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Verhaegen M, Bergot T, Liebana E, Stancanelli G, Streissl F, Mingeot-Leclercq MP, Mahillon J, Bragard C. On the use of antibiotics to control plant pathogenic bacteria: a genetic and genomic perspective. Front Microbiol 2023; 14:1221478. [PMID: 37440885 PMCID: PMC10333595 DOI: 10.3389/fmicb.2023.1221478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 06/08/2023] [Indexed: 07/15/2023] Open
Abstract
Despite growing attention, antibiotics (such as streptomycin, oxytetracycline or kasugamycin) are still used worldwide for the control of major bacterial plant diseases. This raises concerns on their potential, yet unknown impact on antibiotic and multidrug resistances and the spread of their genetic determinants among bacterial pathogens. Antibiotic resistance genes (ARGs) have been identified in plant pathogenic bacteria (PPB), with streptomycin resistance genes being the most commonly reported. Therefore, the contribution of mobile genetic elements (MGEs) to their spread among PPB, as well as their ability to transfer to other bacteria, need to be further explored. The only well-documented example of ARGs vector in PPB, Tn5393 and its highly similar variants (carrying streptomycin resistance genes), is concerning because of its presence outside PPB, in Salmonella enterica and Klebsiella pneumoniae, two major human pathogens. Although its structure among PPB is still relatively simple, in human- and animal-associated bacteria, Tn5393 has evolved into complex associations with other MGEs and ARGs. This review sheds light on ARGs and MGEs associated with PPB, but also investigates the potential role of antibiotic use in resistance selection in plant-associated bacteria.
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Affiliation(s)
- Marie Verhaegen
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Catholic University of Louvain (UCLouvain), Louvain-la-Neuve, Belgium
| | - Thomas Bergot
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Catholic University of Louvain (UCLouvain), Louvain-la-Neuve, Belgium
| | | | | | | | - Marie-Paule Mingeot-Leclercq
- Cellular and Molecular Pharmacology Unit, Louvain Drug Research Institute, UCLouvain, Woluwe-Saint-Lambert, Belgium
| | - Jacques Mahillon
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Catholic University of Louvain (UCLouvain), Louvain-la-Neuve, Belgium
| | - Claude Bragard
- Plant Health Laboratory, Earth and Life Institute, UCLouvain, Louvain-la-Neuve, Belgium
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2
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Huang W, Kong R, Chen L, An Y. Physiological responses and antibiotic-degradation capacity of duckweed ( Lemna aequinoctialis) exposed to streptomycin. FRONTIERS IN PLANT SCIENCE 2022; 13:1065199. [PMID: 36570884 PMCID: PMC9774486 DOI: 10.3389/fpls.2022.1065199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 11/21/2022] [Indexed: 06/12/2023]
Abstract
Aquatic plants are constantly exposed to various water environmental pollutants. Few data on how antibiotics affect duckweed health and its removal ability. The aim of this study was to investigate the impact of streptomycin on the physiological change and uptake capability in duckweed (Lemna aequinoctialis) after exposure at different time points (0, 5, 10, 15 and 20 days). Duckweeds were exposed to streptomycin at a range of concentrations (0.1-10 mM). Results indicated that the high streptomycin concentrations (≥1 mM) resulted in a lower duckweed biomass (21.5-41.5%), RGR (0.258-0.336 g d-1), decrease in total Chl and increase in carotenoids. Antioxidative enzymes, including CAT (18-42.88 U mg protein-1), APX (0.41-0.76 U mg protein-1), and SOD (0.52-0.71 U mg protein-1) were found to accumulate in the streptomycin groups in comparison to the control group. The significant reduction (72-82%) in streptomycin content at 20 d compared to the control (40-55%) suggested that duckweed has a high ability in removing streptomycin. Transcriptome analysis showed that the secondary metabolic pathways including phenylpropanoid biosynthesis and flavonoid biosynthesis were significantly upregulated in the streptomycin setup compared to the control. Therefore, our findings suggested that duckweed can contribute to the streptomycin degradation, which should be highly recommended to the treatment of aquaculture wastewater and domestic sewage.
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Khan SJ, Osborn AM, Eswara PJ. Effect of Sunlight on the Efficacy of Commercial Antibiotics Used in Agriculture. Front Microbiol 2021; 12:645175. [PMID: 34140934 PMCID: PMC8203823 DOI: 10.3389/fmicb.2021.645175] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 04/28/2021] [Indexed: 11/13/2022] Open
Abstract
Antibiotic stewardship is of paramount importance to limit the emergence of antibiotic-resistant bacteria in not only hospital settings, but also in animal husbandry, aquaculture, and agricultural sectors. Currently, large quantities of antibiotics are applied to treat agricultural diseases like citrus greening disease (CGD). The two commonly used antibiotics approved for this purpose are streptomycin and oxytetracycline. Although investigations are ongoing to understand how efficient this process is to control the spread of CGD, to our knowledge, there have been no studies that evaluate the effect of environmental factors such as sunlight on the efficacy of the above-mentioned antibiotics. We conducted a simple disc-diffusion assay to study the efficacy of streptomycin and oxytetracycline after exposure to sunlight for 7- or 14-day periods using Escherichia coli and Bacillus subtilis as the representative strains of Gram-negative and Gram-positive organisms, respectively. Freshly prepared discs and discs stored in the dark for 7 or 14 days served as our controls. We show that the antibiotic potential of oxytetracycline exposed to sunlight dramatically decreases over the course of 14 days against both E. coli and B. subtilis. However, the effectiveness of streptomycin was only moderately impacted by sunlight. It is important to note that antibiotics that last longer in the environment may play a deleterious role in the rise and spread of antibiotic-resistant bacteria. Further studies are needed to substantively analyze the safety and efficacy of antibiotics used for broader environmental applications.
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Affiliation(s)
| | | | - Prahathees J. Eswara
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL, United States
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4
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Al Riachy R, Strub C, Durand N, Guibert B, Guichard H, Constancias F, Chochois V, Lopez-Lauri F, Fontana A, Schorr-Galindo S. Microbiome Status of Cider-Apples, from Orchard to Processing, with a Special Focus on Penicillium expansum Occurrence and Patulin Contamination. J Fungi (Basel) 2021; 7:jof7040244. [PMID: 33805022 PMCID: PMC8063962 DOI: 10.3390/jof7040244] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 03/15/2021] [Accepted: 03/19/2021] [Indexed: 11/22/2022] Open
Abstract
Patulin is a secondary metabolite produced primarily by the fungus Penicillium expansum, responsible for the blue mold disease on apples. It is found in apple products including apple cider when apple juice is added after fermentation. In the present study, two hundred and twenty-five cider-apples of the variety “Bedan”, cultivated in Brittany in France, were sampled from the orchard during harvesting until the storage step, right before processing. The patulin analysis on these samples reported a low contamination at the orchard and a significantly higher-level of contamination in the cider-apples starting from the transporting bin. The percentage of positive samples increased from 6% to 47% after 12 h in the harvesting bin before transporting and reached 95% after 24 h of transporting, decreasing then to 69% at the end of the storage. Penicillium expansum was quantified on the surface of apples using real-time PCR and was observed to be mostly consistent between the harvest and post-harvest steps. It was detected on average, on the surface of 85% of all sampled apples with a mean value around 2.35 × 106Penicillium expansum DNA/g of apple. Moreover, the changes in the fungal and bacterial epiphytic microbiota in the different steps were studied using a metabarcoding approach. The alpha and beta diversity analysis revealed the presence of unique and more diverse bacterial and fungal communities on the surface of apples picked from the orchard compared to the rest of the sampling steps. Potential indigenous biological control agents were identified on the surface of sampled apples. Future perspective includes developing actions of prevention and control of the contamination by Penicillium expansum during the harvest and along the various critical post-harvest stages before transformation in a sustainable development concern.
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Affiliation(s)
- Reem Al Riachy
- Qualisud, Univ Montpellier, CIRAD, Univ d’Avignon, Institut Agro, IRD, Univ de La Réunion, F-34398 Montpellier, France; (N.D.); (B.G.); (F.C.); (V.C.); (F.L.-L.); (A.F.); (S.S.-G.)
- Correspondence: (R.A.R.); (C.S.)
| | - Caroline Strub
- Qualisud, Univ Montpellier, CIRAD, Univ d’Avignon, Institut Agro, IRD, Univ de La Réunion, F-34398 Montpellier, France; (N.D.); (B.G.); (F.C.); (V.C.); (F.L.-L.); (A.F.); (S.S.-G.)
- Correspondence: (R.A.R.); (C.S.)
| | - Noël Durand
- Qualisud, Univ Montpellier, CIRAD, Univ d’Avignon, Institut Agro, IRD, Univ de La Réunion, F-34398 Montpellier, France; (N.D.); (B.G.); (F.C.); (V.C.); (F.L.-L.); (A.F.); (S.S.-G.)
- CIRAD, UMR Qualisud, F-34398 Montpellier, France
| | - Benjamin Guibert
- Qualisud, Univ Montpellier, CIRAD, Univ d’Avignon, Institut Agro, IRD, Univ de La Réunion, F-34398 Montpellier, France; (N.D.); (B.G.); (F.C.); (V.C.); (F.L.-L.); (A.F.); (S.S.-G.)
- CIRAD, UMR Qualisud, F-34398 Montpellier, France
| | - Hugues Guichard
- French Institute for Cider Production (IFPC), Domaine de la Motte, F-35653 Le Rheu, France;
| | - Florentin Constancias
- Qualisud, Univ Montpellier, CIRAD, Univ d’Avignon, Institut Agro, IRD, Univ de La Réunion, F-34398 Montpellier, France; (N.D.); (B.G.); (F.C.); (V.C.); (F.L.-L.); (A.F.); (S.S.-G.)
- CIRAD, UMR Qualisud, F-34398 Montpellier, France
| | - Vincent Chochois
- Qualisud, Univ Montpellier, CIRAD, Univ d’Avignon, Institut Agro, IRD, Univ de La Réunion, F-34398 Montpellier, France; (N.D.); (B.G.); (F.C.); (V.C.); (F.L.-L.); (A.F.); (S.S.-G.)
- CIRAD, UMR Qualisud, F-34398 Montpellier, France
| | - Félicie Lopez-Lauri
- Qualisud, Univ Montpellier, CIRAD, Univ d’Avignon, Institut Agro, IRD, Univ de La Réunion, F-34398 Montpellier, France; (N.D.); (B.G.); (F.C.); (V.C.); (F.L.-L.); (A.F.); (S.S.-G.)
| | - Angélique Fontana
- Qualisud, Univ Montpellier, CIRAD, Univ d’Avignon, Institut Agro, IRD, Univ de La Réunion, F-34398 Montpellier, France; (N.D.); (B.G.); (F.C.); (V.C.); (F.L.-L.); (A.F.); (S.S.-G.)
| | - Sabine Schorr-Galindo
- Qualisud, Univ Montpellier, CIRAD, Univ d’Avignon, Institut Agro, IRD, Univ de La Réunion, F-34398 Montpellier, France; (N.D.); (B.G.); (F.C.); (V.C.); (F.L.-L.); (A.F.); (S.S.-G.)
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5
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Biogeochemical Controls on the Potential for Long-Term Contaminant Leaching from Soils Developing on Historic Coal Mine Spoil. SOIL SYSTEMS 2020. [DOI: 10.3390/soilsystems5010003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Coal mine spoil is widespread in US coal mining regions, and the potential long-term leaching of toxic metal(loid)s is a significant and underappreciated issue. This study aimed to determine the flux of contaminants from historic mine coal spoil at a field site located in Appalachian Ohio (USA) and link pore water composition and solid-phase composition to the weathering reaction stages within the soils. The overall mineralogical and microbial community composition indicates that despite very different soil formation pathways, soils developing on historic coal mine spoil and an undisturbed soil are currently dominated by similar mineral weathering reactions. Both soils contained pyrite coated with clays and secondary oxide minerals. However, mine spoil soil contained abundant residual coal, with abundant Fe- and Mn- (oxy)hydroxides. These secondary phases likely control and mitigate trace metal (Cu, Ni, and Zn) transport from the soils. While Mn was highly mobile in Mn-enriched soils, Fe and Al mobility may be more controlled by dissolved organic carbon dynamics than mineral abundance. There is also likely an underappreciated risk of Mn transport from coal mine spoil, and that mine spoil soils could become a major source of metals if local biogeochemical conditions change.
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6
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O'Connor LMJ, Fugère V, Gonzalez A. Evolutionary Rescue Is Mediated by the History of Selection and Dispersal in Diversifying Metacommunities. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.517434] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Rapid evolution can sometimes prevent population extirpation in stressful environments, but the conditions leading to “evolutionary rescue” in metacommunities are unclear. Here we studied the eco-evolutionary response of microbial metacommunities adapting to selection by the antibiotic streptomycin. Our experiment tested how the history of antibiotic selection and contrasting modes of dispersal influenced diversification and subsequent evolutionary rescue in microbial metacommunities undergoing adaptive radiation. We first tracked the change in diversity and density of Pseudomonas fluorescens morphotypes selected on a gradient of antibiotic stress. We then examined the recovery of these metacommunities following abrupt application of a high concentration of streptomycin lethal to the ancestral organisms. We show that dispersal increases diversity within the stressed metacommunities, that exposure to stress alters diversification dynamics, and that community composition, dispersal, and past exposure to stress mediate the speed at which evolutionary rescue occurs, but not the final outcome of recovery in abundance and diversity. These findings extend recent experiments on evolutionary rescue to the case of metacommunities undergoing adaptive diversification, and should motivate new theory on this question. Our findings are also relevant to evolutionary conservation biology and research on antimicrobial resistance.
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Paynter A, Willis AD. Tuning parameter selection for a penalized estimator of species richness. J Appl Stat 2020; 48:1053-1070. [PMID: 33967371 PMCID: PMC8098713 DOI: 10.1080/02664763.2020.1754359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Our goal is to estimate the true number of classes in a population, called the species richness. We consider the case where multiple frequency count tables have been collected from a homogeneous population, and investigate a penalized maximum likelihood estimator under a negative binomial model. Because high probabilities of unobserved classes increase the variance of species richness estimates, our method penalizes the probability of a class being unobserved. Tuning the penalization parameter is challenging because the true species richness is never known, and so we propose and validate four novel methods for tuning the penalization parameter. We illustrate and contrast the performance of the proposed methods by estimating the strain-level microbial diversity of Lake Champlain over 3 consecutive years, and global human host-associated species-level microbial richness.
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Affiliation(s)
- Alex Paynter
- Department of Biostatistics, University of Washington, Health Sciences Building, Box 357232, 1705 NE Pacific St., Seattle, WA 98195
| | - Amy D Willis
- Department of Biostatistics, University of Washington, Health Sciences Building, Box 357232, 1705 NE Pacific St., Seattle, WA 98195
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8
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Dong X, Rao D, Tian L, Wang Q, Yang K. A slurry microcosm study on the interaction between antibiotics and soil bacterial community. Heliyon 2020; 6:e03348. [PMID: 32055738 PMCID: PMC7005453 DOI: 10.1016/j.heliyon.2020.e03348] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 12/09/2019] [Accepted: 01/30/2020] [Indexed: 12/26/2022] Open
Abstract
Antibiotics released in the environment have attracted great attention. The environmental emission control of antibiotics should be based on the degree of their negative impacts on the environment and ecology. Here, we conducted a series of soil slurry microcosm experiments to investigate the interactions between antibiotics and the soil bacterial community. In the soil slurry, distinctive behaviors were observed for different antibiotics. Beta-lactams (ampicillin and ceftriaxone) experienced fast biodegradation. Kanamycin was adsorbed on soil particles soon after its addition. Nalidixic acid was stable throughout the experimental period (164 h). The main inactivation mechanism of tetracycline was deduced to be hydrolysis. Bacterial communities in slurries with or without antibiotic-treatment were profiled via high-throughput Illumina sequencing of the 16S rRNA gene. Unstable (ceftriaxone) and adsorbed (kanamycin) antibiotics show minor or negligible influences on the soil bacterial community. Stable antibiotics (nalidixic acid and tetracycline) have significantly affected the structure of the bacterial community. Most of enriched bacterial genera by various antibiotics belong to the same phylum, Proteobacteria. Inhibited bacterial phyla by nalidixic acid are Firmicutes and Bacteroidetes, while those inhibited by tetracycline are Firmicutes, Bacteroidetes and Cyanobacteria. According to the PICRUSt prediction of metagenome, influence of antibiotics on overall metabolic function of the bacterial community is rather limited. This study has provided valuable information, from a phylogenetic viewpoint, about the influence of high concentration of antibiotics on soil bacterial community.
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Affiliation(s)
- Xiaohong Dong
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, 610065, China
| | - Dawei Rao
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, 610065, China
| | - Lejin Tian
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, 610065, China
| | - Qizheng Wang
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, 610065, China
| | - Kun Yang
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, 610065, China
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9
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Peil A, Hübert C, Wensing A, Horner M, Emeriewen OF, Richter K, Wöhner T, Chagné D, Orellana-Torrejon C, Saeed M, Troggio M, Stefani E, Gardiner SE, Hanke MV, Flachowsky H, Bus VG. Mapping of fire blight resistance in Malus ×robusta 5 flowers following artificial inoculation. BMC PLANT BIOLOGY 2019; 19:532. [PMID: 31791233 PMCID: PMC6889339 DOI: 10.1186/s12870-019-2154-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 11/21/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND Although the most common path of infection for fire blight, a severe bacterial disease on apple, is via host plant flowers, quantitative trait loci (QTLs) for fire blight resistance to date have exclusively been mapped following shoot inoculation. It is not known whether the same mechanism underlies flower and shoot resistance. RESULTS We report the detection of a fire blight resistance QTL following independent artificial inoculation of flowers and shoots on two F1 segregating populations derived from crossing resistant Malus ×robusta 5 (Mr5) with susceptible 'Idared' and 'Royal Gala' in experimental orchards in Germany and New Zealand, respectively. QTL mapping of phenotypic datasets from artificial flower inoculation of the 'Idared' × Mr5 population with Erwinia amylovora over several years, and of the 'Royal Gala' × Mr5 population in a single year, revealed a single major QTL controlling floral fire blight resistance on linkage group 3 (LG3) of Mr5. This QTL corresponds to the QTL on LG3 reported previously for the 'Idared' × Mr5 and an 'M9' × Mr5 population following shoot inoculation in the glasshouse. Interval mapping of phenotypic data from shoot inoculations of subsets from both flower resistance populations re-confirmed that the resistance QTL is in the same position on LG3 of Mr5 as that for flower inoculation. These results provide strong evidence that fire blight resistance in Mr5 is controlled by a major QTL on LG3, independently of the mode of infection, rootstock and environment. CONCLUSIONS This study demonstrates for the first time that resistance to fire blight caused by Erwinia amylovora is independent of the mode of inoculation at least in Malus ×robusta 5.
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Affiliation(s)
- Andreas Peil
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Pillnitzer Platz 3a, 01326 Dresden, Germany
| | - Christine Hübert
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Fruit Crops and Viticulture, Schwabenheimer str. 101, 69221 Dossenheim, Germany
| | - Annette Wensing
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Fruit Crops and Viticulture, Schwabenheimer str. 101, 69221 Dossenheim, Germany
| | - Mary Horner
- The New Zealand Institute for Plant and Food Research Limited (PFR), Hawke’s Bay Research Centre, Private Bag 1401, Havelock North, 4157 New Zealand
| | - Ofere Francis Emeriewen
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Pillnitzer Platz 3a, 01326 Dresden, Germany
| | - Klaus Richter
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| | - Thomas Wöhner
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Pillnitzer Platz 3a, 01326 Dresden, Germany
| | - David Chagné
- PFR, Palmerston North Research Centre, Private Bag 1600, Palmerston North, 4442 New Zealand
| | | | - Munazza Saeed
- PFR, Palmerston North Research Centre, Private Bag 1600, Palmerston North, 4442 New Zealand
| | - Michela Troggio
- Research and Innovation Centre, Edmund Mach Foundation, 38010 San Michele all’Adige, Italy
| | - Erika Stefani
- Research and Innovation Centre, Edmund Mach Foundation, 38010 San Michele all’Adige, Italy
| | - Susan E. Gardiner
- PFR, Palmerston North Research Centre, Private Bag 1600, Palmerston North, 4442 New Zealand
| | - Magda-Viola Hanke
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Pillnitzer Platz 3a, 01326 Dresden, Germany
| | - Henryk Flachowsky
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Pillnitzer Platz 3a, 01326 Dresden, Germany
| | - Vincent G.M. Bus
- The New Zealand Institute for Plant and Food Research Limited (PFR), Hawke’s Bay Research Centre, Private Bag 1401, Havelock North, 4157 New Zealand
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10
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Affiliation(s)
- Zhiyi Zhang
- Department of Mathematics and Statistics, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Chen Chen
- Department of Mathematics and Statistics, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Jialin Zhang
- Department of Mathematics and Statistics, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
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11
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Abstract
Antibiotics have been used for the management of relatively few bacterial plant diseases and are largely restricted to high-value fruit crops because of the expense involved. Antibiotic resistance in plant-pathogenic bacteria has become a problem in pathosystems where these antibiotics have been used for many years. Where the genetic basis for resistance has been examined, antibiotic resistance in plant pathogens has most often evolved through the acquisition of a resistance determinant via horizontal gene transfer. For example, the strAB streptomycin-resistance genes occur in Erwinia amylovora, Pseudomonas syringae, and Xanthomonas campestris, and these genes have presumably been acquired from nonpathogenic epiphytic bacteria colocated on plant hosts under antibiotic selection. We currently lack knowledge of the effect of the microbiome of commensal organisms on the potential of plant pathogens to evolve antibiotic resistance. Such knowledge is critical to the development of robust resistance management strategies to ensure the safe and effective continued use of antibiotics in the management of critically important diseases.
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Affiliation(s)
- George W Sundin
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, Michigan 48824, USA;
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, Florida 33850, USA
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12
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Pepper IL, Brooks JP, Gerba CP. Antibiotic Resistant Bacteria in Municipal Wastes: Is There Reason for Concern? ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:3949-3959. [PMID: 29505255 DOI: 10.1021/acs.est.7b04360] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Recently, there has been increased concern about the presence of antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARG), in treated domestic wastewaters, animal manures and municipal biosolids. The concern is whether these additional sources of ARB contribute to antibiotic resistance levels in the environment, that is, "environmental antibiotic resistance." ARB and ARG occur naturally in soil and water, and it remains unclear whether the introduction of ARB in liquid and solid municipal and animal wastes via land application have any significant impact on the background levels of antibiotic resistance in the environment, and whether they affect human exposure to ARB. In this current review, we examine and re-evaluate the incidence of ARB and ARG resulting from land application activities, and offer a new perspective on the threat of antibiotic resistance to public health via exposure from nonclinical environmental sources. Based on inputs of ARBs and ARGs from land application, their fate in soil due to soil microbial ecology principles, and background indigenous levels of ARBs and ARGs already present in soil, we conclude that while antibiotic resistance levels in soil are increased temporally by land application of wastes, their persistence is not guaranteed and is in fact variable, and often contradictory based on application site. Furthermore, the application of wastes may not produce the most direct impact of ARGs and ARB on public health. Further investigation is still warranted in agriculture and public health, including continued scrutiny of antibiotic use in both sectors.
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Affiliation(s)
- Ian L Pepper
- Water and Energy Sustainable Technology Center (WEST) , The University of Arizona , 2959 W. Calle Agua Nueva , Tucson , Arizona 85745 , United States
| | - John P Brooks
- Genetics and Sustainable Agriculture Research Unit, USDA ARS , Mississippi State , Mississippi , 39762 , United States
| | - Charles P Gerba
- Water and Energy Sustainable Technology Center (WEST) , The University of Arizona , 2959 W. Calle Agua Nueva , Tucson , Arizona 85745 , United States
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13
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Abstract
In this article, the current knowledge and knowledge gaps in the emergence and spread of antimicrobial resistance (AMR) in livestock and plants and importance in terms of animal and human health are discussed. Some recommendations are provided for generation of the data required in order to develop risk assessments for AMR within agriculture and for risks through the food chain to animals and humans.
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Affiliation(s)
- Sophie Thanner
- Agroscope, Institute for Livestock Sciences, Posieux, Switzerland
| | - David Drissner
- Agroscope, Institute for Food Sciences, Waedenswil, Switzerland
| | - Fiona Walsh
- Department of Biology, Maynooth University, Maynooth, County Kildare, Ireland
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14
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Willis A, Bunge J. Estimating diversity via frequency ratios. Biometrics 2015; 71:1042-9. [PMID: 26038228 DOI: 10.1111/biom.12332] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2014] [Revised: 04/01/2015] [Accepted: 04/01/2015] [Indexed: 01/16/2023]
Abstract
We wish to estimate the total number of classes in a population based on sample counts, especially in the presence of high latent diversity. Drawing on probability theory that characterizes distributions on the integers by ratios of consecutive probabilities, we construct a nonlinear regression model for the ratios of consecutive frequency counts. This allows us to predict the unobserved count and hence estimate the total diversity. We believe that this is the first approach to depart from the classical mixed Poisson model in this problem. Our method is geometrically intuitive and yields good fits to data with reasonable standard errors. It is especially well-suited to analyzing high diversity datasets derived from next-generation sequencing in microbial ecology. We demonstrate the method's performance in this context and via simulation, and we present a dataset for which our method outperforms all competitors.
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Affiliation(s)
- Amy Willis
- Department of Statistical Science, Cornell University, Ithaca, New York, U.S.A
| | - John Bunge
- Department of Statistical Science, Cornell University, Ithaca, New York, U.S.A
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McManus PS. Does a drop in the bucket make a splash? Assessing the impact of antibiotic use on plants. Curr Opin Microbiol 2014; 19:76-82. [PMID: 25006016 DOI: 10.1016/j.mib.2014.05.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 04/29/2014] [Accepted: 05/21/2014] [Indexed: 11/27/2022]
Abstract
Antibiotics are applied to plants to prevent bacterial diseases, although the diversity of antibiotics and total amounts used are dwarfed by antibiotic use in animal agriculture. Nevertheless, the release of antibiotics into the open environment during crop treatment draws scrutiny for its potential impact on the global pool of resistance genes. The main use of antibiotics on plants is application of streptomycin to prevent fire blight, a serious disease of apple and pear trees. A series of recent studies identified and quantified antibiotic resistance genes and profiled bacterial communities in apple orchard plots that were or were not sprayed with streptomycin. While the specific objectives and methods varied, the results of these studies suggest that streptomycin application for fire blight control does not influence bacterial community structure or increase the abundance of resistance genes in orchards.
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Affiliation(s)
- Patricia S McManus
- Department of Plant Pathology, University of Wisconsin-Madison, United States.
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