22.1%; CIP: 30.0% vs. 14.0%) P < 0.001 for all comparisons. Conclusion NTF appears to be the best empiric choice for outpatient treatment of acute uncomplicated cystitis in New York State. TMP-SMX and ciprofloxacin should be avoided empirically. These data also highlight the necessity to obtain uropathogen sensitivity data to confirm empiric therapy or make appropriate adjustments in the outpatient setting. Table 1. Summary of Antimicrobial Susceptibilities Disclosures T. P. Lodise Jr., Motif BioSciences: Board Member, Consulting fee.

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ASSOCIATION OF ESCHERICHIA COLI SEROGROUP 0111 WITH TWO HOSPITAL OUTBREAKS OF EPIDEMIC DIARRHEA OF THE NEWBORN INFANT IN NEW YORK STATE DURING 1947

PEDIATRICS ◽

10.1542/peds.12.4.377 ◽

1953 ◽

Vol 12 (4) ◽

pp. 377-383

Author(s):

ERWIN NETER ◽

ROBERT F. KORNS ◽

RAY E. TRUSSELL

Keyword(s):

Escherichia Coli ◽

New York ◽

Newborn Infant ◽

New York State ◽

York State ◽

E Coli

Escherichia coli serogroup 0111 was isolated in 1952 as the predominant coliform organism from 5 fecal specimens obtained from 7 infants who were suffering from epidemic diarrhea of the newborn infant during two serious hospital outbreaks of this disease in 1947. The specimens had been preserved at a temperature of -40° to -70° C. for five years. The association of certain serogroups of E. coli and epidemic diarrhea of the newborn infant is discussed.

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