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Chick HM, Rees ME, Lewis ML, Williams LK, Bodger O, Harris LG, Rushton S, Wilkinson TS. Using the Traditional Ex Vivo Whole Blood Model to Discriminate Bacteria by Their Inducible Host Responses. Biomedicines 2024; 12:724. [PMID: 38672079 PMCID: PMC11047930 DOI: 10.3390/biomedicines12040724] [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: 02/28/2024] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
Whole blood models are rapid and versatile for determining immune responses to inflammatory and infectious stimuli, but they have not been used for bacterial discrimination. Staphylococcus aureus, S. epidermidis and Escherichia coli are the most common causes of invasive disease, and rapid testing strategies utilising host responses remain elusive. Currently, immune responses can only discriminate between bacterial 'domains' (fungi, bacteria and viruses), and very few studies can use immune responses to discriminate bacteria at the species and strain level. Here, whole blood was used to investigate the relationship between host responses and bacterial strains. Results confirmed unique temporal profiles for the 10 parameters studied: IL-6, MIP-1α, MIP-3α, IL-10, resistin, phagocytosis, S100A8, S100A8/A9, C5a and TF3. Pairwise analysis confirmed that IL-6, resistin, phagocytosis, C5a and S100A8/A9 could be used in a discrimination scheme to identify to the strain level. Linear discriminant analysis (LDA) confirmed that (i) IL-6, MIP-3α and TF3 could predict genera with 95% accuracy; (ii) IL-6, phagocytosis, resistin and TF3 could predict species at 90% accuracy and (iii) phagocytosis, S100A8 and IL-10 predicted strain at 40% accuracy. These data are important because they confirm the proof of concept that host biomarker panels could be used to identify bacterial pathogens.
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Affiliation(s)
- Heather M. Chick
- Microbiology and Infectious Disease, Institute of Life Science, Swansea University Medical School, Swansea SA2 8PP, UK; (H.M.C.); (M.E.R.); (M.L.L.); (L.K.W.); (L.G.H.)
| | - Megan E. Rees
- Microbiology and Infectious Disease, Institute of Life Science, Swansea University Medical School, Swansea SA2 8PP, UK; (H.M.C.); (M.E.R.); (M.L.L.); (L.K.W.); (L.G.H.)
| | - Matthew L. Lewis
- Microbiology and Infectious Disease, Institute of Life Science, Swansea University Medical School, Swansea SA2 8PP, UK; (H.M.C.); (M.E.R.); (M.L.L.); (L.K.W.); (L.G.H.)
| | - Lisa K. Williams
- Microbiology and Infectious Disease, Institute of Life Science, Swansea University Medical School, Swansea SA2 8PP, UK; (H.M.C.); (M.E.R.); (M.L.L.); (L.K.W.); (L.G.H.)
- Department of Animal and Agriculture, Hartpury University, Hartpury, Gloucestershire GL19 3BE, UK
| | - Owen Bodger
- Patient and Population Health an Informatics Research, Swansea University Medical School, Swansea SA2 8PP, UK;
| | - Llinos G. Harris
- Microbiology and Infectious Disease, Institute of Life Science, Swansea University Medical School, Swansea SA2 8PP, UK; (H.M.C.); (M.E.R.); (M.L.L.); (L.K.W.); (L.G.H.)
| | - Steven Rushton
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK;
| | - Thomas S. Wilkinson
- Microbiology and Infectious Disease, Institute of Life Science, Swansea University Medical School, Swansea SA2 8PP, UK; (H.M.C.); (M.E.R.); (M.L.L.); (L.K.W.); (L.G.H.)
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2
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Thomas GA, Paradell Gil T, Müller CT, Rogers HJ, Berger CN. From field to plate: How do bacterial enteric pathogens interact with ready-to-eat fruit and vegetables, causing disease outbreaks? Food Microbiol 2024; 117:104389. [PMID: 37919001 DOI: 10.1016/j.fm.2023.104389] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 09/11/2023] [Accepted: 09/17/2023] [Indexed: 11/04/2023]
Abstract
Ready-to-eat fruit and vegetables are a convenient source of nutrients and fibre for consumers, and are generally safe to eat, but are vulnerable to contamination with human enteric bacterial pathogens. Over the last decade, Salmonella spp., pathogenic Escherichia coli, and Listeria monocytogenes have been linked to most of the bacterial outbreaks of foodborne illness associated with fresh produce. The origins of these outbreaks have been traced to multiple sources of contamination from pre-harvest (soil, seeds, irrigation water, domestic and wild animal faecal matter) or post-harvest operations (storage, preparation and packaging). These pathogens have developed multiple processes for successful attachment, survival and colonization conferring them the ability to adapt to multiple environments. However, these processes differ across bacterial strains from the same species, and across different plant species or cultivars. In a competitive environment, additional risk factors are the plant microbiome phyllosphere and the plant responses; both factors directly modulate the survival of the pathogens on the leaf's surface. Understanding the mechanisms involved in bacterial attachment to, colonization of, and proliferation, on fresh produce and the role of the plant in resisting bacterial contamination is therefore crucial to reducing future outbreaks.
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Affiliation(s)
- Gareth A Thomas
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Teresa Paradell Gil
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Carsten T Müller
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Hilary J Rogers
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Cedric N Berger
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK.
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Wright KM, Marshall J, Wright PJ, Holden NJ. Vacuolar localisation of anthocyanin pigmentation in microgreen cotyledons of basil, cabbage and mustard greens does not impact on colonisation by Shiga-toxigenic Escherichia coli O157:H7. Food Microbiol 2023; 116:104367. [PMID: 37689428 DOI: 10.1016/j.fm.2023.104367] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 08/11/2023] [Accepted: 08/20/2023] [Indexed: 09/11/2023]
Abstract
Microgreens, the immature plants harvested after a few weeks of growth, are perceived as a heathy, nutritious food ingredient but may be susceptible to colonisation by human pathogens including Shiga-toxigenic Escherichia coli (STEC). Some microgreen cultivars accumulate anthocyanins or secrete essential oils which, when extracted or purified, have been reported to inhibit bacterial growth. Therefore, the impact of anthocyanins on bacterial colonisation by STEC (Sakai) was compared for three species that have pigmented cultivars: basil (Ocimum basilicum L.), cabbage (Brassica oleracea L.) and mustard greens (Brassica juncea L.). Inoculation with low concentrations of STEC (Sakai) (3 log10 colony forming units/ml (CFU/ml)) during seed germination resulted in extensive colonisation at the point of harvest, accumulating to ∼ 8 log10 CFU/g FW in all cultivars. Bacterial colonies frequently aligned with anticlinal walls on the surface of epidermal cells of the cotyledons and, in basil, associated with peltate and capitate gland cells. Crude lysates of pigmented and non-pigmented basil cultivars had no impact on STEC (Sakai) growth rates, viability status or biofilm formation. Anthocyanins are located within plant vacuoles of these microgreen cultivars and did not affect colonisation by STEC (Sakai) and pigmentation therefore cannot be considered as a controlling factor in bacterial interactions.
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Affiliation(s)
- Kathryn M Wright
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Jacqueline Marshall
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Peter J Wright
- Marine Scotland Science, 375 Victoria Road, Aberdeen, AB11 9DB, UK
| | - Nicola J Holden
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK; SRUC, Department of Rural Land Use, Craibstone Estate, Aberdeen, AB21 9YA, UK.
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Lagerstrom KM, Hadly EA. Under-Appreciated Phylogroup Diversity of Escherichia coli within and between Animals at the Urban-Wildland Interface. Appl Environ Microbiol 2023:e0014223. [PMID: 37191541 DOI: 10.1128/aem.00142-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
Wild animals have been implicated as reservoirs and even "melting pots" of pathogenic and antimicrobial-resistant bacteria of concern to human health. Though Escherichia coli is common among vertebrate guts and plays a role in the propagation of such genetic information, few studies have explored its diversity beyond humans nor the ecological factors that influence its diversity and distribution in wild animals. We characterized an average of 20 E. coli isolates per scat sample (n = 84) from a community of 14 wild and 3 domestic species. The phylogeny of E. coli comprises 8 phylogroups that are differentially associated with pathogenicity and antibiotic resistance, and we uncovered all of them in one small biological preserve surrounded by intense human activity. Challenging previous assumptions that a single isolate is representative of within-host phylogroup diversity, 57% of individual animals sampled carried multiple phylogroups simultaneously. Host species' phylogroup richness saturated at different levels across species and encapsulated vast within-sample and within-species variation, indicating that distribution patterns are influenced both by isolation source and laboratory sampling depth. Using ecological methods that ensure statistical relevance, we identify trends in phylogroup prevalence associated with host and environmental factors. The vast genetic diversity and broad distribution of E. coli in wildlife populations has implications for biodiversity conservation, agriculture, and public health, as well as for gauging unknown risks at the urban-wildland interface. We propose critical directions for future studies of the "wild side" of E. coli that will expand our understanding of its ecology and evolution beyond the human environment. IMPORTANCE To our knowledge, neither the phylogroup diversity of E. coli within individual wild animals nor that within an interacting multispecies community have previously been assessed. In doing so, we uncovered the globally known phylogroup diversity from an animal community on a preserve imbedded in a human-dominated landscape. We revealed that the phylogroup composition in domestic animals differed greatly from that in their wild counterparts, implying potential human impacts on the domestic animal gut. Significantly, many wild individuals hosted multiple phylogroups simultaneously, indicating the potential for strain-mixing and zoonotic spillback, especially as human encroachment into wildlands increases in the Anthropocene. We reason that due to extensive anthropogenic environmental contamination, wildlife is increasingly exposed to our waste, including E. coli and antibiotics. The gaps in the ecological and evolutionary understanding of E. coli thus necessitate a significant uptick in research to better understand human impacts on wildlife and the risk for zoonotic pathogen emergence.
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Affiliation(s)
| | - Elizabeth A Hadly
- Department of Biology, Stanford University, Stanford, California, USA
- Jasper Ridge Biological Preserve, Stanford University, Stanford, California, USA
- Center for Innovation in Global Health, Stanford University, Stanford, California, USA
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Bhowmik A, Shah SMT, Goswami S, Sirajee AS, Ahsan S. Predominance of Multidrug Resistant Escherichia coli of Environmental Phylotype in Different Environments of Dhaka, Bangladesh. Trop Med Infect Dis 2023; 8:tropicalmed8040226. [PMID: 37104351 PMCID: PMC10145502 DOI: 10.3390/tropicalmed8040226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/15/2023] [Accepted: 03/24/2023] [Indexed: 04/28/2023] Open
Abstract
Considering the ecological diversity of E. coli, the main aim of this study was to determine the prevalence, phylogroup diversity, and antimicrobial susceptibility of E. coli isolated from 383 different clinical and environmental sources. In total, varied prevalence was observed of the 197 confirmed E. coli that were isolated (human-100%, animal-67.5%, prawn-49.23%, soil-30.58%, and water-27.88%). Of these isolates, 70 (36%) were multidrug-resistant (MDR). MDR E. coli was significantly associated with their sources (χ2 = 29.853, p = 0.001). Humans (51.67%) and animals (51.85%) carried more MDR E. coli than other environments. The eae gene indicative of recent fecal contamination was not detected in any isolate, indicating that these E. coli isolates could be present in these environments for a long time and became naturalized. Phylogroup B1 (48.22%) was the predominant group, being present in all hosts analyzed and with the commensal E. coli group A (26.9%) representing the second predominant group. According to chi-square analysis, phylogroup B1 was significantly associated with E. coli from humans (p = 0.024), soil (p < 0.001) and prawn samples (p < 0.001). Human samples were significantly associated with phylogroup B1 (p = 0.024), D (p < 0.001), and F (p = 0.016) of E. coli strains, whereas phylogroup A (p < 0.001), C (p < 0.001), and E (p = 0.015) were associated with animal samples. Correspondence analysis results also indicated the association of these phylogroups with their hosts/sources. The findings of this study exhibited a non-random distribution of phylogenetic groups, though the diversity index was highest for human E. coli phylogroups.
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Affiliation(s)
- Anindita Bhowmik
- Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh
| | - S M Tanjil Shah
- Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh
| | | | | | - Sunjukta Ahsan
- Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh
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Charles Vegdahl A, Schaffner DW. Curli Production Influences Cross-contamination by Escherichia coli O157:H7 When Washing Fresh-cut Romaine Lettuce. J Food Prot 2023; 86:100023. [PMID: 36916579 DOI: 10.1016/j.jfp.2022.100023] [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: 10/09/2022] [Revised: 12/01/2022] [Accepted: 12/03/2022] [Indexed: 12/23/2022]
Abstract
Escherichia coli O157:H7 expresses extracellular proteins called curli that are essential for surface colonization. Transfer rates of E. coli O157:H7 0018+ (curli+), and 0018- (curli-) from inoculated to noninoculated lettuce pieces during washing were quantified in this study. Romaine lettuce pieces were inoculated with ∼6 log CFU on just the surface, just the cut edges, or both surface and cut edges. Samples were dried for 2 h in a biosafety cabinet and then washed with ten (10) noninoculated lettuce pieces in 500 mL of water for 30 s. The curli- strain was more readily removed (3 log reduction) compared to the curli+ (1 log reduction) when only the lettuce surface was inoculated (p > 0.05). The same was true when only the lettuce piece edge was inoculated (p > 0.05), although the magnitude of the reduction was less. There was no significant difference in reduction of curli+ strain between any of the surfaces. There was a significant difference (p < 0.05) in reduction of the curli- strains when comparing the leaf surface (more removal) to the cut leaf edge (less removal). The curli+ strain always showed significantly (p < 0.05) more transfer to noninoculated leaves regardless of the inoculation location. The curli+ strain transferred about -1 log percent (∼0.1%) to noninoculated pieces, while the curli- strain transferred about -2 log percent (∼0.01%) CFU to the noninoculated pieces. Mean log percent transfer was not significantly different within the curli+ or curli- experiments (p > 0.05). When the leaf surface was inoculated, there was about 2 log percent (i.e., close to 100% transfer) into the wash water for both the curli+ and curli- strains. When only the cut edges or surface and edge were inoculated, observed mean transfer rates were lower but not significantly different (p > 0.05). Further research is needed to more fully understand the factors that influence bacterial cross-contamination during the washing of fresh produce.
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Affiliation(s)
- Ann Charles Vegdahl
- Cornell University, Department of Food Science, Geneva, NY 14456, USA; Rutgers University, Department of Food Science, New Brunswick, NJ 08901, USA.
| | - Donald W Schaffner
- Rutgers University, Department of Food Science, New Brunswick, NJ 08901, USA
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Puri D, Fang X, Allison KR. Evidence of a possible multicellular life cycle in Escherichia coli. iScience 2022; 26:105795. [PMID: 36594031 PMCID: PMC9804144 DOI: 10.1016/j.isci.2022.105795] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 10/07/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
Biofilms are surface-attached multicellular microbial communities. Their genetics have been extensively studied, but the cell-scale morphogenetic events of their formation are largely unknown. Here, we recorded the entirety of morphogenesis in Escherichia coli, and discovered a previously unknown multicellular self-assembly process. Unattached, single-cells formed 4-cell rosettes which grew into constant-width chains. After ∼10 cell generations, these multicellular chains attached to surfaces and stopped growing. Chains remained clonal throughout morphogenesis. We showed that this process generates biofilms, which we found are composed of attached clonal chains, aligned in parallel. We investigated genetics of chain morphogenesis: Ag43 facilitates rosette formation and clonality; type-1 fimbriae and curli promote stability and configuration; and extracellular polysaccharide production facilitates attachment. Our study establishes that E. coli, a unicellular organism, can follow a multistage, clonal, genetically-regulated, rosette-initiated multicellular life cycle. These findings have implications for synthetic biology, multicellular development, and the treatment and prevention of bacterial diseases.
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Affiliation(s)
- Devina Puri
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, USA
| | - Xin Fang
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, USA
| | - Kyle R. Allison
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, USA,Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA,Corresponding author
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Wright KM, Wright PJ, Holden NJ. Plant species-dependent transmission of Escherichia coli O157:H7 from the spermosphere to cotyledons and first leaves. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:926-933. [PMID: 35968609 PMCID: PMC9804575 DOI: 10.1111/1758-2229.13115] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
The colonization of six edible plant species: alfalfa, broccoli, coriander, lettuce, parsley and rocket, by the human pathogen Shigatoxigenic Escherichia coli was investigated following two modes of artificial inoculation of seeds, by soaking or watering. The frequency and extent of colonization of cotyledons depended on the mode of inoculation, with three, rapidly germinating species being successfully colonized after overnight soaking, but slower germinating species requiring prolonged exposure to bacteria by watering of the surrounding growth media. Separate analysis of the cotyledons and leaves from individual plants highlighted that successful colonization of the true leaves was also species dependent. For three species, failure of transfer, or lack of nutrients or suitable microhabitat on the leaf surface resulted in infrequent bacterial colonization. Colonization of leaves was lower and generally in proportion to that in cotyledons, if present. The potential risks associated with consumption of leafy produce are discussed.
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Affiliation(s)
| | | | - Nicola Jean Holden
- The James Hutton InstituteInvergowrie, DundeeUK
- SRUC, Department of Rural Land Use, Craibstone EstateAberdeenUK
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Fang Y, Stanford K, Yang X. Lactic Acid Resistance and Population Structure of Escherichia coli from Meat Processing Environment. Microbiol Spectr 2022; 10:e0135222. [PMID: 36194136 PMCID: PMC9602453 DOI: 10.1128/spectrum.01352-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 09/09/2022] [Indexed: 12/30/2022] Open
Abstract
To explore the effect of beef processing on Escherichia coli populations in relation to lactic acid resistance, this study investigated the links among acid response, phylogenetic structure, genome diversity, and genotypes associated with acid resistance of meat plant E. coli. Generic E. coli isolates (n = 700) were from carcasses, fabrication equipment, and beef products. Acid treatment was carried out in Luria-Bertani broth containing 5.5% lactic acid (pH 2.9). Log reductions of E. coli ranged from <0.5 to >5 log CFU/mL (median: 1.37 log). No difference in lactic acid resistance was observed between E. coli populations recovered before and after a processing step or antimicrobial interventions. E. coli from the preintervention carcasses were slightly more resistant than E. coli isolated from equipment, differing by <0.5 log unit. Acid-resistant E. coli (log reduction <1, n = 45) had a higher prevalence of genes related to energy metabolism (ydj, xap, ato) and oxidative stress (fec, ymjC) than the less resistant E. coli (log reduction >1, n = 133). The ydj and ato operons were abundant in E. coli from preintervention carcasses. In contrast, fec genes were abundant in E. coli from equipment surfaces. The preintervention E. coli contained phylogroups A and B1 in relatively equal proportions. Phylogroup B1 predominated (95%) in the population from equipment. Of note, E. coli collected after sanitation shared either the antigens of O8 or H21. Additionally, genome diversity decreased after chilling and equipment sanitation. Overall, beef processing did not select for E. coli resistant to lactic acid but shaped the population structure. IMPORTANCE Antimicrobial interventions have significantly reduced the microbial loads on carcasses/meat products; however, the wide use of chemical and physical biocides has raised concerns over their potential for selecting resistant populations in the beef processing environment. Phenotyping of acid resistance and whole-genome analysis described in this study demonstrated beef processing practices led to differences in acid resistance, genotype, and population structure between carcass- and equipment-associated E. coli but did not select for the acid-resistant population. Results indicate that genes coding for the metabolism of long-chain sugar acids (ydj) and short-chain fatty acids (ato) were more prevalent in carcass-associated than equipment-associated E. coli. These results suggest E. coli from carcasses and equipment surfaces have been exposed to different selective pressures. The findings improve our understanding of the microbial ecology of E. coli in food processing environments and in general.
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Affiliation(s)
- Yuan Fang
- Agriculture and Agri-Food Canada Lacombe Research and Development Centre, Lacombe, Alberta, Canada
| | - Kim Stanford
- University of Lethbridge, Lethbridge, Alberta, Canada
| | - Xianqin Yang
- Agriculture and Agri-Food Canada Lacombe Research and Development Centre, Lacombe, Alberta, Canada
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Verma SK, Chen Q, White JF. Evaluation of colonization and mutualistic endophytic symbiosis of Escherichia coli with tomato and Bermuda grass seedlings. PeerJ 2022; 10:e13879. [PMID: 35971430 PMCID: PMC9375544 DOI: 10.7717/peerj.13879] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 07/19/2022] [Indexed: 01/18/2023] Open
Abstract
Escherichia coli is generally considered a bacterium associated with animal microbiomes. However, we present evidence that E. coli may also mutualistically colonize roots of plant species, even to the extent that it may become endophytic in plants. In this study we used GFP tagged E. coli to observe its colonization and effects on tomato (Solanum lycopersicum) and Bermuda grass (Cynodon dactylon) seedling development and growth. Inoculation with the bacterium significantly improved root development of both seedlings tested. Treatment also increased the photosynthetic pigments in Bermuda grass seedlings. However, effects on shoot length in both seedlings were not significant. This bacterium was found to produce indole acetic acid (IAA) up to 8.68 ± 0.43 µg ml-1 in the broth medium amended with tryptophan. Effects on seedling root growth could, in part, be explained by IAA production. Bacteria successfully colonized the root surfaces and interiors of both seedlings. Tagged bacteria expressing the GFP were observed in the vascular tissues of Bermuda grass seedling roots. Seedlings with bacteria showed greater survival and were healthier than seedlings without bacteria, indicating that E. coli set up a successful mutualistic symbiosis with seedlings. E. coli is not commonly considered to be a plant endophyte but is more generally considered to be a crop contaminant. In this study we show that E. coli may also be an endophyte in plant tissues.
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Affiliation(s)
- Satish K. Verma
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Qiang Chen
- Department of Plant Biology, Rutgers University, New Brunswick, New Jersey, United States of America
| | - James Francis White
- Department of Plant Biology, Rutgers University, New Brunswick, New Jersey, United States of America
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11
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Behruznia M, Gordon DM. Molecular and metabolic characteristics of wastewater associated Escherichia coli strains. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:646-654. [PMID: 35638456 PMCID: PMC9543349 DOI: 10.1111/1758-2229.13076] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 04/18/2022] [Indexed: 06/04/2023]
Abstract
We previously characterized the genetic diversity of Escherichia coli strains isolated from septic tanks in the Canberra region, Australia. In this study, we used repetitive element palindromic (REP) PCR fingerprinting to identify dominant REP-types belonging to phylogroups A and B1 strains across septic tanks. Subsequently, 76 E. coli strains were selected for whole-genome sequencing and phenotype microarrays. Comparative genome analysis was performed to compare septic tank E. coli genomes with a collection of 433 E. coli isolates from different hosts and freshwater. Clonal complexes (CCs) 10 (n = 15) and 399 (n = 10) along with sequence type (ST) 401 (n = 9) were the common lineages in septic tanks. CC10 strains have been detected from animal hosts and freshwater, whereas CC399 and ST401 strains appeared to be associated with septic tanks as they were uncommon in isolates from other sources. Comparative genome analysis revealed that CC399 and ST401 were genetically distinct from other isolates and carried an abundance of niche-specific traits involved in environmental adaptation. These strains also showed distinct metabolic characteristics, such as the ability to utilize pectin, which may provide a fitness advantage under nutrient-limited conditions. The results of this study characterized the adaptive mechanisms allowing E. coli to persist in wastewater.
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Affiliation(s)
- Mahboobeh Behruznia
- Division of Ecology and Evolution, Research School of BiologyThe Australian National UniversityCanberraACT2601Australia
| | - David M. Gordon
- Division of Ecology and Evolution, Research School of BiologyThe Australian National UniversityCanberraACT2601Australia
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Zara ES, Vital PG. Phylogroup typing and carbapenem resistance of Escherichia coli from agricultural samples in Metro Manila, Philippines. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART. B, PESTICIDES, FOOD CONTAMINANTS, AND AGRICULTURAL WASTES 2022; 57:644-656. [PMID: 35852239 DOI: 10.1080/03601234.2022.2096988] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Primary production environment is considered as reservoir of Escherichia coli contamination of produce. E. coli is classified into eight phylogroups which differ in ecological niches, evolutionary history, and phenotypic properties. To understand the population genetic structure and composition of E. coli in primary production environments in Metro Manila, Philippines, a total of 80 E. coli recovered from irrigation water, soil, vegetables, and feces of cat, carabao, chicken, dog, and goat were allocated into distinct phylogroups based on the presence and absence of genetic markers. Results showed that the most prevalent phylogroup was B1 (71.3%), followed by A (18.6%), D (6.3%), B2 (1.3%), E (1.3%), and an unknown phylogroup (1.3%). The most prevalent genetic marker was arpA, followed by TspE4.C2, yjaA, and chuA. The carbapenem resistance of 24 E. coli isolates representing different phylogroups was also evaluated. Intriguingly, all isolates exhibited uniform susceptibility. This is the first report to provide insights into the phylogroup structure and composition, as well as carbapenem resistance of E. coli from primary production in the Philippines, which highlights possible source of and solution for gastrointestinal and enteric diseases.
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Affiliation(s)
- Enrico S Zara
- Natural Sciences Research Institute, University of the Philippines Diliman, Quezon City, Philippines
| | - Pierangeli G Vital
- Natural Sciences Research Institute, University of the Philippines Diliman, Quezon City, Philippines
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Baloyi T, Duvenage S, Du Plessis E, Villamizar-Rodríguez G, Korsten L. Multidrug resistant Escherichia coli from fresh produce sold by street vendors in South African informal settlements. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2022; 32:1513-1528. [PMID: 33706630 DOI: 10.1080/09603123.2021.1896681] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 02/23/2021] [Indexed: 06/12/2023]
Abstract
The aim of this study was to assess the prevalence of commensal and pathogenic Escherichia coli on informally sold fresh produce in South Africa, who harbour and express antimicrobial resistance genes and therefore pose indirect risks to public health. The majority (85.71%) of E. coli isolates from spinach, apples, carrots, cabbage and tomatoes, were multidrug resistant (MDR). Resistance to Aminoglycoside (94.81%), Cephalosporin (93.51%), Penicillin (93.51%) and Chloramphenicol (87.01%) antibiotic classes were most prevalent. Antibiotic resistance genes detected included blaTEM (89.29%), tetA (82.14%), tetB (53.57%), tetL (46.43%), sulI (41.07%), sulII (51.79%), aadA1a (58.93%) and strAB (51.79%). A single isolate was found to harbour eae virulence factor. Moreover, E. coli isolates were grouped into the intra-intestinal infectious phylogenetic group E (28.57%), the rare group C (26.79%), the generalist group B1 (21.43%) and the human commensal group A (16.07%). Presence of MDR E. coli represents a transmission route and significant human health risk.
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Affiliation(s)
- Tintswalo Baloyi
- Department of Science and Innovation-National Research Foundation Centre of Excellence in Food Security, Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - Stacey Duvenage
- Department of Science and Innovation-National Research Foundation Centre of Excellence in Food Security, Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - Erika Du Plessis
- Department of Science and Innovation-National Research Foundation Centre of Excellence in Food Security, Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - Germán Villamizar-Rodríguez
- Department of Science and Innovation-National Research Foundation Centre of Excellence in Food Security, Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - Lise Korsten
- Department of Science and Innovation-National Research Foundation Centre of Excellence in Food Security, Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
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Pellegrini MC, Okada E, González Pasayo RA, Ponce AG. Prevalence of Escherichia coli strains in horticultural farms from Argentina: antibiotic resistance, biofilm formation, and phylogenetic affiliation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:23225-23236. [PMID: 34802078 DOI: 10.1007/s11356-021-17523-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 11/10/2021] [Indexed: 06/13/2023]
Abstract
Escherichia coli is the bacteria most commonly used as an indicator of fecal contamination in agricultural environments. Moreover, E. coli is categorized as a priority pathogen due to its widespread antibiotic resistance. This study aimed to characterize E. coli strains isolated from 10 horticultural farms. Isolates were obtained from samples of vegetable crops (n = 62), the surrounding soil (n = 62), poultry litter (n = 8), and groundwater (n = 6). Phyllo-grouping assignment was performed on the total of E. coli isolates. Antibiograms and quantification of the minimal inhibitory concentration (MIC) were performed with antibiotics commonly used in humans. Biofilm formation capacity was studied by quantifying cells attached to culture tubes. Overall, 21 E. coli isolates were obtained. Three phylogenetic groups (A, B1, and C) and two Escherichia clade IV and IV-V were identified in the collection by polymerase chain reaction. Sixty-seven percent of the E. coli isolates were resistant to amoxicillin-clavulanic acid and/or ampicillin. Amoxicillin MIC values ranged from 11.9 to >190.5 µg/mL and ampicillin MIC values ranged from 3 to >190.5 µg/mL. All the E. coli isolates, resistant and non-resistant, had biofilm forming capacity. The presence of phenotypic resistance on fresh produce and environmental matrices could present significant opportunities for contamination that result in health risks for consumers. To the authors' best knowledge, this is the first environmental assessment of resistant E. coli occurrence in horticultural farms in South America.
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Affiliation(s)
- María Celeste Pellegrini
- Grupo de Investigación en Ingeniería en Alimentos (GIIA), Instituto de Ciencia y Tecnología de alimentos y ambiente (INCITAA, CIC-UNMDP), Facultad de Ingeniería, Universidad Nacional de Mar del Plata, Av. Juan B. Justo 4302, B7602AYL Mar del, Plata, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, CABA, Argentina.
| | - Elena Okada
- Instituto Nacional de Tecnología Agropecuaria (INTA) Centro Regional Buenos Aires Sur. Estación Experimental Agropecuaria Balcarce, Ruta 226 Km 73.5, 7620, Balcarce, Argentina
| | - Ramón Alejandro González Pasayo
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Innovación para la Producción Agropecuaria y Desarrollo Sostenible (IPADS, CONICET-INTA), Ruta 226 km 73.5, Balcarce, 7620, Buenos Aires, Argentina
| | - Alejandra Graciela Ponce
- Grupo de Investigación en Ingeniería en Alimentos (GIIA), Instituto de Ciencia y Tecnología de alimentos y ambiente (INCITAA, CIC-UNMDP), Facultad de Ingeniería, Universidad Nacional de Mar del Plata, Av. Juan B. Justo 4302, B7602AYL Mar del, Plata, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, CABA, Argentina
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Bong CW, Low KY, Chai LC, Lee CW. Prevalence and Diversity of Antibiotic Resistant Escherichia coli From Anthropogenic-Impacted Larut River. Front Public Health 2022; 10:794513. [PMID: 35356018 PMCID: PMC8960044 DOI: 10.3389/fpubh.2022.794513] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 01/20/2022] [Indexed: 11/13/2022] Open
Abstract
Aquatic environments, under frequent anthropogenic pressure, could serve as reservoirs that provide an ideal condition for the acquisition and dissemination of antibiotic resistance genetic determinants. We investigated the prevalence and diversity of antibiotic-resistant Escherichia coli by focusing on their genetic diversity, virulence, and resistance genes in anthropogenic-impacted Larut River. The abundance of E. coli ranged from (estimated count) Est 1 to 4.7 × 105 (colony-forming units per 100 ml) CFU 100 ml−1 to Est 1 to 4.1 × 105 CFU 100 ml−1 with phylogenetic group B1 (46.72%), and A (34.39%) being the most predominant. The prevalence of multiple antibiotic resistance phenotypes of E. coli, with the presence of tet and sul resistance genes, was higher in wastewater effluents than in the river waters. These findings suggested that E. coli could be an important carrier of the resistance genes in freshwater river environments. The phylogenetic composition of E. coli and resistance genes was associated with physicochemical properties and antibiotic residues. These findings indicated that the anthropogenic inputs exerted an effect on the E. coli phylogroup composition, diversification of multiple antibiotic resistance phenotypes, and the distribution of resistance genes in the Larut River.
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Affiliation(s)
- Chui Wei Bong
- Institute of Biological Sciences, Universiti Malaya, Kuala Lumpur, Malaysia
- Institute of Ocean and Earth Sciences (IOES), Universiti Malaya, Kuala Lumpur, Malaysia
- *Correspondence: Chui Wei Bong ;
| | - Kyle Young Low
- Institute of Ocean and Earth Sciences (IOES), Universiti Malaya, Kuala Lumpur, Malaysia
- Institute for Advanced Studies, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Lay Ching Chai
- Institute of Biological Sciences, Universiti Malaya, Kuala Lumpur, Malaysia
- Institute of Ocean and Earth Sciences (IOES), Universiti Malaya, Kuala Lumpur, Malaysia
| | - Choon Weng Lee
- Institute of Biological Sciences, Universiti Malaya, Kuala Lumpur, Malaysia
- Institute of Ocean and Earth Sciences (IOES), Universiti Malaya, Kuala Lumpur, Malaysia
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16
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Ratshilingano MT, du Plessis EM, Duvenage S, Korsten L. Characterization of Multidrug-Resistant Escherichia coli Isolated from Two Commercial Lettuce and Spinach Supply Chains. J Food Prot 2022; 85:122-132. [PMID: 34324673 DOI: 10.4315/jfp-21-125] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 07/24/2021] [Indexed: 11/11/2022]
Abstract
ABSTRACT Leafy green vegetables have increasingly been reported as a reservoir of multidrug-resistant pathogenic Enterobacteriaceae, with Shiga toxin-producing Escherichia coli frequently implicated in disease outbreaks worldwide. This study examined the presence and characteristics of antibiotic resistance, diarrheagenic virulence genes, and phylogenetic groupings of E. coli isolates (n = 51) from commercially produced lettuce and spinach from farms, through processing, and at the point of sale. Multidrug resistance was observed in 33 (64.7%) of the 51 E. coli isolates, with 35.7% (10 of 28) being generic and 100% (23 of 23) being extended-spectrum β-lactamase/AmpC producing. Resistance of E. coli isolates was observed against neomycin (51 of 51, 100%), ampicillin (36 of 51, 70.6%), amoxicillin (35 of 51, 68.6%), tetracycline (23 of 51, 45%), trimethoprim-sulfamethoxazole (22 of 51, 43%), chloramphenicol (13 of 51, 25.5%), Augmentin (6 of 51, 11.8%), and gentamicin (4 of 51, 7.8%), with 100% (51 of 51) susceptibility to imipenem. Virulence gene eae was detected in two E. coli isolates from irrigation water sources only, whereas none of the other virulence genes for which we tested were detected. Most of the E. coli strains belonged to phylogenetic group B2 (25.5%; n = 13), B1 (19.6%; n = 10), and A (17.6%; n = 9), with D (5.9%; n = 3) less distributed. Although diarrheagenic E. coli was not detected, antibiotic resistance in E. coli prevalent in the supply chain was evident. In addition, a clear link between E. coli isolates from irrigation water sources and leafy green vegetables through DNA fingerprinting was established, indicating the potential transfer of E. coli from irrigation water to minimally processed leafy green vegetables. HIGHLIGHTS
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Affiliation(s)
- Muneiwa T Ratshilingano
- Department of Plant and Soil Sciences, University of Pretoria, Hatfield, Pretoria 0002, South Africa
| | - Erika M du Plessis
- Department of Plant and Soil Sciences, University of Pretoria, Hatfield, Pretoria 0002, South Africa
| | - Stacey Duvenage
- Department of Plant and Soil Sciences, University of Pretoria, Hatfield, Pretoria 0002, South Africa
- Department of Science and Innovation-National Research Foundation Centre of Excellence in Food Security, South Africa
| | - Lise Korsten
- Department of Plant and Soil Sciences, University of Pretoria, Hatfield, Pretoria 0002, South Africa
- Department of Science and Innovation-National Research Foundation Centre of Excellence in Food Security, South Africa
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17
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Interplay between Bacterial Clones and Plasmids in the Spread of Antibiotic Resistance Genes in the Gut: Lessons from a Temporal Study in Veal Calves. Appl Environ Microbiol 2021; 87:e0135821. [PMID: 34613750 DOI: 10.1128/aem.01358-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Intestinal carriage of extended spectrum β-lactamase (ESBL)-producing Escherichia coli is a frequent, increasing, and worrying phenomenon, but little is known about the molecular scenario and the evolutionary forces at play. We screened 45 veal calves, known to have high prevalence of carriage, for ESBL-producing E. coli on 514 rectal swabs (one randomly selected colony per sample) collected over 6 months. We characterized the bacterial clones and plasmids carrying blaESBL genes with a combination of genotyping methods, whole genome sequencing, and conjugation assays. One hundred and seventy-three ESBL-producing E. coli isolates [blaCTX-M-1 (64.7%), blaCTX-M-14 (33.5%), or blaCTX-M-15 (1.8%)] were detected, belonging to 32 bacterial clones, mostly of phylogroup A. Calves were colonized successively by different clones with a trend in decreasing carriage. The persistence of a clone in a farm was significantly associated with the number of calves colonized. Despite a high diversity of E. coli clones and blaCTX-M-carrying plasmids, few blaCTX-M gene/plasmid/chromosomal background combinations dominated, due to (i) efficient colonization of bacterial clones and/or (ii) successful plasmid spread in various bacterial clones. The scenario "clone versus plasmid spread" depended on the farm. Thus, epistatic interactions between resistance genes, plasmids, and bacterial clones contribute to optimize fitness in specific environments. IMPORTANCE The gut microbiota is the epicenter of the emergence of resistance. Considerable amount of knowledge on the molecular mechanisms of resistance has been accumulated, but the ecological and evolutionary forces at play in nature are less studied. In this context, we performed a field work on temporal intestinal carriage of extended spectrum β-lactamase (ESBL)-producing Escherichia coli in veal farms. Veal calves are animals with one of the highest levels of ESBL producing E. coli fecal carriage, due to early high antibiotic exposure. We were able to show that calves were colonized successively by different ESBL-producing E. coli clones, and that two main scenarios were at play in the spread of blaCTX-M genes among calves: efficient colonization of several calves by a few bacterial clones and successful plasmid spread in various bacterial clones. Such knowledge should help develop new strategies to fight the emergence of antibiotic-resistance.
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NandaKafle G, Huegen T, Potgieter SC, Steenkamp E, Venter SN, Brözel VS. Niche Preference of Escherichia coli in a Peri-Urban Pond Ecosystem. Life (Basel) 2021; 11:life11101020. [PMID: 34685391 PMCID: PMC8538306 DOI: 10.3390/life11101020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/17/2021] [Accepted: 09/25/2021] [Indexed: 11/23/2022] Open
Abstract
Escherichia coli comprises diverse strains with a large accessory genome, indicating functional diversity and the ability to adapt to a range of niches. Specific strains would display greatest fitness in niches matching their combination of phenotypic traits. Given this hypothesis, we sought to determine whether E. coli in a peri-urban pond and associated cattle pasture display niche preference. Samples were collected from water, sediment, aquatic plants, water snails associated with the pond, as well as bovine feces from cattle in an adjacent pasture. Isolates (120) were obtained after plating on Membrane Lactose Glucuronide Agar (MLGA). We used the uidA and mutS sequences for all isolates to determine phylogeny by maximum likelihood, and population structure through gene flow analysis. PCR was used to allocate isolates to phylogroups and to determine the presence of pathogenicity/virulence genes (stxI, stxII, eaeA, hlyA, ST, and LT). Antimicrobial resistance was determined using a disk diffusion assay for Tetracycline, Gentamicin, Ciprofloxacin, Meropenem, Ceftriaxone, and Azithromycin. Our results showed that isolates from water, sediment, and water plants were similar by phylogroup distribution, virulence gene distribution, and antibiotic resistance while both snail and feces populations were significantly different. Few of the feces isolates were significantly similar to aquatic ones, and most of the snail isolates were also different. Population structure analysis indicated three genetic backgrounds associated with bovine, snail, and aquatic environments. Collectively these data support niche preference of E. coli isolates occurring in this ecosystem.
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Affiliation(s)
- Gitanjali NandaKafle
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA; (G.N.); (T.H.)
| | - Taylor Huegen
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA; (G.N.); (T.H.)
| | - Sarah C. Potgieter
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0004, South Africa; (S.C.P.); (E.S.); (S.N.V.)
| | - Emma Steenkamp
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0004, South Africa; (S.C.P.); (E.S.); (S.N.V.)
| | - Stephanus N. Venter
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0004, South Africa; (S.C.P.); (E.S.); (S.N.V.)
| | - Volker S. Brözel
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA; (G.N.); (T.H.)
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0004, South Africa; (S.C.P.); (E.S.); (S.N.V.)
- Correspondence:
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19
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Saraceno M, Gómez Lugo S, Ortiz N, Gómez BM, Sabio Y García CA, Frankel N, Graziano M. Unraveling the ecological processes modulating the population structure of Escherichia coli in a highly polluted urban stream network. Sci Rep 2021; 11:14679. [PMID: 34282205 PMCID: PMC8289912 DOI: 10.1038/s41598-021-94198-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 07/07/2021] [Indexed: 02/06/2023] Open
Abstract
Escherichia coli dynamics in urban watersheds are affected by a complex balance among external inputs, niche modulation and genetic variability. To explore the ecological processes influencing E. coli spatial patterns, we analyzed its abundance and phylogenetic structure in water samples from a stream network with heterogeneous urban infrastructure and environmental conditions. Our results showed that environmental and infrastructure variables, such as macrophyte coverage, DIN and sewerage density, mostly explained E. coli abundance. Moreover, main generalist phylogroups A and B1 were found in high proportion, which, together with an observed negative relationship between E. coli abundance and phylogroup diversity, suggests that their dominance might be due to competitive exclusion. Lower frequency phylogroups were associated with sites of higher ecological disturbance, mainly involving simplified habitats, higher drainage infrastructure and septic tank density. In addition to the strong negative relationship between phylogroup diversity and dominance, the occurrence of these phylogroups would be associated with increased facilitated dispersal. Nutrients also contributed to explaining phylogroup distribution. Our study proposes the differential contribution of distinct ecological processes to the patterns of E. coli in an urban watershed, which is useful for the monitoring and management of fecal pollution.
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Affiliation(s)
- Martín Saraceno
- Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), CONICET - Universidad de Buenos Aires, 1428, Buenos Aires, Argentina
- Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, 1428, Buenos Aires, Argentina
| | - Sebastián Gómez Lugo
- Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, 1428, Buenos Aires, Argentina
| | - Nicolás Ortiz
- Instituto Nacional del Agua, 1804, Ezeiza, Argentina
| | | | - Carmen A Sabio Y García
- Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, 1428, Buenos Aires, Argentina
| | - Nicolás Frankel
- Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, 1428, Buenos Aires, Argentina
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET - Universidad de Buenos Aires, 1428, Buenos Aires, Argentina
| | - Martín Graziano
- Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), CONICET - Universidad de Buenos Aires, 1428, Buenos Aires, Argentina.
- Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, 1428, Buenos Aires, Argentina.
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20
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Tharek M, Khairuddin D, Najimudin N, Ghazali AH. Plant Growth Promoting Potentials of Beneficial Endophytic Escherichia coli USML2 in Association with Rice Seedlings. Trop Life Sci Res 2021; 32:119-143. [PMID: 33936555 PMCID: PMC8054666 DOI: 10.21315/tlsr2021.32.1.8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
An endophytic Escherichia coli USML2 originally isolated from the inner part of an oil palm (Elaeis guineensis Jacq.) leaf tissue was inoculated to rice seedlings to investigate its ability in colonising plant inner tissues and promoting growth. Infection of E. coli USML2 was initiated by colonisation on the root surface, invasion of the interior root system followed by endophytic spreading. Inoculation of E. coli USML2 in the rice rhizosphere zone resulted in a significant increase in leaf numbers (33.3%), chlorophyll content (33.3%), shoot height (34.8%) and plant dry weight (90.4%) of 42 days old rice seedlings as compared to the control. These findings also demonstrated the ability of E. coli USML2 to spread endophytically which serves as a beneficial strategy for the bacterium to colonise the host plant and gain protection against adverse soil conditions. The genome of E. coli USML2 had also revealed predicted genes essential for endophytic bacterial colonisation and plant growth promotion which further proven potentials of E. coli USML2 as Plant Growth Promoting Endophyte (PGPE).
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Affiliation(s)
- Munirah Tharek
- School of Biological Sciences, Universiti Sains Malaysia, 11800 USM Pulau Pinang, Malaysia
| | - Dzulaikha Khairuddin
- Department of Water Resources and Environmental System, Faculty of Civil Engineering, Universiti Teknologi MARA, 40450 Shah Alam, Selangor, Malaysia
| | - Nazalan Najimudin
- School of Biological Sciences, Universiti Sains Malaysia, 11800 USM Pulau Pinang, Malaysia
| | - Amir Hamzah Ghazali
- School of Biological Sciences, Universiti Sains Malaysia, 11800 USM Pulau Pinang, Malaysia
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21
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Singh NS, Singhal N, Kumar M, Virdi JS. High Prevalence of Drug Resistance and Class 1 Integrons in Escherichia coli Isolated From River Yamuna, India: A Serious Public Health Risk. Front Microbiol 2021; 12:621564. [PMID: 33633708 PMCID: PMC7899961 DOI: 10.3389/fmicb.2021.621564] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 01/05/2021] [Indexed: 11/16/2022] Open
Abstract
Globally, urban water bodies have emerged as an environmental reservoir of antimicrobial resistance (AMR) genes because resistant bacteria residing here might easily disseminate these traits to other waterborne pathogens. In the present study, we have investigated the AMR phenotypes, prevalent plasmid-mediated AMR genes, and integrons in commensal strains of Escherichia coli, the predominant fecal indicator bacteria isolated from a major urban river of northern India Yamuna. The genetic environment of blaCTX–M–15 was also investigated. Our results indicated that 57.5% of the E. coli strains were resistant to at least two antibiotic classes and 20% strains were multidrug resistant, i.e., resistant to three or more antibiotic classes. The multiple antibiotic resistance index of about one-third of the E. coli strains was quite high (>0.2), reflecting high contamination of river Yamuna with antibiotics. With regard to plasmid-mediated AMR genes, blaTEM–1 was present in 95% of the strains, followed by qnrS1 and armA (17% each), blaCTX–M–15 (15%), strA-strB (12%), and tetA (7%). Contrary to the earlier reports where blaCTX–M–15 was mostly associated with pathogenic phylogroup B2, our study revealed that the CTX-M-15 type extended-spectrum β-lactamases (ESBLs) were present in the commensal phylogroups A and B1, also. The genetic organization of blaCTX–M–15 was similar to that reported for E. coli, isolated from other parts of the world; and ISEcp1 was present upstream of blaCTX–M–15. The integrons of classes 2 and 3 were absent, but class 1 integron gene intI1 was present in 75% of the isolates, denoting its high prevalence in E. coli of river Yamuna. These evidences indicate that due to high prevalence of plasmid-mediated AMR genes and intI1, commensal E. coli can become vehicles for widespread dissemination of AMR in the environment. Thus, regular surveillance and management of urban rivers is necessary to curtail the spread of AMR and associated health risks.
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Affiliation(s)
- Nambram Somendro Singh
- Department of Microbiology, University of Delhi South Campus, New Delhi, India.,Department of Biophysics, University of Delhi South Campus, New Delhi, India
| | - Neelja Singhal
- Department of Biophysics, University of Delhi South Campus, New Delhi, India
| | - Manish Kumar
- Department of Biophysics, University of Delhi South Campus, New Delhi, India
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22
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Nowicki S, deLaurent ZR, de Villiers EP, Githinji G, Charles KJ. The utility of Escherichia coli as a contamination indicator for rural drinking water: Evidence from whole genome sequencing. PLoS One 2021; 16:e0245910. [PMID: 33481909 PMCID: PMC7822521 DOI: 10.1371/journal.pone.0245910] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 01/09/2021] [Indexed: 12/12/2022] Open
Abstract
Across the water sector, Escherichia coli is the preferred microbial water quality indicator and current guidance upholds that it indicates recent faecal contamination. This has been challenged, however, by research demonstrating growth of E. coli in the environment. In this study, we used whole genome sequencing to investigate the links between E. coli and recent faecal contamination in drinking water. We sequenced 103 E. coli isolates sampled from 9 water supplies in rural Kitui County, Kenya, including points of collection (n = 14) and use (n = 30). Biomarkers for definitive source tracking remain elusive, so we analysed the phylogenetic grouping, multi-locus sequence types (MLSTs), allelic diversity, and virulence and antimicrobial resistance (AMR) genes of the isolates for insight into their likely source. Phylogroup B1, which is generally better adapted to water environments, is dominant in our samples (n = 69) and allelic diversity differences (z = 2.12, p = 0.03) suggest that naturalised populations may be particularly relevant at collection points with lower E. coli concentrations (<50 / 100mL). The strains that are more likely to have originated from human and/or recent faecal contamination (n = 50), were found at poorly protected collection points (4 sites) or at points of use (12 sites). We discuss the difficulty of interpreting health risk from E. coli grab samples, especially at household level, and our findings support the use of E. coli risk categories and encourage monitoring that accounts for sanitary conditions and temporal variability.
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Affiliation(s)
- Saskia Nowicki
- School of Geography and the Environment, University of Oxford, Oxford, United Kingdom
| | - Zaydah R. deLaurent
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Etienne P. de Villiers
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
- Department of Public Health, Pwani University, Kilifi, Kenya
| | - George Githinji
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Katrina J. Charles
- School of Geography and the Environment, University of Oxford, Oxford, United Kingdom
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Kamal SM, Cimdins-Ahne A, Lee C, Li F, Martín-Rodríguez AJ, Seferbekova Z, Afasizhev R, Wami HT, Katikaridis P, Meins L, Lünsdorf H, Dobrindt U, Mogk A, Römling U. A recently isolated human commensal Escherichia coli ST10 clone member mediates enhanced thermotolerance and tetrathionate respiration on a P1 phage-derived IncY plasmid. Mol Microbiol 2020; 115:255-271. [PMID: 32985020 PMCID: PMC7984374 DOI: 10.1111/mmi.14614] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 09/16/2020] [Accepted: 09/17/2020] [Indexed: 12/29/2022]
Abstract
The ubiquitous human commensal Escherichia coli has been well investigated through its model representative E. coli K‐12. In this work, we initially characterized E. coli Fec10, a recently isolated human commensal strain of phylogroup A/sequence type ST10. Compared to E. coli K‐12, the 4.88 Mbp Fec10 genome is characterized by distinct single‐nucleotide polymorphisms and acquisition of genomic islands. In addition, E. coli Fec10 possesses a 155.86 kbp IncY plasmid, a composite element based on phage P1. pFec10 harbours multiple cargo genes such as coding for a tetrathionate reductase and its corresponding regulatory two‐component system. Among the cargo genes is also the Transmissible Locus of Protein Quality Control (TLPQC), which mediates tolerance to lethal temperatures in bacteria. The disaggregase ClpGGI of TLPQC constitutes a major determinant of the thermotolerance of E. coli Fec10. We confirmed stand‐alone disaggregation activity, but observed distinct biochemical characteristics of ClpGGI‐Fec10 compared to the nearly identical Pseudomonas aeruginosa ClpGGI‐SG17M. Furthermore, we noted a unique contribution of ClpGGI‐Fec10 to the exquisite thermotolerance of E. coli Fec10, suggesting functional differences between both disaggregases in vivo. Detection of thermotolerance in 10% of human commensal E. coli isolates hints to the successful establishment of food‐borne heat‐resistant strains in the human gut.
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Affiliation(s)
- Shady Mansour Kamal
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.,Department of Microbiology and Immunology, Faculty of Pharmaceutical Sciences & Pharmaceutical Industries, Future University in Egypt, Cairo, Egypt
| | | | - Changhan Lee
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Fengyang Li
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | | | - Zaira Seferbekova
- Kharkevich Institute for Information Transmission Problems, RAS, Moscow, Russia.,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Robert Afasizhev
- Kharkevich Institute for Information Transmission Problems, RAS, Moscow, Russia
| | | | - Panagiotis Katikaridis
- Center for Molecular Biology, University of Heidelberg (ZMBH), German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Lena Meins
- Center for Molecular Biology, University of Heidelberg (ZMBH), German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | | | - Ulrich Dobrindt
- Institute of Hygiene, University of Münster, Münster, Germany
| | - Axel Mogk
- Center for Molecular Biology, University of Heidelberg (ZMBH), German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Ute Römling
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
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24
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Breckell G, Silander OK. Complete Genome Sequences of 47 Environmental Isolates of Escherichia coli. Microbiol Resour Announc 2020; 9:e00222-20. [PMID: 32943554 PMCID: PMC7498420 DOI: 10.1128/mra.00222-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 08/21/2020] [Indexed: 12/14/2022] Open
Abstract
Escherichia coli is commonly considered a host-associated bacterium. However, there is evidence that some strains occupy environmental (non-host-associated) niches. Here, we report the complete genomes of 47 Escherichia coli environmental isolates. These will be useful for understanding the dynamics of plasmids, phages, and other repetitive genetic elements.
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Affiliation(s)
- Georgia Breckell
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
| | - Olin K Silander
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
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25
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Barth SA, Weber M, Schaufler K, Berens C, Geue L, Menge C. Metabolic Traits of Bovine Shiga Toxin-Producing Escherichia Coli (STEC) Strains with Different Colonization Properties. Toxins (Basel) 2020; 12:toxins12060414. [PMID: 32580365 PMCID: PMC7354573 DOI: 10.3390/toxins12060414] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/10/2020] [Accepted: 06/17/2020] [Indexed: 01/14/2023] Open
Abstract
Cattle harbor Shiga toxin-producing Escherichia coli (STEC) in their intestinal tract, thereby providing these microorganisms with an ecological niche, but without this colonization leading to any clinical signs. In a preceding study, genotypic characterization of bovine STEC isolates unveiled that their ability to colonize cattle persistently (STECper) or only sporadically (STECspo) is more closely associated with the overall composition of the accessory rather than the core genome. However, the colonization pattern could not be unequivocally linked to the possession of classical virulence genes. This study aimed at assessing, therefore, if the presence of certain phenotypic traits in the strains determines their colonization pattern and if these can be traced back to distinctive genetic features. STECspo strains produced significantly more biofilm than STECper when incubated at lower temperatures. Key substrates, the metabolism of which showed a significant association with colonization type, were glyoxylic acid and L-rhamnose, which were utilized by STECspo, but not or only by some STECper. Genomic sequences of the respective glc and rha operons contained mutations and frameshifts in uptake and/or regulatory genes, particularly in STECper. These findings suggest that STECspo conserved features leveraging survival in the environment, whereas the acquisition of a persistent colonization phenotype in the cattle reservoir was accompanied by the loss of metabolic properties and genomic mutations in the underlying genetic pathways.
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Affiliation(s)
- Stefanie A. Barth
- Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Naumburger Str. 96a, 07743 Jena, Germany; (M.W.); (C.B.); (L.G.); (C.M.)
- Correspondence: ; Tel.: +49-3641-804-2270; Fax: +49-3641-804-2482
| | - Michael Weber
- Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Naumburger Str. 96a, 07743 Jena, Germany; (M.W.); (C.B.); (L.G.); (C.M.)
| | - Katharina Schaufler
- Free University Berlin, Institute of Microbiology and Epizootics, Robert-von-Ostertag-Str. 7-13, 14163 Berlin, Germany;
- University of Greifswald, Pharmaceutical Microbiology, Friedrich-Ludwig-Jahn-Str. 17, 17489 Greifswald, Germany
| | - Christian Berens
- Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Naumburger Str. 96a, 07743 Jena, Germany; (M.W.); (C.B.); (L.G.); (C.M.)
| | - Lutz Geue
- Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Naumburger Str. 96a, 07743 Jena, Germany; (M.W.); (C.B.); (L.G.); (C.M.)
| | - Christian Menge
- Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Naumburger Str. 96a, 07743 Jena, Germany; (M.W.); (C.B.); (L.G.); (C.M.)
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26
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Touchon M, Perrin A, de Sousa JAM, Vangchhia B, Burn S, O’Brien CL, Denamur E, Gordon D, Rocha EPC. Phylogenetic background and habitat drive the genetic diversification of Escherichia coli. PLoS Genet 2020; 16:e1008866. [PMID: 32530914 PMCID: PMC7314097 DOI: 10.1371/journal.pgen.1008866] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 06/24/2020] [Accepted: 05/18/2020] [Indexed: 12/15/2022] Open
Abstract
Escherichia coli is mostly a commensal of birds and mammals, including humans, where it can act as an opportunistic pathogen. It is also found in water and sediments. We investigated the phylogeny, genetic diversification, and habitat-association of 1,294 isolates representative of the phylogenetic diversity of more than 5,000 isolates from the Australian continent. Since many previous studies focused on clinical isolates, we investigated mostly other isolates originating from humans, poultry, wild animals and water. These strains represent the species genetic diversity and reveal widespread associations between phylogroups and isolation sources. The analysis of strains from the same sequence types revealed very rapid change of gene repertoires in the very early stages of divergence, driven by the acquisition of many different types of mobile genetic elements. These elements also lead to rapid variations in genome size, even if few of their genes rise to high frequency in the species. Variations in genome size are associated with phylogroup and isolation sources, but the latter determine the number of MGEs, a marker of recent transfer, suggesting that gene flow reinforces the association of certain genetic backgrounds with specific habitats. After a while, the divergence of gene repertoires becomes linear with phylogenetic distance, presumably reflecting the continuous turnover of mobile element and the occasional acquisition of adaptive genes. Surprisingly, the phylogroups with smallest genomes have the highest rates of gene repertoire diversification and fewer but more diverse mobile genetic elements. This suggests that smaller genomes are associated with higher, not lower, turnover of genetic information. Many of these genomes are from freshwater isolates and have peculiar traits, including a specific capsule, suggesting adaptation to this environment. Altogether, these data contribute to explain why epidemiological clones tend to emerge from specific phylogenetic groups in the presence of pervasive horizontal gene transfer across the species. Previous large scale studies on the evolution of E. coli focused on clinical isolates emphasizing virulence and antibiotic resistance in medically important lineages. Yet, most E. coli strains are either human commensals or not associated with humans at all. Here, we analyzed a large collection of non-clinical isolates of the species to assess the mechanisms of gene repertoire diversification in the light of isolation sources and phylogeny. We show that gene repertoires evolve so rapidly by the high turnover of mobile genetic elements that epidemiologically indistinguishable strains can be phenotypically extremely heterogeneous, illustrating the velocity of bacterial adaptation and the importance of accounting for the information on the whole genome at the epidemiological scale. Phylogeny and habitat shape the genetic diversification of E. coli to similar extents. Surprisingly, freshwater strains seem specifically adapted to this environment, breaking the paradigm that E. coli environmental isolates are systematically fecal contaminations. As a consequence, the evolution of this species is also shaped by environmental habitats, and it may diversify by acquiring genes and mobile elements from environmental bacteria (and not just from gut bacteria). This may facilitate the acquisition of virulence factors and antibiotic resistance in the strains that become pathogenic.
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Affiliation(s)
- Marie Touchon
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, 25-28 rue Dr Roux, Paris, 75015, France
- * E-mail:
| | - Amandine Perrin
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, 25-28 rue Dr Roux, Paris, 75015, France
- Sorbonne Université, Collège doctoral, F-75005 Paris, France
| | - Jorge André Moura de Sousa
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, 25-28 rue Dr Roux, Paris, 75015, France
| | - Belinda Vangchhia
- Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT, Australia
- Department of Veterinary Microbiology, College of Veterinary Sciences & Animal Husbandry, Central Agricultural University, Selesih, Aizawl, Mizoram, India
| | - Samantha Burn
- Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT, Australia
| | - Claire L. O’Brien
- School of Medicine, University of Wollongong, Northfields Ave Wollongong, Australia
| | - Erick Denamur
- Université de Paris, IAME, UMR 1137, INSERM, Paris, 75018, France
- AP-HP, Laboratoire de Génétique Moléculaire, Hôpital Bichat, 75018, Paris, France
| | - David Gordon
- Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT, Australia
| | - Eduardo PC Rocha
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, 25-28 rue Dr Roux, Paris, 75015, France
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27
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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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28
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Disayathanoowat T, Li H, Supapimon N, Suwannarach N, Lumyong S, Chantawannakul P, Guo J. Different Dynamics of Bacterial and Fungal Communities in Hive-Stored Bee Bread and Their Possible Roles: A Case Study from Two Commercial Honey Bees in China. Microorganisms 2020; 8:microorganisms8020264. [PMID: 32075309 PMCID: PMC7074699 DOI: 10.3390/microorganisms8020264] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 02/13/2020] [Accepted: 02/13/2020] [Indexed: 12/13/2022] Open
Abstract
This study investigated both bacterial and fungal communities in corbicular pollen and hive-stored bee bread of two commercial honey bees, Apis mellifera and Apis cerana, in China. Although both honey bees favor different main floral sources, the dynamics of each microbial community is similar. During pH reduction in hive-stored bee bread, results from conventional culturable methods and next-generation sequencing showed a declining bacterial population but a stable fungal population. Different honey bee species and floral sources might not affect the core microbial community structure but could change the number of bacteria. Corbicular pollen was colonized by the Enterobacteriaceae bacterium (Escherichia-Shiga, Panteoa, Pseudomonas) group; however, the number of bacteria significantly decreased in hive-stored bee bread in less than 72 h. In contrast, Acinetobacter was highly abundant and could utilize protein sources. In terms of the fungal community, the genus Cladosporium remained abundant in both corbicular pollen and hive-stored bee bread. This filamentous fungus might encourage honey bees to reserve pollen by releasing organic acids. Furthermore, several filamentous fungi had the potential to inhibit both commensal/contaminant bacteria and the growth of pathogens. Filamentous fungi, in particular, the genus Cladosporium, could support pollen preservation of both honey bee species.
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Affiliation(s)
- Terd Disayathanoowat
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China;
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand; (N.S.); (N.S.); (S.L.); (P.C.)
- Research Center in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
- Research Center of Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai 50200, Thailand
- Correspondence: (T.D.); (J.G.)
| | - HuanYuan Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China;
| | - Natapon Supapimon
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand; (N.S.); (N.S.); (S.L.); (P.C.)
| | - Nakarin Suwannarach
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand; (N.S.); (N.S.); (S.L.); (P.C.)
- Research Center of Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Saisamorn Lumyong
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand; (N.S.); (N.S.); (S.L.); (P.C.)
- Research Center of Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai 50200, Thailand
- Academy of Science, The Royal Society of Thailand, Bangkok 10300, Thailand
| | - Panuwan Chantawannakul
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand; (N.S.); (N.S.); (S.L.); (P.C.)
- Research Center in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Jun Guo
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China;
- Correspondence: (T.D.); (J.G.)
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29
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Oblessuc PR, Matiolli CC, Melotto M. Novel molecular components involved in callose-mediated Arabidopsis defense against Salmonella enterica and Escherichia coli O157:H7. BMC PLANT BIOLOGY 2020; 20:16. [PMID: 31914927 PMCID: PMC6950905 DOI: 10.1186/s12870-019-2232-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 12/30/2019] [Indexed: 05/26/2023]
Abstract
BACKGROUND Food contamination with Salmonella enterica and enterohemorrhagic Escherichia coli is among the leading causes of foodborne illnesses worldwide and crop plants are associated with > 50% of the disease outbreaks. However, the mechanisms underlying the interaction of these human pathogens with plants remain elusive. In this study, we have explored plant resistance mechanisms against these enterobacteria and the plant pathogen Pseudomonas syringae pv. tomato (Pst) DC3118, as an opportunity to improve food safety. RESULTS We found that S. enterica serovar Typhimurium (STm) transcriptionally modulates stress responses in Arabidopsis leaves, including induction of two hallmark processes of plant defense: ROS burst and cell wall modifications. Analyses of plants with a mutation in the potentially STm-induced gene EXO70H4 revealed that its encoded protein is required for stomatal defense against STm and E. coli O157:H7, but not against Pst DC3118. In the apoplast however, EXO70H4 is required for defense against STm and Pst DC3118, but not against E. coli O157:H7. Moreover, EXO70H4 is required for callose deposition, but had no function in ROS burst, triggered by all three bacteria. The salicylic acid (SA) signaling and biosynthesis proteins NPR1 and ICS1, respectively, were involved in stomatal and apoplastic defense, as well as callose deposition, against human and plant pathogens. CONCLUSIONS The results show that EXO70H4 is involved in stomatal and apoplastic defenses in Arabidopsis and suggest that EXO70H4-mediated defense play a distinct role in guard cells and leaf mesophyll cells in a bacteria-dependent manner. Nonetheless, EXO70H4 contributes to callose deposition in response to both human and plant pathogens. NPR1 and ICS1, two proteins involved in the SA signaling pathway, are important to inhibit leaf internalization and apoplastic persistence of enterobacteria and proliferation of phytopathogens. These findings highlight the existence of unique and shared plant genetic components to fight off diverse bacterial pathogens providing specific targets for the prevention of foodborne diseases.
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Affiliation(s)
- Paula Rodrigues Oblessuc
- Department of Plant Sciences, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | | | - Maeli Melotto
- Department of Plant Sciences, University of California, One Shields Avenue, Davis, CA, 95616, USA.
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30
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Gonzalez-Alba JM, Baquero F, Cantón R, Galán JC. Stratified reconstruction of ancestral Escherichia coli diversification. BMC Genomics 2019; 20:936. [PMID: 31805853 PMCID: PMC6896753 DOI: 10.1186/s12864-019-6346-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 11/28/2019] [Indexed: 12/15/2022] Open
Abstract
Background Phylogenetic analyses of the bacterial genomes based on the simple classification in core- genes and accessory genes pools could offer an incomplete view of the evolutionary processes, of which some are still unresolved. A combined strategy based on stratified phylogeny and ancient molecular polymorphisms is proposed to infer detailed evolutionary reconstructions by using a large number of whole genomes. This strategy, based on the highest number of genomes available in public databases, was evaluated for improving knowledge of the ancient diversification of E. coli. This staggered evolutionary scenario was also used to investigate whether the diversification of the ancient E. coli lineages could be associated with particular lifestyles and adaptive strategies. Results Phylogenetic reconstructions, exploiting 6220 available genomes in Genbank, established the E. coli core genome in 1023 genes, representing about 20% of the complete genome. The combined strategy using stratified phylogeny plus molecular polymorphisms inferred three ancient lineages (D, EB1A and FGB2). Lineage D was the closest to E. coli root. A staggered diversification could also be proposed in EB1A and FGB2 lineages and the phylogroups into these lineages. Several molecular markers suggest that each lineage had different adaptive trajectories. The analysis of gained and lost genes in the main lineages showed that functions of carbohydrates utilization (uptake of and metabolism) were gained principally in EB1A lineage, whereas loss of environmental-adaptive functions in FGB2 lineage were observed, but this lineage showed higher accumulated mutations and ancient recombination events. The population structure of E. coli was re-evaluated including up to 7561 new sequenced genomes, showing a more complex population structure of E. coli, as a new phylogroup, phylogroup I, was proposed. Conclusions A staggered reconstruction of E. coli phylogeny is proposed, indicating evolution from three ancestral lineages to reach all main known phylogroups. New phylogroups were confirmed, suggesting an increasingly complex population structure of E. coli. However these new phylogroups represent < 1% of the global E. coli population. A few key evolutionary forces have driven the diversification of the two main E. coli lineages, metabolic flexibility in one of them and colonization-virulence in the other.
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Affiliation(s)
- José Maria Gonzalez-Alba
- Servicio de Microbiología. Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain.,CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Fernando Baquero
- Servicio de Microbiología. Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain.,CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.,Unidad de Resistencia a Antibióticos y Virulencia Bacteriana, Madrid, Spain
| | - Rafael Cantón
- Servicio de Microbiología. Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain.,Red Española de Investigación en Patología Infecciosa (REIPI), Madrid, Spain
| | - Juan Carlos Galán
- Servicio de Microbiología. Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain. .,CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain. .,Unidad de Resistencia a Antibióticos y Virulencia Bacteriana, Madrid, Spain.
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31
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Fagerström A, Mölling P, Khan FA, Sundqvist M, Jass J, Söderquist B. Comparative distribution of extended-spectrum beta-lactamase-producing Escherichia coli from urine infections and environmental waters. PLoS One 2019; 14:e0224861. [PMID: 31697734 PMCID: PMC6837386 DOI: 10.1371/journal.pone.0224861] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 10/23/2019] [Indexed: 01/07/2023] Open
Abstract
Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli have been reported in natural environments, and may be released through wastewater. In this study, the genetic relationship between ESBL-producing E. coli collected from patient urine samples (n = 45, both hospitalized patients and out-patients) and from environmental water (n = 82, from five locations), during the same time period, was investigated. Three independent water samples were collected from the municipal wastewater treatment plant, both incoming water and treated effluent water; the receiving river and lake; and a bird sanctuary near the lake, on two different occasions. The water was filtered and cultured on selective chromID ESBL agar plates in order to detect and isolate ESBL-producing E. coli. Illumina whole genome sequencing was performed on all bacterial isolates (n = 127). Phylogenetic group B2 was more common among the clinical isolates than the environmental isolates (44.4% vs. 17.1%, p < 0.01) due to a significantly higher prevalence of sequence type (ST) 131 (33.3% vs. 13.4%, p < 0.01). ST131 was, however, one of the most prevalent STs among the environmental isolates. There was no significant difference in diversity between the clinical isolates (DI 0.872 (0.790-0.953)) and the environmental isolates (DI 0.947 (0.920-0.969)). The distribution of ESBL genes was similar: blaCTX-M-15 dominated, followed by blaCTX-M-14 and blaCTX-M-27 in both the clinical (60.0%, 8.9%, and 6.7%) and the environmental isolates (62.2%, 12.2%, and 8.5%). Core genome multi-locus sequence typing showed that five environmental isolates, from incoming wastewater, treated wastewater, Svartån river and Hjälmaren lake, were indistinguishable or closely related (≤10 allele differences) to clinical isolates. Isolates of ST131, serotype O25:H4 and fimtype H30, from the environment were as closely related to the clinical isolates as the isolates from different patients were. This study confirms that ESBL-producing E. coli are common in the aquatic environment even in low-endemic regions and suggests that wastewater discharge is an important route for the release of ESBL-producing E. coli into the aquatic environment.
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Affiliation(s)
- Anna Fagerström
- Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
- * E-mail:
| | - Paula Mölling
- Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Faisal Ahmad Khan
- The Life Science Centre–Biology, School of Science and Technology, Örebro University, Örebro, Sweden
| | - Martin Sundqvist
- Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Jana Jass
- The Life Science Centre–Biology, School of Science and Technology, Örebro University, Örebro, Sweden
| | - Bo Söderquist
- Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
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32
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Sharma RS, Karmakar S, Kumar P, Mishra V. Application of filamentous phages in environment: A tectonic shift in the science and practice of ecorestoration. Ecol Evol 2019; 9:2263-2304. [PMID: 30847110 PMCID: PMC6392359 DOI: 10.1002/ece3.4743] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 08/25/2018] [Accepted: 10/30/2018] [Indexed: 02/06/2023] Open
Abstract
Theories in soil biology, such as plant-microbe interactions and microbial cooperation and antagonism, have guided the practice of ecological restoration (ecorestoration). Below-ground biodiversity (bacteria, fungi, invertebrates, etc.) influences the development of above-ground biodiversity (vegetation structure). The role of rhizosphere bacteria in plant growth has been largely investigated but the role of phages (bacterial viruses) has received a little attention. Below the ground, phages govern the ecology and evolution of microbial communities by affecting genetic diversity, host fitness, population dynamics, community composition, and nutrient cycling. However, few restoration efforts take into account the interactions between bacteria and phages. Unlike other phages, filamentous phages are highly specific, nonlethal, and influence host fitness in several ways, which make them useful as target bacterial inocula. Also, the ease with which filamentous phages can be genetically manipulated to express a desired peptide to track and control pathogens and contaminants makes them useful in biosensing. Based on ecology and biology of filamentous phages, we developed a hypothesis on the application of phages in environment to derive benefits at different levels of biological organization ranging from individual bacteria to ecosystem for ecorestoration. We examined the potential applications of filamentous phages in improving bacterial inocula to restore vegetation and to monitor changes in habitat during ecorestoration and, based on our results, recommend a reorientation of the existing framework of using microbial inocula for such restoration and monitoring. Because bacterial inocula and biomonitoring tools based on filamentous phages are likely to prove useful in developing cost-effective methods of restoring vegetation, we propose that filamentous phages be incorporated into nature-based restoration efforts and that the tripartite relationship between phages, bacteria, and plants be explored further. Possible impacts of filamentous phages on native microflora are discussed and future areas of research are suggested to preclude any potential risks associated with such an approach.
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Affiliation(s)
- Radhey Shyam Sharma
- Bioresources and Environmental Biotechnology Laboratory, Department of Environmental StudiesUniversity of DelhiDelhiIndia
| | - Swagata Karmakar
- Bioresources and Environmental Biotechnology Laboratory, Department of Environmental StudiesUniversity of DelhiDelhiIndia
| | - Pankaj Kumar
- Bioresources and Environmental Biotechnology Laboratory, Department of Environmental StudiesUniversity of DelhiDelhiIndia
| | - Vandana Mishra
- Bioresources and Environmental Biotechnology Laboratory, Department of Environmental StudiesUniversity of DelhiDelhiIndia
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Corzo-Ariyama HA, García-Heredia A, Heredia N, García S, León J, Jaykus L, Solís-Soto L. Phylogroups, pathotypes, biofilm formation and antimicrobial resistance of Escherichia coli isolates in farms and packing facilities of tomato, jalapeño pepper and cantaloupe from Northern Mexico. Int J Food Microbiol 2019; 290:96-104. [DOI: 10.1016/j.ijfoodmicro.2018.10.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Revised: 08/15/2018] [Accepted: 10/05/2018] [Indexed: 01/05/2023]
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Spider mites escape bacterial infection by avoiding contaminated food. Oecologia 2018; 189:111-122. [DOI: 10.1007/s00442-018-4316-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 11/22/2018] [Indexed: 11/26/2022]
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35
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Méric G, Mageiros L, Pensar J, Laabei M, Yahara K, Pascoe B, Kittiwan N, Tadee P, Post V, Lamble S, Bowden R, Bray JE, Morgenstern M, Jolley KA, Maiden MCJ, Feil EJ, Didelot X, Miragaia M, de Lencastre H, Moriarty TF, Rohde H, Massey R, Mack D, Corander J, Sheppard SK. Disease-associated genotypes of the commensal skin bacterium Staphylococcus epidermidis. Nat Commun 2018; 9:5034. [PMID: 30487573 PMCID: PMC6261936 DOI: 10.1038/s41467-018-07368-7] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 10/23/2018] [Indexed: 01/05/2023] Open
Abstract
Some of the most common infectious diseases are caused by bacteria that naturally colonise humans asymptomatically. Combating these opportunistic pathogens requires an understanding of the traits that differentiate infecting strains from harmless relatives. Staphylococcus epidermidis is carried asymptomatically on the skin and mucous membranes of virtually all humans but is a major cause of nosocomial infection associated with invasive procedures. Here we address the underlying evolutionary mechanisms of opportunistic pathogenicity by combining pangenome-wide association studies and laboratory microbiology to compare S. epidermidis from bloodstream and wound infections and asymptomatic carriage. We identify 61 genes containing infection-associated genetic elements (k-mers) that correlate with in vitro variation in known pathogenicity traits (biofilm formation, cell toxicity, interleukin-8 production, methicillin resistance). Horizontal gene transfer spreads these elements, allowing divergent clones to cause infection. Finally, Random Forest model prediction of disease status (carriage vs. infection) identifies pathogenicity elements in 415 S. epidermidis isolates with 80% accuracy, demonstrating the potential for identifying risk genotypes pre-operatively.
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Affiliation(s)
- Guillaume Méric
- The Milner Centre for Evolution, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Leonardos Mageiros
- The Milner Centre for Evolution, University of Bath, Claverton Down, Bath, BA2 7AY, UK
- Swansea University Medical School, Swansea University, Singleton Campus, Swansea, SA2 8PP, UK
| | - Johan Pensar
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, 00100, Finland
| | - Maisem Laabei
- The Milner Centre for Evolution, University of Bath, Claverton Down, Bath, BA2 7AY, UK
- Medical Protein Chemistry, Department of Translational Medicine, Lund University, Malmö, 205 02, Sweden
| | - Koji Yahara
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Ben Pascoe
- The Milner Centre for Evolution, University of Bath, Claverton Down, Bath, BA2 7AY, UK
- MRC Cloud-based Infrastructure for Microbial Bioinformatics (CLIMB) Consortium, Bath, BA2 7AY, UK
| | - Nattinee Kittiwan
- Integrative Research Centre for Veterinary Preventive Medicine, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | | | - Virginia Post
- AO Research Institute Davos, Davos, 7270, Switzerland
| | - Sarah Lamble
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Rory Bowden
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - James E Bray
- Department of Zoology, University of Oxford, Oxford, OX1 3SZ, UK
| | - Mario Morgenstern
- Department of Orthopaedic Surgery and Traumatology, University Hospital Basel, Basel, 4031, Switzerland
| | - Keith A Jolley
- Department of Zoology, University of Oxford, Oxford, OX1 3SZ, UK
| | | | - Edward J Feil
- The Milner Centre for Evolution, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Xavier Didelot
- Department of Infectious Disease Epidemiology, Imperial College, London, SW7 2AZ, UK
| | - Maria Miragaia
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, 2775-412, Portugal
| | - Herminia de Lencastre
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, 2775-412, Portugal
- Laboratory of Microbiology and Infectious Diseases, The Rockefeller University, New York, New York, 10065, USA
| | | | - Holger Rohde
- Institut für Medizinische Mikrobiologie, Virologie & Hygiene, Universität Hamburg, Hamburg, 20246, Germany
| | - Ruth Massey
- The Milner Centre for Evolution, University of Bath, Claverton Down, Bath, BA2 7AY, UK
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - Dietrich Mack
- Bioscientia Labor Ingelheim, Institut für Medizinische Diagnostik GmbH, Ingelheim, 55218, Germany
| | - Jukka Corander
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, 00100, Finland
- Department of Biostatistics, University of Oslo, Oslo, 0372, Norway
- Pathogen Genomics, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Samuel K Sheppard
- The Milner Centre for Evolution, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
- MRC Cloud-based Infrastructure for Microbial Bioinformatics (CLIMB) Consortium, Bath, BA2 7AY, UK.
- Department of Zoology, University of Oxford, Oxford, OX1 3SZ, UK.
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Abstract
Some bacteria can transfer to new host species, and this poses a risk to human health. Indeed, an estimated 60% of all human pathogens have originated from other animal species. Similarly, human-to-animal transitions are recognized as a major threat to sustainable livestock production, and emerging pathogens impose an increasing burden on crop yield and global food security. Recent advances in high-throughput sequencing technologies have enabled comparative genomic analyses of bacterial populations from multiple hosts. Such studies are providing new insights into the evolutionary processes that underpin the establishment of bacteria in new host niches. A better understanding of the genetic and mechanistic basis for bacterial host adaptation may reveal novel targets for controlling infection or inform the design of approaches to limit the emergence of new pathogens.
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Affiliation(s)
- Samuel K Sheppard
- Milner Centre for Evolution, Department of Biology & Biotechnology, University of Bath, Claverton Down, Bath, UK
| | - David S Guttman
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Ontario, Canada
| | - J Ross Fitzgerald
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh, UK.
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Ocaña de Jesús RL, Gutiérrez Ibáñez AT, Sánchez Pale JR, Mariezcurrena Berasain MD, Eslava Campos CA, Laguna Cerda A. [Persistence, internalization and translocation of Escherichia coli O157:H7, O157:H16 and O105ab in plants and tomato fruits (Solanum lycopersicum L.)]. Rev Argent Microbiol 2018; 50:408-416. [PMID: 29709245 DOI: 10.1016/j.ram.2017.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 11/28/2017] [Accepted: 12/09/2017] [Indexed: 10/17/2022] Open
Abstract
The presence of pathogenic bacteria, such as Escherichia coli affects the quality and safety of vegetables that are consumed fresh and is associated with serious health problems. The objective of this study was to determine if three different strains of E. coli can penetrate and remain in plants and tomato fruits. A completely randomized experimental design was followed for which a tomato crop ("Cid" variety) was established under greenhouse conditions and three treatments were evaluated, T1 (E. coli O157:H7), T2 (E. coli from tomato cultivation [EcT] O157:H16), T3 (E. coli from spinach cultivation [EcH] O105ab) and a T4 control, with 100 plants each and four forms of inoculation: in the substrate, steam, petiole and the peduncle. Samples were carried out in vegetative stage, flowering, fruiting and physiological maturity to quantify in petri dish CFU/g and know if the bacteria managed to move around and recover in root, stem, flower and fruit. The phylogenetic groups that corresponded to the bacteria recovered were confirmed by biochemical tests, serotyping and PCR. At 120 days the recovery of bacteria in the plant was 23% (E. coli O157:H7), 28% (EcT O157:H16) and 55% (EcH O105ab) whit inoculation to the substrate while the inoculation by puncture the recovery was (in the same order) of 5%, 3%, and 4% at 30 days; 37%, 35% and 30% at 90 days; and 42%, 39% and 13% at 65 days. The strains submit the ability to enter the tomato plant and to stay in it and transported to the fruit, without producing that indicate their presence.
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Affiliation(s)
- Rosa L Ocaña de Jesús
- Facultad de Ciencias Agrícolas, Universidad Autónoma del Estado de México, Toluca, México
| | - Ana T Gutiérrez Ibáñez
- Facultad de Ciencias Agrícolas, Universidad Autónoma del Estado de México, Toluca, México.
| | - Jesús R Sánchez Pale
- Facultad de Ciencias Agrícolas, Universidad Autónoma del Estado de México, Toluca, México
| | | | - Carlos A Eslava Campos
- Laboratorio de Patogenicidad Bacteriana, Unidad de Hemato Oncología e Investigación, Hospital Infantil de México Federico Gómez'/División de Investigación, Facultad de Medicina (UNAM), Ciudad de México, México
| | - Antonio Laguna Cerda
- Facultad de Ciencias Agrícolas, Universidad Autónoma del Estado de México, Toluca, México
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Wright KM, Holden NJ. Quantification and colonisation dynamics of Escherichia coli O157:H7 inoculation of microgreens species and plant growth substrates. Int J Food Microbiol 2018; 273:1-10. [DOI: 10.1016/j.ijfoodmicro.2018.02.025] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 02/23/2018] [Accepted: 02/27/2018] [Indexed: 02/02/2023]
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Landscape-Scale Factors Affecting the Prevalence of Escherichia coli in Surface Soil Include Land Cover Type, Edge Interactions, and Soil pH. Appl Environ Microbiol 2018. [PMID: 29523546 DOI: 10.1128/aem.02714-17] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli is deposited into soil with feces and exhibits subsequent population decline with concomitant environmental selection. Environmentally persistent strains exhibit longer survival times during this selection process, and some strains have adapted to soil and sediments. A georeferenced collection of E. coli isolates was developed comprising 3,329 isolates from 1,428 soil samples that were collected from a landscape spanning the transition from the grasslands to the eastern deciduous forest biomes. The isolate collection and sample database were analyzed together to discover how land cover, site characteristics, and soil chemistry influence the prevalence of cultivable E. coli in surface soil. Soils from forests and pasture lands had equally high prevalences of E. coli Edge interactions were also observed among land cover types, with proximity to forests and pastures affecting the likelihood of E. coli isolation from surrounding soils. E. coli is thought to be more prevalent in sediments with high moisture, but this was observed only in grass- or crop-dominated lands in this study. Because differing E. coli phylogroups are thought to have differing ecology profiles, isolates were also typed using a novel single-nucleotide polymorphism (SNP) genotyping assay. Phylogroup B1 was the dominant group isolated from soil, as has been reported in all other surveys of environmental E. coli Although differences were small, isolates belonging to phylogroups B2 and D were associated with wooded areas, slightly more acidic soils, and soil sampling after rainfall events. In contrast, isolates from phylogroups B1 and E were associated with pasture lands.IMPORTANCE The consensus is that complex niches or life cycles should select for complex genomes in organisms. There is much unexplained biodiversity in E. coli, and its cycling through complex extrahost environments may be a cause. In order to understand the evolutionary processes that lead to adaptation for survival and growth in soil, an isolate collection that associates soil conditions and isolate genome sequences is required. An equally important question is whether traits selected in soil or other extrahost habitats can be transmitted to E. coli residing in hosts via gene flow. The new findings about the distribution of E. coli in soil at the landscape scale (i) enhance our capability to study how extrahost environments influence the evolution of E. coli and other bacteria, (ii) advance our knowledge of the environmental biology of this microbe, and (iii) further affirm the emerging scientific consensus that E. coli in waterways originates from nonpoint sources not associated with human activity or livestock farming.
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40
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Verma P, Saharan VV, Nimesh S, Singh AP. Phenotypic and virulence traits of Escherichia coli and Salmonella strains isolated from vegetables and fruits from India. J Appl Microbiol 2018. [PMID: 29512849 DOI: 10.1111/jam.13754] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
AIMS The present study was designed to assess the phenotypic traits and virulence determinants of vegetable-/fruit-origin Escherichia coli and Salmonella strains. METHODS AND RESULTS A total of 520 fresh vegetables/fruits samples were analysed for the presence of E. coli, including Shiga toxin-producing E. coli (STEC), and Salmonella. The vegetable-/fruit-origin E. coli and Salmonella strains were further assessed for antimicrobial resistance, biofilm formation, extracellular matrix production and in vitro invasion/intracellular survivability assays. A total of 73 E. coli, including four STEC, and 26 Salmonella strains were recovered from vegetables/fruits in the present study. Most of the E. coli and Salmonella isolates were able to form biofilm with higher production of cellulose/curli-fimbriae. Furthermore, more resistance was observed in E. coli isolates (61·6%) than in Salmonella isolates (38·5%) against tested antimicrobials. Additionally, invasion/intracellular survival results showed that majority of the E. coli and Salmonella isolates were able to efficiently invade/replicate intracellularly in the human epithelial cells. CONCLUSIONS Our results demonstrate that vegetable-/fruit-origin E. coli and Salmonella significantly exhibited distinct phenotypic/virulence traits which could be linked to their plant-associated lifestyle with food safety issues. SIGNIFICANCE AND IMPACT OF THE STUDY The present study provides valuable baseline information that E. coli and Salmonella may use plants as an alternative host with significant clinical importance.
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Affiliation(s)
- P Verma
- Department of Microbiology, School of Life Science, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - V V Saharan
- Department of Microbiology, School of Life Science, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - S Nimesh
- Department of Biotechnology, School of Life Science, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - A P Singh
- Department of Microbiology, School of Life Science, Central University of Rajasthan, Ajmer, Rajasthan, India
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41
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Cook KL, Givan EC, Mayton HM, Parekh RR, Taylor R, Walker SL. Using the agricultural environment to select better surrogates for foodborne pathogens associated with fresh produce. Int J Food Microbiol 2017; 262:80-88. [PMID: 28968533 DOI: 10.1016/j.ijfoodmicro.2017.09.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 08/25/2017] [Accepted: 09/24/2017] [Indexed: 01/26/2023]
Abstract
Despite continuing efforts to reduce foodborne pathogen contamination of fresh produce, significant outbreaks continue to occur. Identification of appropriate surrogates for foodborne pathogens facilitates relevant research to identify reservoirs and amplifiers of these contaminants in production and processing environments. Therefore, the objective of this study was to identify environmental Escherichia coli isolates from manures (poultry, swine and dairy) and surface water sources with properties similar to those of the produce associated foodborne pathogens E. coli O157:H7 and Salmonella enterica serotype Typhimurium. The most similar environmental E. coli isolates were from poultry (n=3) and surface water (n=1) sources. The best environmental E. coli surrogates had cell surface characteristics (zeta potential, hydrophobicity and exopolysaccharide composition) that were similar (i.e., within 15%) to those of S. Typhimurium and/or formed biofilms more often when grown in low nutrient media prepared from lettuce lysates (24%) than when grown on high nutrient broth (7%). The rate of attachment of environmental isolates to lettuce leaves was also similar to that of S. Typhimurium. In contrast, E. coli O157:H7, a commonly used E. coli quality control strain and swine isolates behaved similarly; all were in the lowest 10% of isolates for biofilm formation and leaf attachment. These data suggest that the environment may provide a valuable resource for selection of surrogates for foodborne pathogens.
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Affiliation(s)
- Kimberly L Cook
- USDA-ARS, Food Animal Environmental Systems Research Unit, Bowling Green, KY, USA.
| | - Ethan C Givan
- Western Kentucky University, Department of Public Health, Bowling Green, KY, USA.
| | - Holly M Mayton
- University of California, Bourns College of Engineering, Riverside, CA, USA.
| | - Rohan R Parekh
- USDA-ARS, Food Animal Environmental Systems Research Unit, Bowling Green, KY, USA.
| | - Ritchie Taylor
- Western Kentucky University, Department of Public Health, Bowling Green, KY, USA.
| | - Sharon L Walker
- University of California, Bourns College of Engineering, Riverside, CA, USA.
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42
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Plessis EMD, Govender S, Pillay B, Korsten L. Exploratory Study into the Microbiological Quality of Spinach and Cabbage Purchased from Street Vendors and Retailers in Johannesburg, South Africa. J Food Prot 2017; 80:1726-1733. [PMID: 28922029 DOI: 10.4315/0362-028x.jfp-16-540] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Knowledge of the microbiological quality and prevalence of antibiotic resistance and virulence genes in bacterial isolates from leafy green vegetables supplied by formal suppliers (retailers) and informal suppliers (street vendors) in South Africa is limited. Because leafy vegetables have been implicated in foodborne disease outbreaks worldwide, 180 cabbage and spinach samples were collected from three major retailers and nine street vendors in Johannesburg, South Africa. Escherichia coli and coliforms were enumerated using Petrifilm plates. The prevalence of Listeria monocytogenes, Salmonella, and Shigella was determined using real-time PCR analysis. Identities of presumptive E. coli isolates from the fresh produce were confirmed using matrix-assisted laser desorption-ionization time of flight mass spectroscopy. Isolates were characterized using phenotypic (antibiotic resistance) and genotypic (phylogenetic and virulence gene) analysis. Hygiene indicator bacteria levels on spinach from formal and informal retailers exceeded the maximum level specified by the Department of Health guidelines for fresh fruit and vegetables. E. coli counts for street vendor spinach were higher (P < 0.0789) than those for retailer spinach. E. coli was present in only two cabbage samples, at 0.0035 CFU/g. L. monocytogenes and Salmonella were detected in 7.2 and 5% of the 180 samples, respectively, based on real-time PCR analysis; Shigella was not detected. Of the 29 spinach E. coli isolates, 37.9% were multidrug resistant. Virulence genes eae and stx1 were present in 14 and 3% of the spinach E. coli isolates, respectively; the stx2 gene was not detected. Eighty-six percent of these isolates belonged to phylogroup A, 3% belonged to group C, 7% belonged to group E, and 3% belonged to clade 1. The results from the current exploratory study on the microbiological quality of spinach bought from selected retailers highlight the need for continued surveillance on a larger scale, especially in the informal sector, to characterize the potential health risks to the consumer.
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Affiliation(s)
- Erika M du Plessis
- 1 Centre of Excellence in Food Security, Department of Plant and Soil Sciences, University of Pretoria, Hatfield, Pretoria 0002, South Africa; and
| | - Sarasha Govender
- 2 Department of Microbiology, School of Life Sciences, Westville Campus, University of KwaZulu-Natal, Private Bag X 54001, Durban 4000, South Africa
| | - Bala Pillay
- 2 Department of Microbiology, School of Life Sciences, Westville Campus, University of KwaZulu-Natal, Private Bag X 54001, Durban 4000, South Africa
| | - Lise Korsten
- 1 Centre of Excellence in Food Security, Department of Plant and Soil Sciences, University of Pretoria, Hatfield, Pretoria 0002, South Africa; and
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Yahara K, Méric G, Taylor AJ, de Vries SPW, Murray S, Pascoe B, Mageiros L, Torralbo A, Vidal A, Ridley A, Komukai S, Wimalarathna H, Cody AJ, Colles FM, McCarthy N, Harris D, Bray JE, Jolley KA, Maiden MCJ, Bentley SD, Parkhill J, Bayliss CD, Grant A, Maskell D, Didelot X, Kelly DJ, Sheppard SK. Genome-wide association of functional traits linked with Campylobacter jejuni survival from farm to fork. Environ Microbiol 2017; 19:361-380. [PMID: 27883255 DOI: 10.1111/1462-2920.13628] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 11/16/2016] [Accepted: 11/18/2016] [Indexed: 01/07/2023]
Abstract
Campylobacter jejuni is a major cause of bacterial gastroenteritis worldwide, primarily associated with the consumption of contaminated poultry. C. jejuni lineages vary in host range and prevalence in human infection, suggesting differences in survival throughout the poultry processing chain. From 7343 MLST-characterised isolates, we sequenced 600 C. jejuni and C. coli isolates from various stages of poultry processing and clinical cases. A genome-wide association study (GWAS) in C. jejuni ST-21 and ST-45 complexes identified genetic elements over-represented in clinical isolates that increased in frequency throughout the poultry processing chain. Disease-associated SNPs were distinct in these complexes, sometimes organised in haplotype blocks. The function of genes containing associated elements was investigated, demonstrating roles for cj1377c in formate metabolism, nuoK in aerobic survival and oxidative respiration, and cj1368-70 in nucleotide salvage. This work demonstrates the utility of GWAS for investigating transmission in natural zoonotic pathogen populations and provides evidence that major C. jejuni lineages have distinct genotypes associated with survival, within the host specific niche, from farm to fork.
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Affiliation(s)
- Koji Yahara
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Guillaume Méric
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Aidan J Taylor
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
| | - Stefan P W de Vries
- Department of Veterinary Medicine, University of Cambridge, Madingley, Cambridge, UK
| | - Susan Murray
- Swansea University Medical School, Institute of Life Science, Swansea University, Swansea, UK
| | - Ben Pascoe
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK.,MRC CLIMB Consortium, Oxford Bath, UK
| | - Leonardos Mageiros
- Swansea University Medical School, Institute of Life Science, Swansea University, Swansea, UK
| | - Alicia Torralbo
- Swansea University Medical School, Institute of Life Science, Swansea University, Swansea, UK
| | - Ana Vidal
- Animal and Plant Health Agency (APHA), Addlestone, UK
| | - Anne Ridley
- Animal and Plant Health Agency (APHA), Addlestone, UK
| | - Sho Komukai
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Alison J Cody
- Department of Zoology, Oxford University, Oxford, UK
| | | | - Noel McCarthy
- Department of Zoology, Oxford University, Oxford, UK.,NIHR Health Protections Research Unit in Gastrointestinal Infections, University of Oxford, Oxford, UK
| | - David Harris
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - James E Bray
- Department of Zoology, Oxford University, Oxford, UK
| | | | - Martin C J Maiden
- Department of Zoology, Oxford University, Oxford, UK.,NIHR Health Protections Research Unit in Gastrointestinal Infections, University of Oxford, Oxford, UK
| | - Stephen D Bentley
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | | | - Andrew Grant
- Department of Veterinary Medicine, University of Cambridge, Madingley, Cambridge, UK
| | - Duncan Maskell
- Department of Veterinary Medicine, University of Cambridge, Madingley, Cambridge, UK
| | - Xavier Didelot
- Department of Infectious Disease Epidemiology, Imperial College, London, UK
| | - David J Kelly
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
| | - Samuel K Sheppard
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK.,MRC CLIMB Consortium, Oxford Bath, UK.,Department of Zoology, Oxford University, Oxford, UK
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44
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Procopio NA, Atherholt TB, Goodrow SM, Lester LA. The Likelihood of Coliform Bacteria in NJ Domestic Wells Based on Precipitation and Other Factors. GROUND WATER 2017; 55:722-735. [PMID: 28369797 DOI: 10.1111/gwat.12518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 03/01/2017] [Accepted: 03/02/2017] [Indexed: 05/20/2023]
Abstract
The influence of precipitation on coliform bacteria detection rates in domestic wells was investigated using data collected through the New Jersey Private Well Testing Act. Measured precipitation data from the National Weather Service (NWS) monitoring stations was compared to estimated data from the Multisensor Precipitation Estimate (MPE) in order to determine which source of data to include in the analyses. A strong concordance existed between these two precipitations datasets; therefore, MPE data was utilized as it is geographically more specific to individual wells. Statewide, 10 days of cumulative precipitation prior to testing was found to be an optimal period influencing the likelihood of coliform detections in wells. A logistic regression model was developed to predict the likelihood of coliform occurrence in wells from 10 days of cumulative precipitation data and other predictive variables including geology, season, coliform bacteria analysis method, pH, and nitrate concentration. Total coliform (TC) and fecal coliform or Escherichia coli (FC/EC) were detected more frequently when the preceding 10 days of cumulative precipitation exceeded 34.5 and 54 mm, respectively. Furthermore, the likelihood of coliform detection was highest in wells located in the bedrock region, during summer and autumn, analyzed with the enzyme substrate method, with pH between 5 and 6.99, and (for FC/EC but not TC) nitrate greater than 10 mg/L. Thus, the likelihood of coliform presence in domestic wells can be predicted from readily available environmental factors including timing and magnitude of precipitation, offering outreach opportunities and potential changes to coliform testing recommendations.
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Affiliation(s)
- Nicholas A Procopio
- Division of Science, Research and Environmental Health, New Jersey Department of Environmental Protection, 428 East State St., Trenton, NJ, 08625-0420
| | - Thomas B Atherholt
- Division of Science, Research and Environmental Health, New Jersey Department of Environmental Protection, 428 East State St., Trenton, NJ, 08625-0420
| | - Sandra M Goodrow
- Division of Science, Research and Environmental Health, New Jersey Department of Environmental Protection, 428 East State St., Trenton, NJ, 08625-0420
| | - Lori A Lester
- Division of Science, Research and Environmental Health, New Jersey Department of Environmental Protection, 428 East State St., Trenton, NJ, 08625-0420
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45
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Woodcock DJ, Krusche P, Strachan NJC, Forbes KJ, Cohan FM, Méric G, Sheppard SK. Genomic plasticity and rapid host switching can promote the evolution of generalism: a case study in the zoonotic pathogen Campylobacter. Sci Rep 2017; 7:9650. [PMID: 28851932 PMCID: PMC5575054 DOI: 10.1038/s41598-017-09483-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 07/25/2017] [Indexed: 11/16/2022] Open
Abstract
Horizontal gene transfer accelerates bacterial adaptation to novel environments, allowing selection to act on genes that have evolved in multiple genetic backgrounds. This can lead to ecological specialization. However, little is known about how zoonotic bacteria maintain the ability to colonize multiple hosts whilst competing with specialists in the same niche. Here we develop a stochastic evolutionary model and show how genetic transfer of host segregating alleles, distributed as predicted for niche specifying genes, and the opportunity for host transition could interact to promote the emergence of host generalist lineages of the zoonotic bacterium Campylobacter. Using a modelling approach we show that increasing levels of homologous recombination enhance the efficiency with which selection can fix combinations of beneficial alleles, speeding adaptation. We then show how these predictions change in a multi-host system, with low levels of recombination, consistent with real r/m estimates, increasing the standing variation in the population, allowing a more effective response to changes in the selective landscape. Our analysis explains how observed gradients of host specialism and generalism can evolve in a multihost system through the transfer of ecologically important loci among coexisting strains.
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Affiliation(s)
- Dan J Woodcock
- Warwick Systems Biology Centre, Coventry House, University of Warwick, Coventry, CV47AL, UK
| | - Peter Krusche
- Warwick Systems Biology Centre, Coventry House, University of Warwick, Coventry, CV47AL, UK
| | - Norval J C Strachan
- School of Biological Sciences, University of Aberdeen, Cruickshank Building. St Machar Drive, Aberdeen, AB24 3UU, UK
| | - Ken J Forbes
- School of Medicine and Dentistry, The University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
| | - Frederick M Cohan
- Department of Biology, Wesleyan University, Middletown, CT, 06459-0170, USA
| | - Guillaume Méric
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Samuel K Sheppard
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK.
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46
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Jang J, Hur HG, Sadowsky MJ, Byappanahalli MN, Yan T, Ishii S. Environmental Escherichia coli: ecology and public health implications-a review. J Appl Microbiol 2017; 123:570-581. [PMID: 28383815 DOI: 10.1111/jam.13468] [Citation(s) in RCA: 331] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 03/29/2017] [Accepted: 03/31/2017] [Indexed: 12/19/2022]
Abstract
Escherichia coli is classified as a rod-shaped, Gram-negative bacterium in the family Enterobacteriaceae. The bacterium mainly inhabits the lower intestinal tract of warm-blooded animals, including humans, and is often discharged into the environment through faeces or wastewater effluent. The presence of E. coli in environmental waters has long been considered as an indicator of recent faecal pollution. However, numerous recent studies have reported that some specific strains of E. coli can survive for long periods of time, and potentially reproduce, in extraintestinal environments. This indicates that E. coli can be integrated into indigenous microbial communities in the environment. This naturalization phenomenon calls into question the reliability of E. coli as a faecal indicator bacterium (FIB). Recently, many studies reported that E. coli populations in the environment are affected by ambient environmental conditions affecting their long-term survival. Large-scale studies of population genetics revealed the diversity and complexity of E. coli strains in various environments, which are affected by multiple environmental factors. This review examines the current knowledge on the ecology of E. coli strains in various environments with regard to its role as a FIB and as a naturalized member of indigenous microbial communities. Special emphasis is given on the growth of pathogenic E. coli in the environment, and the population genetics of environmental members of the genus Escherichia. The impact of environmental E. coli on water quality and public health is also discussed.
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Affiliation(s)
- J Jang
- BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - H-G Hur
- School of Environmental Science and Engineering, Gwangju Institute of Science and Technology, Gwangju, Korea
| | - M J Sadowsky
- BioTechnology Institute, University of Minnesota, St. Paul, MN, USA.,Department of Soil, Water, and Climate, University of Minnesota, St. Paul, MN, USA
| | - M N Byappanahalli
- Lake Michigan Ecological Research Station, Great Lakes Science Center, U.S. Geological Survey, Chesterton, IN, USA
| | - T Yan
- Department of Civil and Environmental Engineering, University of Hawai'i at Manoa, Honolulu, HI, USA
| | - S Ishii
- BioTechnology Institute, University of Minnesota, St. Paul, MN, USA.,Department of Soil, Water, and Climate, University of Minnesota, St. Paul, MN, USA
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47
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Tymensen L, Booker CW, Hannon SJ, Cook SR, Zaheer R, Read R, McAllister TA. Environmental Growth of Enterococci and Escherichia coli in Feedlot Catch Basins and a Constructed Wetland in the Absence of Fecal Input. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:5386-5395. [PMID: 28430425 DOI: 10.1021/acs.est.6b06274] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Population structures of fecal indicator bacteria (FIB) isolated from catch basins, a constructed wetland, and feces from a beef cattle feedlot were compared over a two-year period. Enterococcus hirae accounted for 92% of the fecal isolates, whereas secondary environments were characterized by greater relative abundance of environmentally adapted species including Enterococcus casseliflavus. While enterococci densities in the catch basins and wetland were similar under wet and drought conditions, E. hirae predominated during rainy periods, while E. casseliflavus predominated during drought conditions. Environmentally adapted species accounted for almost half of the erythromycin resistant enterococci isolated from the wetland. Densities of Escherichia coli were also comparable during wet versus drought conditions, and the relative abundance of strains from environmentally adapted clades was greater in secondary environments compared to feces. Unlike enterococci, fewer environmentally adapted E. coli strains were isolated on selective media containing ceftriaxone from the wetland compared to feces, suggesting resistance to this antibiotic may not be well maintained in the absence of selective pressure. Overall, these findings suggest that secondary environments select for environmentally adapted FIB. While these species and clades tend to be of limited clinical relevance, they could potentially serve as reservoirs of antimicrobial resistance.
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Affiliation(s)
- Lisa Tymensen
- Irrigation and Farm Water Branch, Alberta Agriculture and Forestry , 100, 5401 1st Avenue South, Lethbridge, Alberta, Canada , T1J 4 V6
| | - Calvin W Booker
- Feedlot Health Management Services, Ltd. , Okotoks, Alberta, Canada , T1S 2A2
| | - Sherry J Hannon
- Feedlot Health Management Services, Ltd. , Okotoks, Alberta, Canada , T1S 2A2
| | - Shaun R Cook
- Irrigation and Farm Water Branch, Alberta Agriculture and Forestry , 100, 5401 1st Avenue South, Lethbridge, Alberta, Canada , T1J 4 V6
- Agriculture and Agri-Food Canada , Lethbridge, Alberta, Canada , T1J 4B1
| | - Rahat Zaheer
- Agriculture and Agri-Food Canada , Lethbridge, Alberta, Canada , T1J 4B1
| | - Ron Read
- Microbiology, Immunology and Infectious Diseases, University of Calgary , Calgary, Alberta, Canada , T1Y 6J4
| | - Tim A McAllister
- Agriculture and Agri-Food Canada , Lethbridge, Alberta, Canada , T1J 4B1
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48
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Whole-Genome Sequence of Endophytic Plant Growth-Promoting Escherichia coli USML2. GENOME ANNOUNCEMENTS 2017; 5:5/19/e00305-17. [PMID: 28495774 PMCID: PMC5427209 DOI: 10.1128/genomea.00305-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Escherichia coli strain USML2 was originally isolated from the inner leaf tissues of surface-sterilized phytopathogenic-free oil palm (Elaeis guineensis Jacq.). We present here the whole-genome sequence of this plant-endophytic strain. The genome consists of a single circular chromosome of 4,502,758 bp, 4,315 predicted coding sequences, and a G+C content of 50.8%.
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49
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Rossi E, Cimdins A, Lüthje P, Brauner A, Sjöling Å, Landini P, Römling U. "It's a gut feeling" - Escherichia coli biofilm formation in the gastrointestinal tract environment. Crit Rev Microbiol 2017; 44:1-30. [PMID: 28485690 DOI: 10.1080/1040841x.2017.1303660] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Escherichia coli can commonly be found, either as a commensal, probiotic or a pathogen, in the human gastrointestinal (GI) tract. Biofilm formation and its regulation is surprisingly variable, although distinct regulatory pattern of red, dry and rough (rdar) biofilm formation arise in certain pathovars and even clones. In the GI tract, environmental conditions, signals from the host and from commensal bacteria contribute to shape E. coli biofilm formation within the multi-faceted multicellular communities in a complex and integrated fashion. Although some major regulatory networks, adhesion factors and extracellular matrix components constituting E. coli biofilms have been recognized, these processes have mainly been characterized in vitro and in the context of interaction of E. coli strains with intestinal epithelial cells. However, direct observation of E. coli cells in situ, and the vast number of genes encoding surface appendages on the core or accessory genome of E. coli suggests the complexity of the biofilm process to be far from being fully understood. In this review, we summarize biofilm formation mechanisms of commensal, probiotic and pathogenic E. coli in the context of the gastrointestinal tract.
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Affiliation(s)
- Elio Rossi
- a Department of Biosciences , Università degli Studi di Milano , Milan , Italy.,b Novo Nordisk Center for Biosustainabiliy , Technical University of Denmark , Kgs. Lyngby , Denmark
| | - Annika Cimdins
- c Department of Microbiology, Tumor and Cell Biology (MTC) , Karolinska Institutet , Stockholm , Sweden.,d Institute of Hygiene, University of Münster , Münster , Germany
| | - Petra Lüthje
- c Department of Microbiology, Tumor and Cell Biology (MTC) , Karolinska Institutet , Stockholm , Sweden.,e Division of Clinical Microbiology, Department of Laboratory Medicine , Karolinska Institutet and Karolinska University Hospital Huddinge , Stockholm , Sweden
| | - Annelie Brauner
- c Department of Microbiology, Tumor and Cell Biology (MTC) , Karolinska Institutet , Stockholm , Sweden
| | - Åsa Sjöling
- c Department of Microbiology, Tumor and Cell Biology (MTC) , Karolinska Institutet , Stockholm , Sweden
| | - Paolo Landini
- a Department of Biosciences , Università degli Studi di Milano , Milan , Italy
| | - Ute Römling
- c Department of Microbiology, Tumor and Cell Biology (MTC) , Karolinska Institutet , Stockholm , Sweden
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50
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Wright KM, Crozier L, Marshall J, Merget B, Holmes A, Holden NJ. Differences in internalization and growth of Escherichia coli O157:H7 within the apoplast of edible plants, spinach and lettuce, compared with the model species Nicotiana benthamiana. Microb Biotechnol 2017; 10:555-569. [PMID: 28169510 PMCID: PMC5404196 DOI: 10.1111/1751-7915.12596] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 12/14/2016] [Indexed: 11/30/2022] Open
Abstract
Internalization of food-borne bacteria into edible parts of fresh produce plants represents a serious health risk. Therefore, internalization of verocytotoxigenic E. coli O157:H7 isolate Sakai was assessed in two species associated with outbreaks, spinach (Spinacia oleracea) and lettuce (Lactuca sativa) and compared to the model species Nicotiana benthamiana. Internalization occurred in the leaves and roots of spinach and lettuce throughout a 10 day time-course. The plant species, tissue type and inoculum dose all impacted the outcome. A combination of low inoculum dose (~102 CFU) together with light microscopy imaging highlighted marked differences in the fate of endophytic E. coli O157:H7 Sakai. In the fresh produce species, bacterial growth was restricted but viable cells persisted over 20 days, whereas there was > 400-fold (~2.5 Log10 ) increase in growth in N. benthamiana. Colony formation occurred adjacent to epidermal cells and mesophyll cells or close to vascular bundles of N. benthamiana and contained components of a biofilm matrix, including curli expression and elicitation, extracellular DNA and a limited presence of cellulose. Together the data show that internalization is a relevant issue in crop production and that crop species and tissue need to be considered as food safety risk parameters.
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Affiliation(s)
| | - Louise Crozier
- Cell and Molecular SciencesThe James Hutton InstituteDundeeUK
| | | | - Bernhard Merget
- Cell and Molecular SciencesThe James Hutton InstituteDundeeUK
| | - Ashleigh Holmes
- Cell and Molecular SciencesThe James Hutton InstituteDundeeUK
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