Last data update: May 20, 2024. (Total: 46824 publications since 2009)
Records 1-13 (of 13 Records) |
Query Trace: Lafon P [original query] |
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Evaluation of the Illumina iSeq whole genome sequencing system for enteric disease surveillance and outbreak detection
Trees E , Poates A , Sabol A , LaFon P , Truong J , Lindsey R . J Microbiol Methods 2023 211 106784 The Illumina iSeq low-capacity sequencing platform was evaluated for use in foodborne disease surveillance and outbreak detection. The platform produced high quality sequence data comparable to that of the Illumina MiSeq and was cost-effective with fast turn-around time in low sample volume environments. |
Gen-FS coordinated proficiency test data for genomic foodborne pathogen surveillance, 2017 and 2018 exercises.
Timme RE , Lafon PC , Balkey M , Adams JK , Wagner D , Carleton H , Strain E , Hoffmann M , Sabol A , Rand H , Lindsey R , Sheehan D , Baugher JD , Trees E . Sci Data 2020 7 (1) 402 The US PulseNet and GenomeTrakr laboratory networks work together within the Genomics for Food Safety (Gen-FS) consortium to collect and analyze genomic data for foodborne pathogen surveillance (species include Salmonella enterica, Listeria monocytogenes, Escherichia coli (STECs), and Campylobactor). In 2017 these two laboratory networks started harmonizing their respective proficiency test exercises, agreeing on distributing a single strain-set and following the same standard operating procedure (SOP) for genomic data collection, running a jointly coordinated annual proficiency test exercise. In this data release we are publishing the reference genomes and raw data submissions for the 2017 and 2018 proficiency test exercises. |
Implementing insurance billing in local health department sexually transmitted disease clinics in Virginia, 2017
McGee F , Carter A , Lafon E , Chesson H . Sex Transm Dis 2020 47 (8) e21-e23 In 2017, the Virginia Department of Health (VDH) implemented billing of insurance in local health department sexually transmitted disease (STD) clinics. We examined data collected by VDH related to clinic encounters, billing, and revenue from STD clinics statewide. Implementing insurance billing created a new revenue stream for local health departments. |
Multiple-locus variable-number tandem repeat analysis for strain discrimination of non-O157 Shiga toxin-producing Escherichia coli.
Timmons C , Trees E , Ribot EM , Gerner-Smidt P , LaFon P , Im S , Ma LM . J Microbiol Methods 2016 125 70-80 Non-O157 Shiga toxin-producing Escherichia coli (STEC) are foodborne pathogens of growing concern worldwide that have been associated with several recent multistate and multinational outbreaks of foodborne illness. Rapid and sensitive molecular-based bacterial strain discrimination methods are critical for timely outbreak identification and contaminated food source traceback. One such method, multiple-locus variable-number tandem repeat analysis (MLVA), is being used with increasing frequency in foodborne illness outbreak investigations to augment the current gold standard bacterial subtyping technique, pulsed-field gel electrophoresis (PFGE). The objective of this study was to develop a MLVA assay for intra- and inter-serogroup discrimination of six major non-O157 STEC serogroups-O26, O111, O103, O121, O45, and O145-and perform a preliminary internal validation of the method on a limited number of clinical isolates. The resultant MLVA scheme consists of ten variable number tandem repeat (VNTR) loci amplified in three multiplex PCR reactions. Sixty-five unique MLVA types were obtained among 84 clinical non-O157 STEC strains comprised of geographically diverse sporadic and outbreak related isolates. Compared to PFGE, the developed MLVA scheme allowed similar discrimination among serogroups O26, O111, O103, and O121 but not among O145 and O45. To more fully compare the discriminatory power of this preliminary MLVA method to PFGE and to determine its epidemiological congruence, a thorough internal and external validation needs to be performed on a carefully selected large panel of strains, including multiple isolates from single outbreaks. |
Insights into the environmental reservoir of pathogenic Vibrio parahaemolyticus using comparative genomics.
Hazen TH , Lafon PC , Garrett NM , Lowe TM , Silberger DJ , Rowe LA , Frace M , Parsons MB , Bopp CA , Rasko DA , Sobecky PA . Front Microbiol 2015 6 204 Vibrio parahaemolyticus is an aquatic halophilic bacterium that occupies estuarine and coastal marine environments, and is a leading cause of seafood-borne food poisoning cases. To investigate the environmental reservoir and potential gene flow that occurs among V. parahaemolyticus isolates, the virulence-associated gene content and genome diversity of a collection of 133 V. parahaemolyticus isolates were analyzed. Phylogenetic analysis of housekeeping genes, and pulsed-field gel electrophoresis, demonstrated that there is genetic similarity among V. parahaemolyticus clinical and environmental isolates. Whole-genome sequencing and comparative analysis of six representative V. parahaemolyticus isolates was used to identify genes that are unique to the clinical and environmental isolates examined. Comparative genomics demonstrated an O3:K6 environmental isolate, AF91, which was cultured from sediment collected in Florida in 2006, has significant genomic similarity to the post-1995 O3:K6 isolates. However, AF91 lacks the majority of the virulence-associated genes and genomic islands associated with these highly virulent post-1995 O3:K6 genomes. These findings demonstrate that although they do not contain most of the known virulence-associated regions, some V. parahaemolyticus environmental isolates exhibit significant genetic similarity to clinical isolates. This highlights the dynamic nature of the V. parahaemolyticus genome allowing them to transition between aquatic and host-pathogen states. |
Suitability of the molecular subtyping methods intergenic spacer region, direct genome restriction analysis, and pulsed-field gel electrophoresis for clinical and environmental Vibrio parahaemolyticus isolates.
Ludeke CH , Fischer M , LaFon P , Cooper K , Jones JL . Foodborne Pathog Dis 2014 11 (7) 520-8 Vibrio parahaemolyticus is the leading cause of infectious illness associated with seafood consumption in the United States. Molecular fingerprinting of strains has become a valuable research tool for understanding this pathogen. However, there are many subtyping methods available and little information on how they compare to one another. For this study, a collection of 67 oyster and 77 clinical V. parahaemolyticus isolates were analyzed by three subtyping methods-intergenic spacer region (ISR-1), direct genome restriction analysis (DGREA), and pulsed-field gel electrophoresis (PFGE)-to determine the utility of these methods for discriminatory subtyping. ISR-1 analysis, run as previously described, provided the lowest discrimination of all the methods (discriminatory index [DI]=0.8665). However, using a broader analytical range than previously reported, ISR-1 clustered isolates based on origin (oyster versus clinical) and had a DI=0.9986. DGREA provided a DI=0.9993-0.9995, but did not consistently cluster the isolates by any identifiable characteristics (origin, serotype, or virulence genotype) and approximately 15% of isolates were untypeable by this method. PFGE provided a DI=0.9998 when using the combined pattern analysis of both restriction enzymes, SfiI and NotI. This analysis was more discriminatory than using either enzyme pattern alone and primarily grouped isolates by serotype, regardless of strain origin (clinical or oyster) or presence of currently accepted virulence markers. These results indicate that PFGE and ISR-1 are more reliable methods for subtyping V. parahemolyticus, rather than DGREA. Additionally, ISR-1 may provide an indication of pathogenic potential; however, more detailed studies are needed. These data highlight the diversity within V. parahaemolyticus and the need for appropriate selection of subtyping methods depending on the study objectives. |
Outbreak of Salmonella enterica serotype I 4,5,12:i:- infections: the challenges of hypothesis generation and microwave cooking
Mody RK , Meyer S , Trees E , White PL , Nguyen T , Sowadsky R , Henao OL , Lafon PC , Austin J , Azzam I , Griffin PM , Tauxe RV , Smith K , Williams IT . Epidemiol Infect 2013 142 (5) 1-11 We investigated an outbreak of 396 Salmonella enterica serotype I 4,5,12:i:- infections to determine the source. After 7 weeks of extensive hypothesis-generation interviews, no refined hypothesis was formed. Nevertheless, a case-control study was initiated. Subsequently, an iterative hypothesis-generation approach used by a single interviewing team identified brand A not-ready-to-eat frozen pot pies as a likely vehicle. The case-control study, modified to assess this new hypothesis, along with product testing indicated that the turkey variety of pot pies was responsible. Review of product labels identified inconsistent language regarding preparation, and the cooking instructions included undefined microwave wattage categories. Surveys found that most patients did not follow the product's cooking instructions and did not know their oven's wattage. The manufacturer voluntarily recalled pot pies and improved the product's cooking instructions. This investigation highlights the value of careful hypothesis-generation and the risks posed by frozen not-ready-to-eat microwavable foods. |
US outbreak of human Salmonella infections associated with aquatic frogs, 2008-2011
Mettee Zarecki SL , Bennett SD , Hall J , Yaeger J , Lujan K , Adams-Cameron M , Winpisinger Quinn K , Brenden R , Biggerstaff G , Hill VR , Sholtes K , Garrett NM , Lafon PC , Behravesh CB , Sodha SV . Pediatrics 2013 131 (4) 724-31 OBJECTIVE: Although amphibians are known Salmonella carriers, no such outbreaks have been reported. We investigated a nationwide outbreak of human Salmonella Typhimurium infections occurring predominantly among children from 2008 to 2011. METHODS: We conducted a matched case-control study. Cases were defined as persons with Salmonella Typhimurium infection yielding an isolate indistinguishable from the outbreak strain. Controls were persons with recent infection with Salmonella strains other than the outbreak strain and matched to cases by age and geography. Environmental samples were obtained from patients' homes; traceback investigations were conducted. RESULTS: We identified 376 cases from 44 states from January 1, 2008, to December 31, 2011; 29% (56/193) of patients were hospitalized and none died. Median patient age was 5 years (range <1-86 years); 69% were children <10 years old (253/367). Among 114 patients interviewed, 69 (61%) reported frog exposure. Of patients who knew frog type, 79% (44/56) reported African dwarf frogs (ADF), a type of aquatic frog. Among 18 cases and 29 controls, illness was significantly associated with frog exposure (67% cases versus 3% controls, matched odds ratio 12.4, 95% confidence interval 1.9-infinity). Environmental samples from aquariums containing ADFs in 8 patients' homes, 2 ADF distributors, and a day care center yielded isolates indistinguishable from the outbreak strain. Traceback investigations of ADFs from patient purchases converged to a common ADF breeding facility. Environmental samples from the breeding facility yielded the outbreak strain. CONCLUSIONS: ADFs were the source of this nationwide pediatric predominant outbreak. Pediatricians should routinely inquire about pet ownership and advise families about illness risks associated with animals. |
Surveillance of parapoxvirus among ruminants in Virginia and Connecticut.
Roess AA , McCollum AM , Gruszynski K , Zhao H , Davidson W , Lafon N , Engelmeyer T , Moyer B , Godfrey C , Kilpatrick H , Labonte A , Murphy J , Carroll DS , Li Y , Damon IK . Zoonoses Public Health 2013 60 (8) 543-8 In 2008, two deer hunters in Virginia and Connecticut were infected with a unique strain of pseudocowpox virus, a parapoxvirus. To estimate the prevalence of this virus, and in an attempt to define the reservoir, Parapoxvirus surveillance was undertaken between November 2009 and January 2010. 125 samples from four ruminant species (cows, goat, sheep and white-tailed deer) were collected in Virginia, and nine samples from white-tailed deer were collected in Connecticut. We found no evidence that the parapoxvirus species that infected the deer hunters is circulating among domesticated ruminants or white-tailed deer. However, parapoxvirus DNA of a different parapoxvirus species, bovine papular stomatitis virus (BPSV), was detected in 31 samples obtained from asymptomatic cattle in Virginia. Parapoxvirus DNA-positive cattle originated from the same counties indicating probable transmission among animals. Molecular analysis identified BPSV as the parapoxvirus affecting animals. Asymptomatic parapoxvirus infections in livestock, particularly young animals, may be common, and further investigation will inform our knowledge of virus transmission. |
Outbreak of human Salmonella Typhimurium infections linked to contact with baby poultry from a single agricultural feed store chain and mail-order hatchery, 2009
Loharikar A , Vawter S , Warren K , Deasy M 3rd , Moll M , Sandt C , Gilhousen R , Villamil E , Rhorer A , Briere E , Schwensohn C , Trees E , Lafon P , Adams JK , Le B , Behravesh CB . Pediatr Infect Dis J 2012 32 (1) 8-12 BACKGROUND: Over thirty outbreaks of human salmonellosis linked to contact with live poultry from mail-order hatcheries were reported to CDC between 1990-2010. In May 2009, we investigated an outbreak of human Salmonella Typhimurium infections, primarily affecting children. METHODS: A case was defined as a person with the outbreak strain of Salmonella Typhimurium, as determined by pulsed-field gel electrophoresis (PFGE) and multiple-locus variable-number tandem repeat analysis (MLVA), in a Pennsylvania or New York resident with illness onset between May 1- September 1, 2009. We conducted a case-control study to examine the relationship between illness and live poultry contact. Controls were age- and geographically-matched. Traceback and environmental investigations were conducted. RESULTS: We identified 36 case-patients in Pennsylvania and New York; 36% were children aged ≤5 years. Case-patients were more likely than controls to report live baby poultry contact (matched odds ratio [mOR]: 17.0; 95% Confidence Interval [CI]:2.7-710.5), contact with chicks (mOR:14.0; 95% CI:2.1-592.0), ducklings (mOR:8.0; 95% CI:1.1-355.0), and visiting agricultural feed stores (mOR:6.0; 95% CI:1.3-55.2). Most (83%) visited agricultural Feed Store Chain Y, a national agricultural feed store chain, which received poultry from Hatchery C, which is supplied by multiple egg sources. Salmonella Typhimurium was isolated from a source duck flock, but had a different PFGE pattern than the outbreak strain. CONCLUSION: Live baby poultry remain an important source of human salmonellosis, particularly among children. Preventing these infections requires comprehensive interventions at hatcheries and agricultural feed stores; pediatricians should inform patients of risks associated with live poultry contact. |
Four multistate outbreaks of human Salmonella infections associated with live poultry contact, United States, 2009
Loharikar A , Briere E , Schwensohn C , Weninger S , Wagendorf J , Scheftel J , Garvey A , Warren K , Villamil E , Rudroff JA , Kurkjian K , Levine S , Colby K , Morrison B , May A , Anderson S , Daly E , Marsden-Haug N , Erdman MM , Gomez T , Rhorer A , Castleman J , Adams JK , Theobald L , Lafon P , Trees E , Mitchell J , Sotir MJ , Behravesh CB . Zoonoses Public Health 2012 59 (5) 347-54 Outbreaks of human salmonellosis associated with live poultry contact have been reported since 1955. Multiple Salmonella serotypes have been associated with these outbreaks, and specific outbreak strains have been repeatedly linked to single hatcheries over multiple years. During 2009, four multistate outbreaks of human Salmonella infections associated with direct and indirect exposure to live poultry purchased from mail-order hatcheries and agricultural feed stores were identified, resulting in 165 culture-confirmed cases in 30 states. This report describes the epidemiologic, environmental and laboratory investigations conducted by state and local health departments, state departments of agriculture, the U.S. Department of Agriculture (USDA), Animal and Plant Health Inspection Service (APHIS), National Poultry Improvement Plan (NPIP) and National Veterinary Services Laboratories (NVSL), and the Centers for Disease Control and Prevention (CDC). Case-patients were identified through PulseNet, the national molecular subtyping network for foodborne disease surveillance, and interviewed using the CDC standard live poultry contact questionnaire that asks about poultry-related exposures during the 7 days before illness onset. These outbreaks highlight the need to focus efforts on strategies to decrease and prevent human illness associated with live poultry contact through comprehensive interventions at the mail-order hatchery, agricultural feed store and consumer levels. Additional consumer education and interventions at mail-order hatcheries and venues where live poultry are sold, including agricultural feed stores, are necessary to prevent transmission of Salmonella from poultry to humans. |
Multilaboratory validation study of standardized multiple-locus variable-number tandem repeat analysis protocol for shiga toxin-producing escherichia coli O157: a novel approach to normalize fragment size data between capillary electrophoresis platforms
Hyytia-Trees E , Lafon P , Vauterin P , Ribot EM . Foodborne Pathog Dis 2009 7 (2) 129-36 The PulseNet USA subtyping network recently established a standardized protocol for multiple-locus variable-number tandem repeat analysis (MLVA) to characterize Shiga toxin-producing Escherichia coli O157. To enable data comparisons from different laboratories in the same database, reproducibility and high quality of the data must be ensured. The aim of this study was to test the robustness and reproducibility of the proposed standardized protocol by subjecting it to a multilaboratory validation process and to address any discrepancies that may have arisen from the study. A set of 50 strains was tested in 10 PulseNet participating laboratories that used capillary electrophoresis instruments from two manufacturers. Six out of the 10 laboratories were able to generate correct MLVA types for 46 (92%) or more strains. The discrepancies in MLVA type assignment were caused mainly by difficulties in optimizing polymerase chain reactions that were attributed to technical inexperience of the staff and suboptimal quality of reagents and instrumentation. It was concluded that proper training of staff must be an integral part of technology transfer. The interlaboratory reproducibility of fragment sizing was excellent when the same capillary electrophoresis platform was used. However, sizing discrepancies of up to six base pairs for the same fragment were detected between the two platforms. These discrepancies were attributed to different dye and polymer chemistries employed by the manufacturers. A novel software script was developed to assign alleles based on two platform-specific (Beckman Coulter CEQ8000 and Applied Biosystems Genetic Analyzer 3130xl) look-up tables containing fragment size ranges for all alleles. The new allele assignment method was validated at the PulseNet central laboratory using a diverse set of 502 Shiga toxin-producing Escherichia coli O157 isolates. The validation confirmed that the script reliably assigned the same allele for the same fragment regardless of the platform used to size the fragment. |
Rapid identification of vibrio parahaemolyticus by whole-cell matrix-assisted laser desorption ionization-time of flight mass spectrometry
Hazen TH , Martinez RJ , Chen Y , Lafon PC , Garrett NM , Parsons MB , Bopp CA , Sullards MC , Sobecky PA . Appl Environ Microbiol 2009 75 (21) 6745-56 Vibrio parahaemolyticus is a pathogenic marine bacterium that is the main causative agent of bacterial seafood borne gastroenteritis in the United States. An increase in the frequency of V. parahaemolyticus-related infections during the last decade has been attributed to the emergence of an O3:K6 pandemic clone in 1995. The diversity of the O3:K6 pandemic clone and serovariants has been examined using multiple molecular techniques including multilocus sequence analysis (MLSA), pulsed-field gel electrophoresis (PFGE), and group-specific PCR (GS-PCR) analysis. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has become a powerful tool for rapidly distinguishing between related bacterial species. In the current study we demonstrate the development of a whole-cell MALDI-TOF MS method for the identification of V. parahaemolyticus from other Vibrio spp. We identified 30 peaks that were present only in the spectra of the V. parahaemolyticus strains examined in this study that may be developed as MALDI-TOF MS biomarkers for identification of V. parahaemolyticus. We detected variation in the MALDI-TOF spectra of V. parahaemolyticus strains isolated from different geographical locations and at different times. The MALDI-TOF MS spectra of the V. parahaemolyticus strains examined were distinct from the other Vibrios examined including the closely related V. alginolyticus, V. harveyi, and V. campbellii. The results of this study demonstrate the first use of whole-cell MALDI-TOF MS analysis for the rapid identification of V. parahaemolyticus. |
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