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Mullally CA, Fahriani M, Mowlaboccus S, Coombs GW. Non- faecium non- faecalis enterococci: a review of clinical manifestations, virulence factors, and antimicrobial resistance. Clin Microbiol Rev 2024; 37:e0012123. [PMID: 38466110 DOI: 10.1128/cmr.00121-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2024] Open
Abstract
SUMMARYEnterococci are a diverse group of Gram-positive bacteria that are typically found as commensals in humans, animals, and the environment. Occasionally, they may cause clinically relevant diseases such as endocarditis, septicemia, urinary tract infections, and wound infections. The majority of clinical infections in humans are caused by two species: Enterococcus faecium and Enterococcus faecalis. However, there is an increasing number of clinical infections caused by non-faecium non-faecalis (NFF) enterococci. Although NFF enterococcal species are often overlooked, studies have shown that they may harbor antimicrobial resistance (AMR) genes and virulence factors that are found in E. faecium and E. faecalis. In this review, we present an overview of the NFF enterococci with a particular focus on human clinical manifestations, epidemiology, virulence genes, and AMR genes.
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Affiliation(s)
- Christopher A Mullally
- Antimicrobial Resistance and Infectious Diseases (AMRID) Research Laboratory, Murdoch University, Murdoch, Western Australia, Australia
- The Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Marhami Fahriani
- Antimicrobial Resistance and Infectious Diseases (AMRID) Research Laboratory, Murdoch University, Murdoch, Western Australia, Australia
| | - Shakeel Mowlaboccus
- Antimicrobial Resistance and Infectious Diseases (AMRID) Research Laboratory, Murdoch University, Murdoch, Western Australia, Australia
- The Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, Australia
- PathWest Laboratory Medicine-WA, Department of Microbiology, Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - Geoffrey W Coombs
- Antimicrobial Resistance and Infectious Diseases (AMRID) Research Laboratory, Murdoch University, Murdoch, Western Australia, Australia
- The Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, Australia
- PathWest Laboratory Medicine-WA, Department of Microbiology, Fiona Stanley Hospital, Murdoch, Western Australia, Australia
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2
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Leopold M, Kabicher A, Pap IJ, Ströbele B, Zarfel G, Farnleitner AH, Kirschner AKT. A comparative study on antibiotic resistant Escherichia coli isolates from Austrian patients and wastewater-influenced Danube River water and biofilms. Int J Hyg Environ Health 2024; 258:114361. [PMID: 38552533 DOI: 10.1016/j.ijheh.2024.114361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 03/04/2024] [Accepted: 03/22/2024] [Indexed: 04/06/2024]
Abstract
Antimicrobial resistance (AMR) poses a major threat to human health worldwide. AMR can be introduced into natural aquatic ecosystems, for example, from clinical facilities via wastewater emissions. Understanding AMR patterns in environmental populations of bacterial pathogens is important to elucidate propagation routes and develop mitigation strategies. In this study, AMR patterns of Escherichia coli isolates from urinary tract infections and colonised urinary catheters of inpatients and outpatients were compared to isolates from the Danube River within the same catchment in Austria to potentially link environmental with clinical resistance patterns. Susceptibility to 20 antibiotics was tested for 697 patient, 489 water and 440 biofilm isolates. The resistance ratios in patient isolates were significantly higher than in the environmental isolates and higher resistance ratios were found in biofilm in comparison to water isolates. The role of the biofilm as potential sink of resistances was reflected by two extended-spectrum beta-lactamase (ESBL) producing isolates in the biofilm while none were found in water, and by higher amoxicillin/clavulanic acid resistance ratios in biofilm compared to patient isolates. Although, resistances to last-line antibiotics such as carbapenems and tigecycline were found in the patient and in the environmental isolates, they still occurred at low frequency.
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Affiliation(s)
- Melanie Leopold
- Division Water Quality and Health, Department Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Krems, Austria; Institute for Chemical, Environmental and Bioscience Engineering, Research Group Microbiology and Molecular Diagnostics, Technische Universität Wien, Vienna, Austria
| | - Angelika Kabicher
- Division Water Quality and Health, Department Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Krems, Austria; Institute for Chemical, Environmental and Bioscience Engineering, Research Group Microbiology and Molecular Diagnostics, Technische Universität Wien, Vienna, Austria
| | - Ildiko-Julia Pap
- Clinical Institute for Hygiene and Microbiology, University Clinic St. Pölten, Austria
| | - Barbara Ströbele
- Clinical Institute for Hygiene and Microbiology, University Clinic St. Pölten, Austria
| | - Gernot Zarfel
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Austria
| | - Andreas H Farnleitner
- Division Water Quality and Health, Department Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Krems, Austria; Institute for Chemical, Environmental and Bioscience Engineering, Research Group Microbiology and Molecular Diagnostics, Technische Universität Wien, Vienna, Austria
| | - Alexander K T Kirschner
- Division Water Quality and Health, Department Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Krems, Austria; Institute for Hygiene and Applied Immunology - Water Microbiology, Medical University Vienna, Austria.
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3
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Lin C, Feng Y, Xie X, Zhang H, Wu J, Zhu Y, Yu J, Feng J, Su W, Lai S, Zhang A. Antimicrobial resistance characteristics and phylogenetic relationships of pleuromutilin-resistant Enterococcus isolates from different environmental samples along a laying hen production chain. J Environ Sci (China) 2024; 137:195-205. [PMID: 37980008 DOI: 10.1016/j.jes.2023.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 01/10/2023] [Accepted: 01/12/2023] [Indexed: 11/20/2023]
Abstract
Antimicrobial resistance in the laying hen production industry has become a serious public health problem. The antimicrobial resistance and phylogenetic relationships of the common conditional pathogen Enterococcus along the laying hen production chain have not been systematically clarified. 105 Enterococcus isolates were obtained from 115 environmental samples (air, dust, feces, flies, sewage, and soil) collected along the laying hen production chain (breeding chicken, chick, young chicken, and commercial laying hen). These Enterococcus isolates exhibited resistance to some clinically relevant antibiotics, such as tetracycline (92.4%), streptomycin (92.4%), and erythromycin (91.4%), and all strains had multidrug resistance phenotypes. Whole genome sequencing characterized 29 acquired antibiotic resistance genes (ARGs) that conferred resistance to 11 classes of antibiotics in 51 pleuromutilin-resistant Enterococcus isolates, and lsa(E), which mediates resistance to pleuromutilins, always co-occurred with lnu(B). Alignments with the Mobile Genetic Elements database identified four transposons (Tn554, Tn558, Tn6261, and Tn6674) with several ARGs (erm(A), ant(9)-la, fex(A), and optrA) that mediated resistance to many clinically important antibiotics. Moreover, we identified two new transposons that carried ARGs in the Tn554 family designated as Tn7508 and Tn7492. A complementary approach based on conventional multi-locus sequence typing and whole genome single nucleotide polymorphism analysis showed that phylogenetically related pleuromutilin-resistant Enterococcus isolates were widely distributed in various environments on different production farms. Our results indicate that environmental contamination by antimicrobial-resistant Enterococcus requires greater attention, and they highlight the risk of pleuromutilin-resistant Enterococcus and ARGs disseminating along the laying hen production chain, thereby warranting effective disinfection.
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Affiliation(s)
- Cong Lin
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yuxuan Feng
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Xianjun Xie
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Haoyu Zhang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Jie Wu
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yixiao Zhu
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Jing Yu
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Jingyi Feng
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Wen Su
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Shanming Lai
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Anyun Zhang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China.
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4
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Cho S, Hiott LM, Read QD, Damashek J, Westrich J, Edwards M, Seim RF, Glinski DA, Bateman McDonald JM, Ottesen EA, Lipp EK, Henderson WM, Jackson CR, Frye JG. Distribution of Antibiotic Resistance in a Mixed-Use Watershed and the Impact of Wastewater Treatment Plants on Antibiotic Resistance in Surface Water. Antibiotics (Basel) 2023; 12:1586. [PMID: 37998788 PMCID: PMC10668835 DOI: 10.3390/antibiotics12111586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/28/2023] [Accepted: 10/31/2023] [Indexed: 11/25/2023] Open
Abstract
The aquatic environment has been recognized as a source of antibiotic resistance (AR) that factors into the One Health approach to combat AR. To provide much needed data on AR in the environment, a comprehensive survey of antibiotic-resistant bacteria (ARB), antibiotic resistance genes (ARGs), and antibiotic residues was conducted in a mixed-use watershed and wastewater treatment plants (WWTPs) within the watershed to evaluate these contaminants in surface water. A culture-based approach was used to determine prevalence and diversity of ARB in surface water. Low levels of AR Salmonella (9.6%) and Escherichia coli (6.5%) were detected, while all Enterococcus were resistant to at least one tested antibiotic. Fewer than 20% of extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae (17.3%) and carbapenem-resistant Enterobacteriaceae (CRE) (7.7%) were recovered. Six ARGs were detected using qPCR, primarily the erythromycin-resistance gene, ermB. Of the 26 antibiotics measured, almost all water samples (98.7%) had detectable levels of antibiotics. Analysis of wastewater samples from three WWTPs showed that WWTPs did not completely remove AR contaminants. ARGs and antibiotics were detected in all the WWTP effluent discharges, indicating that WWTPs are the source of AR contaminants in receiving water. However, no significant difference in ARGs and antibiotics between the upstream and downstream water suggests that there are other sources of AR contamination. The widespread occurrence and abundance of medically important antibiotics, bacteria resistant to antibiotics used for human and veterinary purposes, and the genes associated with resistance to these antibiotics, may potentially pose risks to the local populations exposed to these water sources.
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Affiliation(s)
- Sohyun Cho
- Poultry Microbiological Safety and Processing Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA 30605, USA; (S.C.); (L.M.H.); (C.R.J.)
- Oak Ridge Institute for Science and Education, Oak Ridge, TN 37830, USA;
| | - Lari M. Hiott
- Poultry Microbiological Safety and Processing Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA 30605, USA; (S.C.); (L.M.H.); (C.R.J.)
| | - Quentin D. Read
- Agricultural Research Service, U.S. Department of Agriculture, Southeast Area, Raleigh, NC 27606, USA;
| | - Julian Damashek
- Department of Biology, Utica University, Utica, NY 13502, USA;
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA; (J.W.); (E.A.O.)
| | - Jason Westrich
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA; (J.W.); (E.A.O.)
| | - Martinique Edwards
- Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA; (M.E.); (E.K.L.)
| | - Roland F. Seim
- Oak Ridge Institute for Science and Education, Oak Ridge, TN 37830, USA;
- Center for Environmental Measurement and Modeling, Office of Research and Development, U.S. Environmental Protection Agency, Athens, GA 30605, USA; (D.A.G.); (W.M.H.)
| | - Donna A. Glinski
- Center for Environmental Measurement and Modeling, Office of Research and Development, U.S. Environmental Protection Agency, Athens, GA 30605, USA; (D.A.G.); (W.M.H.)
| | - Jacob M. Bateman McDonald
- Lewis F. Rogers Institute for Environmental and Spatial Analysis, University of North Georgia, Oakwood, GA 30566, USA;
| | - Elizabeth A. Ottesen
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA; (J.W.); (E.A.O.)
| | - Erin K. Lipp
- Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA; (M.E.); (E.K.L.)
| | - William Matthew Henderson
- Center for Environmental Measurement and Modeling, Office of Research and Development, U.S. Environmental Protection Agency, Athens, GA 30605, USA; (D.A.G.); (W.M.H.)
| | - Charlene R. Jackson
- Poultry Microbiological Safety and Processing Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA 30605, USA; (S.C.); (L.M.H.); (C.R.J.)
| | - Jonathan G. Frye
- Poultry Microbiological Safety and Processing Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA 30605, USA; (S.C.); (L.M.H.); (C.R.J.)
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5
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Davis BC, Keenum I, Calarco J, Liguori K, Milligan E, Pruden A, Harwood VJ. Towards the standardization of Enterococcus culture methods for waterborne antibiotic resistance monitoring: A critical review of trends across studies. WATER RESEARCH X 2022; 17:100161. [PMID: 36466738 PMCID: PMC9712764 DOI: 10.1016/j.wroa.2022.100161] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 11/15/2022] [Accepted: 11/17/2022] [Indexed: 06/17/2023]
Abstract
Antibiotic resistance is a major 21st century One Health (humans, animals, environment) challenge whose spread limits options to treat bacterial infections. There is growing interest in monitoring water environments, including surface water and wastewater, which have been identified as key recipients, pathways, and sources of antibiotic resistant bacteria (ARB). Aquatic environments also facilitate the transmission and amplification of ARB. Enterococcus spp. often carry clinically-important antibiotic resistance genes and are of interest as environmental monitoring targets. Enterococcus spp. are Gram-positive bacteria that are typically of fecal origin; however, they are also found in relevant environmental niches, with various species and strains that are opportunistic human pathogens. Although the value of environmental monitoring of antibiotic-resistant Enterococcus has been recognized by both national and international organizations, lack of procedural standardization has hindered generation of comparable data needed to implement integrated surveillance programs. Here we provide a comprehensive methodological review to assess the techniques used for the culturing and characterization of antibiotic-resistant Enterococcus across water matrices for the purpose of environmental monitoring. We analyzed 117 peer-reviewed articles from 33 countries across six continents. The goal of this review is to provide a critical analysis of (i) the various methods applied globally for isolation, confirmation, and speciation of Enterococcus isolates, (ii) the different methods for profiling antibiotic resistance among enterococci, and (iii) the current prevalence of resistance to clinically-relevant antibiotics among Enterococcus spp. isolated from various environments. Finally, we provide advice regarding a path forward for standardizing culturing of Enterococcus spp. for the purpose of antibiotic resistance monitoring in wastewater and wastewater-influenced waters within a global surveillance framework.
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Affiliation(s)
- Benjamin C. Davis
- Via Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia
| | - Ishi Keenum
- Via Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia
| | - Jeannette Calarco
- Department of Integrative Biology, University of South Florida, Tampa, Florida
| | - Krista Liguori
- Via Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia
| | - Erin Milligan
- Via Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia
| | - Amy Pruden
- Via Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia
| | - Valerie J. Harwood
- Department of Integrative Biology, University of South Florida, Tampa, Florida
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6
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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: 11] [Impact Index Per Article: 5.5] [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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Agga GE, Silva PJ, Martin RS. Tetracycline- and Macrolide-Resistant Enterococcus Species Isolated from a Mink Farm in the United States. Microb Drug Resist 2022; 28:734-743. [PMID: 35575717 DOI: 10.1089/mdr.2021.0438] [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: 12/27/2022] Open
Abstract
Enterococcus species are a normal flora of animals and humans. However, life-threatening opportunistic infections can be caused by antimicrobial resistant strains. Fecal (n = 42) and feed (n = 8) samples were obtained from a mink farm and cultured for the enumeration and detection of erythromycin-resistant (a macrolide; ERYr)- and tetracycline-resistant (TETr) enterococci. ERYr and TETr enterococci were detected from all fecal (mean concentrations = 6 and 7 logs, respectively) and feed (mean concentrations = 5 and 4 logs, respectively) samples. While Enterococcus faecalis and Enterococcus faecium were detected at equal proportions among the fecal TETr isolates, E. faecium predominated among ERYr fecal isolates. All ERYr and 90% of the TETr isolates (n = 50) were multidrug resistant (resistant to three or more antimicrobial classes). Among ERYr isolates, while 83% of E. faecalis (n = 12) were positive for erm(B), 58% of E. faecium (n = 38) isolates were positive for msr(C). Among ERYr isolates, tet(M) was detected from 92% of E. faecalis (n = 12) and 97% of E. faecium (n = 38) isolates. Conversely, however, erm(B) was detected in 18% of E. faecalis (n = 22) and 33% of E. faecium (n = 27) TETr isolates. Our study provides a baseline for future efforts to reduce antimicrobial resistance and improve antimicrobial stewardship in commercial mink production facilities.
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Affiliation(s)
- Getahun E Agga
- Food Animal Environmental Systems Research Unit, Agricultural Research Service, United States Department of Agriculture (USDA), Bowling Green, Kentucky, USA
| | - Philip J Silva
- Food Animal Environmental Systems Research Unit, Agricultural Research Service, United States Department of Agriculture (USDA), Bowling Green, Kentucky, USA
| | - Randal S Martin
- Utah Water Research Laboratory, Department of Civil and Environmental Engineering, Utah State University, Logan, Utah, USA
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Solaiman S, Patterson R, Davey K, Katz Y, Payne-Sturges D, R Sapkota A, Micallef SA. Effects of season and water type on the distribution and antimicrobial resistance of Enterococcus faecalis and E. faecium from surface and reclaimed water. J Appl Microbiol 2022; 133:477-487. [PMID: 35396758 DOI: 10.1111/jam.15570] [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] [Received: 03/03/2022] [Revised: 04/04/2022] [Accepted: 04/05/2022] [Indexed: 11/30/2022]
Abstract
AIMS To evaluate the safety of irrigation water sources based on phenotypic antimicrobial resistance (AMR) in Enterococcus spp., a potential environmental reservoir for AMR determinants. METHODS AND RESULTS Eleven sites representing fresh and brackish water rivers, ponds and reclaimed water, were sampled over two years. Samples (n=333) yielded 198 unique isolates of E. faecalis and E. faecium which were tested for antimicrobial susceptibility by microbroth dilution. Species distribution was influenced by water type and season. E. faecalis was more likely found in freshwater rivers and in summer, and E. faecium in reclaimed water and in spring. Only 11% of isolates were pansusceptible, while 48.5% and 26.3% were single (SDR) and multidrug resistant (MDR), respectively. MDR was more likely detected in E. faecium than E. faecalis. Winter isolates were more likely than summer isolates to exhibit MDR than SDR. CONCLUSIONS E. faecalis and E. faecium in surface and reclaimed water exhibited diverse phenotypic AMR and a low-level resistance to clinically important antimicrobials such as ampicillin, vancomycin and linezolid. SIGNIFICANCE AND IMPACT OF THE STUDY Single and multidrug resistance in E. faecalis and E. faecium varied by season but not water type. AMR prevalence can assist decisions on the safety of irrigation water sources for fresh produce crops.
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Affiliation(s)
- Sultana Solaiman
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Rebecca Patterson
- Maryland Institute of Applied and Environmental Health, School of Public Health, University of Maryland, College Park, MD, USA
| | - Kaitlyn Davey
- Department of Nutrition and Food Sciences, University of Maryland, College Park, MD, USA
| | - Yisrael Katz
- Department of Biological Sciences, University of Maryland, College Park, MD, USA
| | - Devon Payne-Sturges
- Maryland Institute of Applied and Environmental Health, School of Public Health, University of Maryland, College Park, MD, USA
| | - Amy R Sapkota
- Maryland Institute of Applied and Environmental Health, School of Public Health, University of Maryland, College Park, MD, USA
| | - Shirley A Micallef
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA.,Centre for Food Safety and Security System, University of Maryland, College Park, MD, USA
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9
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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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10
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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: 0] [Impact Index Per Article: 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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11
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Devane ML, Moriarty E, Weaver L, Cookson A, Gilpin B. Fecal indicator bacteria from environmental sources; strategies for identification to improve water quality monitoring. WATER RESEARCH 2020; 185:116204. [PMID: 32745743 DOI: 10.1016/j.watres.2020.116204] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 07/13/2020] [Accepted: 07/19/2020] [Indexed: 06/11/2023]
Abstract
In tropical to temperate environments, fecal indicator bacteria (FIB), such as enterococci and Escherichia coli, can persist and potentially multiply, far removed from their natural reservoir of the animal gut. FIB isolated from environmental reservoirs such as stream sediments, beach sand and vegetation have been termed "naturalized" FIB. In addition, recent research suggests that the intestines of poikilothermic animals such as fish may be colonized by enterococci and E. coli, and therefore, these animals may contribute to FIB concentrations in the aquatic environment. Naturalized FIB that are derived from fecal inputs into the environment, and subsequently adapted to maintain their population within the non-host environment are termed "naturalized enteric FIB". In contrast, an additional theory suggests that some "naturalized" FIB diverged from enteric FIB many millions of years ago and are now normal inhabitants of the environment where they are referred to as "naturalized non-enteric FIB". In the case of the Escherichia genus, the naturalized non-enteric members are identified as E. coli during routine water quality monitoring. An over-estimation of the health risk could result when these naturalized, non-enteric FIB, (that is, not derived from avian or mammalian fecal contamination), contribute to water quality monitoring results. It has been postulated that these environmental FIB belonging to the genera Escherichia and Enterococcus can be differentiated from enteric FIB by genetic methods because they lack some of the genes required for colonization of the host intestine, and have acquired genes that aid survival in the environment. Advances in molecular tools such as next generation sequencing will aid the identification of genes peculiar or "enriched" in particular habitats to discriminate between enteric and environmental FIB. In this appraisal, we have reviewed the research studying "naturalized" FIB, and discussed the techniques for their differentiation from enteric FIB. This differentiation includes the important distinction between enteric FIB derived from fresh and non-recent fecal inputs, and those truly non-enteric environmental microbes, which are currently identified as FIB during routine water quality monitoring. The inclusion of tools for the identification of naturalized FIB (enteric or environmental) would be a valuable resource for future studies assessing water quality.
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Affiliation(s)
- Megan L Devane
- Institute of Environmental Science and Research Ltd., 27 Creyke Rd, Ilam, Christchurch, New Zealand.
| | - Elaine Moriarty
- Institute of Environmental Science and Research Ltd., 27 Creyke Rd, Ilam, Christchurch, New Zealand
| | - Louise Weaver
- Institute of Environmental Science and Research Ltd., 27 Creyke Rd, Ilam, Christchurch, New Zealand
| | - Adrian Cookson
- AgResearch Ltd., Hopkirk Research Institute, Massey University, Palmerston North, New Zealand; mEpiLab, School of Veterinary Sciences, Massey University, Palmerston North, New Zealand
| | - Brent Gilpin
- Institute of Environmental Science and Research Ltd., 27 Creyke Rd, Ilam, Christchurch, New Zealand
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12
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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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13
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Antimicrobial Resistance Gene Detection and Plasmid Typing Among Multidrug Resistant Enterococci Isolated from Freshwater Environment. Microorganisms 2020; 8:microorganisms8091338. [PMID: 32887339 PMCID: PMC7563215 DOI: 10.3390/microorganisms8091338] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 08/27/2020] [Accepted: 08/31/2020] [Indexed: 12/14/2022] Open
Abstract
In this study, mechanisms of antimicrobial resistance (AR) as well as the abundance and diversity of plasmids were determined among multidrug resistant (MDR) enterococci from surface water in GA, USA. A total of 51 enterococci isolates were screened for the presence of 27 AR genes conferring resistance to ciprofloxacin, erythromycin, tylosin, kanamycin, streptomycin, lincomycin, Quinupristin/Dalfopristin (Q/D), and tetracycline. A plasmid classification system based on replication genes was used to detect 19 defined Gram-positive plasmid replicon families. Twelve genes were identified as conferring resistance to erythromycin and tylosin (erm(B) and erm(C)), kanamycin (aph(3′)-IIIa), streptomycin (ant(6)-Ia), lincomycin (lnu(B)), Q/D (vat(E)), ciprofloxacin (qnrE. faecalis), and tetracycline (tet(K), tet(L), tet(M), tet(O) and tet(S)). Twelve different rep-families were identified in two-thirds of the isolates. While AR genes commonly found in human and animals were detected in this study among environmental enterococci, resistance genes could not be determined for many of the isolates, which indicates that diverse AR mechanisms exist among enterococci, and the understanding of AR mechanisms for environmental enterococci is limited. Diverse rep-families were identified among the enterococci recovered from the aquatic environment, and these rep-families appear to be quite different from those recovered from other sources. This work expands knowledge of AR gene reservoirs and enterococcal plasmids across a wider range of environments.
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14
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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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15
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Escherichia coli Antimicrobial Resistance Variability in Water Runoff and Soil from a Remnant Native Prairie, an Improved Pasture, and a Cultivated Agricultural Watershed. WATER 2020. [DOI: 10.3390/w12051251] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Although many previous studies have examined patterns of antimicrobial resistance (AMR) and multidrug resistance (MDR) from domestic animals and farm environments, comparatively little is known about the environmental sources and natural reservoirs of AMR and MDR. In this study, we collected stormwater runoff and soil samples from three watersheds in Texas. Escherichia coli (E. coli) were enumerated, isolated, and analyzed for resistance patterns. E. coli from all sites, irrespective of land use, displayed the presence of AMR/MDR. Higher levels of AMR/MDR were observed in water compared to soil. More isolates were resistant to cephalothin than other antibiotics. For water isolates, 94% was resistant to cephalothin, 27% to tetracycline, and 15% to ampicillin. Across all sites, a large percentage of water isolates demonstrated MDR with 34% resistant to ≥2 antibiotics and 11% to ≥3 antibiotics. All AMR soil isolates were resistant to cephalothin (87% of the total soil isolates), but only 8.9% were MDR. High cephalothin resistance observed in both soil and water suggests the presence of native, cephalothin-resistant E. coli. Higher MDR observed within water compared to the soil populations suggests that resistance sources other than soil, such as more recent fecal depositions as opposed to residual AMR in soil, could have contributed to higher antibiotic-resistant E. coli in runoff.
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