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Franklin AM, Weller DL, Durso LM, Bagley M, Davis BC, Frye JG, Grim CJ, Ibekwe AM, Jahne MA, Keely SP, Kraft AL, McConn BR, Mitchell RM, Ottesen AR, Sharma M, Strain EA, Tadesse DA, Tate H, Wells JE, Williams CF, Cook KL, Kabera C, McDermott PF, Garland JL. A one health approach for monitoring antimicrobial resistance: developing a national freshwater pilot effort. FRONTIERS IN WATER 2024; 6:10.3389/frwa.2024.1359109. [PMID: 38855419 PMCID: PMC11157689 DOI: 10.3389/frwa.2024.1359109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Antimicrobial resistance (AMR) is a world-wide public health threat that is projected to lead to 10 million annual deaths globally by 2050. The AMR public health issue has led to the development of action plans to combat AMR, including improved antimicrobial stewardship, development of new antimicrobials, and advanced monitoring. The National Antimicrobial Resistance Monitoring System (NARMS) led by the United States (U.S) Food and Drug Administration along with the U.S. Centers for Disease Control and U.S. Department of Agriculture has monitored antimicrobial resistant bacteria in retail meats, humans, and food animals since the mid 1990's. NARMS is currently exploring an integrated One Health monitoring model recognizing that human, animal, plant, and environmental systems are linked to public health. Since 2020, the U.S. Environmental Protection Agency has led an interagency NARMS environmental working group (EWG) to implement a surface water AMR monitoring program (SWAM) at watershed and national scales. The NARMS EWG divided the development of the environmental monitoring effort into five areas: (i) defining objectives and questions, (ii) designing study/sampling design, (iii) selecting AMR indicators, (iv) establishing analytical methods, and (v) developing data management/analytics/metadata plans. For each of these areas, the consensus among the scientific community and literature was reviewed and carefully considered prior to the development of this environmental monitoring program. The data produced from the SWAM effort will help develop robust surface water monitoring programs with the goal of assessing public health risks associated with AMR pathogens in surface water (e.g., recreational water exposures), provide a comprehensive picture of how resistant strains are related spatially and temporally within a watershed, and help assess how anthropogenic drivers and intervention strategies impact the transmission of AMR within human, animal, and environmental systems.
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Affiliation(s)
- Alison M. Franklin
- United States (U.S.) Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, United States
| | - Daniel L. Weller
- U.S. Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Lisa M. Durso
- U.S. Department of Agriculture, Agricultural Research Service (USDA, ARS), Agroecosystem Management Research, Lincoln, NE, United States
| | - Mark Bagley
- United States (U.S.) Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, United States
| | - Benjamin C. Davis
- United States (U.S.) Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, United States
| | - Jonathan G. Frye
- USDA ARS, U.S. National Poultry Research Center, Poultry Microbiological Safety and Processing Research Unit, Athens, GA, United States
| | - Christopher J. Grim
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, United States
| | - Abasiofiok M. Ibekwe
- USDA, ARS, Agricultural Water Efficiency and Salinity Research Unit, Riverside, CA, United States
| | - Michael A. Jahne
- United States (U.S.) Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, United States
| | - Scott P. Keely
- United States (U.S.) Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, United States
| | - Autumn L. Kraft
- Oak Ridge Institute for Science and Education, USDA, ARS, Beltsville, MD, United States
| | - Betty R. McConn
- Oak Ridge Institute for Science and Education, USDA, ARS, Beltsville, MD, United States
| | - Richard M. Mitchell
- Environmental Protection Agency, Office of Water, Washington, DC, United States
| | - Andrea R. Ottesen
- Center for Veterinary Medicine, National Antimicrobial Resistance Monitoring System (NARMS), U.S. Food and Drug Administration, Laurel, MD, United States
| | - Manan Sharma
- USDA, ARS Environmental Microbial and Food Safety Laboratory, Beltsville, MD, United States
| | - Errol A. Strain
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, United States
| | - Daniel A. Tadesse
- Center for Veterinary Medicine, National Antimicrobial Resistance Monitoring System (NARMS), U.S. Food and Drug Administration, Laurel, MD, United States
| | - Heather Tate
- Center for Veterinary Medicine, National Antimicrobial Resistance Monitoring System (NARMS), U.S. Food and Drug Administration, Laurel, MD, United States
| | - Jim E. Wells
- USDA, ARS, U.S. Meat Animal Research Center, Meat Safety and Quality, Clay Center, NE, United States
| | - Clinton F. Williams
- USDA, ARS, US Arid-Land Agricultural Research Center, Maricopa, AZ, United States
| | - Kim L. Cook
- USDA, ARS Nutrition, Food Safety and Quality National Program Staff, Beltsville, MD, United States
| | - Claudine Kabera
- Center for Veterinary Medicine, National Antimicrobial Resistance Monitoring System (NARMS), U.S. Food and Drug Administration, Laurel, MD, United States
| | - Patrick F. McDermott
- Center for Veterinary Medicine, National Antimicrobial Resistance Monitoring System (NARMS), U.S. Food and Drug Administration, Laurel, MD, United States
| | - Jay L. Garland
- United States (U.S.) Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, United States
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Damashek J, Westrich JR, McDonald JMB, Teachey ME, Jackson CR, Frye JG, Lipp EK, Capps KA, Ottesen EA. Non-point source fecal contamination from aging wastewater infrastructure is a primary driver of antibiotic resistance in surface waters. WATER RESEARCH 2022; 222:118853. [PMID: 35870389 DOI: 10.1016/j.watres.2022.118853] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 07/06/2022] [Accepted: 07/09/2022] [Indexed: 06/15/2023]
Abstract
Antibiotic resistance is a global threat to human health. Many surface water resources are environmental hotspots of antibiotic resistant gene (ARG) transfer, with agricultural runoff and human waste highlighted as common sources of ARGs to aquatic systems. Here we quantified fecal marker genes and ARGs in 992 stream water samples collected seasonally during a 5-year period from 115 sites across the Upper Oconee watershed (Georgia, USA), an area characterized by gradients of agricultural and urban development. Widespread fecal contamination was found from humans (48% of samples), ruminants (55%), and poultry (19%), and 73% of samples tested positive for at least one of the six targeted ARGs (ermB, tet(B), blaCTX-M-1, blaKPC, blaSHV, and qnrS). While ARGs were strongly correlated with human fecal markers, many highly contaminated samples were not associated with sewage outfalls, an expected source of fecal and ARG pollution. To determine sources of contamination, we synthesized ARG and fecal marker data with geospatial data on land use/land cover and wastewater infrastructure across the watershed. This novel analysis found strong correlations between ARGs and measures of sewer density, sewer length, and septic system age within sample watersheds, indicating non-point sources of fecal contamination from aging wastewater infrastructure can be critical disseminators of anthropogenic ARGs in the environment.
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Affiliation(s)
- Julian Damashek
- Department of Microbiology, University of Georgia, 120 Cedar Street, Athens, GA 30602, USA
| | - Jason R Westrich
- Department of Microbiology, University of Georgia, 120 Cedar Street, Athens, GA 30602, USA
| | - Jacob M Bateman McDonald
- Lewis F. Rogers Institute for Environmental and Spatial Analysis, University of North Georgia, 2636 Mathis Drive, Oakwood, GA 30566, USA
| | - Morgan E Teachey
- Department of Microbiology, University of Georgia, 120 Cedar Street, Athens, GA 30602, USA
| | - Charlene R Jackson
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, U.S. National Poultry Research Center, USDA-ARS, 950 College Station Road, Athens, GA 30605, USA
| | - Jonathan G Frye
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, U.S. National Poultry Research Center, USDA-ARS, 950 College Station Road, Athens, GA 30605, USA
| | - Erin K Lipp
- Department of Environmental Health Science, University of Georgia, 150 East Green Street, Athens, GA 30602, USA
| | - Krista A Capps
- Odum School of Ecology, University of Georgia, 140 East Green Street, Athens, GA 30602, USA; Savannah River Ecology Laboratory, University of Georgia, SRS Building 737A, Aiken, SC 29808, USA
| | - Elizabeth A Ottesen
- Department of Microbiology, University of Georgia, 120 Cedar Street, Athens, GA 30602, USA.
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3
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Analysis of Salmonella enterica Isolated from a Mixed-Use Watershed in Georgia, USA: Antimicrobial Resistance, Serotype Diversity, and Genetic Relatedness to Human Isolates. Appl Environ Microbiol 2022; 88:e0039322. [PMID: 35532233 DOI: 10.1128/aem.00393-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
As the cases of Salmonella enterica infections associated with contaminated water are increasing, this study was conducted to address the role of surface water as a reservoir of S. enterica serotypes. We sampled rivers and streams (n = 688) over a 3-year period (2015 to 2017) in a mixed-use watershed in Georgia, USA, and 70.2% of the total stream samples tested positive for Salmonella. A total of 1,190 isolates were recovered and characterized by serotyping, antimicrobial susceptibility testing, and pulsed-field gel electrophoresis (PFGE). A wide range of serotypes was identified, including those commonly associated with humans and animals, with S. enterica serotype Muenchen being predominant (22.7%) and each serotype exhibiting a high degree of strain diversity by PFGE. About half (46.1%) of the isolates had PFGE patterns indistinguishable from those of human clinical isolates in the CDC PulseNet database. A total of 52 isolates (4.4%) were resistant to antimicrobials, out of which 43 isolates were multidrug resistant (MDR; resistance to two or more classes of antimicrobials). These 52 resistant Salmonella isolates were screened for the presence of antimicrobial resistance genes, plasmid replicons, and class 1 integrons, out of which four representative MDR isolates were selected for whole-genome sequencing analysis. The results showed that 28 MDR isolates resistant to 10 antimicrobials had blacmy-2 on an A/C plasmid. Persistent contamination of surface water with a high diversity of Salmonella strains, some of which are drug resistant and genetically indistinguishable from human isolates, supports a role of environmental surface water as a reservoir for and transmission route of this pathogen. IMPORTANCE Salmonella has been traditionally considered a foodborne pathogen, as it is one of the most common etiologies of foodborne illnesses worldwide; however, recent Salmonella outbreaks attributed to fresh produce and water suggest a potential environmental source of Salmonella that causes some human illnesses. Here, we investigated the prevalence, diversity, and antimicrobial resistance of Salmonella isolated from a mixed-use watershed in Georgia, USA, in order to enhance the overall understanding of waterborne Salmonella. The persistence and widespread distribution of Salmonella in surface water confirm environmental sources of the pathogen. A high proportion of waterborne Salmonella with clinically significant serotypes and genetic similarity to strains of human origin supports the role of environmental water as a significant reservoir of Salmonella and indicates a potential waterborne transmission of Salmonella to humans. The presence of antimicrobial-resistant and MDR Salmonella demonstrates additional risks associated with exposure to contaminated environmental water.
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Bell RL, Kase JA, Harrison LM, Balan KV, Babu U, Chen Y, Macarisin D, Kwon HJ, Zheng J, Stevens EL, Meng J, Brown EW. The Persistence of Bacterial Pathogens in Surface Water and Its Impact on Global Food Safety. Pathogens 2021; 10:1391. [PMID: 34832547 PMCID: PMC8617848 DOI: 10.3390/pathogens10111391] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/15/2021] [Accepted: 10/19/2021] [Indexed: 11/17/2022] Open
Abstract
Water is vital to agriculture. It is essential that the water used for the production of fresh produce commodities be safe. Microbial pathogens are able to survive for extended periods of time in water. It is critical to understand their biology and ecology in this ecosystem in order to develop better mitigation strategies for farmers who grow these food crops. In this review the prevalence, persistence and ecology of four major foodborne pathogens, Shiga toxin-producing Escherichia coli (STEC), Salmonella, Campylobacter and closely related Arcobacter, and Listeria monocytogenes, in water are discussed. These pathogens have been linked to fresh produce outbreaks, some with devastating consequences, where, in a few cases, the contamination event has been traced to water used for crop production or post-harvest activities. In addition, antimicrobial resistance, methods improvements, including the role of genomics in aiding in the understanding of these pathogens, are discussed. Finally, global initiatives to improve our knowledge base of these pathogens around the world are touched upon.
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Affiliation(s)
- Rebecca L. Bell
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD 20740, USA; (J.A.K.); (Y.C.); (D.M.); (H.J.K.); (J.Z.); (E.W.B.)
| | - Julie A. Kase
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD 20740, USA; (J.A.K.); (Y.C.); (D.M.); (H.J.K.); (J.Z.); (E.W.B.)
| | - Lisa M. Harrison
- Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, Food and Drug Administration, Laurel, MD 20708, USA; (L.M.H.); (K.V.B.); (U.B.)
| | - Kannan V. Balan
- Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, Food and Drug Administration, Laurel, MD 20708, USA; (L.M.H.); (K.V.B.); (U.B.)
| | - Uma Babu
- Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, Food and Drug Administration, Laurel, MD 20708, USA; (L.M.H.); (K.V.B.); (U.B.)
| | - Yi Chen
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD 20740, USA; (J.A.K.); (Y.C.); (D.M.); (H.J.K.); (J.Z.); (E.W.B.)
| | - Dumitru Macarisin
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD 20740, USA; (J.A.K.); (Y.C.); (D.M.); (H.J.K.); (J.Z.); (E.W.B.)
| | - Hee Jin Kwon
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD 20740, USA; (J.A.K.); (Y.C.); (D.M.); (H.J.K.); (J.Z.); (E.W.B.)
| | - Jie Zheng
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD 20740, USA; (J.A.K.); (Y.C.); (D.M.); (H.J.K.); (J.Z.); (E.W.B.)
| | - Eric L. Stevens
- Office of the Center Director, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD 20740, USA;
| | - Jianghong Meng
- Joint Institute for Food Safety and Applied Nutrition, Center for Food Safety and Security Systems, University of Maryland, College Park, MD 20742, USA;
| | - Eric W. Brown
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD 20740, USA; (J.A.K.); (Y.C.); (D.M.); (H.J.K.); (J.Z.); (E.W.B.)
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5
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Genomic population structure associated with repeated escape of Salmonella enterica ATCC14028s from the laboratory into nature. PLoS Genet 2021; 17:e1009820. [PMID: 34570761 PMCID: PMC8496778 DOI: 10.1371/journal.pgen.1009820] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 10/07/2021] [Accepted: 09/10/2021] [Indexed: 11/19/2022] Open
Abstract
Salmonella enterica serovar Typhimurium strain ATCC14028s is commercially available from multiple national type culture collections, and has been widely used since 1960 for quality control of growth media and experiments on fitness (“laboratory evolution”). ATCC14028s has been implicated in multiple cross-contaminations in the laboratory, and has also caused multiple laboratory infections and one known attempt at bioterrorism. According to hierarchical clustering of 3002 core gene sequences, ATCC14028s belongs to HierCC cluster HC20_373 in which most internal branch lengths are only one to three SNPs long. Many natural Typhimurium isolates from humans, domesticated animals and the environment also belong to HC20_373, and their core genomes are almost indistinguishable from those of laboratory strains. These natural isolates have infected humans in Ireland and Taiwan for decades, and are common in the British Isles as well as the Americas. The isolation history of some of the natural isolates confirms the conclusion that they do not represent recent contamination by the laboratory strain, and 10% carry plasmids or bacteriophages which have been acquired in nature by HGT from unrelated bacteria. We propose that ATCC14028s has repeatedly escaped from the laboratory environment into nature via laboratory accidents or infections, but the escaped micro-lineages have only a limited life span. As a result, there is a genetic gap separating HC20_373 from its closest natural relatives due to a divergence between them in the late 19th century followed by repeated extinction events of escaped HC20_373. Clades of closely related bacteria exist in nature. Individual isolates from such clades are often distinguishable by genomic sequencing because genomic sequence differences can be acquired over a few years due to neutral drift and natural selection. The evolution of laboratory strains is often largely frozen, physically due to storage conditions and genetically due to long periods of storage. Thus, laboratory strains can normally be readily distinguished from natural isolates because they show much less diversity. However, laboratory strain ATCC14028s shows modest levels of sequence diversity because it has been shipped around the world to multiple laboratories and is routinely used for analyses of laboratory evolution. Closely related natural isolates also exist, but their genetic diversity is not dramatically greater at the core genome level. Indeed, many scientists doubt that such isolates are natural, and interpret them as undetected contamination by the laboratory strain. We present data indicating that ATCC14028s has repeatedly escaped from the laboratory through inadvertent contamination of the environment, infection of technical staff and deliberate bioterrorism. The escapees survive in nature long enough that some acquire mobile genomic elements by horizontal gene transfer, but eventually they go extinct. As a result, even extensive global databases of natural isolates lack closely related isolates whose ancestors diverged from ATCC14028s within the last 100 years.
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Hernandez SM, Maurer JJ, Yabsley MJ, Peters VE, Presotto A, Murray MH, Curry S, Sanchez S, Gerner-Smidt P, Hise K, Huang J, Johnson K, Kwan T, Lipp EK. Free-Living Aquatic Turtles as Sentinels of Salmonella spp. for Water Bodies. Front Vet Sci 2021; 8:674973. [PMID: 34368271 PMCID: PMC8339271 DOI: 10.3389/fvets.2021.674973] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/25/2021] [Indexed: 11/13/2022] Open
Abstract
Reptile-associated human salmonellosis cases have increased recently in the United States. It is not uncommon to find healthy chelonians shedding Salmonella enterica. The rate and frequency of bacterial shedding are not fully understood, and most studies have focused on captive vs. free-living chelonians and often in relation to an outbreak. Their ecology and significance as sentinels are important to understanding Salmonella transmission. In 2012-2013, Salmonella prevalence was determined for free-living aquatic turtles in man-made ponds in Clarke and Oconee Counties, in northern Georgia (USA) and the correlation between species, basking ecology, demographics (age/sex), season, or landcover with prevalence was assessed. The genetic relatedness between turtle and archived, human isolates, as well as, other archived animal and water isolates reported from this study area was examined. Salmonella was isolated from 45 of 194 turtles (23.2%, range 14-100%) across six species. Prevalence was higher in juveniles (36%) than adults (20%), higher in females (33%) than males (18%), and higher in bottom-dwelling species (31%; common and loggerhead musk turtles, common snapping turtles) than basking species (15%; sliders, painted turtles). Salmonella prevalence decreased as forest cover, canopy cover, and distance from roads increased. Prevalence was also higher in low-density, residential areas that have 20-49% impervious surface. A total of 9 different serovars of two subspecies were isolated including 3 S. enterica subsp. arizonae and 44 S. enterica subsp. enterica (two turtles had two serotypes isolated from each). Among the S. enterica serovars, Montevideo (n = 13) and Rubislaw (n = 11) were predominant. Salmonella serovars Muenchen, Newport, Mississippi, Inverness, Brazil, and Paratyphi B. var L(+) tartrate positive (Java) were also isolated. Importantly, 85% of the turtle isolates matched pulsed-field gel electrophoresis patterns of human isolates, including those reported from Georgia. Collectively, these results suggest that turtles accumulate Salmonella present in water bodies, and they may be effective sentinels of environmental contamination. Ultimately, the Salmonella prevalence rates in wild aquatic turtles, especially those strains shared with humans, highlight a significant public health concern.
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Affiliation(s)
- Sonia M Hernandez
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, United States.,Department of Population Health, Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - John J Maurer
- Department of Population Health, Poultry Diagnostic and Research Center, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Michael J Yabsley
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, United States.,Department of Population Health, Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Valerie E Peters
- Department of Biological Sciences, Eastern Kentucky University, Richmond, KY, United States
| | - Andrea Presotto
- Department of Geography, University of Georgia, Athens, GA, United States
| | - Maureen H Murray
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, United States.,Department of Population Health, Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA, United States.,Davee Center for Epidemiology and Endocrinology and the Urban Wildlife Institute, Lincoln Park Zoo, Chicago, IL, United States
| | - Shannon Curry
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, United States.,Department of Population Health, Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Susan Sanchez
- Athens Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Peter Gerner-Smidt
- Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Kelley Hise
- Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Joyce Huang
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, United States.,Department of Population Health, Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Kasey Johnson
- Department of Population Health, Poultry Diagnostic and Research Center, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Tiffany Kwan
- Department of Population Health, Poultry Diagnostic and Research Center, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Erin K Lipp
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA, United States
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7
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Dungan RS, Bjorneberg DL. Antimicrobial Resistance in Escherichia coli and Enterococcal Isolates From Irrigation Return Flows in a High-Desert Watershed. Front Microbiol 2021; 12:660697. [PMID: 34054760 PMCID: PMC8149595 DOI: 10.3389/fmicb.2021.660697] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/13/2021] [Indexed: 11/25/2022] Open
Abstract
Irrigation return flows (IRFs) collect surface runoff and subsurface drainage, causing them to have elevated contaminant and bacterial levels, and making them a potential source of pollutants. The purpose of this study was to determine antimicrobial susceptibility among Escherichia coli and enterococcal isolates that were collected from IRFs in a south-central Idaho watershed. Environmental isolates can be a potentially important source of antimicrobial resistance (AMR) and IRFs may be one way resistance genes are transported out of agroecosystems. Water samples were collected from nine IRFs and one background site (canal water from Snake River) on a biweekly basis during 2018. Escherichia coli and enterococci were enumerated via a most probable number (MPN) technique, then subsamples were plated on selective media to obtain isolates. Isolates of E. coli (187) or enterococci (185) were tested for antimicrobial susceptibility using Sensititre broth microdilution plates. For E. coli, 13% (25/187) of isolates were resistant to tetracycline, with fewer numbers being resistant to 13 other antimicrobials, with none resistant to gentamicin. While 75% (141/187) of the E. coli isolates were pan-susceptible, 12 multidrug resistance (MDR) patterns with 17 isolates exhibiting resistance to up to seven drug classes (10 antimicrobials). For the enterococcal species, only 9% (16/185) of isolates were pan-susceptible and the single highest resistance was to lincomycin (138/185; 75%) followed by nitrofurantoin (56/185; 30%) and quinupristin/dalfopristin (34/185; 18%). In addition, 13 enterococcal isolates belonging to Enterococcus faecalis, Enterococcus faecium, Enterococcus casseliflavus, and Enterococcus thailandicus, were determined to be MDR to up to six different antimicrobial drug classes. None of the enterococcal isolates were resistant to gentamycin, linezolid, tigecycline, and vancomycin.
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Affiliation(s)
- Robert S Dungan
- Northwest Irrigation and Soils Research Laboratory, Agricultural Research Service, United States Department of Agriculture, Kimberly, ID, United States
| | - David L Bjorneberg
- Northwest Irrigation and Soils Research Laboratory, Agricultural Research Service, United States Department of Agriculture, Kimberly, ID, United States
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8
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Deaven AM, Ferreira CM, Reed EA, Chen See JR, Lee NA, Almaraz E, Rios PC, Marogi JG, Lamendella R, Zheng J, Bell RL, Shariat NW. Salmonella Genomics and Population Analyses Reveal High Inter- and Intraserovar Diversity in Freshwater. Appl Environ Microbiol 2021; 87:e02594-20. [PMID: 33397693 PMCID: PMC8104997 DOI: 10.1128/aem.02594-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 12/21/2020] [Indexed: 01/04/2023] Open
Abstract
Freshwater can support the survival of the enteric pathogen Salmonella, though temporal Salmonella diversity in a large watershed has not been assessed. At 28 locations within the Susquehanna River basin, 10-liter samples were assessed in spring and summer over 2 years. Salmonella prevalence was 49%, and increased river discharge was the main driver of Salmonella presence. The amplicon-based sequencing tool, CRISPR-SeroSeq, was used to determine serovar population diversity and detected 25 different Salmonella serovars, including up to 10 serovars from a single water sample. On average, there were three serovars per sample, and 80% of Salmonella-positive samples contained more than one serovar. Serovars Give, Typhimurium, Thompson, and Infantis were identified throughout the watershed and over multiple collections. Seasonal differences were evident: serovar Give was abundant in the spring, whereas serovar Infantis was more frequently identified in the summer. Eight of the ten serovars most commonly associated with human illness were detected in this study. Crucially, six of these serovars often existed in the background, where they were masked by a more abundant serovar(s) in a sample. Serovars Enteritidis and Typhimurium, especially, were masked in 71 and 78% of samples where they were detected, respectively. Whole-genome sequencing-based phylogeny demonstrated that strains within the same serovar collected throughout the watershed were also very diverse. The Susquehanna River basin is the largest system where Salmonella prevalence and serovar diversity have been temporally and spatially investigated, and this study reveals an extraordinary level of inter- and intraserovar diversity.IMPORTANCESalmonella is a leading cause of bacterial foodborne illness in the United States, and outbreaks linked to fresh produce are increasing. Understanding Salmonella ecology in freshwater is of importance, especially where irrigation practices or recreational use occur. As the third largest river in the United States east of the Mississippi, the Susquehanna River is the largest freshwater contributor to the Chesapeake Bay, and it is the largest river system where Salmonella diversity has been studied. Rainfall and subsequent high river discharge rates were the greatest indicators of Salmonella presence in the Susquehanna and its tributaries. Several Salmonella serovars were identified, including eight commonly associated with foodborne illness. Many clinically important serovars were present at a low frequency within individual samples and so could not be detected by conventional culture methods. The technologies employed here reveal an average of three serovars in a 10-liter sample of water and up to 10 serovars in a single sample.
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Affiliation(s)
- Abigail M Deaven
- Department of Population Health, University of Georgia, Athens, Georgia, USA
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania, USA
| | - Christina M Ferreira
- Division of Microbiology, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Elizabeth A Reed
- Division of Microbiology, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | | | - Nora A Lee
- Biology Department, Juniata College, Huntingdon, Pennsylvania, USA
| | - Eduardo Almaraz
- Biology Department, Juniata College, Huntingdon, Pennsylvania, USA
| | - Paula C Rios
- Department of Population Health, University of Georgia, Athens, Georgia, USA
| | - Jacob G Marogi
- Division of Microbiology, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | | | - Jie Zheng
- Division of Microbiology, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Rebecca L Bell
- Division of Microbiology, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Nikki W Shariat
- Department of Population Health, University of Georgia, Athens, Georgia, USA
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9
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Achtman M, Zhou Z, Alikhan NF, Tyne W, Parkhill J, Cormican M, Chiou CS, Torpdahl M, Litrup E, Prendergast DM, Moore JE, Strain S, Kornschober C, Meinersmann R, Uesbeck A, Weill FX, Coffey A, Andrews-Polymenis H, Curtiss 3rd R, Fanning S. Genomic diversity of Salmonella enterica -The UoWUCC 10K genomes project. Wellcome Open Res 2021; 5:223. [PMID: 33614977 PMCID: PMC7869069 DOI: 10.12688/wellcomeopenres.16291.2] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/25/2021] [Indexed: 12/31/2022] Open
Abstract
Background: Most publicly available genomes of Salmonella enterica are from human disease in the US and the UK, or from domesticated animals in the US. Methods: Here we describe a historical collection of 10,000 strains isolated between 1891-2010 in 73 different countries. They encompass a broad range of sources, ranging from rivers through reptiles to the diversity of all S. enterica isolated on the island of Ireland between 2000 and 2005. Genomic DNA was isolated, and sequenced by Illumina short read sequencing. Results: The short reads are publicly available in the Short Reads Archive. They were also uploaded to EnteroBase, which assembled and annotated draft genomes. 9769 draft genomes which passed quality control were genotyped with multiple levels of multilocus sequence typing, and used to predict serovars. Genomes were assigned to hierarchical clusters on the basis of numbers of pair-wise allelic differences in core genes, which were mapped to genetic Lineages within phylogenetic trees. Conclusions: The University of Warwick/University College Cork (UoWUCC) project greatly extends the geographic sources, dates and core genomic diversity of publicly available S. enterica genomes. We illustrate these features by an overview of core genomic Lineages within 33,000 publicly available Salmonella genomes whose strains were isolated before 2011. We also present detailed examinations of HC400, HC900 and HC2000 hierarchical clusters within exemplar Lineages, including serovars Typhimurium, Enteritidis and Mbandaka. These analyses confirm the polyphyletic nature of multiple serovars while showing that discrete clusters with geographical specificity can be reliably recognized by hierarchical clustering approaches. The results also demonstrate that the genomes sequenced here provide an important counterbalance to the sampling bias which is so dominant in current genomic sequencing.
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Affiliation(s)
- Mark Achtman
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Zhemin Zhou
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | | | - William Tyne
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Martin Cormican
- National Salmonella, Shigella and Listeria Reference Laboratory, Galway, H91 YR71, Ireland
| | - Chien-Shun Chiou
- Central Regional Laboratory, Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taichung, None, Taiwan
| | - Mia Torpdahl
- Statens Serum Institut, Copenhagen S, DK-2300, Denmark
| | - Eva Litrup
- Statens Serum Institut, Copenhagen S, DK-2300, Denmark
| | - Deirdre M. Prendergast
- Backweston complex, Department of Agriculture, Food and the Marine (DAFM), Celbridge, Co. Kildare, W23 X3PH, Ireland
| | - John E. Moore
- Northern Ireland Public Health Laboratory, Department of Bacteriology, Belfast City Hospital, Belfast, BT9 7AD, UK
| | - Sam Strain
- Animal Health and Welfare NI, Dungannon, BT71 6JT, UK
| | - Christian Kornschober
- Institute for Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety (AGES), Graz, 8010, Austria
| | - Richard Meinersmann
- US National Poultry Research Center, USDA Agricultural Research Service, Athens, GA, 30605, USA
| | - Alexandra Uesbeck
- Institute for Medical Microbiology, Immunology, and Hygiene, University of Cologne, Cologne, 50935, Germany
| | - François-Xavier Weill
- Unité des bactéries pathogènes entériques, Institut Pasteur, Paris, cedex 15, France
| | - Aidan Coffey
- Cork Institute of Technology, Cork, T12P928, Ireland
| | - Helene Andrews-Polymenis
- Dept. of Microbial Pathogenesis and Immunology, College of Medicine Texas A&M University, Bryan, TX, 77807, USA
| | - Roy Curtiss 3rd
- Dept. of Infectious Diseases & Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, 32611, USA
| | - Séamus Fanning
- UCD-Centre for Food Safety, University College Dublin, Dublin, D04 N2E5, Ireland
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10
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Cho S, Hiott LM, Woodley TA, Frye JG, Jackson CR. Evaluation of a new chromogenic agar for the detection of environmental Enterococcus. J Microbiol Methods 2020; 178:106082. [PMID: 33039542 DOI: 10.1016/j.mimet.2020.106082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/02/2020] [Accepted: 10/03/2020] [Indexed: 11/28/2022]
Abstract
CHROMagar Enterococcus (CHR), a new chromogenic medium not yet available for commercial purchase, was evaluated for the isolation of Enterococcus from environmental water samples. Its performance was evaluated in comparison to commercially available media, Enterococcosel agar and m-Enterococcus agar. Three consecutive tests were conducted with each test being performed with a newer batch of the CHR medium with improved media composition per batch. The recovery rate, positive predictive value, and sensitivity of the CHR medium improved with the subsequent re-formulation of the media components from 93.9%, 63%, and 92.6%, respectively, with the first batch of CHR, to 96.2%, 97.4%, and 95.7%, respectively, with the newest batch of CHR. The results showed that the newer batches of CHR performed better than the previous versions and are comparable to the other two commercial media tested. The CHR medium has been developed to decrease the turnaround time to approximately 18 h and be read more easily due to bigger colony morphology. The superior growth of colonies on CHR compared with other media in a shorter period of time can aid in the early detection of enterococci and may offer a user-friendly alternative to other media for the isolation of enterococci.
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Affiliation(s)
- Sohyun Cho
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, United States Department of Agriculture, Agricultural Research Service, Athens, GA 30605, USA.
| | - Lari M Hiott
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, United States Department of Agriculture, Agricultural Research Service, Athens, GA 30605, USA.
| | - Tiffanie A Woodley
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, United States Department of Agriculture, Agricultural Research Service, Athens, GA 30605, USA.
| | - Jonathan G Frye
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, United States Department of Agriculture, Agricultural Research Service, Athens, GA 30605, USA.
| | - Charlene R Jackson
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, United States Department of Agriculture, Agricultural Research Service, Athens, GA 30605, USA.
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11
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Achtman M, Zhou Z, Alikhan NF, Tyne W, Parkhill J, Cormican M, Chiou CS, Torpdahl M, Litrup E, Prendergast DM, Moore JE, Strain S, Kornschober C, Meinersmann R, Uesbeck A, Weill FX, Coffey A, Andrews-Polymenis H, Curtiss 3rd R, Fanning S. Genomic diversity of Salmonella enterica -The UoWUCC 10K genomes project. Wellcome Open Res 2020; 5:223. [PMID: 33614977 PMCID: PMC7869069 DOI: 10.12688/wellcomeopenres.16291.1] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2020] [Indexed: 01/25/2023] Open
Abstract
Background: Most publicly available genomes of Salmonella enterica are from human disease in the US and the UK, or from domesticated animals in the US. Methods: Here we describe a historical collection of 10,000 strains isolated between 1891-2010 in 73 different countries. They encompass a broad range of sources, ranging from rivers through reptiles to the diversity of all S. enterica isolated on the island of Ireland between 2000 and 2005. Genomic DNA was isolated, and sequenced by Illumina short read sequencing. Results: The short reads are publicly available in the Short Reads Archive. They were also uploaded to EnteroBase, which assembled and annotated draft genomes. 9769 draft genomes which passed quality control were genotyped with multiple levels of multilocus sequence typing, and used to predict serovars. Genomes were assigned to hierarchical clusters on the basis of numbers of pair-wise allelic differences in core genes, which were mapped to genetic Lineages within phylogenetic trees. Conclusions: The University of Warwick/University College Cork (UoWUCC) project greatly extends the geographic sources, dates and core genomic diversity of publicly available S. enterica genomes. We illustrate these features by an overview of core genomic Lineages within 33,000 publicly available Salmonella genomes whose strains were isolated before 2011. We also present detailed examinations of HC400, HC900 and HC2000 hierarchical clusters within exemplar Lineages, including serovars Typhimurium, Enteritidis and Mbandaka. These analyses confirm the polyphyletic nature of multiple serovars while showing that discrete clusters with geographical specificity can be reliably recognized by hierarchical clustering approaches. The results also demonstrate that the genomes sequenced here provide an important counterbalance to the sampling bias which is so dominant in current genomic sequencing.
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Affiliation(s)
- Mark Achtman
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Zhemin Zhou
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | | | - William Tyne
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Martin Cormican
- National Salmonella, Shigella and Listeria Reference Laboratory, Galway, H91 YR71, Ireland
| | - Chien-Shun Chiou
- Central Regional Laboratory, Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taichung, None, Taiwan
| | - Mia Torpdahl
- Statens Serum Institut, Copenhagen S, DK-2300, Denmark
| | - Eva Litrup
- Statens Serum Institut, Copenhagen S, DK-2300, Denmark
| | - Deirdre M. Prendergast
- Backweston complex, Department of Agriculture, Food and the Marine (DAFM), Celbridge, Co. Kildare, W23 X3PH, Ireland
| | - John E. Moore
- Northern Ireland Public Health Laboratory, Department of Bacteriology, Belfast City Hospital, Belfast, BT9 7AD, UK
| | - Sam Strain
- Animal Health and Welfare NI, Dungannon, BT71 6JT, UK
| | - Christian Kornschober
- Institute for Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety (AGES), Graz, 8010, Austria
| | - Richard Meinersmann
- US National Poultry Research Center, USDA Agricultural Research Service, Athens, GA, 30605, USA
| | - Alexandra Uesbeck
- Institute for Medical Microbiology, Immunology, and Hygiene, University of Cologne, Cologne, 50935, Germany
| | - François-Xavier Weill
- Unité des bactéries pathogènes entériques, Institut Pasteur, Paris, cedex 15, France
| | - Aidan Coffey
- Cork Institute of Technology, Cork, T12P928, Ireland
| | - Helene Andrews-Polymenis
- Dept. of Microbial Pathogenesis and Immunology, College of Medicine Texas A&M University, Bryan, TX, 77807, USA
| | - Roy Curtiss 3rd
- Dept. of Infectious Diseases & Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, 32611, USA
| | - Séamus Fanning
- UCD-Centre for Food Safety, University College Dublin, Dublin, D04 N2E5, Ireland
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12
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Meinersmann RJ, Berrang ME, Bradshaw JK, Molina M, Cosby DE, Genzlinger LL, Snyder BJ. Recovery of thermophilic Campylobacter by three sampling methods from river sites in Northeast Georgia, USA, and their antimicrobial resistance genes. Lett Appl Microbiol 2020; 71:102-107. [PMID: 31560126 PMCID: PMC9109067 DOI: 10.1111/lam.13224] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 09/13/2019] [Accepted: 09/18/2019] [Indexed: 02/01/2023]
Abstract
Sixteen sites in the watershed of the South Fork of the Broad River (SFBR) in Northeastern Georgia, USA, were sampled in two seasons to detect Campylobacter. Sites were classified as mostly influenced by forest, pasture, wastewater pollution control plants (WPC) or mixed use. Sampling was repeated in the late spring and late fall for 2 years for a total of 126 samples. Free-catch water and sediment grab samples were taken at each site; Moore's swabs were placed for up to 3 days at most sites. A total of 56 isolates of thermophilic Campylobacter were recovered. Thirteen samplings were positive by two or three methods, and 26 samplings were positive by only one method; once by Moore's swab only and 25 times by free-catch water only. Campylobacter was detected at 58% of cattle pasture sites, 30% of forested sites and 81% of WPC sites. Twenty-one of the isolates carried antimicrobial resistance genes, mostly blaOXA-61. Free-catch water samples were more efficient than Moore's swabs or sediment samples for recovery of Campylobacter, which was more likely to be detected in streams near cattle pastures and human communities than in forested land. SIGNIFICANCE AND IMPACT OF THE STUDY: The role of environmental water in transmitting Campylobacter was investigated, and methods for recovery of the organism were compared. The sequence types of recovered Campylobacter correlated with adjacent land use without regard to the method used to isolate the organisms. Sequence types and antimicrobial resistance genes associated with cattle were most prevalent near pastures. Even though types were recurrent at a given site, types appeared to be lost or replaced as the water flowed downstream.
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Affiliation(s)
| | - M E Berrang
- USDA Agricultural Research Service, Athens, GA, USA
| | - J K Bradshaw
- Environmental Protection Agency, Athens, GA, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA
| | - M Molina
- Environmental Protection Agency, Athens, GA, USA
| | - D E Cosby
- USDA Agricultural Research Service, Athens, GA, USA
| | | | - B J Snyder
- Environmental Protection Agency, Athens, GA, USA
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13
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Cho S, Jackson C, Frye J. The prevalence and antimicrobial resistance phenotypes of
Salmonella
,
Escherichia coli
and
Enterococcus
sp. in surface water. Lett Appl Microbiol 2020; 71:3-25. [DOI: 10.1111/lam.13301] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/09/2020] [Accepted: 04/13/2020] [Indexed: 12/25/2022]
Affiliation(s)
- S. Cho
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit United States Department of Agriculture, Agricultural Research Service Athens GA United States of America
| | - C.R. Jackson
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit United States Department of Agriculture, Agricultural Research Service Athens GA United States of America
| | - J.G. Frye
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit United States Department of Agriculture, Agricultural Research Service Athens GA United States of America
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14
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Cho S, Hiott LM, McDonald JM, Barrett JB, McMillan EA, House SL, Adams ES, Frye JG, Jackson CR. Diversity and antimicrobial resistance of Enterococcus from the Upper Oconee Watershed, Georgia. J Appl Microbiol 2020; 128:1221-1233. [PMID: 31834656 DOI: 10.1111/jam.14550] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 11/15/2019] [Accepted: 12/03/2019] [Indexed: 01/01/2023]
Abstract
AIM It is well-known that enterococci are abundant in the environment; however, the role of surface water as a reservoir of antimicrobial-resistant enterococci remains largely undefined. In this study, surface water samples were collected over a 2-year period from the Upper Oconee watershed, Athens, GA to examine enterococci and their antimicrobial resistance. METHODS AND RESULTS Approximately 97% (445/458) of the samples were positive for enterococci and a total of 637 enterococci were isolated. The predominant species were Enterococcus casseliflavus (33·6%) followed by Enterococcus faecalis (26·5%) and Enterococcus hirae (13·2%). Regardless of species, the highest levels of resistance were to lincomycin (88·5%) and tetracycline (13%); isolates also exhibited resistance to newer antimicrobials, daptomycin (8·9%) and tigecycline (6·4%). Multidrug resistance (resistance ≥3 antimicrobial classes) was observed to as many as five classes of antimicrobials. Resistant enterococci appeared to be randomly dispersed over the seasons rather than clustered by species or antimicrobial resistance. CONCLUSIONS This study demonstrated that surface waters contain a large population of diverse species of antimicrobial-resistant enterococci, including resistance to new antimicrobials. SIGNIFICANCE AND IMPACT OF THE STUDY These results may indicate the potential of human intestinal illness and/or colonization of the human gut with resistant enterococci as enterococci correlate with increased disease risk to humans during recreational exposure to water.
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Affiliation(s)
- S Cho
- Department of Microbiology, University of Georgia, Athens, GA, USA
| | - L M Hiott
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, USDA-ARS Russell Research Center, Athens, GA, USA
| | - J M McDonald
- Lewis F. Rogers Institute for Environmental and Spatial Analysis, University of North Georgia, Oakwood, GA, USA
| | - J B Barrett
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, USDA-ARS Russell Research Center, Athens, GA, USA
| | - E A McMillan
- Department of Microbiology, University of Georgia, Athens, GA, USA
| | - S L House
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, USDA-ARS Russell Research Center, Athens, GA, USA
| | - E S Adams
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, USDA-ARS Russell Research Center, Athens, GA, USA
| | - J G Frye
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, USDA-ARS Russell Research Center, Athens, GA, USA
| | - C R Jackson
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, USDA-ARS Russell Research Center, Athens, GA, USA
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15
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Cho S, Hiott LM, Barrett JB, McMillan EA, House SL, Humayoun SB, Adams ES, Jackson CR, Frye JG. Prevalence and characterization of Escherichia coli isolated from the Upper Oconee Watershed in Northeast Georgia. PLoS One 2018; 13:e0197005. [PMID: 29738574 PMCID: PMC5940194 DOI: 10.1371/journal.pone.0197005] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 04/24/2018] [Indexed: 01/06/2023] Open
Abstract
Surface waters are important sources of water for drinking, industrial, agricultural, and recreational uses; hence, contamination of water by fecal, pathogenic, or antimicrobial resistant (AR) bacteria is a major environmental and public health concern. However, very little data is available on prevalence of these bacteria in surface water throughout a watershed. This study aimed to characterize Escherichia coli present in the Upper Oconee Watershed, a mixed-use watershed in Athens, GA, USA for potential pathogenicity and AR. E. coli were enumerated by colony counts, cultured by enrichment and direct plating, and characterized by phylo-groups, diarrheagenic pathotypes, and antimicrobial susceptibility. From the analysis, 99.3% (455/458) of the total samples were positive for E. coli resulting in 496 isolates. E. coli counts were as high as 1.2×104 CFU/100 ml, which is above the United States Environmental Protection Agency (U.S. EPA) threshold for recreational water (235 CFU/100 ml based on a one-time measurement). Phylo-groups B2 (31.7%; 157/496) and B1 (30.8%; 153/496) were the most prevalent among the isolates. Enteropathogenic E. coli (EPEC) (19/496) and Shiga toxin-producing E. coli (STEC) (1/496) were the only diarrheagenic pathotypes detected. AR was observed in 6.9% (34/496) of the isolates, 15 of which were multidrug resistant (MDR; resistance to two or more classes of antimicrobials). Tetracycline resistance was most often detected (76.5%; 26/34), followed by ampicillin (32.4%; 11/34), streptomycin (23.5%; 8/34), sulfisoxazole (23.5%; 8/34), and nalidixic acid (14.7%; 5/34). Results from this study showed that E. coli is prevalent in high levels in the Upper Oconee Watershed, suggesting possible widespread fecal contamination. The presence of pathogenic, AR E. coli in the watershed indicates that environmental water can serve as a reservoir of resistant bacteria that may be transferred to humans through drinking and recreational activities.
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Affiliation(s)
- Sohyun Cho
- Department of Microbiology, University of Georgia, Athens, Georgia, United States of America
| | - Lari M. Hiott
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, United States Department of Agriculture, Agricultural Research Service, Athens, Georgia, United States of America
| | - John B. Barrett
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, United States Department of Agriculture, Agricultural Research Service, Athens, Georgia, United States of America
| | - Elizabeth A. McMillan
- Department of Microbiology, University of Georgia, Athens, Georgia, United States of America
| | - Sandra L. House
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, United States Department of Agriculture, Agricultural Research Service, Athens, Georgia, United States of America
| | - Shaheen B. Humayoun
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, United States Department of Agriculture, Agricultural Research Service, Athens, Georgia, United States of America
| | - Eric S. Adams
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, United States Department of Agriculture, Agricultural Research Service, Athens, Georgia, United States of America
| | - Charlene R. Jackson
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, United States Department of Agriculture, Agricultural Research Service, Athens, Georgia, United States of America
| | - Jonathan G. Frye
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, United States Department of Agriculture, Agricultural Research Service, Athens, Georgia, United States of America
- * E-mail:
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16
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Hernandez SM, Welch CN, Peters VE, Lipp EK, Curry S, Yabsley MJ, Sanchez S, Presotto A, Gerner-Smidt P, Hise KB, Hammond E, Kistler WM, Madden M, Conway AL, Kwan T, Maurer JJ. Urbanized White Ibises (Eudocimus albus) as Carriers of Salmonella enterica of Significance to Public Health and Wildlife. PLoS One 2016; 11:e0164402. [PMID: 27768705 PMCID: PMC5074519 DOI: 10.1371/journal.pone.0164402] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 09/23/2016] [Indexed: 11/18/2022] Open
Abstract
Worldwide, Salmonella spp. is a significant cause of disease for both humans and wildlife, with wild birds adapted to urban environments having different opportunities for pathogen exposure, infection, and transmission compared to their natural conspecifics. Food provisioning by people may influence these factors, especially when high-density mixed species flocks aggregate. White Ibises (Eudocimus albus), an iconic Everglades species in decline in Florida, are becoming increasingly common in urbanized areas of south Florida where most are hand-fed. We examined the prevalence of Salmonella shedding by ibises to determine the role of landscape characteristics where ibis forage and their behavior, on shedding rates. We also compared Salmonella isolated from ibises to human isolates to better understand non-foodborne human salmonellosis. From 2010-2013, 13% (n = 261) adult/subadult ibises and 35% (n = 72) nestlings sampled were shedding Salmonella. The prevalence of Salmonella shedding by ibises significantly decreased as the percent of Palustrine emergent wetlands and herbaceous grasslands increased, and increased as the proportion of open-developed land types (e.g. parks, lawns, golf courses) increased, suggesting that natural ecosystem land cover types supported birds with a lower prevalence of infection. A high diversity of Salmonella serotypes (n = 24) and strain types (43 PFGE types) were shed by ibises, of which 33% of the serotypes ranked in the top 20 of high significance for people in the years of the study. Importantly, 44% of the Salmonella Pulsed-Field Gel Electrophoresis patterns for ibis isolates (n = 43) matched profiles in the CDC PulseNet USA database. Of these, 20% came from Florida in the same three years we sampled ibis. Importantly, there was a negative relationship between the amount of Palustrine emergent wetland and the number of Salmonella isolates from ibises that matched human cases in the PulseNet database (p = 0.056). Together, our results indicate that ibises are good indicators of salmonellae strains circulating in their environment and they have both the potential and opportunity to transmit salmonellae to people. Finally, they may act as salmonellae carriers to natural environments where other more highly-susceptible groups (nestlings) may be detrimentally affected.
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Affiliation(s)
- Sonia M. Hernandez
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, United States of America
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Catharine N. Welch
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, United States of America
| | - Valerie E. Peters
- Institute for Environment and Sustainability, Department of Zoology, Miami University, Columbia, Ohio, United States of America
| | - Erin K. Lipp
- Department of Environmental Health Science, University of Georgia, Athens, Georgia, United States of America
| | - Shannon Curry
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, United States of America
| | - Michael J. Yabsley
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, United States of America
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Susan Sanchez
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Andrea Presotto
- Department of Geography, University of Georgia, Athens, Georgia, United States of America
| | - Peter Gerner-Smidt
- Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, Georgia, United States of America
| | - Kelley B. Hise
- Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, Georgia, United States of America
| | - Elizabeth Hammond
- Lion Country Safari Park, Loxahatchee, Florida, United States of America
| | - Whitney M. Kistler
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Marguerite Madden
- Department of Geography, University of Georgia, Athens, Georgia, United States of America
| | - April L. Conway
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, United States of America
| | - Tiffany Kwan
- Poultry Diagnostic and Research Center, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - John J. Maurer
- Poultry Diagnostic and Research Center, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
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17
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Bradshaw JK, Snyder BJ, Oladeinde A, Spidle D, Berrang ME, Meinersmann RJ, Oakley B, Sidle RC, Sullivan K, Molina M. Characterizing relationships among fecal indicator bacteria, microbial source tracking markers, and associated waterborne pathogen occurrence in stream water and sediments in a mixed land use watershed. WATER RESEARCH 2016; 101:498-509. [PMID: 27295624 DOI: 10.1016/j.watres.2016.05.014] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 03/31/2016] [Accepted: 05/03/2016] [Indexed: 06/06/2023]
Abstract
Bed sediments of streams and rivers may store high concentrations of fecal indicator bacteria (FIB) and pathogens. Due to resuspension events, these contaminants can be mobilized into the water column and affect overall water quality. Other bacterial indicators such as microbial source tracking (MST) markers, developed to determine potential sources of fecal contamination, can also be resuspended from bed sediments. The primary objective of this study was to predict occurrence of waterborne pathogens in water and streambed sediments using a simple statistical model that includes traditionally measured FIB, environmental parameters and source allocation, using MST markers as predictor variables. Synoptic sampling events were conducted during baseflow conditions downstream from agricultural (AG), forested (FORS), and wastewater pollution control plant (WPCP) land uses. Concentrations of FIB and MST markers were measured in water and sediments, along with occurrences of the enteric pathogens Campylobacter, Listeria and Salmonella, and the virulence gene that carries Shiga toxin, stx2. Pathogens were detected in water more often than in underlying sediments. Shiga toxin was significantly related to land use, with concentrations of the ruminant marker selected as an independent variable that could correctly classify 76% and 64% of observed Shiga toxin occurrences in water and sediment, respectively. FIB concentrations and water quality parameters were also selected as independent variables that correctly classified Shiga toxin occurrences in water and sediment (54%-87%), and Salmonella occurrences in water (96%). Relationships between pathogens and indicator variables were generally inconsistent and no single indicator adequately described occurrence of all pathogens. Because of inconsistent relationships between individual pathogens and FIB/MST markers, incorporating a combination of FIB, water quality measurements, and MST markers may be the best way to assess microbial water quality in mixed land use systems.
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Affiliation(s)
- J Kenneth Bradshaw
- Oak Ridge Institute for Science and Education, P.O. Box 117, Oak Ridge, TN 37831, USA; Ecosystems Research Division, Office of Research and Development, National Exposure Research Laboratory, U.S. Environmental Protection Agency, 960 College Station RD, Athens, GA 30605, USA
| | - Blake J Snyder
- Oak Ridge Institute for Science and Education, P.O. Box 117, Oak Ridge, TN 37831, USA; Ecosystems Research Division, Office of Research and Development, National Exposure Research Laboratory, U.S. Environmental Protection Agency, 960 College Station RD, Athens, GA 30605, USA
| | - Adelumola Oladeinde
- Ecosystems Research Division, Office of Research and Development, National Exposure Research Laboratory, U.S. Environmental Protection Agency, 960 College Station RD, Athens, GA 30605, USA
| | - David Spidle
- Ecosystems Research Division, Office of Research and Development, National Exposure Research Laboratory, U.S. Environmental Protection Agency, 960 College Station RD, Athens, GA 30605, USA
| | - Mark E Berrang
- Agricultural Research Service, U.S. Department of Agriculture, 950 College Station RD, Athens, GA 30605, USA
| | - Richard J Meinersmann
- Agricultural Research Service, U.S. Department of Agriculture, 950 College Station RD, Athens, GA 30605, USA
| | - Brian Oakley
- Western University of Health Sciences, College of Veterinary Medicine, 309 E. 2nd St, Pomona, CA 91711, USA
| | - Roy C Sidle
- University of the Sunshine Coast, Sustainability Research Centre, 90 Sippy Downs Drive, Sippy Downs, Queensland 4556, Australia
| | - Kathleen Sullivan
- Ecosystems Research Division, Office of Research and Development, National Exposure Research Laboratory, U.S. Environmental Protection Agency, 960 College Station RD, Athens, GA 30605, USA
| | - Marirosa Molina
- Ecosystems Research Division, Office of Research and Development, National Exposure Research Laboratory, U.S. Environmental Protection Agency, 960 College Station RD, Athens, GA 30605, USA.
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Maurer JJ, Martin G, Hernandez S, Cheng Y, Gerner-Smidt P, Hise KB, Tobin D’Angelo M, Cole D, Sanchez S, Madden M, Valeika S, Presotto A, Lipp EK. Diversity and Persistence of Salmonella enterica Strains in Rural Landscapes in the Southeastern United States. PLoS One 2015; 10:e0128937. [PMID: 26131552 PMCID: PMC4489491 DOI: 10.1371/journal.pone.0128937] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 05/01/2015] [Indexed: 11/22/2022] Open
Abstract
Salmonellosis cases in the in the United States show distinct geographical trends, with the southeast reporting among the highest rates of illness. In the state of Georgia, USA, non-outbreak associated salmonellosis is especially high in the southern low-lying coastal plain. Here we examined the distribution of Salmonella enterica in environmental waters and associated wildlife in two distinct watersheds, one in the Atlantic Coastal Plain (a high case rate rural area) physiographic province and one in the Piedmont (a lower case rate rural area). Salmonella were isolated from the two regions and compared for serovar and strain diversity, as well as distribution, between the two study areas, using both a retrospective and prospective design. Thirty-seven unique serovars and 204 unique strain types were identified by pulsed-field gel electrophoresis (PFGE). Salmonella serovars Braenderup, Give, Hartford, and Muenchen were dominant in both watersheds. Two serovars, specifically S. Muenchen and S. Rubislaw, were consistently isolated from both systems, including water and small mammals. Conversely, 24 serovars tended to be site-specific (64.8%, n = 37). Compared to the other Salmonella serovars isolated from these sites, S. Muenchen and S. Rubislaw exhibited significant genetic diversity. Among a subset of PFGE patterns, approximately half of the environmental strain types matched entries in the USA PulseNet database of human cases. Ninety percent of S. Muenchen strains from the Little River basin (the high case rate area) matched PFGE entries in PulseNet compared to 33.33% of S. Muenchen strains from the North Oconee River region (the lower case rate area). Underlying the diversity and turnover of Salmonella strains observed for these two watersheds is the persistence of specific Salmonella serovars and strain types that may be adapted to these watersheds and landscapes.
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Affiliation(s)
- John J. Maurer
- Department of Population Health, University of Georgia, Athens, Georgia, United States of America
| | - Gordon Martin
- Department of Environmental Health Science, University of Georgia, Athens, Georgia, United States of America
| | - Sonia Hernandez
- Department of Population Health, University of Georgia, Athens, Georgia, United States of America
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, United States of America
| | - Ying Cheng
- Department of Population Health, University of Georgia, Athens, Georgia, United States of America
| | - Peter Gerner-Smidt
- Centers for Disease and Control and Prevention, Atlanta, Georgia, United States of America
| | - Kelley B. Hise
- Centers for Disease and Control and Prevention, Atlanta, Georgia, United States of America
| | | | - Dana Cole
- Department of Environmental Health Science, University of Georgia, Athens, Georgia, United States of America
- Centers for Disease and Control and Prevention, Atlanta, Georgia, United States of America
| | - Susan Sanchez
- Department of Infectious Diseases, University of Georgia, Athens, Georgia, United States of America
| | - Marguerite Madden
- Department of Geography, University of Georgia, Athens, Georgia, United States of America
| | - Steven Valeika
- Department of Epidemiology and Biostatistics, University of Georgia, Athens, Georgia, United States of America
| | - Andrea Presotto
- Department of Geography, University of Georgia, Athens, Georgia, United States of America
| | - Erin K. Lipp
- Department of Environmental Health Science, University of Georgia, Athens, Georgia, United States of America
- * E-mail:
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Meinersmann RJ, Berrang ME, Little E. Campylobacter spp. recovered from the Upper Oconee River Watershed, Georgia in a 4-year study. MICROBIAL ECOLOGY 2013; 65:22-27. [PMID: 22945232 DOI: 10.1007/s00248-012-0117-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Accepted: 08/14/2012] [Indexed: 06/01/2023]
Abstract
Waterways should be considered in the migration routes of Campylobacter, and the genus has been isolated from several water sources. Inferences on migration routes can be made from tracking genetic types in populations found in specific habitats and testing how they are linked to other types. Water samples were taken over a 4-year period from waterways in the Upper Oconee River Watershed, Georgia, to recover isolates of thermophilic Campylobacter. The isolates were typed by multilocus sequence typing (MLST) and analyzed to determine the overall diversity of Campylobacter in that environment. Forty-seven independent isolates were recovered from 560 samples (8.4 %). Two (~4 %) isolates were Campylobacter coli, three (~6 %) isolates were putatively identified as Campylobacter lari, and the remaining 42 (~90 %) were Campylobacter jejuni. The C. jejuni and C. coli isolates were typed by the Oxford MLST scheme. Thirty sequence types (STs) were identified including 13 STs that were not found before in the MLST database, including 24 novel alleles. Of the 17 previously described STs, 10 have been isolated from humans, 6 from environmental water, and 6 from wild birds (five types from multiple sources). Seven sites had multiple positive samples, and on two occasions, the same ST was isolated at the same site. The most common type was STST61 with four isolates, and the most common clonal complex was CC179 with nine isolates. CC179 has been commonly associated with environmental water. Although some Campylobacter STs that were found in the Oconee River engage in widespread migration, most are tightly associated with or unique to environmental water sources.
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Affiliation(s)
- R J Meinersmann
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, Russell Research Center, USDA Agricultural Research Service, 950 College Station Rd, Athens, GA 30605, USA.
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Levantesi C, Bonadonna L, Briancesco R, Grohmann E, Toze S, Tandoi V. Salmonella in surface and drinking water: Occurrence and water-mediated transmission. Food Res Int 2012. [DOI: 10.1016/j.foodres.2011.06.037] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Lanthier M, Scott A, Zhang Y, Cloutier M, Durie D, Henderson V, Wilkes G, Lapen D, Topp E. Distribution of selected virulence genes and antibiotic resistance in Enterococcus species isolated from the South Nation River drainage basin, Ontario, Canada. J Appl Microbiol 2010; 110:407-21. [DOI: 10.1111/j.1365-2672.2010.04893.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Salmonella infections in the common raccoon (Procyon lotor) in western Pennsylvania. J Clin Microbiol 2008; 46:3084-6. [PMID: 18596136 DOI: 10.1128/jcm.00685-08] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ten Salmonella enterica serotypes were isolated from fecal samples collected from anesthetized raccoons (n = 738) trapped in six Pennsylvania counties from 2003 to 2005. Comparison of raccoon pulsed-field gel electrophoresis (PFGE) pulse type data with the Pennsylvania Department of Health PFGE database revealed that the patterns of seven Salmonella serotypes matched those isolated from humans with salmonellosis.
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