Kelly Goodwin | National Oceanographic Data Center (original) (raw)

Papers by Kelly Goodwin

Microbial source tracking qPCR Water quality Coliform a b s t r a c t Microbial source tracking (... more Microbial source tracking qPCR Water quality Coliform a b s t r a c t Microbial source tracking (MST) methods were evaluated in the Source Identification Protocol Project (SIPP), in which 27 laboratories compared methods to identify host sources of fecal pollution from blinded water samples containing either one or two different fecal types collected from California. This paper details lessons learned from the SIPP study and makes recommendations to further advance the field of MST. Overall, results from the SIPP study demonstrated that methods are available that can correctly identify whether particular host sources including humans, cows and birds have contributed to contamination in a body of water. However, differences between laboratory protocols and data processing affected results and complicated interpretation of MST method performance in some cases. This was an issue particularly for samples that tested positive (non-zero C t values) but below the limits of quantification or detection of a PCR assay. Although false positives were observed, such samples in the SIPP study often contained the fecal pollution

Recreational water quality Enterococci Seawater Beach sand a b s t r a c t Incidences of Staphylo... more Recreational water quality Enterococci Seawater Beach sand a b s t r a c t Incidences of Staphylococcus aureus and methicillin resistant S. aureus (MRSA) have risen worldwide prompting a need to better understand routes of human exposure and whether standard bacterial water quality monitoring practices adequately account for this potential threat. Beach water and sand samples were analyzed during summer months for S. aureus, enterococci, and MRSA at three southern California beaches (Avalon, Doheny, Malibu Surfrider). S. aureus frequently was detected in samples of seawater (59%, n ¼ 328) and beach sand (53%, n ¼ 358). MRSA sometimes was detected in seawater (1.6%, n ¼ 366) and sand (2.7%, n ¼ 366) at relatively low concentrations. Site specific differences were observed, with Avalon Beach presenting the highest concentrations of S. aureus and Malibu Surfrider the lowest in both seawater and sand. S. aureus concentrations in seawater and sand were correlated to each other and to a variety of other parameters. Multiple linear regression on the combined beach data indicated that significant explanatory variables for S. aureus in seawater were S. aureus in sand, water temperature, enterococci in seawater, and the number of swimmers. In sand, S. aureus concentrations were related to S. aureus in seawater, water temperature, enterococci in seawater, and inversely to surf height classification. Only the correlation to water temperature held for individually analyzed beaches and for S. aureus concentrations in both seawater and sand. To provide context for these results, the prevalence of S. aureus in sand was compared to published fomite studies, and results suggested that beach prevalence was similar to that in homes. journal home page: www.elsevier.com/loca te/watres w a t e r r e s e a r c h 4 6 ( 2 0 1 2 ) 4 1 9 5 e4 2 0 7

Many PCR-based methods for microbial source tracking (MST) have been developed and validated with... more Many PCR-based methods for microbial source tracking (MST) have been developed and validated within individual research laboratories. Inter-laboratory validation of these methods, however, has been minimal, and the effects of protocol standardization regimes

Marine Pollution Bulletin, 2005

Monitoring waters for indicator bacteria is required to protect the public from exposure to fecal... more Monitoring waters for indicator bacteria is required to protect the public from exposure to fecal pollution. Our proof-of-concept study describes a method for detecting fecal coliforms. The coliform Escherichia coli was used as a model fecal indicator. DNA probe-coated magnetic beads in combination with the electrochemical monitoring of the oxidation state of guanine nucleotides should allow for direct detection of bacterial RNA. To demonstrate this concept, we used voltammetry in connection with pencil electrodes to detect isolated E. coli 16S rRNA. Using this approach, 10 7 cells of E. coli were detected in a quantitative, reproducible fashion in 4 h. Detection was achieved without a nucleic acid amplification step. The specificity of the assay for coliforms was demonstrated by testing against a panel of bacterial RNA. We also show that E. coli RNA can be detected directly from cell extracts. The method could be used for on-site detection and shows promise for adaptation into automated biosensors for water-quality monitoring.

Nature Microbiology, 2016

Genome-enabled technologies have supported a dramatic increase in our ability to study microbial ... more Genome-enabled technologies have supported a dramatic increase in our ability to study microbial communities in environments and hosts. Taking stock of previously funded microbiome research can help to identify common themes, under-represented areas and research priorities to consider moving forward. To assess the status of US microbiome research, a team of government scientists conducted an analysis of federally funded microbiome research. Microbiomes were defined as host-, ecosystem- or habitat-associated communities of microorganisms, and microbiome research was defined as those studies that emphasize community-level analyses using &amp;amp;amp;#39;omics technologies. Single pathogen, single strain and culture-based studies were not included, except symbiosis studies that served as models for more complex communities. Fourteen governmental organizations participated in the data call. The analysis examined three broad research themes, eight environments and eight microbial categories. Human microbiome research was larger than any other environment studied, and the basic biology research theme accounted for half of the total research activities. Computational biology and bioinformatics, reference databases and biorepositories, standardized protocols and high-throughput tools were commonly identified needs. Longitudinal and functional studies and interdisciplinary research were also identified as needs. This study has implications for the funding of future microbiome research, not only in the United States but beyond.

GigaScience, 2015

Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinf... more Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world's oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits.

Journal of Atmospheric Chemistry, 2014

Your article is protected by copyright and all rights are held exclusively by Springer Science +B... more Your article is protected by copyright and all rights are held exclusively by Springer Science +Business Media Dordrecht. This e-offprint is for personal use only and shall not be selfarchived in electronic repositories. If you wish to self-archive your article, please use the accepted manuscript version for posting on your own website. You may further deposit the accepted manuscript version in any repository, provided it is only made publicly available 12 months after official publication or later and provided acknowledgement is given to the original source of publication and a link is inserted to the published article on Springer's website. The link must be accompanied by the following text: "The final publication is available at link.springer.com".

GigaScience, 2014

The co-authors of this paper hereby state their intention to work together to launch the Genomic ... more The co-authors of this paper hereby state their intention to work together to launch the Genomic Observatories Network (GOs Network) for which this document will serve as its Founding Charter. We define a Genomic Observatory as an ecosystem and/or site subject to long-term scientific research, including (but not limited to) the sustained study of genomic biodiversity from single-celled microbes to multicellular organisms.An international group of 64 scientists first published the call for a global network of Genomic Observatories in January 2012. The vision for such a network was expanded in a subsequent paper and developed over a series of meetings in Bremen (Germany), Shenzhen (China), Moorea (French Polynesia), Oxford (UK), Pacific Grove (California, USA), Washington (DC, USA), and London (UK). While this community-building process continues, here we express our mutual intent to establish the GOs Network formally, and to describe our shared vision for its future. The views expres...

Water Research, 2012

Water Research, 2011

A v a i l a b l e a t w w w . s c i e n c e d i r e c t . c o m j o u r n a l h o m e p a g e : w... more A v a i l a b l e a t w w w . s c i e n c e d i r e c t . c o m j o u r n a l h o m e p a g e : w w w . e l s e v i e r . c o m / l o c a t e / w a t r e s w a t e r r e s e a r c h 4 5 ( 2 0 1 1 ) 3 2 7 9 e3 2 9 0 0043-1354/$ e see front matter ª

Water Research, 2013

The contribution of fecal pollution from dogs in urbanized areas can be significant and is an oft... more The contribution of fecal pollution from dogs in urbanized areas can be significant and is an often underestimated problem. Microbial source tracking methods (MST) utilizing quantitative PCR of dog-associated gene sequences encoding 16S rRNA of Bacteroidales are a Abbreviations: cp, gene copy numbers; Ct, cycle threshold; DNQ, detected but not quantifiable; FIB, fecal indicator bacteria; LLOQ, lower limit of quantification; LOD, limit of detection; MST, microbial source tracking; ND, not detected; PCR, polymerase chain reaction; qPCR, quantitative polymerase chain reaction; ROQ, range of quantification; SIPP, Source Identification Protocol Project; TMDL, total maximum daily load.

Water Research, 2009

MRSA Recreational water quality CHROMagar clfA mecA a b s t r a c t Beach seawater and sand were ... more MRSA Recreational water quality CHROMagar clfA mecA a b s t r a c t Beach seawater and sand were analyzed for Staphylococcus aureus and methicillin resistant S. aureus (MRSA) for samples collected from Avalon, and Doheny Beach, CA. Membrane filtration followed by incubation on CHROMagarÔ Staph aureus (SCA) and CHROMagarÔ MRSA (C-MRSA) was used to enumerate S. aureus and MRSA, respectively. Media performance was evaluated by comparing identification via colony morphology and latex agglutination tests to PCR (clfA, 16S, and mecA genes). Due to background color and crowding, picking colonies from membrane filters and streaking for isolation were sometimes necessary. The specificity of SCA and C-MRSA was improved if colony isolates were identified by the presence of a matte halo in addition to mauve color; however routine agglutination testing of isolates did not appear warranted. Using the appearance of a colony on the membrane filter in conjunction with isolate appearance, the positive % agreement, the negative % agreement, and the % positive predictive accuracy for SCA was 84%, 95%, and 99% respectively, and for C-MRSA it was 85%, 98%, and 92%, respectively. Sensitivity and specificity of SCA and C-MRSA with membrane-filtered beach samples were optimized through identification experience, control of filter volume and incubation time, and isolation of colonies needing further identification. With optimization, SCA and C-MRSA could be used for enumeration of S. aureus and MRSA from samples of beach water and sand. For the sites studied here, the frequency of detection of S. aureus ranged from 60 to 76% and 53 to 79% for samples of beach seawater and sand, respectively. The frequency of detection of MRSA ranged from 2 to 9% and 0 to 12% for samples of seawater and sand, respectively.

Marine Pollution Bulletin, 2013

The need for quantitative molecular methods is growing in environmental, food, and medical fields... more The need for quantitative molecular methods is growing in environmental, food, and medical fields but is hindered by low and variable DNA extraction and by co-extraction of PCR inhibitors. DNA extracts from Enterococcus faecium, seawater, and seawater spiked with E. faecium and Vibrio parahaemolyticus were tested by qPCR for target recovery and inhibition. Conventional and novel methods were tested, including Synchronous Coefficient of Drag Alteration (SCODA) and lysis and purification systems used on an automated genetic sensor (the Environmental Sample Processor, ESP). Variable qPCR target recovery and inhibition were measured, significantly affecting target quantification. An aggressive lysis method that utilized chemical, enzymatic, and mechanical disruption enhanced target recovery compared to commercial kit protocols. SCODA purification did not show marked improvement over commercial spin columns. Overall, data suggested a general need to improve sample preparation and to accurately assess and account for DNA recovery and inhibition in qPCR applications.

Journal of Water and Health, 2011

The Gulf of Mexico Alliance (GOMA) was tasked by the five Gulf State Governors to identify major ... more The Gulf of Mexico Alliance (GOMA) was tasked by the five Gulf State Governors to identify major issues affecting the Gulf of Mexico (GoM) and to set priorities for ameliorating these problems. One priority identified by GOMA is the need to improve detection methods for water quality indicators, pathogens and microbial source tracking. The United States Environmental Protection Agency (USEPA) is tasked with revising water quality criteria by 2012; however, the locations traditionally studied by the USEPA are not representative of the GoM and this has raised concern about whether or not the new criteria will be appropriate. This paper outlines a number of concerns, including deadlines associated with the USEPA Consent Decree, which may prevent inclusion of research needed to produce a well-developed set of methods and criteria appropriate for all regulated waters.