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Wong LC, Rodenburg U, Leite RR, Korthals GW, Pover J, Koerten H, Kuramae EE, Bodelier PLE. Exploring microbial diversity and interactions for asbestos modifying properties. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 951:175577. [PMID: 39155010 DOI: 10.1016/j.scitotenv.2024.175577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 07/25/2024] [Accepted: 08/14/2024] [Indexed: 08/20/2024]
Abstract
Asbestos poses a substantial environmental health risk, and biological treatment offers a promising approach to mitigate its impact by altering its chemical composition. However, the dynamics of microbial co-inoculation in asbestos bioremediation remain poorly understood. This study investigates the effect of microbial single cultures and co-cultures on modifying crocidolite and chrysotile fibers, focusing on the extraction of iron and magnesium. Seventy bacterial and eighty-three fungal strains were isolated from five diverse sites, characterized phylogenetically using the 16S rRNA gene and ITS region, respectively, and assessed for siderophore and organic acid production. Most bacterial strains were identified as Pseudomonas, while Penicillium predominated among fungal strains. Ten bacterial and 25 fungal strains were found to produce both organic compounds. Four microbial co-cultures (one bacterium-bacterium, two fungus-bacterium, and one fungus-fungus) exhibiting synergistic effects in plate assays, alongside their respective single cultures, were incubated with crocidolite and chrysotile. ICP-OES analysis revealed that in crocidolite, the co-culture HRF19-HRB12 removed more iron than their single cultures, while Penicillium TPF36 showed the highest iron removal. The co-culture of two Pseudomonas strains (HRB12-RB5) exhibited the highest magnesium concentration in the supernatant. In chrysotile, the co-culture HRB12-RB5 removed more iron than their individual cultures, with Penicillium TFSF27 exhibiting the highest iron concentration in the solution. Penicillium TFSF27 and the co-culture TFSF27-TPF36 demonstrated the highest magnesium removal. SEM-XRMA analysis showed a significant reduction in iron and magnesium content, confirming elemental extraction from the fibers' structure. This study significantly broadens the range of microbial strains capable of modifying asbestos fibers and underscores the potential of microbial co-cultures in asbestos remediation.
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Affiliation(s)
- Lina C Wong
- Microbial Ecology Department, Netherlands Institute of Ecology (NIOO), Droevendaalsesteeg 10, 6708 PB, Wageningen, the Netherlands
| | - Umi Rodenburg
- Wageningen University and Research, Wageningen, the Netherlands
| | - Raycenne R Leite
- Microbial Ecology Department, Netherlands Institute of Ecology (NIOO), Droevendaalsesteeg 10, 6708 PB, Wageningen, the Netherlands
| | | | - Judith Pover
- SGI Compliance, Hongkongstraat 5, 3047 BR Rotterdam, the Netherlands
| | - Henk Koerten
- SGI Compliance, Hongkongstraat 5, 3047 BR Rotterdam, the Netherlands
| | - Eiko E Kuramae
- Microbial Ecology Department, Netherlands Institute of Ecology (NIOO), Droevendaalsesteeg 10, 6708 PB, Wageningen, the Netherlands; Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Paul L E Bodelier
- Microbial Ecology Department, Netherlands Institute of Ecology (NIOO), Droevendaalsesteeg 10, 6708 PB, Wageningen, the Netherlands.
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2
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Singh S, Koo OK. A Comprehensive Review Exploring the Protective Role of Specific Commensal Gut Bacteria against Salmonella. Pathogens 2024; 13:642. [PMID: 39204243 PMCID: PMC11356920 DOI: 10.3390/pathogens13080642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2024] [Revised: 07/25/2024] [Accepted: 07/30/2024] [Indexed: 09/03/2024] Open
Abstract
Gut microbiota is a diverse community of microorganisms that constantly work to protect the gut against pathogens. Salmonella stands out as a notorious foodborne pathogen that interacts with gut microbes, causing an imbalance in the overall composition of microbiota and leading to dysbiosis. This review focuses on the interactions between Salmonella and the key commensal bacteria such as E. coli, Lactobacillus, Clostridium, Akkermansia, and Bacteroides. The review highlights the role of these gut bacteria and their synergy in combating Salmonella through several mechanistic interactions. These include the production of siderophores, which compete with Salmonella for essential iron; the synthesis of short-chain fatty acids (SCFAs), which exert antimicrobial effects and modulate the gut environment; the secretion of bacteriocins, which directly inhibit Salmonella growth; and the modulation of cytokine responses, which influences the host's immune reaction to infection. While much research has explored Salmonella, this review aims to better understand how specific gut bacteria engage with the pathogen, revealing distinct defense mechanisms tailored to each species and how their synergy may lead to enhanced protection against Salmonella. Furthermore, the combination of these commensal bacteria could offer promising avenues for bacteria-mediated therapy during Salmonella-induced gut infections in the future.
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Affiliation(s)
| | - Ok Kyung Koo
- Department of Food Science & Technology, Chungnam National University, Daejeon 34134, Republic of Korea;
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3
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Zou Z, Robinson JI, Steinberg LK, Henderson JP. Uropathogenic Escherichia coli wield enterobactin-derived catabolites as siderophores. J Biol Chem 2024; 300:105554. [PMID: 38072063 PMCID: PMC10788543 DOI: 10.1016/j.jbc.2023.105554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 11/20/2023] [Accepted: 12/05/2023] [Indexed: 12/19/2023] Open
Abstract
Uropathogenic Escherichia coli (UPEC) secrete multiple siderophore types to scavenge extracellular iron(III) ions during clinical urinary tract infections, despite the metabolic costs of biosynthesis. Here, we find the siderophore enterobactin (Ent) and its related products to be prominent components of the iron-responsive extracellular metabolome of a model UPEC strain. Using defined Ent biosynthesis and import mutants, we identify lower molecular weight dimeric exometabolites as products of incomplete siderophore catabolism, rather than prematurely released biosynthetic intermediates. In E. coli, iron acquisition from iron(III)-Ent complexes requires intracellular esterases that hydrolyze the siderophore. Although UPEC are equipped to consume the products of completely hydrolyzed Ent, we find that Ent and its derivatives may be incompletely hydrolyzed to yield products with retained siderophore activity. These results are consistent with catabolic inefficiency as means to obtain more than one iron ion per siderophore molecule. This is compatible with an evolved UPEC strategy to maximize the nutritional returns from metabolic investments in siderophore biosynthesis.
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Affiliation(s)
- Zongsen Zou
- Center for Women's Infectious Diseases Research, Washington University School of Medicine, St Louis, Missouri, USA; Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St Louis, Missouri, USA
| | - John I Robinson
- Center for Women's Infectious Diseases Research, Washington University School of Medicine, St Louis, Missouri, USA; Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St Louis, Missouri, USA
| | - Lindsey K Steinberg
- Center for Women's Infectious Diseases Research, Washington University School of Medicine, St Louis, Missouri, USA; Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St Louis, Missouri, USA
| | - Jeffrey P Henderson
- Center for Women's Infectious Diseases Research, Washington University School of Medicine, St Louis, Missouri, USA; Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St Louis, Missouri, USA.
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4
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Stein NV, Eder M, Burr F, Stoss S, Holzner L, Kunz HH, Jung H. The RND efflux system ParXY affects siderophore secretion in Pseudomonas putida KT2440. Microbiol Spectr 2023; 11:e0230023. [PMID: 37800935 PMCID: PMC10715066 DOI: 10.1128/spectrum.02300-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 08/28/2023] [Indexed: 10/07/2023] Open
Abstract
IMPORTANCE Gram-negative bacteria from the Pseudomonas group are survivors in various environmental niches. For example, the bacteria secrete siderophores to capture ferric ions under deficiency conditions. Tripartite efflux systems are involved in the secretion of siderophores, which are also important for antibiotic resistance. For one of these efflux systems, the resistance-nodulation-cell division transporter ParXY from the model organism Pseudomonas putida KT2440, we show that it influences the secretion of the siderophore pyoverdine in addition to its already known involvement in antibiotic resistance. Phenotypically, its role in pyoverdine secretion is only apparent when other pyoverdine secretion systems are inactive. The results confirm that the different tripartite efflux systems have overlapping substrate specificities and can at least partially functionally substitute for each other, especially in important physiological activities such as supplying the cell with iron ions. This fact must be taken into account when developing specific inhibitors for tripartite efflux systems.
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Affiliation(s)
- Nicola Victoria Stein
- Microbiology, Faculty of Biology, Ludwig Maximilian University Munich, Martinsried, Germany
| | - Michelle Eder
- Microbiology, Faculty of Biology, Ludwig Maximilian University Munich, Martinsried, Germany
| | - Fabienne Burr
- Microbiology, Faculty of Biology, Ludwig Maximilian University Munich, Martinsried, Germany
| | - Sarah Stoss
- Microbiology, Faculty of Biology, Ludwig Maximilian University Munich, Martinsried, Germany
| | - Lorenz Holzner
- Plant Biochemistry and Physiology, Faculty of Biology, Ludwig Maximilian University Munich, Martinsried, Germany
| | - Hans-Henning Kunz
- Plant Biochemistry and Physiology, Faculty of Biology, Ludwig Maximilian University Munich, Martinsried, Germany
| | - Heinrich Jung
- Microbiology, Faculty of Biology, Ludwig Maximilian University Munich, Martinsried, Germany
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5
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Zou Z, Robinson JI, Steinberg LK, Henderson JP. Uropathogenic Escherichia coli wield enterobactin-derived catabolites as siderophores. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.25.550588. [PMID: 37546885 PMCID: PMC10402112 DOI: 10.1101/2023.07.25.550588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Uropathogenic E. coli (UPEC) secrete multiple siderophore types to scavenge extracellular iron(III) ions during clinical urinary tract infections, despite the metabolic costs of biosynthesis. Here we find the siderophore enterobactin and its related products to be prominent components of the iron-responsive extracellular metabolome of a model UPEC strain. Using defined enterobactin biosynthesis and import mutants, we identify lower molecular weight, dimeric exometabolites as products of incomplete siderophore catabolism, rather than prematurely released biosynthetic intermediates. In E. coli, iron acquisition from iron(III)-enterobactin complexes requires intracellular esterases that hydrolyze the siderophore. Although UPEC are equipped to consume the products of completely hydrolyzed enterobactin, we find that enterobactin and its derivatives may be incompletely hydrolyzed to yield products with retained siderophore activity. These results are consistent with catabolic inefficiency as means to obtain more than one iron ion per siderophore molecule. This is compatible with an evolved UPEC strategy to maximize the nutritional returns from metabolic investments in siderophore biosynthesis.
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Affiliation(s)
- Zongsen Zou
- Center for Women’s Infectious Diseases Research, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Internal Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - John I. Robinson
- Center for Women’s Infectious Diseases Research, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Internal Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Lindsey K. Steinberg
- Center for Women’s Infectious Diseases Research, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Internal Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jeffrey P. Henderson
- Center for Women’s Infectious Diseases Research, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Internal Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
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6
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Celis AI, Relman DA, Huang KC. The impact of iron and heme availability on the healthy human gut microbiome in vivo and in vitro. Cell Chem Biol 2023; 30:110-126.e3. [PMID: 36603582 PMCID: PMC9913275 DOI: 10.1016/j.chembiol.2022.12.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 07/12/2022] [Accepted: 12/14/2022] [Indexed: 01/06/2023]
Abstract
Responses of the indigenous human gut commensal microbiota to iron are poorly understood because of an emphasis on in vitro studies of pathogen iron sensitivity. In a study of iron supplementation in healthy humans, we identified gradual microbiota shifts in some participants correlated with bacterial iron internalization. To identify direct effects due to taxon-specific iron sensitivity, we used participant stool samples to derive diverse in vitro communities. Iron supplementation of these communities caused small compositional shifts, mimicking those in vivo, whereas iron deprivation dramatically inhibited growth with irreversible, cumulative reduction in diversity and replacement of dominant species. Sensitivity of individual species to iron deprivation in axenic culture generally predicted iron dependency in a community. Finally, exogenous heme acted as a source of inorganic iron to prevent depletion of some species. Our results highlight the complementarity of in vivo and in vitro studies in understanding how environmental factors affect gut microbiotas.
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Affiliation(s)
- Arianna I Celis
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - David A Relman
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Infectious Diseases Section, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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7
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Wolf PG, Bernabe BP, Oliveira ML, Hamm A, McLeod A, Olender S, Castellanos K, Loman BR, Gaskins HR, Fitzgibbon M, Tussing-Humphreys L. Effect of Diets Varying in Iron and Saturated Fat on the Gut Microbiota and Intestinal Inflammation: A Crossover Feeding Study among Older Females with Obesity. Nutr Cancer 2023; 75:876-889. [PMID: 36625531 PMCID: PMC10023443 DOI: 10.1080/01635581.2022.2163668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 12/23/2022] [Accepted: 12/23/2022] [Indexed: 01/11/2023]
Abstract
Obesity is considered an independent risk factor for colorectal cancer (CRC). Altered nutrient metabolism, particularly changes to digestion and intestinal absorption, may play an important role in the development of CRC. Iron can promote the formation of tissue-damaging and immune-modulating reactive oxygen species. We conducted a crossover, controlled feeding study to examine the effect of three, 3-week diets varying in iron and saturated fat content on the colonic milieu and systemic markers among older females with obesity. Anthropometrics, fasting venous blood and stool were collected before and after each diet. There was a minimum 3-week washout period between diets. Eighteen participants consumed the three diets (72% Black; mean age 60.4 years; mean body mass index 35.7 kg/m2). Results showed no effect of the diets on intestinal inflammation (fecal calprotectin) or circulating iron, inflammation, and metabolic markers. Pairwise comparisons revealed less community diversity between samples (beta diversity, calculated from 16S rRNA amplicon sequences) among participants when consuming a diet low in iron and high in saturated fat vs. when consuming a diet high in iron and saturated fat. More studies are needed to investigate if dietary iron represents a salient target for CRC prevention among individuals with obesity.
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Affiliation(s)
- Patricia G. Wolf
- Institute for Health Research and Policy, University of Illinois Chicago, Chicago, IL, USA
- University of Illinois Cancer Center, University of Illinois Chicago, Chicago, IL, USA
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Department of Nutrition Science, Purdue University, West Lafayette, IN, USA
| | | | - Manoela Lima Oliveira
- Department of Kinesiology and Nutrition, University of Illinois Chicago, Chicago, Illinois, USA
| | - Alyshia Hamm
- Department of Kinesiology and Nutrition, University of Illinois Chicago, Chicago, Illinois, USA
| | - Andrew McLeod
- Institute for Health Research and Policy, University of Illinois Chicago, Chicago, IL, USA
- Department of Kinesiology and Nutrition, University of Illinois Chicago, Chicago, Illinois, USA
| | - Sarah Olender
- Department of Kinesiology and Nutrition, University of Illinois Chicago, Chicago, Illinois, USA
| | - Karla Castellanos
- Department of Medicine, University of Illinois Chicago, Chicago, Illinois, USA
| | - Brett R. Loman
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - H. Rex Gaskins
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA
- Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Marian Fitzgibbon
- Institute for Health Research and Policy, University of Illinois Chicago, Chicago, IL, USA
- University of Illinois Cancer Center, University of Illinois Chicago, Chicago, IL, USA
- Department of Pediatrics, University of Illinois at Chicago, Chicago, IL, USA
| | - Lisa Tussing-Humphreys
- University of Illinois Cancer Center, University of Illinois Chicago, Chicago, IL, USA
- Department of Kinesiology and Nutrition, University of Illinois Chicago, Chicago, Illinois, USA
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8
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Production and Potential Genetic Pathways of Three Different Siderophore Types in Streptomyces tricolor Strain HM10. FERMENTATION 2022. [DOI: 10.3390/fermentation8080346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Siderophores are iron-chelating low-molecular-weight compounds that bind iron (Fe3+) with a high affinity for transport into the cell. The newly isolated strain Streptomyces tricolor HM10 secretes a pattern of secondary metabolites. Siderophore molecules are the representatives of such secondary metabolites. S. tricolor HM10 produces catechol, hydroxamate, and carboxylate types of siderophores. Under 20 μM FeCl3 conditions, S. tricolor HM10 produced up to 6.00 µg/mL of catechol siderophore equivalent of 2,3-DHBA (2,3-dihydroxybenzoic acid) after 4 days from incubation. In silico analysis of the S. tricolor HM10 genome revealed three proposed pathways for siderophore biosynthesis. The first pathway, consisting of five genes, predicted the production of catechol-type siderophore similar to petrobactin from Bacillus anthracis str. Ames. The second proposed pathway, consisting of eight genes, is expected to produce a hydroxamate-type siderophore similar to desferrioxamine B/E from Streptomyces sp. ID38640, S. griseus NBRC 13350, and/or S. coelicolor A3(2). The third pathway exhibited a pattern identical to the carboxylate xanthoferrin siderophore from Xanthomonas oryzae. Thus, Streptomyces strain HM10 could produce three different types of siderophore, which could be an incentive to use it as a new source for siderophore production in plant growth-promoting, environmental bioremediation, and drug delivery strategy.
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Singh P, Chauhan PK, Upadhyay SK, Singh RK, Dwivedi P, Wang J, Jain D, Jiang M. Mechanistic Insights and Potential Use of Siderophores Producing Microbes in Rhizosphere for Mitigation of Stress in Plants Grown in Degraded Land. Front Microbiol 2022; 13:898979. [PMID: 35898908 PMCID: PMC9309559 DOI: 10.3389/fmicb.2022.898979] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 06/09/2022] [Indexed: 12/20/2022] Open
Abstract
Plant growth performance under a stressful environment, notably in the agriculture field, is directly correlated with the rapid growth of the human population, which triggers the pressure on crop productivity. Plants perceived many stresses owing to degraded land, which induces low plant productivity and, therefore, becomes a foremost concern for the future to face a situation of food scarcity. Land degradation is a very notable environmental issue at the local, regional, and global levels for agriculture. Land degradation generates global problems such as drought desertification, heavy metal contamination, and soil salinity, which pose challenges to achieving many UN Sustainable Development goals. The plant itself has a varied algorithm for the mitigation of stresses arising due to degraded land; the rhizospheric system of the plant has diverse modes and efficient mechanisms to cope with stress by numerous root-associated microbes. The suitable root-associated microbes and components of root exudate interplay against stress and build adaptation against stress-mediated mechanisms. The problem of iron-deficient soil is rising owing to increasing degraded land across the globe, which hampers plant growth productivity. Therefore, in the context to tackle these issues, the present review aims to identify plant-stress status owing to iron-deficient soil and its probable eco-friendly solution. Siderophores are well-recognized iron-chelating agents produced by numerous microbes and are associated with the rhizosphere. These siderophore-producing microbes are eco-friendly and sustainable agents, which may be managing plant stresses in the degraded land. The review also focuses on the molecular mechanisms of siderophores and their chemistry, cross-talk between plant root and siderophores-producing microbes to combat plant stress, and the utilization of siderophores in plant growth on degraded land.
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Affiliation(s)
- Pratiksha Singh
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi Minzu University, Nanning, China
| | - Prabhat K. Chauhan
- Department of Environmental Science, Veer Bahadur Singh Purvanchal University, Jaunpur, India
| | - Sudhir K. Upadhyay
- Department of Environmental Science, Veer Bahadur Singh Purvanchal University, Jaunpur, India
- Sudhir K. Upadhyay
| | - Rajesh Kumar Singh
- Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Padmanabh Dwivedi
- Department of Plant Physiology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
| | - Jing Wang
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi Minzu University, Nanning, China
| | - Devendra Jain
- Department of Molecular Biology and Biotechnology, Maharana Pratap University of Agriculture and Technology, Udaipur, India
| | - Mingguo Jiang
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi Minzu University, Nanning, China
- *Correspondence: Mingguo Jiang
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Elankumaran P, Cummins ML, Browning GF, Marenda MS, Reid CJ, Djordjevic SP. Genomic and Temporal Trends in Canine ExPEC Reflect Those of Human ExPEC. Microbiol Spectr 2022; 10:e0129122. [PMID: 35674442 PMCID: PMC9241711 DOI: 10.1128/spectrum.01291-22] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 05/24/2022] [Indexed: 11/25/2022] Open
Abstract
Companion animals and humans are known to share extraintestinal pathogenic Escherichia coli (ExPEC), but the extent of E. coli sequence types (STs) that cause extraintestinal diseases in dogs is not well understood. Here, we generated whole-genome sequences of 377 ExPEC collected by the University of Melbourne Veterinary Hospital from dogs over an 11-year period from 2007 to 2017. Isolates were predominantly from urogenital tract infections (219, 58.1%), but isolates from gastrointestinal specimens (51, 13.5%), general infections (72, 19.1%), and soft tissue infections (34, 9%) were also represented. A diverse collection of 53 STs were identified, with 18 of these including at least five sequences. The five most prevalent STs were ST372 (69, 18.3%), ST73 (31, 8.2%), ST127 (22, 5.8%), ST80 (19, 5.0%), and ST58 (14, 3.7%). Apart from ST372, all of these are prominent human ExPEC STs. Other common ExPEC STs identified included ST12, ST131, ST95, ST141, ST963, ST1193, ST88, and ST38. Virulence gene profiles, antimicrobial resistance carriage, and trends in plasmid carriage for specific STs were generally reflective of those seen in humans. Many of the prominent STs were observed repetitively over an 11-year time span, indicating their persistence in the dogs in the community, which is most likely driven by household sharing of E. coli between humans and their pets. The case of ST372 as a dominant canine lineage observed sporadically in humans is flagged for further investigation. IMPORTANCE Pathogenic E. coli that causes extraintestinal infections (ExPEC) in humans and canines represents a significant burden in hospital and veterinary settings. Despite the obvious interrelationship between dogs and humans favoring both zoonotic and anthropozoonotic infections, whole-genome sequencing projects examining large numbers of canine-origin ExPEC are lacking. In support of anthropozoonosis, we found that most STs from canine infections are dominant human ExPEC STs (e.g., ST73, ST127, ST131) with similar genomic traits, such as plasmid carriage and virulence gene burden. In contrast, we identified ST372 as the dominant canine ST and a sporadic cause of infection in humans, supporting zoonotic transfer. Furthermore, we highlight that, as is the case in humans, STs in canine disease are consistent over time, implicating the gastrointestinal tract as the major community reservoir, which is likely augmented by exposure to human E. coli via shared diet and proximity.
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Affiliation(s)
- Paarthiphan Elankumaran
- Australian Institute for Microbiology and Infection, School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Max L. Cummins
- Australian Institute for Microbiology and Infection, School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Glenn F. Browning
- Asia-Pacific Centre for Animal Health, Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville and Werribee, Victoria, Australia
| | - Marc S. Marenda
- Asia-Pacific Centre for Animal Health, Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville and Werribee, Victoria, Australia
| | - Cameron J. Reid
- Australian Institute for Microbiology and Infection, School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Steven P. Djordjevic
- Australian Institute for Microbiology and Infection, School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, New South Wales, Australia
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11
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Antibiotic resistance and siderophores production by clinical Escherichia coli strains. BIOTECHNOLOGIA 2022; 103:169-184. [PMID: 36606072 PMCID: PMC9642952 DOI: 10.5114/bta.2022.116211] [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: 07/04/2021] [Revised: 02/17/2022] [Accepted: 03/01/2022] [Indexed: 01/09/2023] Open
Abstract
The phenomenon of antibiotic resistance has dramatically increased in the last few decades, especially in enterobacterial pathogens. Different strains of Escherichia coli have been reported to produce a variety of structurally different siderophores. In the present study, 32 E. coli strains were collected from different clinical settings in Cairo, Egypt and subjected to the antibiotic susceptibility test by using 19 antibiotics belonging to 7 classes of chemical groups. The results indicated that 31 strains could be considered as extensively drug-resistant and only one strain as pan drug-resistant. Siderophores production by all the tested E. coli strains was determined qualitatively and quantitatively. Two E. coli strains coded 21 and 49 were found to be the most potent siderophores producers, with 79.9 and 46.62%, respectively. Bacterial colonies with cured plasmids derived from strain 49 showed susceptibility to all the tested antibiotics. Furthermore, E. coli DH5α cells transformed with the plasmid isolated from E. coli strain 21 or E. coli strain 49 were found to be susceptible to ansamycins, quinolones, and sulfonamide groups of antibiotics. In contrast, both plasmid-cured and plasmid-transformed strains did not produce siderophores, indicating that the genes responsible for siderophores production were located on plasmids and regulated by genes located on the chromosome. On the basis of the obtained results, it could be concluded that there is a positive correlation between antibiotic resistance, especially to quinolones and sulfonamide groups, and siderophores production by E. coli strains used in this study.
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12
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Nunes PHS, Valiatti TB, Santos ACDM, Nascimento JADS, Santos-Neto JF, Rocchetti TT, Yu MCZ, Hofling-Lima AL, Gomes TAT. Evaluation of the Pathogenic Potential of Escherichia coli Strains Isolated from Eye Infections. Microorganisms 2022; 10:microorganisms10061084. [PMID: 35744602 PMCID: PMC9229993 DOI: 10.3390/microorganisms10061084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/13/2022] [Accepted: 05/21/2022] [Indexed: 11/29/2022] Open
Abstract
While primarily Gram-positive bacteria cause bacterial eye infections, several Gram-negative species also pose eye health risks. Currently, few studies have tried to understand the pathogenic mechanisms involved in E. coli eye infections. Therefore, this study aimed to establish the pathogenic potential of E. coli strains isolated from eye infections. Twenty-two strains isolated between 2005 and 2019 from patients with keratitis or conjunctivitis were included and submitted to traditional polymerase chain reactions (PCR) to define their virulence profile, phylogeny, clonal relationship, and sequence type (ST). Phenotypic assays were employed to determine hemolytic activity, antimicrobial susceptibility, and adhesion to human primary corneal epithelial cells (PCS-700-010). The phylogenetic results indicated that groups B2 and ST131 were the most frequent. Twenty-five virulence genes were found among our strains, with ecp, sitA, fimA, and fyuA being the most prevalent. Two strains presented a hemolytic phenotype, and resistance to ciprofloxacin and ertapenem was found in six strains and one strain, respectively. Regarding adherence, all but one strains adhered in vitro to corneal cells. Our results indicate significant genetic and virulence variation among ocular strains and point to an ocular pathogenic potential related to multiple virulence mechanisms.
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Affiliation(s)
- Pedro Henrique Soares Nunes
- Laboratório Experimental de Patogenicidade de Enterobactérias (LEPE), Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia (DMIP), Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), Sao Paulo 04023-062, Brazil; (P.H.S.N.); (T.B.V.); (A.C.d.M.S.); (J.A.d.S.N.); (J.F.S.-N.)
- Laboratório de Oftalmologia (LOFT), Departamento de Oftalmologia e Ciências Visuais, Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), Sao Paulo 04023-062, Brazil; (T.T.R.); (M.C.Z.Y.); (A.L.H.-L.)
| | - Tiago Barcelos Valiatti
- Laboratório Experimental de Patogenicidade de Enterobactérias (LEPE), Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia (DMIP), Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), Sao Paulo 04023-062, Brazil; (P.H.S.N.); (T.B.V.); (A.C.d.M.S.); (J.A.d.S.N.); (J.F.S.-N.)
- Laboratório Alerta, Disciplina de Infectologia, Departamento de Medicina, Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), Sao Paulo 04039-032, Brazil
| | - Ana Carolina de Mello Santos
- Laboratório Experimental de Patogenicidade de Enterobactérias (LEPE), Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia (DMIP), Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), Sao Paulo 04023-062, Brazil; (P.H.S.N.); (T.B.V.); (A.C.d.M.S.); (J.A.d.S.N.); (J.F.S.-N.)
| | - Júllia Assis da Silva Nascimento
- Laboratório Experimental de Patogenicidade de Enterobactérias (LEPE), Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia (DMIP), Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), Sao Paulo 04023-062, Brazil; (P.H.S.N.); (T.B.V.); (A.C.d.M.S.); (J.A.d.S.N.); (J.F.S.-N.)
| | - José Francisco Santos-Neto
- Laboratório Experimental de Patogenicidade de Enterobactérias (LEPE), Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia (DMIP), Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), Sao Paulo 04023-062, Brazil; (P.H.S.N.); (T.B.V.); (A.C.d.M.S.); (J.A.d.S.N.); (J.F.S.-N.)
| | - Talita Trevizani Rocchetti
- Laboratório de Oftalmologia (LOFT), Departamento de Oftalmologia e Ciências Visuais, Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), Sao Paulo 04023-062, Brazil; (T.T.R.); (M.C.Z.Y.); (A.L.H.-L.)
| | - Maria Cecilia Zorat Yu
- Laboratório de Oftalmologia (LOFT), Departamento de Oftalmologia e Ciências Visuais, Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), Sao Paulo 04023-062, Brazil; (T.T.R.); (M.C.Z.Y.); (A.L.H.-L.)
| | - Ana Luisa Hofling-Lima
- Laboratório de Oftalmologia (LOFT), Departamento de Oftalmologia e Ciências Visuais, Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), Sao Paulo 04023-062, Brazil; (T.T.R.); (M.C.Z.Y.); (A.L.H.-L.)
| | - Tânia Aparecida Tardelli Gomes
- Laboratório Experimental de Patogenicidade de Enterobactérias (LEPE), Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia (DMIP), Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), Sao Paulo 04023-062, Brazil; (P.H.S.N.); (T.B.V.); (A.C.d.M.S.); (J.A.d.S.N.); (J.F.S.-N.)
- Correspondence: ; Tel.: +55-11-5576-4848
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13
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Indigenous microbial populations of abandoned mining sites and their role in natural attenuation. Arch Microbiol 2022; 204:251. [PMID: 35411412 DOI: 10.1007/s00203-022-02861-6] [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: 07/23/2021] [Revised: 03/17/2022] [Accepted: 03/20/2022] [Indexed: 11/02/2022]
Abstract
Environmental contamination by toxic effluents discharged by anthropogenic activities including the mining industries has increased extensively in the recent past. Microbial communities and their biofilms inhabiting these extreme habitats have developed different adaptive strategies in metabolizing and transforming the persistent pollutants. They also play a crucial role in natural attenuation of these abandoned mining sites and act as a major driver of many biogeochemical processes, which helps in ecological rehabilitation and is a viable approach for restoration of wide stretches of land. In this review, the types of mine wastes including the overburden and mine drainage and the types of microbial communities thriving in such environments were probed in detail. The types of biofilms formed along with their possible role in metal bioremediation were also reviewed. This review also provides an overview of the shift in microbial communities in natural reclamation process and also provides an insight into the restoration of the enzyme activities of the soils which may help in further revegetation of abundant mining areas in a sustainable manner. Moreover, the role of indigenous microbiota in bioremediation of heavy metals and their plant growth-promoting activity weres discussed to assess their role in phytoremedial processes.
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14
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WHO Critical Priority Escherichia coli as One Health Challenge for a Post-Pandemic Scenario: Genomic Surveillance and Analysis of Current Trends in Brazil. Microbiol Spectr 2022; 10:e0125621. [PMID: 35234515 PMCID: PMC8941879 DOI: 10.1128/spectrum.01256-21] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The dissemination of carbapenem-resistant and third generation cephalosporin-resistant pathogens is a critical issue that is no longer restricted to hospital settings. The rapid spread of critical priority pathogens in Brazil is notably worrying, considering its continental dimension, the diversity of international trade, livestock production, and human travel. We conducted a nationwide genomic investigation under a One Health perspective that included Escherichia coli strains isolated from humans and nonhuman sources, over 45 years (1974–2019). One hundred sixty-seven genomes were analyzed extracting clinically relevant information (i.e., resistome, virulome, mobilome, sequence types [STs], and phylogenomic). The endemic status of extended-spectrum β-lactamase (ESBL)-positive strains carrying a wide diversity of blaCTX-M variants, and the growing number of colistin-resistant isolates carrying mcr-type genes was associated with the successful expansion of international ST10, ST38, ST115, ST131, ST354, ST410, ST648, ST517, and ST711 clones; phylogenetically related and shared between human and nonhuman hosts, and polluted aquatic environments. Otherwise, carbapenem-resistant ST48, ST90, ST155, ST167, ST224, ST349, ST457, ST648, ST707, ST744, ST774, and ST2509 clones from human host harbored blaKPC-2 and blaNDM-1 genes. A broad resistome to other clinically relevant antibiotics, hazardous heavy metals, disinfectants, and pesticides was further predicted. Wide virulome associated with invasion/adherence, exotoxin and siderophore production was related to phylogroup B2. The convergence of wide resistome and virulome has contributed to the persistence and rapid spread of international high-risk clones of critical priority E. coli at the human-animal-environmental interface, which must be considered a One Health challenge for a post-pandemic scenario. IMPORTANCE A One Health approach for antimicrobial resistance must integrate whole-genome sequencing surveillance data of critical priority pathogens from human, animal and environmental sources to track hot spots and routes of transmission and developing effective prevention and control strategies. As part of the Grand Challenges Explorations: New Approaches to Characterize the Global Burden of Antimicrobial Resistance Program, we present genomic data of WHO critical priority carbapenemase-resistant, ESBL-producing, and/or colistin-resistant Escherichia coli strains isolated from humans and nonhuman sources in Brazil, a country with continental proportions and high levels of antimicrobial resistance. The present study provided evidence of epidemiological and clinical interest, highlighting that the convergence of wide virulome and resistome has contributed to the persistence and rapid spread of international high-risk clones of E. coli at the human-animal-environmental interface, which must be considered a One Health threat that requires coordinated actions to reduce its incidence in humans and nonhuman hosts.
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15
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Antibiotic resistance, virulence, and phylogenetic analysis of Escherichia coli strains isolated from free-living birds in human habitats. PLoS One 2022; 17:e0262236. [PMID: 35020771 PMCID: PMC8754294 DOI: 10.1371/journal.pone.0262236] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 12/20/2021] [Indexed: 12/11/2022] Open
Abstract
Wild birds can be colonized by bacteria, which are often resistant to antibiotics and have various virulence profiles. The aim of this study was to analyze antibiotic resistance mechanisms and virulence profiles in relation to the phylogenetic group of E. coli strains that were isolated from the GI tract of wildfowl. Out of 241 faecal samples, presence of E. coli resistant to a cephalosporin (ESBL/AmpC) was estimated for 33 isolates (13,7%). Based on the analysis of the coexistence of 4 genes encoding ESBLs/AmpC (blaCTX-M, blaTEM,blaSHV, blaAmpC) and class 1 and 2 integrons genes (intI1, intI2) a subset of two resistance profiles was observed among the investigated E. coli isolates carrying blaAmpC, blaSHV, and blaCTX-M, blaTEM, class 1 and 2 integrons, respectively. The E. coli isolates were categorized into 4 phylogenetic groups A (39.4%), B2 (24.25%), D (24.25%) and B1 (12.1%). The pathogenic B2 and D groups were mainly typical for the Laridae family. Among the 28 virulence factors (Vfs) detected in pathogenic phylogenetic groups B2 and D, 7 were exclusively found in those groups (sfa, vat, tosA, tosB, hly, usp, cnf), while 4 VFs (fecA, fyuA, irp2, kspMTII) showed a statistically significant association (P≤0.05) with phylogroups A and B1. Our results indicated that strains belonging to commensal phylogroups A/B1 possess extensive iron acquisition systems (93,9%) and autotransporters (60,6%), typical for pathogens, hence we suggest that these strains evolve towards higher levels of virulence. This study, which is a point assessment of the virulence and drug resistance potential of wild birds, confirms the importance of taking wild birds as a reservoir of strains that pose a growing threat to humans. The E. coli analyzed in our study derive from different phylogenetic groups and possess an arsenal of antibiotic resistance genes and virulence factors that contribute to their ability to cause diseases.
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16
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Reid CJ, Cummins ML, Börjesson S, Brouwer MSM, Hasman H, Hammerum AM, Roer L, Hess S, Berendonk T, Nešporová K, Haenni M, Madec JY, Bethe A, Michael GB, Schink AK, Schwarz S, Dolejska M, Djordjevic SP. A role for ColV plasmids in the evolution of pathogenic Escherichia coli ST58. Nat Commun 2022; 13:683. [PMID: 35115531 PMCID: PMC8813906 DOI: 10.1038/s41467-022-28342-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 01/11/2022] [Indexed: 12/15/2022] Open
Abstract
Escherichia coli ST58 has recently emerged as a globally disseminated uropathogen that often progresses to sepsis. Unlike most pandemic extra-intestinal pathogenic E. coli (ExPEC), which belong to pathogenic phylogroup B2, ST58 belongs to the environmental/commensal phylogroup B1. Here, we present a pan-genomic analysis of a global collection of 752 ST58 isolates from diverse sources. We identify a large ST58 sub-lineage characterized by near ubiquitous carriage of ColV plasmids, which carry genes encoding virulence factors, and by a distinct accessory genome including genes typical of the Yersiniabactin High Pathogenicity Island. This sub-lineage includes three-quarters of all ExPEC sequences in our study and has a broad host range, although poultry and porcine sources predominate. By contrast, strains isolated from cattle often lack ColV plasmids. Our data indicate that ColV plasmid acquisition contributed to the divergence of the major ST58 sub-lineage, and different sub-lineages inhabit poultry, swine and cattle.
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Affiliation(s)
- Cameron J Reid
- iThree Institute, University of Technology Sydney, Ultimo, NSW, 2007, Australia.
| | - Max L Cummins
- iThree Institute, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Stefan Börjesson
- Department of Animal Health and Antimicrobial Strategies, National Veterinary Institute (SVA), 75189, Uppsala, Sweden
- Department of Microbiology, Public Health Agency of Sweden, 17182, Solna, Sweden
| | | | - Henrik Hasman
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen S, Denmark
| | - Anette M Hammerum
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen S, Denmark
| | - Louise Roer
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen S, Denmark
| | - Stefanie Hess
- Institute of Microbiology, Technische Universität Dresden, Dresden, Germany
| | - Thomas Berendonk
- Institute of Hydrobiology, Technische Universität Dresden, Dresden, Germany
| | - Kristina Nešporová
- CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czech Republic
- Department of Biology and Wildlife Disease, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Marisa Haenni
- Université de Lyon-ANSES, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Jean-Yves Madec
- Université de Lyon-ANSES, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Astrid Bethe
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, 14163, Berlin, Germany
| | - Geovana B Michael
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, 14163, Berlin, Germany
| | - Anne-Kathrin Schink
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, 14163, Berlin, Germany
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, 14163, Berlin, Germany
| | - Monika Dolejska
- CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czech Republic
- Department of Biology and Wildlife Disease, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czech Republic
- Biomedical Center, Charles University, Charles, Czech Republic
| | - Steven P Djordjevic
- iThree Institute, University of Technology Sydney, Ultimo, NSW, 2007, Australia.
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17
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Starčič Erjavec M, Jeseničnik K, Elam LP, Kastrin A, Predojević L, Sysoeva TA. Complete sequence of classic F-type plasmid pRK100 shows unique conservation over time and geographic location. Plasmid 2022; 119-120:102618. [PMID: 35077724 PMCID: PMC8978152 DOI: 10.1016/j.plasmid.2022.102618] [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: 09/09/2021] [Revised: 01/13/2022] [Accepted: 01/16/2022] [Indexed: 12/05/2022]
Abstract
Plasmids exhibit great diversity of gene content and host ranges and are famous for quick adaptation to the genetic background of the bacterial host cell. In addition to observing ever evolving plasmids, some plasmids have conserved backbones: a stable core composition and arrangement of genes in addition to variable regions. There are a few reports of extremely conserved plasmids. Here we report the complete sequence of pRK100 plasmid - a large, well-characterized conjugative F-like plasmid found in an Escherichia coli strain isolated from a urinary tract infection patient in 1990. The sequence shows that the 142 kb-long pRK100 plasmid is nearly identical to plasmids circulating in distant geographical locations and found in different host E. coli strains between 2007 and 2017. We also performed additional functional characterization of pRK100. Our results showed that pRK100 does not have a strong pathogenicity phenotype in porcine primary bladder epithelial cell culture. Moreover, the conjugation of pRK100 seems to strongly depend on recipient characteristics. These observations and identification of the pRK100 plasmid in different strain genotypes leave the extreme sequence conservation and broad distribution of this plasmid unexplained.
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Affiliation(s)
- Marjanca Starčič Erjavec
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Karmen Jeseničnik
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Lauren P Elam
- Department of Biological Sciences, The University of Alabama in Huntsville, 301 Sparkman Dr, Huntsville, AL 35899, USA
| | - Andrej Kastrin
- Institute for Biostatistics and Medical Informatics, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, SI-1000 Ljubljana, Slovenia
| | - Luka Predojević
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Tatyana A Sysoeva
- Department of Biological Sciences, The University of Alabama in Huntsville, 301 Sparkman Dr, Huntsville, AL 35899, USA.
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18
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Martin MJ, Corey BW, Sannio F, Hall LR, MacDonald U, Jones BT, Mills EG, Harless C, Stam J, Maybank R, Kwak Y, Schaufler K, Becker K, Hübner NO, Cresti S, Tordini G, Valassina M, Cusi MG, Bennett JW, Russo TA, McGann PT, Lebreton F, Docquier JD. Anatomy of an extensively drug-resistant Klebsiella pneumoniae outbreak in Tuscany, Italy. Proc Natl Acad Sci U S A 2021; 118:e2110227118. [PMID: 34819373 PMCID: PMC8640832 DOI: 10.1073/pnas.2110227118] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/11/2021] [Indexed: 01/13/2023] Open
Abstract
A protracted outbreak of New Delhi metallo-β-lactamase (NDM)-producing carbapenem-resistant Klebsiella pneumoniae started in Tuscany, Italy, in November 2018 and continued in 2020 and through 2021. To understand the regional emergence and transmission dynamics over time, we collected and sequenced the genomes of 117 extensively drug-resistant, NDM-producing K. pneumoniae isolates cultured over a 20-mo period from 76 patients at several healthcare facilities in southeast Tuscany. All isolates belonged to high-risk clone ST-147 and were typically nonsusceptible to all first-line antibiotics. Albeit sporadic, resistances to colistin, tigecycline, and fosfomycin were also observed as a result of repeated, independent mutations. Genomic analysis revealed that ST-147 isolates circulating in Tuscany were monophyletic and highly genetically related (including a network of 42 patients from the same hospital and sharing nearly identical isolates), and shared a recent ancestor with clinical isolates from the Middle East. While the blaNDM-1 gene was carried by an IncFIB-type plasmid, our investigations revealed that the ST-147 lineage from Italy also acquired a hybrid IncFIB/IncHIB-type plasmid carrying the 16S methyltransferase armA gene as well as key virulence biomarkers often found in hypervirulent isolates. This plasmid shared extensive homologies with mosaic plasmids circulating globally including from ST-11 and ST-307 convergent lineages. Phenotypically, the carriage of this hybrid plasmid resulted in increased siderophore production but did not confer virulence to the level of an archetypical, hypervirulent K. pneumoniae in a subcutaneous model of infection with immunocompetent CD1 mice. Our findings highlight the importance of performing genomic surveillance to identify emerging threats.
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Affiliation(s)
- Melissa J Martin
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD 20910
| | - Brendan W Corey
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD 20910
| | - Filomena Sannio
- Dipartimento di Biotecnologie Mediche, University of Siena I-53100 Siena, Italy
| | - Lindsey R Hall
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD 20910
| | - Ulrike MacDonald
- Veterans Administration Western New York Healthcare System, University at Buffalo, State University of New York, Buffalo, NY 14215
- Department of Medicine, University at Buffalo, State University of New York, Buffalo, NY 14203
| | - Brendan T Jones
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD 20910
| | - Emma G Mills
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD 20910
| | - Casey Harless
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD 20910
| | - Jason Stam
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD 20910
| | - Rosslyn Maybank
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD 20910
| | - Yoon Kwak
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD 20910
| | - Katharina Schaufler
- Institute of Pharmacy, Pharmaceutical Microbiology, University of Greifswald, 17489 Greifswald, Germany
- Institute of Infection Medicine, Christian-Albrecht University of Kiel, 24105 Kiel, Germany
- Institute of Infection Medicine, University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Karsten Becker
- Friedrich Loeffler Institute of Medical Microbiology, University of Greifswald, 17475 Greifswald, Germany
| | - Nils-Olaf Hübner
- Central Unit for Infection Prevention and Control, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Stefania Cresti
- Dipartimento di Biotecnologie Mediche, University of Siena I-53100 Siena, Italy
- Unita Operativa Complessa di Microbiologia e Virologia, Azienda Ospedaliera Universitaria Senese, I-53100 Siena, Italy
| | - Giacinta Tordini
- Dipartimento di Biotecnologie Mediche, University of Siena I-53100 Siena, Italy
- Unita Operativa Complessa di Microbiologia e Virologia, Azienda Ospedaliera Universitaria Senese, I-53100 Siena, Italy
| | - Marcello Valassina
- Unita Operativa Complessa di Microbiologia e Virologia, Azienda Ospedaliera Universitaria Senese, I-53100 Siena, Italy
| | - Maria Grazia Cusi
- Dipartimento di Biotecnologie Mediche, University of Siena I-53100 Siena, Italy
- Unita Operativa Complessa di Microbiologia e Virologia, Azienda Ospedaliera Universitaria Senese, I-53100 Siena, Italy
| | - Jason W Bennett
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD 20910
| | - Thomas A Russo
- Veterans Administration Western New York Healthcare System, University at Buffalo, State University of New York, Buffalo, NY 14215
- Department of Medicine, University at Buffalo, State University of New York, Buffalo, NY 14203
- Department of Microbiology and Immunology, University at Buffalo, State University of New York, Buffalo, NY 14203
- The Witebsky Center for Microbial Pathogenesis, University at Buffalo, State University of New York, Buffalo, NY 14203
| | - Patrick T McGann
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD 20910
| | - Francois Lebreton
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD 20910;
| | - Jean-Denis Docquier
- Dipartimento di Biotecnologie Mediche, University of Siena I-53100 Siena, Italy;
- Centre d'Ingénierie des Protéines-InBioS, Université de Liège B-4000 Liège, Belgium
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19
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Mould DL, Hogan DA. Intraspecies heterogeneity in microbial interactions. Curr Opin Microbiol 2021; 62:14-20. [PMID: 34034081 DOI: 10.1016/j.mib.2021.04.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 04/08/2021] [Accepted: 04/13/2021] [Indexed: 11/18/2022]
Abstract
Microbial interactions are increasingly recognized as an integral part of microbial physiology. Cell-cell communication mediated by quorum sensing and metabolite exchange is a formative element of microbial interactions. However, loss-of-function mutations in quorum-sensing components are common across diverse species. Furthermore, quorum sensing is modulated by small molecules and environmental conditions that may be altered in the presence of other microbial species. Recent evidence highlights how strain heterogeneity impacts microbial interactions. There is great potential for microbial interactions to act as selective pressures that influence the emergence of common mutations in quorum-sensing genes across the bacterial and fungal domains.
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Affiliation(s)
- Dallas L Mould
- Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Deborah A Hogan
- Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA.
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20
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Klebba PE, Newton SMC, Six DA, Kumar A, Yang T, Nairn BL, Munger C, Chakravorty S. Iron Acquisition Systems of Gram-negative Bacterial Pathogens Define TonB-Dependent Pathways to Novel Antibiotics. Chem Rev 2021; 121:5193-5239. [PMID: 33724814 PMCID: PMC8687107 DOI: 10.1021/acs.chemrev.0c01005] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Iron is an indispensable metabolic cofactor in both pro- and eukaryotes, which engenders a natural competition for the metal between bacterial pathogens and their human or animal hosts. Bacteria secrete siderophores that extract Fe3+ from tissues, fluids, cells, and proteins; the ligand gated porins of the Gram-negative bacterial outer membrane actively acquire the resulting ferric siderophores, as well as other iron-containing molecules like heme. Conversely, eukaryotic hosts combat bacterial iron scavenging by sequestering Fe3+ in binding proteins and ferritin. The variety of iron uptake systems in Gram-negative bacterial pathogens illustrates a range of chemical and biochemical mechanisms that facilitate microbial pathogenesis. This document attempts to summarize and understand these processes, to guide discovery of immunological or chemical interventions that may thwart infectious disease.
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Affiliation(s)
- Phillip E Klebba
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506, United States
| | - Salete M C Newton
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506, United States
| | - David A Six
- Venatorx Pharmaceuticals, Inc., 30 Spring Mill Drive, Malvern, Pennsylvania 19355, United States
| | - Ashish Kumar
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506, United States
| | - Taihao Yang
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506, United States
| | - Brittany L Nairn
- Department of Biological Sciences, Bethel University, 3900 Bethel Drive, St. Paul, Minnesota 55112, United States
| | - Colton Munger
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas 66506, United States
| | - Somnath Chakravorty
- Jacobs School of Medicine and Biomedical Sciences, SUNY Buffalo, Buffalo, New York 14203, United States
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21
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Yañez-Yazlle MF, Romano-Armada N, Acreche MM, Rajal VB, Irazusta VP. Halotolerant bacteria isolated from extreme environments induce seed germination and growth of chia (Salvia hispanica L.) and quinoa (Chenopodium quinoa Willd.) under saline stress. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 218:112273. [PMID: 33940441 DOI: 10.1016/j.ecoenv.2021.112273] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 04/16/2021] [Accepted: 04/18/2021] [Indexed: 06/12/2023]
Abstract
The aim of the study was to characterize halotolerant bacteria and to evaluate their plant growth promotion potential on chia and quinoa seedlings under saline stress. Isolated microorganisms were evaluated for nitrogen fixation, phosphate solubilization, and production of siderophores and indole acetic acid. Three strains and two consortia were selected: Halomonas sp. (SFS), Micrococcus luteus (SA211), Bacillus sp. (HX11), C1 (SA211 + SFS), and C2 (SA211 + HX11). In vitro assays using water agar and half-strength Murashige-Skoog plates showed that an increase in salinity led to an increased seedlings mortality and a decrease in germination (lower than 40%), in total length (varying between 16% and 87% decreases), root length (from 60% to 92% lesser length) and dry weight (from 7% to 86% lower weight). Also, the relative growth index (RGI) decreased for both crops in most treatments, except those with HX11 and C2. These treatments had the highest growth parameters and RGI values in presence of high salinity in chia (50 and 100 mmol/L NaCl) and quinoa (200 and 400 mmol/L NaCl). SA211, the highest producer of indole acetic acid, showed a detrimental effect and anomalous phenotype on plants. Our results suggest that Bacillus sp. HX11, with multiple plant growth promotion traits and tolerance to saline stress, has a great potential as a bioinoculant in saline conditions and could be used as a biofertilizer for crop production.
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Affiliation(s)
- María Florencia Yañez-Yazlle
- Instituto de Investigaciones para la Industria Química (INIQUI), Universidad Nacional de Salta (UNSa) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Salta, Argentina; Facultad de Ciencias Naturales, UNSa, Salta, Argentina
| | - Neli Romano-Armada
- Instituto de Investigaciones para la Industria Química (INIQUI), Universidad Nacional de Salta (UNSa) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Salta, Argentina; Facultad de Ingeniería, UNSa, Salta, Argentina
| | - Martín Moises Acreche
- Estación Experimental (EEA) Salta, Instituto Nacional de Tecnología Agropecuaria (INTA), Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Verónica Beatriz Rajal
- Instituto de Investigaciones para la Industria Química (INIQUI), Universidad Nacional de Salta (UNSa) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Salta, Argentina; Facultad de Ingeniería, UNSa, Salta, Argentina; Singapore Centre for Environmental Life Sciences Engineering (SCELSE), School of Biological Sciences, Nanyang Technological University (NTU), Singapore
| | - Verónica Patricia Irazusta
- Instituto de Investigaciones para la Industria Química (INIQUI), Universidad Nacional de Salta (UNSa) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Salta, Argentina; Facultad de Ciencias Naturales, UNSa, Salta, Argentina.
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22
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Štumpf S, Hostnik G, Primožič M, Leitgeb M, Bren U. Generation Times of E. coli Prolong with Increasing Tannin Concentration while the Lag Phase Extends Exponentially. PLANTS (BASEL, SWITZERLAND) 2020; 9:plants9121680. [PMID: 33271746 PMCID: PMC7760653 DOI: 10.3390/plants9121680] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 11/27/2020] [Accepted: 11/29/2020] [Indexed: 05/10/2023]
Abstract
The current study examines the effect of tannins and tannin extracts on the lag phase duration, growth rate, and generation time of Escherichia coli. Effects of castalagin, vescalagin, gallic acid, Colistizer, tannic acid as well as chestnut, mimosa, and quebracho extracts were determined on E. coli's growth phases using the broth microdilution method and obtained by turbidimetric measurements. E. coli responds to the stress caused by the investigated antimicrobial agents with reduced growth rates, longer generation times, and extended lag phases. Prolongation of the lag phase was relatively small at low tannin concentrations, while it became more pronounced at concentrations above half the MIC. Moreover, for the first time, it was observed that lag time extensions follow a strict exponential relationship with increasing tannin concentrations. This feature is very likely a direct consequence of the tannin complexation of certain essential ions from the growth medium, making them unavailable to E. coli for its growth.
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Affiliation(s)
- Sara Štumpf
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Maribor 2000, Slovenia; (S.Š.); (G.H.); (M.P.); (M.L.)
| | - Gregor Hostnik
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Maribor 2000, Slovenia; (S.Š.); (G.H.); (M.P.); (M.L.)
| | - Mateja Primožič
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Maribor 2000, Slovenia; (S.Š.); (G.H.); (M.P.); (M.L.)
| | - Maja Leitgeb
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Maribor 2000, Slovenia; (S.Š.); (G.H.); (M.P.); (M.L.)
- Faculty of Medicine, University of Maribor, Maribor 2000, Slovenia
| | - Urban Bren
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Maribor 2000, Slovenia; (S.Š.); (G.H.); (M.P.); (M.L.)
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Koper 6000, Slovenia
- Correspondence: ; Tel.: +386-2-2294-421
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23
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Rahayuningtyas I, Indrawati A, Wibawan IWT, Palupi MF, Istiyaningsih I. Phylogenetic group determination and plasmid virulence gene profiles of colistin-resistant Escherichia coli originated from the broiler meat supply chain in Bogor, Indonesia. Vet World 2020; 13:1807-1814. [PMID: 33132591 PMCID: PMC7566268 DOI: 10.14202/vetworld.2020.1807-1814] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 07/21/2020] [Indexed: 11/23/2022] Open
Abstract
Background and Aim: Pathogenic Escherichia coli contamination along the broiler meat supply chain is a serious public health concern. This bacterial infection with multidrug-resistant can lead to treatment failure. Several studies have revealed that avian pathogenic E. coli (APEC) and human extraintestinal pathogenic E. coli (ExPEC) showed a close genetic relationship and may share virulence genes. This study aimed to determine the phylogenetic group and virulence gene profiles in colistin-resistant E. coli obtained from the broiler meat supply chain in Bogor, West Java, Indonesia. Materials and Methods: Fifty-eight archive isolates originated from the cloacal swab, litter, drinking water, inside plucker swab, fresh meat at small scale poultry slaughterhouses, and traditional markets were used in this study. All the isolates were characterized by a polymerase chain reaction to determine the phylogenetic group (A, B1, B2, or D) and virulence gene profiles with APEC marker genes (iutA, hlyF, iss, iroN, and ompT). Results: Phylogenetic grouping revealed that the isolates belong to A group (34.48%), D group (34.48%), B1 group (17.24%), and B2 group (13.79%). The virulence gene prevalence was as follows: iutA (36%), hlyF (21%), ompT (21%), iroN (10%), and iss (9%). The B2 group presented with more virulence genes combinations. iroN, hlyF, and ompT genes were positively associated with the B2 group (p≤0.05). Conclusion: Our results highlight the role of colistin-resistant E. coli originated from the broiler meat supply chain as a potential reservoir for human ExPEC virulence genes.
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Affiliation(s)
- Irma Rahayuningtyas
- Department of Animal Disease and Veterinary Public Health, Faculty of Veterinary Medicine, IPB University-Bogor, Indonesia.,National Veterinary Drug Assay Laboratory, Directorate General of Livestock and Animal Health, Ministry of Agriculture of the Republic of Indonesia, Indonesia
| | - Agustin Indrawati
- Department of Animal Disease and Veterinary Public Health, Faculty of Veterinary Medicine, IPB University-Bogor, Indonesia
| | - I Wayan Teguh Wibawan
- Department of Animal Disease and Veterinary Public Health, Faculty of Veterinary Medicine, IPB University-Bogor, Indonesia
| | - Maria Fatima Palupi
- National Veterinary Drug Assay Laboratory, Directorate General of Livestock and Animal Health, Ministry of Agriculture of the Republic of Indonesia, Indonesia
| | - Istiyaningsih Istiyaningsih
- National Veterinary Drug Assay Laboratory, Directorate General of Livestock and Animal Health, Ministry of Agriculture of the Republic of Indonesia, Indonesia
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24
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Luna BM, Ershova K, Yan J, Ulhaq A, Nielsen TB, Hsieh S, Pantapalangkoor P, Vanscoy B, Ambrose P, Rudin S, Hujer K, Bonomo RA, Actis L, Skaar EP, Spellberg B. Adjunctive transferrin to reduce the emergence of antibiotic resistance in Gram-negative bacteria. J Antimicrob Chemother 2020; 74:2631-2639. [PMID: 31170282 PMCID: PMC6736376 DOI: 10.1093/jac/dkz225] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 04/15/2019] [Accepted: 04/29/2019] [Indexed: 11/14/2022] Open
Abstract
Background New strategies are needed to slow the emergence of antibiotic resistance among bacterial pathogens. In particular, society is experiencing a crisis of antibiotic-resistant infections caused by Gram-negative bacterial pathogens and novel therapeutics are desperately needed to combat such diseases. Acquisition of iron from the host is a nearly universal requirement for microbial pathogens—including Gram-negative bacteria—to cause infection. We have previously reported that apo-transferrin (lacking iron) can inhibit the growth of Staphylococcus aureus in culture and diminish emergence of resistance to rifampicin. Objectives To define the potential of apo-transferrin to inhibit in vitro growth of Klebsiella pneumoniae and Acinetobacter baumannii, key Gram-negative pathogens, and to reduce emergence of resistance to antibiotics. Methods The efficacy of apo-transferrin alone or in combination with meropenem or ciprofloxacin against K. pneumoniae and A. baumannii clinical isolates was tested by MIC assay, time–kill assay and assays for the selection of resistant mutants. Results We confirmed that apo-transferrin had detectable MICs for all strains tested of both pathogens. Apo-transferrin mediated an additive antimicrobial effect for both antibiotics against multiple strains in time–kill assays. Finally, adding apo-transferrin to ciprofloxacin or meropenem reduced the emergence of resistant mutants during 20 day serial passaging of both species. Conclusions These results suggest that apo-transferrin may have promise to suppress the emergence of antibiotic-resistant mutants when treating infections caused by Gram-negative bacteria.
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Affiliation(s)
- Brian M Luna
- Department of Medicine, Keck School of Medicine at the University of Southern California (USC), Los Angeles, CA, USA.,Molecular Microbiology and Immunology, Keck School of Medicine at the University of Southern California (USC), Los Angeles, CA, USA
| | - Ksenia Ershova
- Department of Medicine, Keck School of Medicine at the University of Southern California (USC), Los Angeles, CA, USA.,Molecular Microbiology and Immunology, Keck School of Medicine at the University of Southern California (USC), Los Angeles, CA, USA
| | - Jun Yan
- Department of Medicine, Keck School of Medicine at the University of Southern California (USC), Los Angeles, CA, USA.,Molecular Microbiology and Immunology, Keck School of Medicine at the University of Southern California (USC), Los Angeles, CA, USA
| | - Amber Ulhaq
- Department of Medicine, Keck School of Medicine at the University of Southern California (USC), Los Angeles, CA, USA.,Molecular Microbiology and Immunology, Keck School of Medicine at the University of Southern California (USC), Los Angeles, CA, USA
| | - Travis B Nielsen
- Department of Medicine, Keck School of Medicine at the University of Southern California (USC), Los Angeles, CA, USA.,Molecular Microbiology and Immunology, Keck School of Medicine at the University of Southern California (USC), Los Angeles, CA, USA
| | - Sarah Hsieh
- Department of Medicine, Keck School of Medicine at the University of Southern California (USC), Los Angeles, CA, USA.,Molecular Microbiology and Immunology, Keck School of Medicine at the University of Southern California (USC), Los Angeles, CA, USA
| | - Paul Pantapalangkoor
- Department of Medicine, Keck School of Medicine at the University of Southern California (USC), Los Angeles, CA, USA.,Molecular Microbiology and Immunology, Keck School of Medicine at the University of Southern California (USC), Los Angeles, CA, USA
| | - Brian Vanscoy
- Institute for Clinical Pharmacodynamics, Schenectady, NY, USA
| | - Paul Ambrose
- Institute for Clinical Pharmacodynamics, Schenectady, NY, USA
| | - Sue Rudin
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA.,Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Kristine Hujer
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA.,Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Robert A Bonomo
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA.,Department of Medicine, Case Western Reserve University, Cleveland, OH, USA.,Departments of Pharmacology, Molecular Biology and Microbiology, Biochemistry, and Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH, USA
| | - Luis Actis
- Department of Microbiology, Miami University, Oxford, OH, USA
| | - Eric P Skaar
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Brad Spellberg
- Department of Medicine, Keck School of Medicine at the University of Southern California (USC), Los Angeles, CA, USA.,Molecular Microbiology and Immunology, Keck School of Medicine at the University of Southern California (USC), Los Angeles, CA, USA
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25
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Rahmani HK, Tabar GH, Badouei MA, Khoramian B. Development of three multiplex-PCR assays for virulence profiling of different iron acquisition systems in Escherichia coli. IRANIAN JOURNAL OF MICROBIOLOGY 2020; 12:281-288. [PMID: 32994898 PMCID: PMC7502150 DOI: 10.18502/ijm.v12i4.3930] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
BACKGROUND AND OBJECTIVES Escherichia coli is responsible for various enteric and extraintestinal infections in animals and humans. Iron as an essential nutrient, has a proven role in pathogenicity of E. coli. Pathogenic E. coli benefits of having complicated systems for iron acquisition but our current knowledge is limited because of complexity of these systems. In the present study, three multiplex-PCR assays were developed to screen nine different virulence genes related to diverse iron acquisition systems in E. coli. MATERIALS AND METHODS The multiplex-PCR systems were designed and optimized in three panels. Each panel includes a triplex-PCR cocktail. The panels are as follow: panel 1: iroN, iutA and fecA; panel 2: fyuA, sitA and irp2; and panel 3: iucD, chuA and tonB. A total of 39 pathogenic E. coli was screened according to the designed multiplex-PCR. RESULTS In total, the top three frequent genes were tonB (100%), fecA (66.6%) and sitA (58.9%). With the exception of fecA and tonB, comparing the prevalence of genes among different origin of isolates (human, cattle, poultry and pigeon) showed significant associations (P < 0.05). Moreover, the iroN, sitA and iucD genes were significantly prevalent (P < 0.05) among members of extraintestinal pathogenic E. coli in comparison with the group of diarrheagenic E. coli. CONCLUSION The current multiplex-PCR assays could be a valuable, rapid and economic tool to investigate diverse iron acquisition systems in E. coli for more precise virulence typing of pathogenic or commensal strains.
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Affiliation(s)
- Hamideh Kalateh Rahmani
- Department of Pathobiology, School of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Gholamreza Hashemi Tabar
- Department of Pathobiology, School of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mahdi Askari Badouei
- Department of Pathobiology, School of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Babak Khoramian
- Department of Clinical Sciences, School of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
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26
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Pérez-Etayo L, González D, Vitas AI. The Aquatic Ecosystem, a Good Environment for the Horizontal Transfer of Antimicrobial Resistance and Virulence-Associated Factors Among Extended Spectrum β-lactamases Producing E. coli. Microorganisms 2020; 8:microorganisms8040568. [PMID: 32326434 PMCID: PMC7232254 DOI: 10.3390/microorganisms8040568] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 04/09/2020] [Accepted: 04/12/2020] [Indexed: 12/31/2022] Open
Abstract
One of the main public health problems nowadays is the increase of antimicrobial resistance, both in the hospital environment and outside it (animal environment, food and aquatic ecosystems, among others). It is necessary to investigate the virulence-associated factors and the ability of horizontal gene transfer among bacteria for a better understanding of the pathogenicity and the mechanisms of dissemination of resistant bacteria. Therefore, the objective of this work was to detect several virulence factors genes (fimA, papC, papG III, cnf1, hlyA and aer) and to determine the conjugative capacity in a wide collection of extended-spectrum β-lactamases-producing E. coli isolated from different sources (human, food, farms, rivers, and wastewater treatment plants). Regarding virulence genes, fimA, papC, and aer were distributed throughout all the studied environments, papG III was mostly related to clinical strains and wastewater is a route of dissemination for cnf1 and hlyA. Strains isolated from aquatic environments showed an average conjugation frequencies of 1.15 × 10−1 ± 5 × 10−1, being significantly higher than those observed in strains isolated from farms and food (p < 0.05), with frequencies of 1.53 × 10−4 ± 2.85 × 10−4 and 9.61 × 10−4 ± 1.96 × 10−3, respectively. The reported data suggest the importance that the aquatic environment (especially WWTPs) acquires for the exchange of genes and the dispersion of resistance. Therefore, specific surveillance programs of AMR indicators in wastewaters from animal or human origin are needed, in order to apply sanitation measures to reduce the burden of resistant bacteria arriving to risky environments as WWTPs.
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Affiliation(s)
- Lara Pérez-Etayo
- Department of Microbiology and Parasitology, University of Navarra, 31008 Pamplona, Spain; (D.G.); (A.I.V.)
- Correspondence: ; Tel.: +34-948-425-600
| | - David González
- Department of Microbiology and Parasitology, University of Navarra, 31008 Pamplona, Spain; (D.G.); (A.I.V.)
- Instituto de Investigación Sanitaria de Navarra (IDISNA), 31008 Pamplona, Spain
| | - Ana Isabel Vitas
- Department of Microbiology and Parasitology, University of Navarra, 31008 Pamplona, Spain; (D.G.); (A.I.V.)
- Instituto de Investigación Sanitaria de Navarra (IDISNA), 31008 Pamplona, Spain
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27
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Abstract
Natural products from microorganisms are important small molecules that play roles in various biological processes like cellular growth, motility, nutrient acquisition, stress response, biofilm formation, and defense. It is hypothesized that pathogens exploit these molecules to regulate virulence and persistence during infections. Here, we present selected examples of signaling natural products from human pathogenic bacteria that use these metabolites to gain a competitive advantage. Targeting these signaling systems provides novel strategies to antimicrobial treatments.
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Affiliation(s)
- Zhijuan Hu
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, 201 Gilman Hall, Berkeley, California 94720, United States
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, 201 Gilman Hall, Berkeley, California 94720, United States
- Chan Zuckerberg Biohub, San Francisco, California 94158, United States
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29
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Hussain A, Shaik S, Ranjan A, Suresh A, Sarker N, Semmler T, Wieler LH, Alam M, Watanabe H, Chakravortty D, Ahmed N. Genomic and Functional Characterization of Poultry Escherichia coli From India Revealed Diverse Extended-Spectrum β-Lactamase-Producing Lineages With Shared Virulence Profiles. Front Microbiol 2019; 10:2766. [PMID: 31849903 PMCID: PMC6901389 DOI: 10.3389/fmicb.2019.02766] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 11/13/2019] [Indexed: 01/16/2023] Open
Abstract
Extended-spectrum β-lactamases (ESBLs) form the most important resistance determinants prevalent worldwide. Data on ESBL-producing Escherichia coli from poultry and livestock are scarce in India. We present data on the functional and genomic characterization of ESBL-producing E. coli obtained from poultry in India. The whole genome sequences of 28 ESBL-producing E. coli were analyzed comprising of 12 broiler chicken E. coli isolates, 11 free-range chicken E. coli isolates, and 5 human extraintestinal pathogenic E. coli. All of the 28 ESBL-producing E. coli isolates were tested for antibiotic susceptibilities, in vitro conjugation, and virulence-associated phenotypic characteristics. A total of 13 sequence types were identified from the poultry E. coli, which included globally successful sequence types such as ST117 (9%), ST131 (4.3%), and ST10 (4.3%). The most common ESBL gene detected in poultry E. coli genomes was blaCTX-M-15 (17%). Also, FIB (73%) and FII (73%) were the most common plasmid replicons identified. Conjugation experiments demonstrated 54 (7/13), 30 (3/10), and 40% (2/5) of broiler, free-range, and human ExPEC E. coli to be able to transfer their ESBL genes, respectively. The in vitro virulence-associated phenotypic tests revealed the broiler, free-range, and human ExPEC isolates to be comparable in biofilm formation, resistance to serum bactericidal activity, adherence, and invasion capabilities. Our overall results showed prevalence of virulence phenotypes among the diverse ESBL-producing E. coli from poultry; while certain E. coli clones from broiler-poultry may indeed have the potential to cause infection in humans.
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Affiliation(s)
- Arif Hussain
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India.,International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Sabiha Shaik
- Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, India
| | - Amit Ranjan
- Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, India
| | - Arya Suresh
- Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, India
| | - Nishat Sarker
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Torsten Semmler
- Methodology and Research Infrastructure, Robert Koch Institute, Berlin, Germany
| | - Lothar H Wieler
- Methodology and Research Infrastructure, Robert Koch Institute, Berlin, Germany
| | - Munirul Alam
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Haruo Watanabe
- International University of Health and Welfare, Tokyo, Japan
| | - Dipshikha Chakravortty
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Niyaz Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh.,Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, India
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30
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Guerrieri CG, Pereira MF, Galdino ACM, Dos Santos ALS, Elias WP, Schuenck RP, Spano LC. Typical and Atypical Enteroaggregative Escherichia coli Are Both Virulent in the Galleria mellonella Model. Front Microbiol 2019; 10:1791. [PMID: 31456762 PMCID: PMC6700222 DOI: 10.3389/fmicb.2019.01791] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 07/19/2019] [Indexed: 12/16/2022] Open
Abstract
Enteroaggregative Escherichia coli (EAEC) is an emerging pathotype responsible for acute and persistent diarrhea. It can be classified as typical and atypical strains, respectively, based on the presence or absence of the AggR regulon, suggesting a higher virulence for typical EAEC. This study aims to evaluate in the Galleria mellonella model if there are differences in the virulence profiles among clinical strains of typical and atypical EAEC, prototype strains EAEC C1096, 042 and its aggR mutant. The clinical EAEC strains (n = 20) were analyzed for the presence of 22 putative virulence factors of EAEC or extraintestinal E. coli by PCR, as well as phenotypic characteristics of virulence (enzymes, siderophore, and biofilm). The survival of the larvae was analyzed after inoculation of 104-107 CFU/larva; the monitoring of bacterial growth in vivo and hemocyte quantification was determined after inoculation of the prototype strains (105 CFU/larva) at different periods after infection. The strains of typical and atypical EAEC presented the same virulence profile for the larva, regardless of the amount or type of genes and phenotypic aspects of virulence analyzed. In addition, the EAEC 042 aggR mutant strain showed a significant reduction in the mortality of the inoculated larvae compared to the wild-type strain. In conclusion, the results obtained herein demonstrate that the virulence of EAEC seems to be related to the AggR regulon, but not exclusively, and atypical EAEC strains may be as virulent as typical ones in vivo in the G. mellonella model.
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Affiliation(s)
- Caroline Gastaldi Guerrieri
- Laboratory of Virology and Infectious Gastroenteritis, Department of Pathology, Health Sciences Center, Federal University of Espírito Santo, Vitória, Brazil
| | - Monalessa Fábia Pereira
- Laboratory of Virology and Infectious Gastroenteritis, Department of Pathology, Health Sciences Center, Federal University of Espírito Santo, Vitória, Brazil
| | - Anna Clara Milesi Galdino
- Laboratory of Advanced Studies of Emerging and Resistant Microorganisms, Department of General Microbiology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - André Luis Souza Dos Santos
- Laboratory of Advanced Studies of Emerging and Resistant Microorganisms, Department of General Microbiology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Ricardo Pinto Schuenck
- Laboratory of Virology and Infectious Gastroenteritis, Department of Pathology, Health Sciences Center, Federal University of Espírito Santo, Vitória, Brazil
| | - Liliana Cruz Spano
- Laboratory of Virology and Infectious Gastroenteritis, Department of Pathology, Health Sciences Center, Federal University of Espírito Santo, Vitória, Brazil
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Antibiotic Resistance, Virulence Factors, Phenotyping, and Genotyping of E. coli Isolated from the Feces of Healthy Subjects. Microorganisms 2019; 7:microorganisms7080251. [PMID: 31405113 PMCID: PMC6722543 DOI: 10.3390/microorganisms7080251] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 07/31/2019] [Accepted: 08/07/2019] [Indexed: 12/26/2022] Open
Abstract
Escherichia coli may innocuously colonize the intestine of healthy subjects or may instigate infections in the gut or in other districts. This study investigated intestinal E. coli isolated from 20 healthy adults. Fifty-one strains were genotyped by molecular fingerprinting and analyzed for genetic and phenotypic traits, encompassing the profile of antibiotic resistance, biofilm production, the presence of surface structures (such as curli and cellulose), and their performance as recipients in conjugation experiments. A phylogroup classification and analysis of 34 virulence determinants, together with genes associated to the pks island (polyketide-peptide genotoxin colibactin) and conjugative elements, was performed. Most of the strains belonged to the phylogroups B1 and B2. The different phylogroups were separated in a principal coordinate space, considering both genetic and functional features, but not considering pulsed-field gel electrophoresis. Within the B2 and F strains, 12 shared the pattern of virulence genes with potential uropathogens. Forty-nine strains were sensitive to all the tested antibiotics. Strains similar to the potential pathogens innocuously inhabited the gut of healthy subjects. However, they may potentially act as etiologic agents of extra-intestinal infections and are susceptible to a wide range of antibiotics. Nevertheless, there is still the possibility to control infections with antibiotic therapy.
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Haddadin RN, Assaf AM, Homsi A, Collier PJ, Shehabi A. Investigating possible association between multidrug resistance and isolate origin with some virulence factors of Escherichia coli strains isolated from infant faeces and fresh green vegetables. J Appl Microbiol 2019; 127:88-98. [PMID: 31034123 DOI: 10.1111/jam.14296] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 04/13/2019] [Accepted: 04/25/2019] [Indexed: 11/30/2022]
Abstract
AIMS In this study, the association between multidrug resistance (MDR) and the expression of some virulence factors were evaluated in Escherichia coli strains isolated from infant faeces and fresh green vegetables. The effect of isolate origin on associated virulence factors was evaluated. In addition, genetic fingerprinting of a sample of these isolates (10 isolates from each group) was studied in order to detect any genetic relatedness among these isolates. METHODS AND RESULTS Escherichia coli isolates were divided into four groups based on their origin (human faeces or plant) and their antibiotic resistance (multiresistance or susceptible). PCR was used to investigate heat-labile and heat-stable enterotoxin genes, and four siderophore genes (aerobactin, enterobactin, salmochelin and yersiniabactin). Genetic fingerprinting of the isolates was performed using enterobacterial repetitive intergenic consensus PCR. Siderophore production was measured by a colorimetric method. Biofilm formation was evaluated by a crystal violet assay. The results of the study showed that the expression of MDR is not significantly associated with an increase in these virulence factors or with biofilm formation. However, the origin of isolates had a significant association with siderophore gene availability and consequently on the concentrations of siderophores released. Genetic fingerprinting indicated that human and plant isolates have the same clonal origin, suggesting their circulation among humans and plants. CONCLUSION Antibiotic-susceptible strains of E. coli may be as virulent as MDR strains. Results also suggest that the environment can play a potential role in selection of strains with specific virulence factors. SIGNIFICANCE AND IMPACT OF THE STUDY Antibiotic-susceptible isolates of Escherichia coli from plant or human origin can be as virulent as the multidrug resistance (MDR) ones. Genetic relatedness was detected among the isolates of plant and human origin, indicating the circulation of these bacteria among human and plants. This could imply a potential role for environmental antimicrobial resistant bacteria in human infection.
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Affiliation(s)
- R N Haddadin
- School of Pharmacy, The University of Jordan, Amman, Jordan
| | - A M Assaf
- School of Pharmacy, The University of Jordan, Amman, Jordan
| | - A Homsi
- School of Pharmacy, The University of Jordan, Amman, Jordan
| | | | - A Shehabi
- School of Medicine, The University of Jordan, Amman, Jordan
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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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Haynes JP, Miller KE, Majestic BJ. Investigation into Photoinduced Auto-Oxidation of Polycyclic Aromatic Hydrocarbons Resulting in Brown Carbon Production. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:682-691. [PMID: 30589540 DOI: 10.1021/acs.est.8b05704] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Brown carbon (BrC) is a collection of oxidized atmospheric aromatic compounds detected worldwide with broad functionality. This multifunctional nature allows BrC to be water-soluble and bioavailable and demonstrate light absorption at multiple wavelengths. Polycyclic aromatic hydrocarbons (PAH) are major primary products of combustion emissions and have long been known to oxidize in the environment as components of secondary organic aerosols. In this study, we have exposed aqueous PAH suspensions to simulated sunlight to investigate oxidized PAH as BrC precursors. Illuminated samples of naphthalene and anthracene demonstrated growth of several new products with absorptions and oxidation consistent with humic-like substances (HULIS). Reactions of aqueous naphthalene, anthracene, and their oxidized derivatives were found to produce chromatographic and spectroscopic evidence of HULIS formation when exposed to sunlight. The association of oxyradicals with HULIS has implications on human health via lung tissue damage; and its absorption character may add to radiative forcing processes in the atmosphere. The overall product characterizations from naphthalene and anthracene indicate reaction mechanism pathways that use oxidized alcohol and quinone as intermediate species.
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Affiliation(s)
- John P Haynes
- Department of Chemistry and Biochemistry , University of Denver , 2190 E Iliff Ave, Olin Hall , Denver , Colorado 80208 , United States
| | - Keith E Miller
- Department of Chemistry and Biochemistry , University of Denver , 2190 E Iliff Ave, Olin Hall , Denver , Colorado 80208 , United States
| | - Brian J Majestic
- Department of Chemistry and Biochemistry , University of Denver , 2190 E Iliff Ave, Olin Hall , Denver , Colorado 80208 , United States
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Qi B, Han M. Microbial Siderophore Enterobactin Promotes Mitochondrial Iron Uptake and Development of the Host via Interaction with ATP Synthase. Cell 2018; 175:571-582.e11. [PMID: 30146159 DOI: 10.1016/j.cell.2018.07.032] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 06/18/2018] [Accepted: 07/23/2018] [Indexed: 02/09/2023]
Abstract
Elucidating the benefits of individual microbiota-derived molecules in host animals is important for understanding the symbiosis between humans and their microbiota. The bacteria-secreted enterobactin (Ent) is an iron scavenging siderophore with presumed negative effects on hosts. However, the high prevalence of Ent-producing commensal bacteria in the human gut raises the intriguing question regarding a potential host mechanism to beneficially use Ent. We discovered an unexpected and striking role of Ent in supporting growth and the labile iron pool in C. elegans. We show that Ent promotes mitochondrial iron uptake and does so, surprisingly, by binding to the ATP synthase α subunit, which acts inside of mitochondria and independently of ATP synthase. We also demonstrated the conservation of this mechanism in mammalian cells. This study reveals a distinct paradigm for the "iron tug of war" between commensal bacteria and their hosts and an important mechanism for mitochondrial iron uptake and homeostasis.
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Affiliation(s)
- Bin Qi
- Howard Hughes Medical Institute and Department of MCDB of University of Colorado at Boulder, Boulder, CO 80309, USA
| | - Min Han
- Howard Hughes Medical Institute and Department of MCDB of University of Colorado at Boulder, Boulder, CO 80309, USA.
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Soutar CD, Stavrinides J. The evolution of three siderophore biosynthetic clusters in environmental and host-associating strains of Pantoea. Mol Genet Genomics 2018; 293:1453-1467. [PMID: 30027301 DOI: 10.1007/s00438-018-1477-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 07/13/2018] [Indexed: 12/22/2022]
Abstract
For many pathogenic members of the Enterobacterales, siderophores play an important role in virulence, yet the siderophores of the host-associating members of the genus Pantoea remain unexplored. We conducted a genome-wide survey of environmental and host-associating strains of Pantoea to identify known and candidate siderophore biosynthetic clusters. Our analysis identified three clusters homologous to those of enterobactin, desferrioxamine, and aerobactin that were prevalent among Pantoea species. Using both phylogenetic and comparative genomic approaches, we demonstrate that the enterobactin-like cluster was present in the common ancestor of all Pantoea, with evidence for three independent losses of the cluster in P. eucalypti, P. eucrina, and the P. ananatis-P. stewartii lineage. The desferrioxamine biosynthetic cluster, previously described and characterized in Pantoea, was horizontally acquired from its close relative Erwinia, with phylogenetic evidence that these transfer events were ancient and occurred between ancestral lineages. The aerobactin cluster was identified in three host-associating species groups, P. septica, P. ananatis, and P. stewartii, with strong evidence for horizontal acquisition from human-pathogenic members of the Enterobacterales. Our work identifies and describes the key siderophore clusters in Pantoea, shows three distinct evolutionary processes driving their diversification, and provides a foundation for exploring the roles that these siderophores may play in human opportunistic infections.
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Affiliation(s)
- Craig D Soutar
- Department of Biology, University of Regina, 3737 Wascana Parkway, Regina, SK, S4S0A2, Canada
| | - John Stavrinides
- Department of Biology, University of Regina, 3737 Wascana Parkway, Regina, SK, S4S0A2, Canada.
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Sharma R, Bhardwaj R, Gautam V, Kohli SK, Kaur P, Bali RS, Saini P, Thukral AK, Arora S, Vig AP. Microbial Siderophores in Metal Detoxification and Therapeutics: Recent Prospective and Applications. PLANT MICROBIOME: STRESS RESPONSE 2018. [DOI: 10.1007/978-981-10-5514-0_15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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Segura A, Auffret P, Klopp C, Bertin Y, Forano E. Draft genome sequence and characterization of commensal Escherichia coli strain BG1 isolated from bovine gastro-intestinal tract. Stand Genomic Sci 2017; 12:61. [PMID: 29046740 PMCID: PMC5634895 DOI: 10.1186/s40793-017-0272-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 09/21/2017] [Indexed: 11/16/2022] Open
Abstract
Escherichia coli is the most abundant facultative anaerobic bacteria in the gastro-intestinal tract of mammals but can be responsible for intestinal infection due to acquisition of virulence factors. Genomes of pathogenic E. coli strains are widely described whereas those of bovine commensal E. coli strains are very scarce. Here, we report the genome sequence, annotation, and features of the commensal E. coli BG1 isolated from the gastro-intestinal tract of cattle. Whole genome sequencing analysis showed that BG1 has a chromosome of 4,782,107 bp coding for 4465 proteins and 97 RNAs. E. coli BG1 belonged to the serotype O159:H21, was classified in the phylogroup B1 and possessed the genetic information encoding "virulence factors" such as adherence systems, iron acquisition and flagella synthesis. A total of 12 adherence systems were detected reflecting the potential ability of BG1 to colonize different segments of the bovine gastro-intestinal tract. E. coli BG1 is unable to assimilate ethanolamine that confers a nutritional advantage to some pathogenic E. coli in the bovine gastro-intestinal tract. Genome analysis revealed the presence of i) 34 amino acids change due to non-synonymous SNPs among the genes encoding ethanolamine transport and assimilation, and ii) an additional predicted alpha helix inserted in cobalamin adenosyltransferase, a key enzyme required for ethanolamine assimilation. These modifications could explain the incapacity of BG1 to use ethanolamine. The BG1 genome can now be used as a reference (control strain) for subsequent evolution and comparative studies.
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Affiliation(s)
- Audrey Segura
- Université Clermont Auvergne, INRA, MEDIS, F-63000 Clermont-Ferrand, France
| | - Pauline Auffret
- Université Clermont Auvergne, INRA, MEDIS, F-63000 Clermont-Ferrand, France
| | - Christophe Klopp
- Plateforme Bioinformatique Toulouse, Midi-Pyrénées UBIA, INRA, Auzeville Castanet-Tolosan, France
| | - Yolande Bertin
- Université Clermont Auvergne, INRA, MEDIS, F-63000 Clermont-Ferrand, France
| | - Evelyne Forano
- Université Clermont Auvergne, INRA, MEDIS, F-63000 Clermont-Ferrand, France
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Genome Sequence of Pantoea ananatis Strain AMG 501, a Plant Growth-Promoting Bacterium Isolated from Rice Leaves Grown in Paddies of Southern Spain. GENOME ANNOUNCEMENTS 2017; 5:5/34/e00848-17. [PMID: 28839029 PMCID: PMC5571415 DOI: 10.1128/genomea.00848-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Pantoea ananatis AMG 501 is a plant growth-promoting bacterium isolated from rice leaves. Its genome was estimated at 5,102,640 bp with 4,994 coding sequences, encompassing genes related to the metabolism of carbohydrates, to the synthesis of auxins, siderophores, and homoserine lactones, and to the type I, II, III, IV, and VI secretion systems.
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Abstract
Lipocalin 2 (Lcn2), an innate immune protein, has emerged as a critical iron regulatory protein during physiological and inflammatory conditions. As a bacteriostatic factor, Lcn2 obstructs the siderophore iron-acquiring strategy of bacteria and thus inhibits bacterial growth. As part of host nutritional immunity, Lcn2 facilitates systemic, cellular, and mucosal hypoferremia during inflammation, in addition to stabilizing the siderophore-bound labile iron pool. In this review, we summarize recent advances in understanding the interaction between Lcn2 and iron, and its effects in various inflammatory diseases. Lcn2 exerts mostly a protective role in infectious and inflammatory bowel diseases, whereas both beneficial and detrimental functions have been documented in neurodegenerative diseases, metabolic syndrome, renal disorders, skin disorders, and cancer. Further animal and clinical studies are necessary to unveil the multifaceted roles of Lcn2 in iron dysregulation during inflammation and to explore its therapeutic potential for treating inflammatory diseases.
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Affiliation(s)
- Xia Xiao
- Department of Nutritional Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802;
| | - Beng San Yeoh
- Department of Nutritional Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802;
| | - Matam Vijay-Kumar
- Department of Nutritional Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802; .,Department of Medicine, The Pennsylvania State University Medical Center, Hershey, Pennsylvania 17033
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Ellermann M, Arthur JC. Siderophore-mediated iron acquisition and modulation of host-bacterial interactions. Free Radic Biol Med 2017; 105:68-78. [PMID: 27780750 PMCID: PMC5401654 DOI: 10.1016/j.freeradbiomed.2016.10.489] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 10/11/2016] [Accepted: 10/19/2016] [Indexed: 02/07/2023]
Abstract
Iron is an essential micronutrient for most life forms including the majority of resident bacteria of the microbiota and their mammalian hosts. Bacteria have evolved numerous mechanisms to competitively acquire iron within host environments, such as the secretion of small molecules known as siderophores that can solubilize iron for bacterial use. However, siderophore biosynthesis and acquisition is not a capability equally harbored by all resident bacteria. Moreover, the structural diversity of siderophores creates variability in the susceptibility to host mechanisms that serve to counteract siderophore-mediated iron acquisition and limit bacterial growth. As a result, the differential capabilities to acquire iron among members of a complex microbial community carry important implications for the growth and function of resident bacteria. Siderophores can also directly influence host function by modulating cellular iron homeostasis, further providing a mechanism by which resident bacteria may influence their local environment at the host-microbial interface. This review will explore the putative mechanisms by which siderophore production by resident bacteria in the intestines may influence microbial community dynamics and host-bacterial interactions with important implications for pathogen- and microbiota-driven diseases including infection, inflammatory bowel diseases and colorectal cancer.
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Affiliation(s)
- Melissa Ellermann
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA
| | - Janelle C Arthur
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA; Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA.
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Mike LA, Smith SN, Sumner CA, Eaton KA, Mobley HLT. Siderophore vaccine conjugates protect against uropathogenic Escherichia coli urinary tract infection. Proc Natl Acad Sci U S A 2016; 113:13468-13473. [PMID: 27821778 PMCID: PMC5127358 DOI: 10.1073/pnas.1606324113] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Uropathogenic Escherichia coli (UPEC) is the primary cause of uncomplicated urinary tract infections (UTIs). Whereas most infections are isolated cases, 1 in 40 women experience recurrent UTIs. The rise in antibiotic resistance has complicated the management of chronic UTIs and necessitates new preventative strategies. Currently, no UTI vaccines are approved for use in the United States, and the development of a highly effective vaccine remains elusive. Here, we have pursued a strategy for eliciting protective immunity by vaccinating with small molecules required for pathogenesis, rather than proteins or peptides. Small iron-chelating molecules called siderophores were selected as antigens to vaccinate against UTI for this vaccine strategy. These pathogen-associated stealth siderophores evade host immune defenses and enhance bacterial virulence. Previous animal studies revealed that vaccination with siderophore receptor proteins protects against UTI. The poor solubility of these integral outer-membrane proteins in aqueous solutions limits their practical utility. Because their cognate siderophores are water soluble, we hypothesized that these bacterial-derived small molecules are prime vaccine candidates. To test this hypothesis, we immunized mice with siderophores conjugated to an immunogenic carrier protein. The siderophore-protein conjugates elicited an adaptive immune response that targeted bacterial stealth siderophores and protected against UTI. Our study has identified additional antigens suitable for a multicomponent UTI vaccine and highlights the potential use of bacterial-derived small molecules as antigens in vaccine therapies.
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Affiliation(s)
- Laura A Mike
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109
| | - Sara N Smith
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109
| | - Christopher A Sumner
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109
| | - Kathryn A Eaton
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109
| | - Harry L T Mobley
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109
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Mosa KA, Saadoun I, Kumar K, Helmy M, Dhankher OP. Potential Biotechnological Strategies for the Cleanup of Heavy Metals and Metalloids. FRONTIERS IN PLANT SCIENCE 2016; 7:303. [PMID: 27014323 PMCID: PMC4791364 DOI: 10.3389/fpls.2016.00303] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Accepted: 02/25/2016] [Indexed: 05/18/2023]
Abstract
Global mechanization, urbanization, and various natural processes have led to the increased release of toxic compounds into the biosphere. These hazardous toxic pollutants include a variety of organic and inorganic compounds, which pose a serious threat to the ecosystem. The contamination of soil and water are the major environmental concerns in the present scenario. This leads to a greater need for remediation of contaminated soils and water with suitable approaches and mechanisms. The conventional remediation of contaminated sites commonly involves the physical removal of contaminants, and their disposition. Physical remediation strategies are expensive, non-specific and often make the soil unsuitable for agriculture and other uses by disturbing the microenvironment. Owing to these concerns, there has been increased interest in eco-friendly and sustainable approaches such as bioremediation, phytoremediation and rhizoremediation for the cleanup of contaminated sites. This review lays particular emphasis on biotechnological approaches and strategies for heavy metal and metalloid containment removal from the environment, highlighting the advances and implications of bioremediation and phytoremediation as well as their utilization in cleaning-up toxic pollutants from contaminated environments.
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Affiliation(s)
- Kareem A. Mosa
- Department of Applied Biology, College of Sciences, University of SharjahSharjah, UAE
- Department of Biotechnology, Faculty of Agriculture, Al-Azhar UniversityCairo, Egypt
- *Correspondence: Kareem A. Mosa,
| | - Ismail Saadoun
- Department of Applied Biology, College of Sciences, University of SharjahSharjah, UAE
| | - Kundan Kumar
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, K. K. Birla Goa CampusGoa, India
| | - Mohamed Helmy
- The Donnelly Centre for Cellular and Biomedical Research, University of Toronto, TorontoON, Canada
| | - Om Parkash Dhankher
- Stockbridge School of Agriculture, University of MassachusettsAmherst, MA, USA
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Chairatana P, Zheng T, Nolan EM. Targeting virulence: salmochelin modification tunes the antibacterial activity spectrum of β-lactams for pathogen-selective killing of Escherichia coli. Chem Sci 2015; 6:4458-4471. [PMID: 28717471 PMCID: PMC5499518 DOI: 10.1039/c5sc00962f] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 05/21/2015] [Indexed: 12/11/2022] Open
Abstract
New antibiotics are required to treat bacterial infections and counteract the emergence of antibiotic resistance. Pathogen-specific antibiotics have several advantages over broad-spectrum drugs, which include minimal perturbation to the commensal microbiota. We present a strategy for targeting antibiotics to bacterial pathogens that utilises the salmochelin-mediated iron uptake machinery of Gram-negative Escherichia coli. Salmochelins are C-glucosylated derivatives of the siderophore enterobactin. The biosynthesis and utilisation of salmochelins are important for virulence because these siderophores allow pathogens to acquire iron and evade the enterobactin-scavenging host-defense protein lipocalin-2. Inspired by the salmochelins, we report the design and chemoenzymatic preparation of glucosylated enterobactin-β-lactam conjugates that harbour the antibiotics ampicillin (Amp) and amoxicillin (Amx), hereafter GlcEnt-Amp/Amx. The GlcEnt scaffolds are based on mono- and diglucosylated Ent where one catechol moiety is functionalized at the C5 position for antibiotic attachment. We demonstrate that GlcEnt-Amp/Amx provide up to 1000-fold enhanced antimicrobial activity against uropathogenic E. coli relative to the parent β-lactams. Moreover, GlcEnt-Amp/Amx based on a diglucosylated Ent (DGE) platform selectively kill uropathogenic E. coli that express the salmochelin receptor IroN in the presence of non-pathogenic E. coli and other bacterial strains that include the commensal microbe Lactobacillus rhamnosus GG. Moreover, GlcEnt-Amp/Amx evade the host-defense protein lipocalin-2, and exhibit low toxicity to mammalian cells. Our work establishes that siderophore-antibiotic conjugates provide a strategy for targeting virulence, narrowing the activity spectrum of antibiotics in clinical use, and achieving selective delivery of antibacterial cargos to pathogenic bacteria on the basis of siderophore receptor expression.
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Affiliation(s)
- Phoom Chairatana
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , MA 02139 , USA . ; ; Tel: +1-617-452-2495
| | - Tengfei Zheng
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , MA 02139 , USA . ; ; Tel: +1-617-452-2495
| | - Elizabeth M Nolan
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , MA 02139 , USA . ; ; Tel: +1-617-452-2495
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