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Leeuwis RHJ, Hall JR, Zanuzzo FS, Smith N, Clow KA, Kumar S, Vasquez I, Goetz FW, Johnson SC, Rise ML, Santander J, Gamperl AK. Climate change can impair bacterial pathogen defences in sablefish via hypoxia-mediated effects on adaptive immunity. Dev Comp Immunol 2024; 156:105161. [PMID: 38521379 DOI: 10.1016/j.dci.2024.105161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/13/2024] [Accepted: 03/13/2024] [Indexed: 03/25/2024]
Abstract
Low-oxygen levels (hypoxia) in aquatic habitats are becoming more common because of global warming and eutrophication. However, the effects on the health/disease status of fishes, the world's largest group of vertebrates, are unclear. Therefore, we assessed how long-term hypoxia affected the immune function of sablefish, an ecologically and economically important North Pacific species, including the response to a formalin-killed Aeromonas salmonicida bacterin. Sablefish were held at normoxia or hypoxia (100% or 40% air saturated seawater, respectively) for 6-16 weeks, while we measured a diverse array of immunological traits. Given that the sablefish is a non-model organism, this involved the development of a species-specific methodological toolbox comprised of qPCR primers for 16 key immune genes, assays for blood antibacterial defences, the assessment of blood immunoglobulin (IgM) levels with ELISA, and flow cytometry and confocal microscopy techniques. We show that innate immune parameters were typically elevated in response to the bacterial antigens, but were not substantially affected by hypoxia. In contrast, hypoxia completely prevented the ∼1.5-fold increase in blood IgM level that was observed under normoxic conditions following bacterin exposure, implying a serious impairment of adaptive immunity. Since the sablefish is naturally hypoxia tolerant, our results demonstrate that climate change-related deoxygenation may be a serious threat to the immune competency of fishes.
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Affiliation(s)
- Robine H J Leeuwis
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, A1C 5S7, Canada.
| | - Jennifer R Hall
- Aquatic Research Cluster, CREAIT Network, Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, A1C 5S7, Canada
| | - Fábio S Zanuzzo
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, A1C 5S7, Canada
| | - Nicole Smith
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, A1C 5S7, Canada
| | - Kathy A Clow
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, A1C 5S7, Canada
| | - Surendra Kumar
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, A1C 5S7, Canada
| | - Ignacio Vasquez
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, A1C 5S7, Canada
| | - Frederick W Goetz
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, 53204, USA
| | - Stewart C Johnson
- Pacific Biological Station, Department of Fisheries and Oceans, Nanaimo, BC, V9T 6N7, Canada
| | - Matthew L Rise
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, A1C 5S7, Canada
| | - Javier Santander
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, A1C 5S7, Canada
| | - A Kurt Gamperl
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, A1C 5S7, Canada
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2
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Huang B, Lv X, Zheng H, Yu H, Zhang Y, Zhang C, Wang J. Microbial organic fertilizer prepared by co-composting of Trichoderma dregs mitigates dissemination of resistance, virulence genes, and bacterial pathogens in soil and rhizosphere. Environ Res 2024; 241:117718. [PMID: 37995998 DOI: 10.1016/j.envres.2023.117718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 11/04/2023] [Accepted: 11/15/2023] [Indexed: 11/25/2023]
Abstract
The use of manure, mycelium dregs and other waste as organic fertilizer is the main source of antibiotic resistance genes (ARGs) and pathogens in farmland. Composting of waste may effectively remove ARGs and pathogens. However, the profiles and drivers of changes in metal resistance genes (MRGs), biocide resistance genes (BRGs), and virulence genes (VGs) in soil-crop rhizosphere systems after compost application remain largely unknown. Here, we prepared two kinds of microbial organic fertilizers (MOF) by using Trichoderma dregs (TDs) and organic fertilizer mixing method (MOF1) and TDs co-composting method (MOF2). The effects of different types and doses of MOF on resistance genes, VGs and pathogens in soil-rhizosphere system and their potential mechanisms were studied. The results showed that co-composting of TDs promoted the decomposition of organic carbon and decreased the absolute abundance of ARGs and mobile genetic elements (MGEs) by 53.4-65.0%. MOF1 application significantly increased the abundance and diversity of soil ARGs, BRGs, and VGs, while low and medium doses of MOF2 significantly decreased their abundance and diversity in soil and rhizosphere. Patterns of positive co-occurrence between MGEs and VGs/MRGs/BRGs/ARGs were observed through statistical analysis and gene arrangements. ARGs/MRGs reductions in MOF2 soil were directly driven by weakened horizontal gene transfer triggered by MGEs. Furthermore, MOF2 reduced soil BRGs/VGs levels by shifting bacterial communities (e.g., reduced bacterial host) or improving soil property. Our study provided new insights into the rational use of waste to minimize the spread of resistomes and VGs in soil.
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Affiliation(s)
- Bin Huang
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Xiaolin Lv
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Hao Zheng
- Institute of Coastal Environmental Pollution Control, Key Laboratory of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, 266100, China
| | - Haitao Yu
- Institute of Plant Protection, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
| | - Yu Zhang
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Chengsheng Zhang
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Jie Wang
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China.
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3
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Feldmeier H. Head lice as vectors of pathogenic microorganisms. Trop Med Health 2023; 51:53. [PMID: 37730694 PMCID: PMC10510260 DOI: 10.1186/s41182-023-00545-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 09/09/2023] [Indexed: 09/22/2023] Open
Abstract
Body lice and head lice are the most common ectoparasites of humans. Head lice (Pediculus humanus capitis) occur worldwide in children and their caretakers, irrespective of their social status. In contrast, body lice (Pediculus humanus corporis) are confined to marginalized population groups in countries of the Global South, homeless people, and refugees. Body lice are known to transmit an array of bacterial pathogens, such as R. prowazekii, R. rickettsii, C. burneti, B. quintana, B. recurrentis, and Y. pestis. The vector capacity of head lice is still a matter of debate. The objective of the review was to scrutinize the existing evidence on the vector capacity of head lice for the transmission of bacterial pathogens. The PUBMED database was searched using a combination of the terms "pediculus humanus" OR "body lice" OR "head lice" AND "pathogen" OR "Rickettsia prowazekii" OR "Bartonella quintana" OR "Borrelia recurrentis" OR "Coxiella burneti" without a time limit. Data from epidemiological studies as well as historical observations demonstrate that body lice and head lice can carry the same array of pathogens. Since the presence of a bacterial pathogen in an arthropod is not sufficient to state that it can be transmitted to humans, and since experimental models are lacking, as yet one cannot conclude with certainty that head lice serve as vectors, although this review presents circumstantial evidence that they do. Adequately designed experimental and epidemiological studies are needed to ascertain the exact transmission potential of head lice.
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Affiliation(s)
- Hermann Feldmeier
- Institute of Microbiology, Infectious Diseases and Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Campus Benjamin Franklin, Hindenburgdamm 30, 12203, Berlin, Germany.
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4
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Usman M, Tang JW, Li F, Lai JX, Liu QH, Liu W, Wang L. Recent advances in surface enhanced Raman spectroscopy for bacterial pathogen identifications. J Adv Res 2023; 51:91-107. [PMID: 36549439 PMCID: PMC10491996 DOI: 10.1016/j.jare.2022.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/15/2022] [Accepted: 11/30/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The rapid and reliable detection of pathogenic bacteria at an early stage is a highly significant research field for public health. However, most traditional approaches for pathogen identification are time-consuming and labour-intensive, which may cause physicians making inappropriate treatment decisions based on an incomplete diagnosis of patients with unknown infections, leading to increased morbidity and mortality. Therefore, novel methods are constantly required to face the emerging challenges of bacterial detection and identification. In particular, Raman spectroscopy (RS) is becoming an attractive method for rapid and accurate detection of bacterial pathogens in recent years, among which the newly developed surface-enhanced Raman spectroscopy (SERS) shows the most promising potential. AIM OF REVIEW Recent advances in pathogen detection and diagnosis of bacterial infections were discussed with focuses on the development of the SERS approaches and its applications in complex clinical settings. KEY SCIENTIFIC CONCEPTS OF REVIEW The current review describes bacterial classification using surface enhanced Raman spectroscopy (SERS) for developing a rapid and more accurate method for the identification of bacterial pathogens in clinical diagnosis. The initial part of this review gives a brief overview of the mechanism of SERS technology and development of the SERS approach to detect bacterial pathogens in complex samples. The development of the label-based and label-free SERS strategies and several novel SERS-compatible technologies in clinical applications, as well as the analytical procedures and examples of chemometric methods for SERS, are introduced. The computational challenges of pre-processing spectra and the highlights of the limitations and perspectives of the SERS technique are also discussed.Taken together, this systematic review provides an overall summary of the SERS technique and its application potential for direct bacterial diagnosis in clinical samples such as blood, urine and sputum, etc.
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Affiliation(s)
- Muhammad Usman
- Department of Intelligent Medical Engineering, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - Jia-Wei Tang
- Department of Intelligent Medical Engineering, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - Fen Li
- Laboratory Medicine, Huai'an Fifth People's Hospital, Huai'an, Jiangsu Province, China
| | - Jin-Xin Lai
- Laboratory Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong Province, China
| | - Qing-Hua Liu
- State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technology, Macao, Macau SAR, China
| | - Wei Liu
- Department of Intelligent Medical Engineering, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, Jiangsu Province, China.
| | - Liang Wang
- Laboratory Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong Province, China.
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5
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Qian S, Chang D, Gu J, Salena BJ, Li Y. In Vitro Selection and Characterization of a DNAzyme Probe for Diverse Pathogenic Strains of Clostridium difficile. Chemistry 2023:e202300240. [PMID: 37086393 DOI: 10.1002/chem.202300240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 04/23/2023]
Abstract
Clostridium difficile frequently causes an infectious disease known as Clostridium difficile infection (CDI) and there are urgent needs for the development of more effective rapid diagnostic tests for CDI. Previously we have developed an RNA-cleaving fluorogenic DNAzyme (RFD) probe named RFD-CD1, which is capable of detecting a specific strain of C. difficile but is too specific to recognize other pathogenic C. difficile strains. To overcome this issue, herein we report RFD-CD2, another RFD that is not only highly specific to C. difficile but also capable of recognizing diverse pathogenic C. difficile strains. Extensive sequence and structure characterization establishes a pseudoknot structure and a significantly minimized sequence for RFD-CD2. As a fluorescence sensor, RFD-CD2 can detect C. difficile at a concentration as low as 100 CFU/mL, making this DNAzyme an attractive molecular probe for rapid diagnosis of CDI caused by diverse strains of C. difficile.
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Affiliation(s)
- Shuwen Qian
- McMaster University, Biochemistry and Biomedical Sciences, CANADA
| | - Dingran Chang
- McMaster University, Biochemistry and Biomedical Sciences, CANADA
| | - Jimmy Gu
- McMaster University, Biochemistry and Biomedical Sciences, CANADA
| | | | - Yingfu Li
- McMaster University, Biochemistry and Biomedical Sciences, 1280 Main Street West, L8S4K1, Hamilton, CANADA
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Koprivova A, Schwier M, Volz V, Kopriva S. Shoot-root interaction in control of camalexin exudation in Arabidopsis. J Exp Bot 2023; 74:2667-2679. [PMID: 36651631 DOI: 10.1093/jxb/erad031] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 01/17/2023] [Indexed: 06/06/2023]
Abstract
Plants exude secondary metabolites from the roots to shape the composition and function of their microbiome. Many of these compounds are known for their anti-microbial activities and play a role in plant immunity, such as the indole-derived phytoalexin camalexin. Here we studied the dynamics of camalexin synthesis and exudation upon interaction of Arabidopsis thaliana with the plant growth promoting bacteria Pseudomonas sp. CH267 or the bacterial pathogen Burkholderia glumae PG1. We show that while camalexin accumulation and exudation is more rapidly but transiently induced upon interaction with the growth promoting bacteria, the pathogen induces higher and more stable camalexin levels. By combination of experiments with cut shoots and roots, and grafting of wild-type plants with mutants in camalexin synthesis, we showed that while camalexin can be produced and released by both organs, in intact plants exuded camalexin originates in the shoots. We also reveal that the root specific CYP71A27 protein specifically affects the outcome of the interaction with the plant growth promoting bacteria and that its transcript levels are controlled by a shoot derived signal. In conclusion, camalexin synthesis seems to be controlled on a whole plant level and is coordinated between the shoots and the roots.
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Affiliation(s)
- Anna Koprivova
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50674 Cologne, Germany
| | - Melina Schwier
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50674 Cologne, Germany
| | - Vanessa Volz
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50674 Cologne, Germany
| | - Stanislav Kopriva
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50674 Cologne, Germany
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7
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Khruengsai S, Sripahco T, Pripdeevech P. Antibacterial activity and synergic effects of the essential oils of Amomum verum Blackw and Zanthoxylum limonella (Dennst.) Alston. Arch Microbiol 2023; 205:102. [PMID: 36862257 DOI: 10.1007/s00203-023-03436-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 01/18/2023] [Accepted: 02/09/2023] [Indexed: 03/03/2023]
Abstract
The antibacterial activity of Amomum verum Blackw, Zanthoxylum limonella (Dennst.) Alston, Zanthoxylum bungeanum, and Zingiber montanum (J. Koenig) Link ex A. Dietr essential oils were investigated against Staphylococcus aureus, Staphylococcus epidermidis, Escherichia coli, and Pseudomonas aeruginosa. The essential oils of A. verum Blackw, Z. limonella (Dennst.) Alston, Z. bungeanum, and Z. montanum (J. Koenig) Link ex A. Dietr displayed strong antibacterial activity with a minimum inhibitory concentration and minimumbactericidal concentration ranging from 0.31 to 1.25 µg/mL and 0.62-5.00 µg/mL, respectively. The chemical composition of A. verum Blackw, Z. limonella (Dennst.) Alston, Z. bungeanum, and Z. montanum (J. Koenig) Link ex A. Dietr essential oils were analysed using gas chromatography-mass spectrometry. 1,8-Cineole and limonene were detected in high amounts in the A. verum Blackw and Z. limonella (Dennst.) Alston essential oils, respectively. The major compound in Z. bungeanum and Z. montanum (J. Koenig) Link ex A. Dietr essential oil was 2,4-dimethylether-phloroacetophenone and terpinene-4-ol, respectively. The antibacterial activities and synergistic effects between these essential oils were further analysed. The combination of A. verum Blackw and Z. limonella (Dennst.) Alston essential oils showed a synergistic effect against all bacterial strains, while the other essential oil combinations showed additive, antagonistic effects, and no interaction. The synergistic effect of the combination between A. verum Blackw and Z. limonella (Dennst.) Alston essential oils could be resulted from 1,8-cineole and limonene which was evaluated to possess strong antibacterial activity.
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Affiliation(s)
| | - Teerapong Sripahco
- School of Science, Mae Fah Luang University, Muang, 57100, Chiang Rai, Thailand
| | - Patcharee Pripdeevech
- School of Science, Mae Fah Luang University, Muang, 57100, Chiang Rai, Thailand. .,Center of Chemical Innovation for Sustainability (CIS), Mae Fah Luang University, Muang, 57100, Chiang Rai, Thailand.
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8
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Wang B, Zou M, Pan Q, Li J. Analysis of Actin Array Rearrangement During the Plant Response to Bacterial Stimuli. Methods Mol Biol 2023; 2604:263-270. [PMID: 36773241 DOI: 10.1007/978-1-0716-2867-6_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Plants are constantly exposed to various environmental stresses, among which, microbial pathogens are one of the major threats. Studies have shown that the host actin cytoskeleton undergoes active rearrangement during the plant-microbe interaction. This actin remodeling is required for plant resistance to bacterial infection. In this chapter, we introduce a protocol routinely used in our laboratory to investigate actin dynamics in response to bacterial cues. We describe the bacterial inoculation methods, plant sample preparation, and imaging techniques used to monitor actin responses in different Arabidopsis cell types including epidermal cells from light-grown leaves and dark-grown hypocotyls, as well as guard cells. We further introduce a high-throughput image analysis method for quantifying cytoskeletal changes. This protocol has allowed us to dissect the host cell contribution to actin remodeling and identify actin-binding proteins as stimulus-response regulators of the cytoskeleton.
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Affiliation(s)
- Bingxiao Wang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Science, Beijing Normal University, Beijing, China
| | - Minxia Zou
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Science, Beijing Normal University, Beijing, China
| | - Qing Pan
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Science, Beijing Normal University, Beijing, China
| | - Jiejie Li
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Science, Beijing Normal University, Beijing, China. .,Key Laboratory of Cell Proliferation and Regulation of Ministry of Education, College of Life Science, Beijing Normal University, Beijing, China.
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9
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Li Y, Deng X, Zhang N, Shen Z, Li R, Shen Q, Salles JF. Rhizosphere suppression hinders antibiotic resistance gene (ARG) spread under bacterial invasion. One Health 2023; 16:100481. [PMID: 36683960 PMCID: PMC9845992 DOI: 10.1016/j.onehlt.2023.100481] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 12/30/2022] [Accepted: 01/01/2023] [Indexed: 01/04/2023] Open
Abstract
The rhizosphere is an extremely important component of the "one health" scenario by linking the soil microbiome and plants, in which the potential enrichment of antibiotic resistance genes (ARGs) might ultimately flow into the human food chain. Despite the increased occurrence of soil-borne diseases, which can lead to increased use of pesticides and antibiotic-producing biocontrol agents, the understanding of the dynamics of ARG spread in the rhizosphere is largely overlooked. Here, tomato seedlings grown in soils conducive and suppressive to the pathogen Ralstonia solanacearum were selected as a model to investigate ARG spread in the rhizosphere with and without pathogen invasion. Metagenomics data revealed that R. solanacearum invasion increased the density of ARGs and mobile genetic elements (MGEs). Although we found ARGs originating from human pathogenic bacteria in both soils, the enrichment was alleviated in the suppressive soil. In summary, the suppressive soil hindered ARG spread through pathogen suppression and had a lower number of taxa carrying antibiotic resistance.
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Affiliation(s)
- Yuchan Li
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Xuhui Deng
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China,Sanya Institute of Nanjing Agricultural University, Sanya 572025, Hainan, China,Corresponding authors at: College of Resources and Environmental Sciences, Nanjing Agricultural University, 210095 Nanjing, China.
| | - Na Zhang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Zongzhuan Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China,Sanya Institute of Nanjing Agricultural University, Sanya 572025, Hainan, China
| | - Rong Li
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China,Sanya Institute of Nanjing Agricultural University, Sanya 572025, Hainan, China,Corresponding authors at: College of Resources and Environmental Sciences, Nanjing Agricultural University, 210095 Nanjing, China.
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Joana Falcao Salles
- Microbial Ecology Cluster, Genomics Research in Ecology and Evolution in Nature, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen 9747AG, the Netherlands
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Leal Sanabria G, Plasencia-Márquez O, Martínez-Zubiaur Y, Silvestre Vañó M, Pérez-López E. First report of potato (Solanum tuberosum L.) blackleg disease caused by Dickeya solani in Mayabeque, Cuba. Plant Dis 2022; 107:1215. [PMID: 36089681 DOI: 10.1094/pdis-07-22-1580-pdn] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Blackleg, caused by Pectobacterium spp. and Dickeya spp., is an important disease of potatoes. During the period from November 20 and March 2021, stems of potato plants showing necrosis and rot symptoms, and chlorotic leaves, were collected from commercial production areas of the Mayabeque province of Cuba (Fig. 1A). After disinfestation of affected stems, small fragments of the stem were cut and macerated in a sterile 0.85% NaCl solution. Serial dilutions of bacterial suspension were prepared and streaked onto nutrient agar in Petri plates. Two colonies per sample showing the characteristic of "fried egg" were selected for further investigation, and an isolated was selected and named D7. The isolated bacterium was rod shaped, gram-negative, motile, oxidase and indole production negative, with anaerobic growth, and able to use lactose as carbon source in Mac Conkey Agar medium. One colony of the isolate D7 was selected and multiplied. Total DNA of the bacteria cells was extracted and used to amplify the genes pelADE (Nassar et al., 1996) and gapA (Cigna et al., 2017), to differentiate Dickeya from Pectobacterium. The sequence obtained showed 99.75% and 99.88% nucleotide identity with Dickeya solani for pelADE (Genbank accession number ON644347) and gapA (Genbank accession number ON644346), respectively. To confirm the pathogenicity of the isolate D7, four 15-day-old potato plants, including two plants of each 'Otolia' and 'Naima' potatoes were inoculated with a bacterial suspension of the isolate D7 (108 CFU/ml) in sterile water by stabbing. Control plants were stabbed with sterile water. Inoculated plants were maintained at 28°C, relative humidity of about 90%, and at 12 h light/12 h dark, as described by (Chen et al. 2014). After 3 to 5 days, typical blackleg disease symptoms (water-soaked lesions and necrosis) developed at the inoculated areas of plants (Fig. 1B). No symptom was observed in the control plants. Bacterium was re-isolated from symptomatic plants and the isolates had the same cultural, physiological, and biochemical characteristics to the isolate D7. To our knowledge, this is the first report of D. solani causing blackleg in potato fields in Cuba. Further studies to determine the spread of this pathogen in potato producing areas in Cuba is underway.
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Affiliation(s)
| | - Odaylin Plasencia-Márquez
- Centro Nacional de Sanidad Agropecuaria, Phytopathology, Carretera de Jamaica y Autopista Nacional, Apdo Postal 10, La Habana, San José de las Lajas, Cuba, 32700;
| | - Yamila Martínez-Zubiaur
- National Center for Animal and Plant Health, Plant Pathology , PO BOX 10, San José de las Lajas , Habana, Cuba, 33700
- National Center for Animal and Plant Health, Plant Pathology , PO BOX 10, San José de las Lajas , Habana, Cuba, 33700;
| | | | - Edel Pérez-López
- Universite Laval, Phytologie, 2480, Boul. Hochelaga, Quebec, Quebec, Canada, G1V 0A6;
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Cai J, Hao Y, Xu R, Zhang Y, Ma Y, Zhang Y, Wang Q. Differential binding of LuxR in response to temperature gauges switches virulence gene expression in Vibrio alginolyticus. Microbiol Res 2022; 263:127114. [PMID: 35878491 DOI: 10.1016/j.micres.2022.127114] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 06/04/2022] [Accepted: 07/05/2022] [Indexed: 12/26/2022]
Abstract
Vibrio pathogens must cope with temperature changes for proper thermo-adaptation and virulence gene expression. LuxR is a quorum-sensing (QS) master regulator of vibrios, playing roles in response to temperature alteration. However, the molecular mechanisms how LuxR is involved in adapting to different temperatures in bacteria have not been precisely elucidated. In this study, using chromatin immunoprecipitation and nucleotide sequencing (ChIP-seq), we identified 272 and 22 enriched loci harboring LuxR-binding peaks at ambient temperature (30 ˚C) and heat shock (42 ˚C) in the Vibrio alginolyticus genome, respectively. Analysis with the MEME (multiple EM for motif elicitation) algorithm indicated that the binding motifs of LuxR varied from temperatures. Three novel binding regions (the promoter of orf00292, orf00397 and fadD) of LuxR were identified and verified that the rising temperature causes the decreasing binding affinity of LuxR to these promoters. Meanwhile, the expression of orf00292, orf00397 and fadD were regulated by LuxR. Moreover, the weak binding of LuxR to the promoter of extracellular protease (Asp) was attributed to the attenuated Asp expression at thermal stress conditions. Taken together, our study demonstrated distinct binding characteristics of LuxR in response to temperature changes, thus highlighting LuxR as a thermo-sensor to switch and control virulence gene expression in V. alginolyticus.
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Affiliation(s)
- Jingxiao Cai
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yuan Hao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Rongjing Xu
- Yantai Tianyuan Aquatic Co. Ltd., Yantai, Shandong, China
| | - Yuanxing Zhang
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, China; Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai 200237, China
| | - Yue Ma
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai 200237, China; Shanghai Collaborative Innovation Center for Biomanufacturing, 130 Meilong Road, Shanghai 200237, China
| | - Yibei Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai 200237, China.
| | - Qiyao Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai 200237, China; Shanghai Collaborative Innovation Center for Biomanufacturing, 130 Meilong Road, Shanghai 200237, China
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12
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Khan F. Strategies for controlling biofilm-forming microbial pathogens on biotic and abiotic surfaces. Curr Drug Targets 2022; 23:956-959. [PMID: 35507795 DOI: 10.2174/1389450123666220429115255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 02/05/2022] [Accepted: 03/17/2022] [Indexed: 11/22/2022]
Affiliation(s)
- Fazlurrahman Khan
- Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, South Korea.,Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, 201306, UP, India
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13
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Sukumaran A, Geddes-McAlister J. Proteomic Profiling of the Interplay Between a Bacterial Pathogen and Host Uncovers Novel Anti-Virulence Strategies. Methods Mol Biol 2022; 2456:253-262. [PMID: 35612747 DOI: 10.1007/978-1-0716-2124-0_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Bottom-up proteomics enables a systems-level analysis of proteins involved in a particular sample set. In this protocol, we describe the workflow to prepare Klebsiella pneumoniae and macrophage cells for co-culture, how to extract and prepare samples for analysis by high-resolution mass spectrometry, and lastly, how to analyze the output data files. This workflow allows for the identification of proteins involved in both the bacterial and host perspective during pathogenesis.
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Affiliation(s)
- Arjun Sukumaran
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
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Farace P, Cravero S, Taibo C, Diodati J, Morsella C, Paolicchi F, Sabio Y García J, Gioffré A. Campylobacter fetus releases S-layered and immunoreactive outer membrane vesicles. Rev Argent Microbiol 2021:S0325-7541(21)00076-6. [PMID: 34412928 DOI: 10.1016/j.ram.2021.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 02/23/2021] [Accepted: 06/07/2021] [Indexed: 11/23/2022] Open
Abstract
The study of outer membrane vesicles (OMVs) became relevant because of their probable important role in the transfer of virulence factors to host cells. Campylobacter fetus is mainly a mammal pathogen whose virulence characterization is still limited. The aim of this study was to evaluate and to characterize the secretion of OMVs in this bacterium. By transmission electron microscopy, we confirmed the production of OMVs in all the strains assayed. Purified OMVs showed a spherical shape and variable size, although comparable to those of other gram-negative bacteria. We also confirmed the presence of the S-layer on the surface of the OMVs of all the strains assayed with the exception of those derived from the NTCC reference strain. In addition, we demonstrated their immunoreactivity by the dot-blot assay. Hence, C. fetus OMVs could contribute to the modulation of the host response and constitute a candidate to be evaluated as an adjuvant of current vaccines used in the veterinary field. This work represents a platform to drive future studies towards the role of these subcellular structures in C. fetus-host interaction.
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15
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Deng Y, Liu S, Feng J, Wu Y, Mao C. What drives putative bacterial pathogens removal within seagrass meadows? Mar Pollut Bull 2021; 166:112229. [PMID: 33711607 DOI: 10.1016/j.marpolbul.2021.112229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 02/21/2021] [Accepted: 02/25/2021] [Indexed: 06/12/2023]
Abstract
To analyze the mechanism of bacterial pathogen removal in seagrass meadows, we compared bacterial pathogens abundance in trapped particles in different seagrass meadows under different intensities of human activities. We compared the particle deposition rates and abundances of bacterial pathogen in Thalassia hemprichii, Enhalus acoroides stands and adjacent unvegetated patches. The bacterial pathogens abundance was much higher in E. acoroides than in adjacent unvegetated patches, however, the trapped particles under T. hemprichii were lower than in nearby unvegetated areas with the exception of the pristine seagrass meadow. These results indicate that seagrass, at least E. acoroides, can remove bacterial pathogens by trapping particles. What is unknown, nevertheless, is how the trapped bacterial pathogens are removed by T. hemprichii. We put forward that antibacterial chemical compounds release from seagrass was stimulated by stress from human activities for inhibition of bacterial pathogen. This putative mechanism needs to be explored in future studies.
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Affiliation(s)
- Yiqin Deng
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Songlin Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Oceanology, South China Sea Institute of Oceanology, Sanya 572100, China.
| | - Juan Feng
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Yunchao Wu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Can Mao
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
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16
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Millar BC, Moore JE. Minimising the risk of cross infection between siblings with cystic fibrosis (CF) within the home: Successful domestic steam disinfection of CF bacterial and foodborne pathogens on common household cutlery and crockery utensils. J Cyst Fibros 2021; 20:708-11. [PMID: 33781700 DOI: 10.1016/j.jcf.2021.03.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 03/09/2021] [Accepted: 03/15/2021] [Indexed: 11/22/2022]
Abstract
Avoidance of cross infection is important between CF siblings living in the same household. In this study, we examined the ability of domestic steam disinfection to eradicate 16 species of CF bacterial and foodborne pathogens from the surface of contaminated crockery and cutlery. Domestic steam disinfection employing baby bottle disinfector devices, when performed properly under manufacturer's instructions, eradicated all organisms tested and offers a relatively inexpensive, simple, versatile and widely available technology for the elimination of common CF bacterial and foodborne pathogens from contaminated crockery and cutlery utensils. Most CF households may already have a baby bottle disinfector device, in order to disinfect nebulizers, respiratory equipment and toothbrushes and therefore employment of this device to disinfect crockery and cutlery would be easily achieved. We therefore advocate the employment of such devices to disinfect such common household utensils, as a critical control in the elimination of these organisms from these sources, thereby enhancing CF sibling safety.
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Chen Z, Erickson DL, Meng J. Polishing the Oxford Nanopore long-read assemblies of bacterial pathogens with Illumina short reads to improve genomic analyses. Genomics 2021; 113:1366-1377. [PMID: 33716184 DOI: 10.1016/j.ygeno.2021.03.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 01/18/2021] [Accepted: 03/08/2021] [Indexed: 11/18/2022]
Abstract
Oxford Nanopore sequencing has been widely used to achieve complete genomes of bacterial pathogens. However, the error rates of Oxford Nanopore long reads are high. Various polishing algorithms using Illumina short reads to correct the errors in Oxford Nanopore long-read assemblies have been developed. The impact of polishing the Oxford Nanopore long-read assemblies of bacterial pathogens with Illumina short reads on improving genomic analyses was evaluated using both simulated and real reads. Ten species (10 strains) were selected for simulated reads, while real reads were tested on 11 species (11 strains). Oxford Nanopore long reads were assembled with Unicycler to produce a draft assembly, followed by three rounds of polishing with Illumina short reads using two polishing tools, Pilon and NextPolish. One round of NextPolish polishing generated genome completeness and accuracy parameters similar to the reference genomes, whereas two or three rounds of Pilon polishing were needed, though contiguity remained unchanged after polishing. The polished assemblies of Escherichia coli O157:H7, Salmonella Typhimurium, and Cronobacter sakazakii with simulated reads did not provide accurate plasmid identifications. One round of NextPolish polishing was needed for accurately identifying plasmids in Staphylococcus aureus and E. coli O26:H11 with real reads, whereas one and two rounds of Pilon polishing were necessary for these two strains, respectively. Polishing failed to provide an accurate antimicrobial resistance (AMR) genotype for S. aureus with real reads. One round of polishing recovered an accurate AMR genotype for Klebsiella pneumoniae with real reads. The reference genome and draft assembly of Citrobacter braakii with real reads differed, which carried blaCMY-83 and fosA6, respectively, while both genes were present after one round of polishing. However, polishing did not improve the assembly of E. coli O26:H11 with real reads to achieve numbers of virulence genes similar to the reference genome. The draft and polished assemblies showed a phylogenetic tree topology comparable with the reference genomes. For multilocus sequence typing and pan-genome analyses, one round of NextPolish polishing was sufficient to obtain accurate results, while two or three rounds of Pilon polishing were needed. Overall, NextPolish outperformed Pilon for polishing the Oxford Nanopore long-read assemblies of bacterial pathogens, though both polishing strategies improved genomic analyses compared to the draft assemblies.
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Affiliation(s)
- Zhao Chen
- Joint Institute for Food Safety and Applied Nutrition, Center for Food Safety and Security Systems, University of Maryland, College Park, MD 20742, USA
| | - David L Erickson
- Joint Institute for Food Safety and Applied Nutrition, Center for Food Safety and Security Systems, University of Maryland, College Park, MD 20742, USA
| | - Jianghong Meng
- Joint Institute for Food Safety and Applied Nutrition, Center for Food Safety and Security Systems, University of Maryland, College Park, MD 20742, USA; Department of Nutrition and Food Science, University of Maryland, College Park, MD 20742, USA.
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18
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Mammo FK, Amoah ID, Gani KM, Pillay L, Ratha SK, Bux F, Kumari S. Microplastics in the environment: Interactions with microbes and chemical contaminants. Sci Total Environ 2020; 743:140518. [PMID: 32653705 DOI: 10.1016/j.scitotenv.2020.140518] [Citation(s) in RCA: 144] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/22/2020] [Accepted: 06/24/2020] [Indexed: 05/02/2023]
Abstract
Microplastics (MPs) are contaminants of emerging concern that have gained considerable attention during the last few decades due to their adverse impact on living organisms and the environment. Recent studies have shown their ubiquitous presence in the environment including the atmosphere, soil, and water. Though several reviews have focused on the occurrence of microplastics in different habitats, little attention has been paid to their interaction with biological and chemical pollutants in the environment. This review therefore presents the state of knowledge on the interaction of MPs with chemicals and microbes in different environments. The distribution of MPs, the association of toxic chemicals with MPs, microbial association with MPs and the microbial-induced fate of MPs in the environment are discussed. The biodegradation and bioaccumulation of MPs by and in microbes and its potential impact on the food chain are also reviewed. The mechanisms driving these interactions and how these, in turn, affect living organisms however are not yet fully understood and require further attention.
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Affiliation(s)
- F K Mammo
- Institute for Water and Wastewater Treatment, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa
| | - I D Amoah
- Institute for Water and Wastewater Treatment, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa
| | - K M Gani
- Institute for Water and Wastewater Treatment, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa
| | - L Pillay
- Institute for Water and Wastewater Treatment, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa
| | - S K Ratha
- Institute for Water and Wastewater Treatment, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa
| | - F Bux
- Institute for Water and Wastewater Treatment, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa
| | - S Kumari
- Institute for Water and Wastewater Treatment, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa.
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Chen Z, Erickson DL, Meng J. Benchmarking hybrid assembly approaches for genomic analyses of bacterial pathogens using Illumina and Oxford Nanopore sequencing. BMC Genomics 2020; 21:631. [PMID: 32928108 PMCID: PMC7490894 DOI: 10.1186/s12864-020-07041-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 08/31/2020] [Indexed: 02/06/2023] Open
Abstract
Background We benchmarked the hybrid assembly approaches of MaSuRCA, SPAdes, and Unicycler for bacterial pathogens using Illumina and Oxford Nanopore sequencing by determining genome completeness and accuracy, antimicrobial resistance (AMR), virulence potential, multilocus sequence typing (MLST), phylogeny, and pan genome. Ten bacterial species (10 strains) were tested for simulated reads of both mediocre- and low-quality, whereas 11 bacterial species (12 strains) were tested for real reads. Results Unicycler performed the best for achieving contiguous genomes, closely followed by MaSuRCA, while all SPAdes assemblies were incomplete. MaSuRCA was less tolerant of low-quality long reads than SPAdes and Unicycler. The hybrid assemblies of five antimicrobial-resistant strains with simulated reads provided consistent AMR genotypes with the reference genomes. The MaSuRCA assembly of Staphylococcus aureus with real reads contained msr(A) and tet(K), while the reference genome and SPAdes and Unicycler assemblies harbored blaZ. The AMR genotypes of the reference genomes and hybrid assemblies were consistent for the other five antimicrobial-resistant strains with real reads. The numbers of virulence genes in all hybrid assemblies were similar to those of the reference genomes, irrespective of simulated or real reads. Only one exception existed that the reference genome and hybrid assemblies of Pseudomonas aeruginosa with mediocre-quality long reads carried 241 virulence genes, whereas 184 virulence genes were identified in the hybrid assemblies of low-quality long reads. The MaSuRCA assemblies of Escherichia coli O157:H7 and Salmonella Typhimurium with mediocre-quality long reads contained 126 and 118 virulence genes, respectively, while 110 and 107 virulence genes were detected in their MaSuRCA assemblies of low-quality long reads, respectively. All approaches performed well in our MLST and phylogenetic analyses. The pan genomes of the hybrid assemblies of S. Typhimurium with mediocre-quality long reads were similar to that of the reference genome, while SPAdes and Unicycler were more tolerant of low-quality long reads than MaSuRCA for the pan-genome analysis. All approaches functioned well in the pan-genome analysis of Campylobacter jejuni with real reads. Conclusions Our research demonstrates the hybrid assembly pipeline of Unicycler as a superior approach for genomic analyses of bacterial pathogens using Illumina and Oxford Nanopore sequencing.
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Affiliation(s)
- Zhao Chen
- Joint Institute for Food Safety and Applied Nutrition, Center for Food Safety and Security Systems, and Department of Nutrition and Food Science, University of Maryland, College Park, MD, 20742, USA
| | - David L Erickson
- Joint Institute for Food Safety and Applied Nutrition, Center for Food Safety and Security Systems, and Department of Nutrition and Food Science, University of Maryland, College Park, MD, 20742, USA
| | - Jianghong Meng
- Joint Institute for Food Safety and Applied Nutrition, Center for Food Safety and Security Systems, and Department of Nutrition and Food Science, University of Maryland, College Park, MD, 20742, USA.
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Zhang H, Zhang Q, Song J, Zhang Z, Chen S, Long Z, Wang M, Yu Y, Fang H. Tracking resistomes, virulence genes, and bacterial pathogens in long-term manure-amended greenhouse soils. J Hazard Mater 2020; 396:122618. [PMID: 32298867 DOI: 10.1016/j.jhazmat.2020.122618] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 02/29/2020] [Accepted: 03/29/2020] [Indexed: 05/03/2023]
Abstract
Organic manure has been implicated as an important source of antibiotic resistance genes (ARGs) in agricultural soils. However, the profiles of biocide resistance genes (BRGs), metal resistance genes (MRGs) and virulence genes (VGs) and their bacterial hosts in manure-amended soils remain largely unknown. Herein, a systematic metagenome-based survey was conducted to comprehensively explore the changes in resistomes, VGs and their bacterial hosts, mobile genetic elements (MGEs), and pathogenic bacteria in manure-amended greenhouse soils. Many manure-borne ARGs, BRGs, MRGs, VGs, and bacterial pathogens could be transferred into soils by applying manures, and their abundance and diversity were markedly positively correlated with greenhouse planting years (manure amendment years). The main ARGs transferred from manures to soils conferred resistance to tetracycline, aminoglycoside, and macrolide-lincosamide-streptogramin. Both statistical analysis and gene arrangements showed a good positive co-occurrence pattern of ARGs/BRGs/MRGs/VGs and MGEs. Furthermore, bacterial hosts of resistomes and VGs were significantly changed in the greenhouse soils in comparison with the field soils. Our findings confirmed the migration and dissemination of resistomes, VGs, and bacterial pathogens, and their accumulation and persistence were correlated with the continuous application of manures.
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Affiliation(s)
- Houpu Zhang
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Qianke Zhang
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Jiajin Song
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Zihan Zhang
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Shiyu Chen
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Zhengnan Long
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Mengcen Wang
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Yunlong Yu
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Hua Fang
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, 310058, China.
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Wang Y, Cui X, Yang B, Xu S, Wei X, Zhao P, Niu F, Sun M, Wang C, Cheng H, Jiang YQ. WRKY55 transcription factor positively regulates leaf senescence and the defense response by modulating the transcription of genes implicated in the biosynthesis of reactive oxygen species and salicylic acid in Arabidopsis. Development 2020; 147:dev.189647. [PMID: 32680933 DOI: 10.1242/dev.189647] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 07/13/2020] [Indexed: 01/19/2023]
Abstract
Reactive oxygen species (ROS) and salicylic acid (SA) are two factors regulating leaf senescence and defense against pathogens. However, how a single gene integrates both ROS and SA pathways remains poorly understood. Here, we show that Arabidopsis WRKY55 transcription factor positively regulates ROS and SA accumulation, and thus leaf senescence and resistance against the bacterial pathogen Pseudomonas syringae WRKY55 is predominantly expressed in senescent leaves and encodes a transcriptional activator localized to nuclei. Both inducible and constitutive overexpression of WRKY55 accelerates leaf senescence, whereas mutants delay it. Transcriptomic sequencing identified 1448 differentially expressed genes, of which 1157 genes are upregulated by WRKY55 expression. Accordingly, the ROS and SA contents in WRKY55-overexpressing plants are higher than those in control plants, whereas the opposite occurs in mutants. Moreover, WRKY55 positively regulates defense against P. syringae Finally, we show that WRKY55 activates the expression of RbohD, ICS1, PBS3 and SAG13 by binding directly to the W-box-containing fragments. Taken together, our work has identified a new WRKY transcription factor that integrates both ROS and SA pathways to regulate leaf senescence and pathogen resistance.
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Affiliation(s)
- Yiqiao Wang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xing Cui
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Bo Yang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Shutao Xu
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiangyan Wei
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Peiyu Zhao
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fangfang Niu
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mengting Sun
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chen Wang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hao Cheng
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuan-Qing Jiang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
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22
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Chan WS, Au CH, Leung SM, Ho DN, Wong EYL, To MY, Ng MK, Chan TL, Ma ESK, Tang BSF. Potential utility of targeted Nanopore sequencing for improving etiologic diagnosis of bacterial and fungal respiratory infection. Diagn Pathol 2020; 15:41. [PMID: 32340617 PMCID: PMC7184685 DOI: 10.1186/s13000-020-00960-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 04/08/2020] [Indexed: 12/14/2022] Open
Abstract
Background Diversified etiology of lower respiratory tract infection renders diagnosis challenging. The mainstay microbial culture is time-consuming and constrained by variable growth requirements. In this study, we explored the use of Nanopore sequencing as a supplementary tool to alleviate this diagnostic bottleneck. Methods We developed a targeted Nanopore method based on amplification of bacterial 16S rRNA gene and fungal internal transcribed spacer region. The performance was compared with routine infectious disease workups on 43 respiratory specimens. Results Nanopore successfully identified majority of microbes (47/54, 87.04%) and 7 possible pathogens not detected by routine workups, which were attributable to the content of microbiological investigations (n = 5) and negative culture (n = 2). The average sequencing time for first target reads was 7 min (1–43 min) plus 5 h of pre-sequencing preparation. Conclusions The Nanopore method described here was rapid, economical and hypothesis-free, which might provide valuable hints to further microbiological follow-up for opportunistic pathogens missed or not detectable by conventional tests.
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Affiliation(s)
- Wai Sing Chan
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | - Chun Hang Au
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | - Sau Man Leung
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | - Dona N Ho
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | | | | | - Man Kin Ng
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | - Tsun Leung Chan
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
| | | | - Bone Siu Fai Tang
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China.
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Semple SL, Bols NC, Lumsden JS, Dixon B. Understanding the pathogenesis of Flavobacterium psychrophilum using the rainbow trout monocyte/macrophage-like cell line, RTS11, as an infection model. Microb Pathog 2019; 139:103910. [PMID: 31809795 DOI: 10.1016/j.micpath.2019.103910] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/28/2019] [Accepted: 12/02/2019] [Indexed: 02/05/2023]
Abstract
The life cycle of Flavobacterium psychrophilum (Fp), the causative agent of bacterial coldwater disease (BCWD) and rainbow trout fry syndrome (RTFS), appears to involve interactions with spleen and head kidney macrophages. To develop an in vitro model for studying this, F. psychrophilum was incubated with a rainbow trout splenic monocyte/macrophage-like cell line (RTS11) and fundamental macrophage functions evaluated. The animal cell basal medium, L15, supplemented with bovine serum (FBS) supports RTS11 maintenance, and surprisingly, L15 with 2% FBS (L15/FBS) also supported F. psychrophilum growth. L15/FBS in which the bacteria had been grown is referred to as F. psychrophilum conditioned medium (FpCM). Adding FpCM to RTS11 cultures caused a small, yet significant, percentage of cells to die, many cells to become more diffuse, and phagocytosis to be temporarily reduced. FpCM also significantly stimulated transcript expression for pro-inflammatory cytokines (IL-1β, TNFα and IL-6) and the anti-inflammatory cytokine (IL-10) after one day of exposure but this upregulation rapidly declined over time. Adding live F. psychrophilum to RTS11 cultures also altered the cellular morphology and stimulated cytokine expression more profoundly than FpCM. Additionally, the phagocytic activity of RTS11 was also significantly impaired by live F. psychrophilum, but not to the same extent as when exposed to FpCM. Adding heat-killed bacteria to RTS11 cultures elicited few changes. These bacteria/RTS11 co-cultures should be useful for gaining a deeper understanding of the pathogenesis of F. psychrophilum and may aid in the development of effective measures to prevent infection and spread of this troublesome disease.
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Affiliation(s)
- Shawna L Semple
- University of Waterloo, Department of Biology, Waterloo, Canada
| | - Niels C Bols
- University of Waterloo, Department of Biology, Waterloo, Canada
| | - John S Lumsden
- University of Guelph, Ontario Veterinary College, Department of Pathobiology, Guelph, Canada
| | - Brian Dixon
- University of Waterloo, Department of Biology, Waterloo, Canada.
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Melo LC, Haenni M, Saras E, Cerdeira L, Moura Q, Boulouis HJ, Madec JY, Lincopan N. Genomic characterisation of a multidrug-resistant TEM-52b extended-spectrum β-lactamase-positive Escherichia coli ST219 isolated from a cat in France. J Glob Antimicrob Resist 2019; 18:223-224. [PMID: 31325616 DOI: 10.1016/j.jgar.2019.07.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 07/05/2019] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVES TEM-52 extended-spectrum β-lactamases (ESBLs) have been detected in members of the Enterobacteriaceae isolated from human and non-human reservoirs, mainly in European countries. Here we report the first draft genome of a multidrug-resistant TEM-52b-positive Escherichia coli isolated from a companion animal in France. METHODS Whole genomic DNA from E. coli 39590 was extracted and was sequenced using an Illumina NextSeq platform. De novo genome assembly was performed using Velvet v.1.2.10 and the draft genome was annotated using the NCBI Prokaryotic Genome Annotation Pipeline v.3.2. Genomic analyses were performed through bioinformatics tools from the Center for Genomic Epidemiology. RESULTS The genome size was calculated as 5362108bp, with 5268 protein-coding sequences and a GC content of 50.5%. E. coli strain 39590 belonged to ST219, serotype O4:H34 and phylogroup E. The antimicrobial resistome consisted of genes encoding resistance to β-lactams (blaTEM-52b), aminoglycosides [aph(3″)-Ib, aph(6)-Id, aadA2, aadA24], phenicols (catA1), sulfonamides (sul1, sul2), trimethoprim (dfrA1, dfrA14), lincosamides (lnuG) and tetracycline (tetA) as well as mutations in gyrA (Ser83Leu, Asp87Asn) and parC (Ser80Ile) conferring resistance to quinolones. Virulome analysis revealed iss, astA and eilA genes, and IncQ1, IncX4, IncX1, IncFIB and IncFIC plasmid incompatibility groups were identified. CONCLUSION This draft genome can be used as a reference sequence for comparative studies using human and non-human E. coli isolates to identify genetic events that have contributed to pathogenicity and adaptation of TEM-52-producing E. coli clones at the human-animal interface as well as to elucidate dynamics of the spread of blaTEM-52 ESBL genes.
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Affiliation(s)
- Luana C Melo
- Department of Microbiology, Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, Brazil.
| | - Marisa Haenni
- Université de Lyon - Unité Antibiorésistance et Virulence Bactériennes, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail, (ANSES), Lyon, France
| | - Estelle Saras
- Université de Lyon - Unité Antibiorésistance et Virulence Bactériennes, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail, (ANSES), Lyon, France
| | - Louise Cerdeira
- Department of Clinical Analysis, School of Pharmacy, Universidade de São Paulo, São Paulo, Brazil
| | - Quézia Moura
- Department of Microbiology, Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, Brazil
| | - Henri-Jean Boulouis
- Université Paris-Est, Ecole Nationale Vétérinaire d'Alfort, Centre Hospitalier Universitaire Vétérinaire d'Alfort (CHUVA), Maisons-Alfort, France
| | - Jean-Yves Madec
- Université de Lyon - Unité Antibiorésistance et Virulence Bactériennes, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail, (ANSES), Lyon, France
| | - Nilton Lincopan
- Department of Microbiology, Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, Brazil; Department of Clinical Analysis, School of Pharmacy, Universidade de São Paulo, São Paulo, Brazil.
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Parajuli P, Rajput MI, Verma NK. Plasmids of Shigella flexneri serotype 1c strain Y394 provide advantages to bacteria in the host. BMC Microbiol 2019; 19:86. [PMID: 31035948 PMCID: PMC6489325 DOI: 10.1186/s12866-019-1455-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 04/11/2019] [Indexed: 11/29/2022] Open
Abstract
Background Shigella flexneri has an extremely complex genome with a significant number of virulence traits acquired by mobile genetic elements including bacteriophages and plasmids. S. flexneri serotype 1c is an emerging etiological agent of bacillary dysentery in developing countries. In this study, the complete nucleotide sequence of two plasmids of S. flexneri serotype 1c strain Y394 was determined and analysed. Results The plasmid pINV-Y394 is an invasive or virulence plasmid of size 221,293 bp composed of a large number of insertion sequences (IS), virulence genes, regulatory and maintenance genes. Three hundred and twenty-eight open reading frames (ORFs) were identified in pINV-Y394, of which about a half (159 ORFs) were identified as IS elements. Ninety-seven ORFs were related to characterized genes (majority of which are associated with virulence and their regulons), and 72 ORFs were uncharacterized or hypothetical genes. The second plasmid pNV-Y394 is of size 10,866 bp and encodes genes conferring resistance against multiple antibiotics of clinical importance. The multidrug resistance gene cassette consists of tetracycline resistance gene tetA, streptomycin resistance gene strA-strB and sulfonamide-resistant dihydropteroate synthase gene sul2. Conclusions These two plasmids together play a key role in the fitness of Y394 in the host environment. The findings from this study indicate that the pathogenic S. flexneri is a highly niche adaptive pathogen which is able to co-evolve with its host and respond to the selection pressure in its environment. Electronic supplementary material The online version of this article (10.1186/s12866-019-1455-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pawan Parajuli
- Division of Biomedical Science and Biochemistry, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Munazza I Rajput
- Division of Biomedical Science and Biochemistry, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Naresh K Verma
- Division of Biomedical Science and Biochemistry, Research School of Biology, The Australian National University, Canberra, ACT, Australia.
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Nobori T, Tsuda K. In planta Transcriptome Analysis of Pseudomonas syringae. Bio Protoc 2018; 8:e2987. [PMID: 34395787 DOI: 10.21769/bioprotoc.2987] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 08/07/2018] [Accepted: 08/09/2018] [Indexed: 11/02/2022] Open
Abstract
Profiling bacterial transcriptome in planta is challenging due to the low abundance of bacterial RNA in infected plant tissues. Here, we describe a protocol to profile transcriptome of a foliar bacterial pathogen, Pseudomonas syringae pv. tomato DC3000, in the leaves of Arabidopsis thaliana at an early stage of infection using RNA sequencing (RNA-Seq). Bacterial cells are first physically isolated from infected leaves, followed by RNA extraction, plant rRNA depletion, cDNA library synthesis, and RNA-Seq. This protocol is likely applicable not only to the A. thaliana-P. syringae pathosystem but also to different plant-bacterial combinations.
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Affiliation(s)
- Tatsuya Nobori
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Kenichi Tsuda
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
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Dai ZM, Xiong Y, He W, Fang Y, Qian YQ, Zhu XJ. Wntless, a conserved Wnt-transport protein, is involved in the innate immune response of Macrobrachium rosenbergii. Fish Shellfish Immunol 2018; 80:437-442. [PMID: 29933109 DOI: 10.1016/j.fsi.2018.06.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 06/13/2018] [Accepted: 06/18/2018] [Indexed: 06/08/2023]
Abstract
Wnt signaling plays important roles in a variety of developmental and pathological processes. Here we show that Wntless, the main regulator for Wnt secretion, is involved in the innate immune response of the giant freshwater prawn, Macrobrachium rosenbergii. The full-length cDNA of the prawn Wntless (named MrWntless) is 2173 bp in length and contains a 1602-bp open reading frame (ORF), which is conceptually translated into a 533-amino acids sequence. MrWntless protein contains a highly conserved Wnt-binding domain which is required for secretion of Wnt ligands, and exhibits 57-67% identity with known Wntless proteins of other animals. MrWntless was found to be expressed in a variety of prawn tissues including heart, gill, muscle, gut, hepatopancreas and ovary. Moreover, MrWntless expression was significantly increased in the hepatopancreas and gill of the prawns challenged by the bacterial pathogen Aeromonas hydrophila and Vibrio parahaemolyticus. Knockdown of MrWntless by RNA interference in prawns led to dramatically decreased MrWntless expression of approximately 70%. Furthermore, the cumulative mortality rate of the prawn injected with MrWntless dsRNA was greatly increased in response to A. hydrophila challenge compared with the control prawns. Taken together, we provide evidence that prawn Wntless is important for their innate immune response against bacterial pathogens.
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Affiliation(s)
- Zhong-Min Dai
- Institute of Life Sciences, College of Life and Environmental Sciences, Hangzhou Normal University, 310036, Hangzhou, Zhejiang, China
| | - Yanan Xiong
- Institute of Life Sciences, College of Life and Environmental Sciences, Hangzhou Normal University, 310036, Hangzhou, Zhejiang, China
| | - Weiran He
- Institute of Life Sciences, College of Life and Environmental Sciences, Hangzhou Normal University, 310036, Hangzhou, Zhejiang, China
| | - Yukun Fang
- Institute of Life Sciences, College of Life and Environmental Sciences, Hangzhou Normal University, 310036, Hangzhou, Zhejiang, China
| | - Ye-Qing Qian
- Women's Hospital, School of Medicine, Zhejiang University, 310006, Hangzhou, Zhejiang, China.
| | - Xiao-Jing Zhu
- Institute of Life Sciences, College of Life and Environmental Sciences, Hangzhou Normal University, 310036, Hangzhou, Zhejiang, China.
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Zhu XJ, Xiong Y, He W, Jin Y, Qian YQ, Liu J, Dai ZM. Molecular cloning and expression analysis of a prawn (Macrobrachium rosenbergii) juvenile hormone esterase-like carboxylesterase following immune challenge. Fish Shellfish Immunol 2018; 80:10-14. [PMID: 29803663 DOI: 10.1016/j.fsi.2018.05.039] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 04/19/2018] [Accepted: 05/23/2018] [Indexed: 06/08/2023]
Abstract
Methyl farnesoate (MF), the crustacean juvenile hormone (JH), plays critical roles in various physiological processes in crustaceans. The titer of MF is precisely regulated by specific carboxylesterase. Here, we report for the first time that the cloning and expression analysis of a JH esterase-like carboxylesterase from the prawn Macrobrachium rosenbergii (named as MrCXE). MrCXE contained a 1935-bp open reading frame (ORF) conceptually translated into a 644-amino acids protein. MrCXE protein shared the highest identity (36%) with JH esterase-like carboxylesterase from the swimming crab, Portunus trituberculatus and exhibited the typical motifs of JH esterase-like carboxylesterases. MrCXE was most abundantly expressed in hepatopancreas, the major tissue for MF metabolism. MrCXE was expressed at a low level in gut and was not detected in other tissues. Additionally, MrCXE expression was upregulated in hepatopancreas by eyestalk ablation to increase MF level. Furthermore, the mRNA level of MrCXE was significantly increased in the hepatopancreas when challenged by the bacterial pathogens Aeromonas hydrophila and Vibrio parahaemolyticus. To our knowledge, this is the first report that the JH esterase-like carboxylesterase is involved in the innate immune response of the crustaceans.
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Affiliation(s)
- Xiao-Jing Zhu
- Zhejiang Key Laboratory of Organ Development and Regeneration, Institute of Life Sciences, College of Life and Environmental Sciences, Hangzhou Normal University, 310036, Hangzhou, Zhejiang, China
| | - Yanan Xiong
- Zhejiang Key Laboratory of Organ Development and Regeneration, Institute of Life Sciences, College of Life and Environmental Sciences, Hangzhou Normal University, 310036, Hangzhou, Zhejiang, China
| | - Weiran He
- Zhejiang Key Laboratory of Organ Development and Regeneration, Institute of Life Sciences, College of Life and Environmental Sciences, Hangzhou Normal University, 310036, Hangzhou, Zhejiang, China
| | - Yuting Jin
- College of Life Sciences, China Jiliang University, 310018, Hangzhou, Zhejiang, China
| | - Ye-Qing Qian
- Women's Hospital, School of Medicine, Zhejiang University, 310006, Hangzhou, Zhejiang, China
| | - Jun Liu
- College of Life Sciences, China Jiliang University, 310018, Hangzhou, Zhejiang, China.
| | - Zhong-Min Dai
- Zhejiang Key Laboratory of Organ Development and Regeneration, Institute of Life Sciences, College of Life and Environmental Sciences, Hangzhou Normal University, 310036, Hangzhou, Zhejiang, China.
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29
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Zhou Y, Zhang J, Wang S, Xu W, Liang W, Yan M, Wang D, Diao B, Pang B, Lu X, Fan F, Li J, Lou J, Zhang L, Wang R, Cui X, Zhao M, Wu R, Cai H, Du X, Cui Z, Gu W, Yang R, Kan B. Bacterial pathogen spectrum of acute diarrheal outpatients in an urbanized rural district in Southwest China. Int J Infect Dis 2018. [PMID: 29518497 DOI: 10.1016/j.ijid.2018.02.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Abstract
OBJECTIVES To conduct a one-year pathogen surveillance of acute diarrheal disease based on outpatient clinics in township hospitals in rural Hongta District of Yunnan Province, China. METHODS Fecal specimens of acute diarrhea cases and relevant epidemiological information were collected. Salmonella, Shigella, Vibrio, Aeromonas, Plesiomonas shigelloides and diarrheogenic Escherichia coli (DEC) were examined. RESULTS Among the 797 stool specimens sampled, 198 samples (24.8%) were positive in pathogen isolation, and 223 strains were isolated. The order of isolation rates from high to low were DEC, Aeromonas, P. shigelloides, Salmonella, Shigella and Vibrio. The overall positive rate in middle school students and preschool children was relatively high; while the overall positive rate of less than 1-year-old infants and above 55 years olds was relatively low. The isolates were analyzed by pulsed-field gel electrophoresis (PFGE). Some cases had the same or very close onset time, and the isolates had similar PFGE patterns, suggesting a possible outbreak once occurred but was not detected by the current infectious disease reporting system. CONCLUSIONS Pathogen infection and transmission in rapidly urbanized rural areas is a serious issue. There is a great need for a more sensitive and accurate mode of monitoring, reporting and outbreak identification of diarrheal disease.
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Affiliation(s)
- Yongming Zhou
- Yunnan Center for Disease Control and Prevention, Yunnan 650022, China
| | - Jingyun Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Shukun Wang
- Yuxi Center for Disease Control and Prevention, Yunnan 653100, China
| | - Wen Xu
- Yunnan Center for Disease Control and Prevention, Yunnan 650022, China
| | - Weili Liang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
| | - Meiying Yan
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Duochun Wang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Baowei Diao
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Bo Pang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Xin Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Fenxia Fan
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Jie Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Jing Lou
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Li Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Ruibai Wang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Xiaoying Cui
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Meng Zhao
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Rui Wu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Hongyan Cai
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Xiaoli Du
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Zhigang Cui
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Wenpeng Gu
- Yunnan Center for Disease Control and Prevention, Yunnan 650022, China
| | - Rusong Yang
- Yunnan Center for Disease Control and Prevention, Yunnan 650022, China
| | - Biao Kan
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China.
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Abstract
The Campylobacter genus is a large and diverse group of Gram-negative bacteria that are known to colonize humans and other mammals, birds, reptiles, and shellfish. While it is now recognized that several emerging Campylobacter species can be associated with human disease, two species, C. jejuni and C. coli, are responsible for the vast majority of bacterial gastroenteritis in humans worldwide. Infection with C. jejuni, in particular, has also been associated with a number of extragastrointestinal manifestations and autoimmune conditions, most notably Guillain-Barré syndrome. The antimicrobial drugs of choice for the treatment of severe Campylobacter infection include macrolides, such as erythromycin, clarithromycin, or azithromycin. Fluoroquinolones, such as ciprofloxacin, are also commonly used for empirical treatment of undiagnosed diarrheal disease. However, resistance to these and other classes of antimicrobial drugs is increasing and is a major public health problem. The US Centers for Disease Control and Prevention estimates that over 300,000 infections per year are caused by drug-resistant Campylobacter. In this chapter, we discuss the taxonomy of the Campylobacter genus, the clinical and global epidemiological aspects of Campylobacter infection, with an emphasis on C. jejuni and C. coli, and issues related to the treatment of infection and antimicrobial resistance mechanisms. We further discuss the use of next-generation sequencing for the detection and surveillance of antimicrobial resistance genes.
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Affiliation(s)
| | - Shaohua Zhao
- U.S. Food and Drug Administration, Laurel, MD, United States
| | - Heather Tate
- U.S. Food and Drug Administration, Laurel, MD, United States
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Deng K, Serment-Moreno V, Welti-Chanes J, Paredes-Sabja D, Fuentes C, Wu X, Torres JA. Inactivation model and risk-analysis design for apple juice processing by high-pressure CO 2. J Food Sci Technol 2018; 55:258-64. [PMID: 29358818 DOI: 10.1007/s13197-017-2933-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 03/18/2017] [Accepted: 10/15/2017] [Indexed: 10/18/2022]
Abstract
Sigmoidal microbial survival curves are observed in high-pressure carbon dioxide (HPCD) pasteurization treatments. The objectives of this study were to use the Gompertz primary model to describe the inactivation in apple juice of the pathogen Escherichia coli CGMCC1.90 and to apply probabilistic engineering to select HPCD treatments meeting at least 5 log10 reductions (SV ≥ 5) at 95% confidence. This required secondary models for the temperature (T, °C) and pressure (P, MPa) dependence of the Gompertz model parameters. The expressions [Formula: see text] and [Formula: see text] selected using goodness-of-fit measures and assessments based on Akaike and Bayesian information criteria were consistent with proposed mechanistic models for HPCD bactericidal effects. Monte Carlo simulations accounting for the variability and uncertainty of the parameter b and c estimates were used to predict SV values for a given time, temperature and CO2 pressure combination and desired confidence boundary. A similar approach used to estimate process times meeting SV ≥ 5 at 95% confidence for a given temperature and CO2 pressure combination, showed that HPCD processes met this requirement only for relatively long processing times, i.e., 35-124 min in the experimental range of 32-42 °C and 10-30 MPa. Therefore, further HPCD research is required to reduce processing time.
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Abstract
Oral mucosal infections appear as localized or generalized lesions. Symptoms range from almost unnoticeable lesions to severe pain. Systemic disease, age, immunocompromised condition, and medication use are common causes. Local causes include dentures, poor oral hygiene, traumatized epithelium, ulcerations, dentures, implants, oral piercing, and reduced salivary secretion. Oral mucosal infections are underdiagnosed and microbiological diagnosis should be more frequently used. Candidiasis is most frequently diagnosed. Clinical appearances are not always clear and are varied, creating a diagnostic challenge. Thorough understanding of clinical appearance and updated information on diagnostic and therapeutic management are essential for successful patient outcome.
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Affiliation(s)
| | - Baddam Venkat Ramana Reddy
- Department of Oral and Maxillofacial Pathology, SIBAR Institute of Dental Sciences, Takkellapadu, Guntur, Andhra Pradesh 522601, India
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Hokunan H, Koyama K, Hasegawa M, Kawamura S, Koseki S. Survival Kinetics of Salmonella enterica and Enterohemorrhagic Escherichia coli on a Plastic Surface at Low Relative Humidity and on Low-Water Activity Foods. J Food Prot 2016; 79:1680-1692. [PMID: 28221855 DOI: 10.4315/0362-028x.jfp-16-081] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We investigated the survival kinetics of Salmonella enterica and enterohemorrhagic Escherichia coli under various water activity (aw) conditions to elucidate the net effect of aw on pathogen survival kinetics and to pursue the development of a predictive model of pathogen survival as a function of aw. Four serotypes of S. enterica (Stanley, Typhimurium, Chester, and Oranienburg) and three serotypes of enterohemorrhagic E. coli ( E. coli O26, E. coli O111, and E. coli O157:H7) were examined. These bacterial strains were inoculated on a plastic plate surface at a constant relative humidity (RH) (22, 43, 58, 68, or 93% RH, corresponding to the aw) or on a surface of almond kernels (aw 0.58), chocolate (aw 0.43), radish sprout seeds (aw 0.58), or Cheddar cheese (aw 0.93) at 5, 15, or 25°C for up to 11 months. Under most conditions, the survival kinetics were nonlinear with tailing regardless of the storage aw, temperature, and bacterial strain. For all bacterial serotypes, there were no apparent differences in pathogen survival kinetics on the plastic surface at a given storage temperature among the tested RH conditions, except for the 93% RH condition. Most bacterial serotypes were rapidly inactivated on Cheddar cheese when stored at 5°C compared with their inactivation on chocolate, almonds, and radish sprout seeds. Distinct trends in bacterial survival kinetics were also observed between almond kernels and radish sprout seeds, even though the aws of these two foods were not significantly different. The survival kinetics of bacteria inoculated on the plastic plate surface showed little correspondence to those of bacteria inoculated on food matrices at an identical aw. Thus, these results demonstrated that, for low-aw foods and/or environments, aw alone is insufficient to account for the survival kinetics of S. enterica and enterohemorrhagic E. coli .
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Affiliation(s)
- Hidekazu Hokunan
- Graduate School of Agricultural Sciences, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan
| | - Kento Koyama
- Graduate School of Agricultural Sciences, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan
| | - Mayumi Hasegawa
- Graduate School of Agricultural Sciences, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan
| | - Shuso Kawamura
- Graduate School of Agricultural Sciences, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan
| | - Shigenobu Koseki
- Graduate School of Agricultural Sciences, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan
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Pan H, Cui B, Huang Y, Yang J, Ba-Thein W. Nasal carriage of common bacterial pathogens among healthy kindergarten children in Chaoshan region, southern China: a cross-sectional study. BMC Pediatr 2016; 16:161. [PMID: 27741941 PMCID: PMC5064895 DOI: 10.1186/s12887-016-0703-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 09/27/2016] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Nasal colonization with bacterial pathogens is associated with risk of invasive respiratory tract infections, but the related information for Chinese healthy children is scarce. METHODS This cross-sectional study was conducted with healthy children from 6 kindergartens in the Chaoshan region, southern China during 2011-2012. Nasal swabs were examined for five common bacterial pathogens: Streptococcus pneumoniae, Haemophilus influenzae, Haemophilus parainfluenzae, Moraxella catarrhalis, and Staphylococcus aureus. RESULTS Among 1,088 children enrolled, 79.6 % (866) were target-bacterial carriers, of which 34.4 % (298/866) were positive for ≥2 bacteria species. The most common pathogen in the bacterial carriers was M. catarrhalis (76.6 %), followed by S. pneumoniae (26.6 %), S. aureus (21.8 %), H. parainfluenzae (12.7 %), and H. influenzae (2.3 %). Multiple logistic regression analyses showed negative associations between age and the overall or multiple bacterial carriage, and between the father's education level and multiple bacterial carriage (all p < 0.05). Age was negatively associated with the carriage of M. catarrhalis and S. pneumoniae, and positively associated with the S. aureus carriage (all p < 0.0001). CONCLUSIONS This study shows high nasal carriage of common pathogenic bacteria and coexistence of multiple pathogens in healthy Chaoshan kindergarten children, with M. catarrhalis as the commonest colonizer. Increasing age of children and higher paternal education are associated with lower risk of bacterial carriage. Longitudinal follow-up studies would be helpful for better understanding the infection risk in bacterial pathogen carriers.
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Affiliation(s)
- Hui Pan
- Shantou-Oxford Clinical Research Unit, Shantou University Medical College, 22 Xinling Road, Jinping, Shantou, Guangdong China
| | - Binglin Cui
- Pediatric Department, First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong China
| | - Yuanchun Huang
- Department of Clinical Microbiology, First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong China
| | - Jiacai Yang
- Department of Urology, Second Affiliated Hospital, Third Military Medical University, Chongqing, China
| | - William Ba-Thein
- Shantou-Oxford Clinical Research Unit, Shantou University Medical College, 22 Xinling Road, Jinping, Shantou, Guangdong China
- Department of Microbiology and Immunology, Shantou University Medical College, Shantou, Guangdong 515041 China
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Abstract
A diverse spectrum of intracellular bacterial pathogens that inhabit the cytosol have evolved the ability to polymerize actin on their surface to power intracellular actin-based motility (ABM). These include species of Listeria, Burkholderia and Rickettsia, as well as Shigella and Mycobacteria Here, we provide an overview of the roles of bacterial ABM in survival and virulence. Moreover, we survey the molecular mechanisms of actin polymerization in host cells and describe how bacterial pathogens mimic or harness the full diversity of these mechanisms for ABM. Finally, we present ABM through a new lens by comparing motility mechanisms between related species of Listeria, Burkholderia, and Rickettsia Through these comparisons, we hope to illuminate how exploitation of different actin polymerization mechanisms influences ABM as well as pathogenicity and virulence in humans and other animals.
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Affiliation(s)
- Julie E Choe
- Department of Molecular & Cell Biology, University of California, Berkeley CA 94720 USA
| | - Matthew D Welch
- Department of Molecular & Cell Biology, University of California, Berkeley CA 94720 USA
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Miller RJH, Chow B, Pillai D, Church D. Development and evaluation of a novel fast broad-range 16S ribosomal DNA PCR and sequencing assay for diagnosis of bacterial infective endocarditis: multi-year experience in a large Canadian healthcare zone and a literature review. BMC Infect Dis 2016; 16:146. [PMID: 27066823 PMCID: PMC4828839 DOI: 10.1186/s12879-016-1476-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 03/22/2016] [Indexed: 11/29/2022] Open
Abstract
Background The study aimed to explore the sensitivity and specificity of a novel fast 16S rDNA PCR and sequencing assay for the improved diagnosis of infective endocarditis (IE) in patients with suspected native or prosthetic heart valve (HV) infection over a multi-year period at our cardiovascular center. Methods Sixty-eight patients were prospectively enrolled who underwent HV replacement for suspected or confirmed IE between February 1, 2009 and September 1, 2014. Patient demographics, medical co-morbidities, Duke’s criteria, culture results, and antibiotic therapy were collected by detailed chart reviews. Dual-priming oligonucleotide primers targeted to 500 bps of the V1-V3 region of the 16S rRNA gene were used to perform fast broad-range 16S rDNA PCR and Sanger sequencing on ribosomal DNA extracted from HV tissues. The performance/diagnostic efficiency of the molecular test was evaluated against blood cultures and Gram stain and culture of HV tissue in patients’ with definite IE according to Duke’s criteria. Results Fifty patients (73.5 %) had definite IE and another 8 (11.8 %) had possible IE according to Duke’s criteria. Cardiac surgery was delayed an average of 15.4 days from the time of the patient’s last positive blood culture, and appropriate antibiotic therapy was given in the pre-operative period. While 44/50 (88 %) patients had a positive blood culture, HV tissue culture was only positive in 23 (46 %) of them. Molecular testing of all HV tissues had sensitivity, specificity, NPV and PPV of 92, 77.8, 77.8 and 92 % compared to 44, 100, 39.1 and 100 % respectively for culture for diagnosis of definite IE. For prosthetic HV tissue, 16S rDNA PCR had sensitivity of 93 % and specificity of 83 % compared to 35 and 100 % respectively for culture. A literature review showed that the diagnostic accuracy of our novel fast broad-range 16S rDNA PCR assay was similar or better than that of previously published studies. Conclusions This novel fast broad-range 16S rDNA PCR/sequencing test had superior sensitivity compared to tissue Gram stain and culture for identifying underlying bacterial pathogen in both native and prosthetic valve endocarditis.
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Affiliation(s)
- Robert J H Miller
- Department of Cardiac Sciences, University of Calgary, Calgary, Alberta, T2N 2T9, Canada
| | - Barbara Chow
- Calgary Laboratory Services, Calgary, Alberta, T2L 2K8, Canada
| | - Dylan Pillai
- Departments of Pathology & Laboratory Medicine and Medicine, University of Calgary, and Calgary Laboratory Services, 9-3535 Research Rd. NW, Calgary, Alberta, T2L 2K8, Canada
| | - Deirdre Church
- Departments of Pathology & Laboratory Medicine and Medicine, University of Calgary, and Calgary Laboratory Services, 9-3535 Research Rd. NW, Calgary, Alberta, T2L 2K8, Canada.
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Abstract
A small subpopulation of non-replicating, multidrug-tolerant bacteria is present within clonal populations of many bacterial species. Known as persisters, these bacteria are probably the cause of relapsing infections such as typhoid fever. Formation of non-growing Salmonella persisters is stimulated by macrophage phagocytosis. This chapter outlines methods to identify and study persisters resulting from interactions between bacterial pathogens and their hosts. We use their antibiotic tolerance for isolation and enumeration and developed a method to study the heterogeneity of growth within clonal populations through single-cell analysis.
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Affiliation(s)
- Robert A Fisher
- Section of Microbiology, Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, South Kensington Campus, Armstrong Road, London, SW7 2AZ, UK
| | - Angela M Cheverton
- Section of Microbiology, Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, South Kensington Campus, Armstrong Road, London, SW7 2AZ, UK
| | - Sophie Helaine
- Section of Microbiology, Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, South Kensington Campus, Armstrong Road, London, SW7 2AZ, UK.
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Bridier A, Hammes F, Canette A, Bouchez T, Briandet R. Fluorescence-based tools for single-cell approaches in food microbiology. Int J Food Microbiol 2015; 213:2-16. [PMID: 26163933 DOI: 10.1016/j.ijfoodmicro.2015.07.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 06/26/2015] [Accepted: 07/03/2015] [Indexed: 12/31/2022]
Abstract
The better understanding of the functioning of microbial communities is a challenging and crucial issue in the field of food microbiology, as it constitutes a prerequisite to the optimization of positive and technological microbial population functioning, as well as for the better control of pathogen contamination of food. Heterogeneity appears now as an intrinsic and multi-origin feature of microbial populations and is a major determinant of their beneficial or detrimental functional properties. The understanding of the molecular and cellular mechanisms behind the behavior of bacteria in microbial communities requires therefore observations at the single-cell level in order to overcome "averaging" effects inherent to traditional global approaches. Recent advances in the development of fluorescence-based approaches dedicated to single-cell analysis provide the opportunity to study microbial communities with an unprecedented level of resolution and to obtain detailed insights on the cell structure, metabolism activity, multicellular behavior and bacterial interactions in complex communities. These methods are now increasingly applied in the field of food microbiology in different areas ranging from research laboratories to industry. In this perspective, we reviewed the main fluorescence-based tools used for single-cell approaches and their concrete applications with specific focus on food microbiology.
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Affiliation(s)
| | - F Hammes
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - A Canette
- INRA, UMR1319 Micalis, Jouy-en-Josas, France; AgroParisTech, UMR Micalis, Jouy-en-Josas, France
| | | | - R Briandet
- INRA, UMR1319 Micalis, Jouy-en-Josas, France; AgroParisTech, UMR Micalis, Jouy-en-Josas, France.
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Radji M, Fauziah S, Aribinuko N. Antibiotic sensitivity pattern of bacterial pathogens in the intensive care unit of Fatmawati Hospital, Indonesia. Asian Pac J Trop Biomed 2015; 1:39-42. [PMID: 23569722 DOI: 10.1016/s2221-1691(11)60065-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Revised: 09/27/2010] [Accepted: 10/15/2010] [Indexed: 10/28/2022] Open
Abstract
OBJECTIVE To evaluate the sensitivity pattern of bacterial pathogens in the intensive care unit (ICU) of a tertiary care of Fatmawati Hospital Jakarta Indonesia. METHODS A cross sectional retrospective study of bacterial pathogen was carried out on a total of 722 patients that were admitted to the ICU of Fatmawati Hospital Jakarta Indonesia during January 2009 to March 2010. All bacteria were identified by standard microbiologic methods, and their antibiotic susceptibility testing was performed using disk diffusion method. RESULTS Specimens were collected from 385 patients who were given antimicrobial treatment, of which 249 (64.68%) were cultured positive and 136 (35.32%) were negative. The most predominant isolate was Pseudomonas aeruginosa (P. aeruginosa) (26.5%) followed by Klebsiella pneumoniae (K. pneumoniae) (15.3%) and Staphylococcus epidermidis (14.9%). P. aeruginosa isolates showed high rate of resistance to cephalexin (95.3%), cefotaxime (64.1%), and ceftriaxone (60.9%). Amikacin was the most effective (84.4%) antibiotic against P. aeruginosa followed by imipenem (81.2%), and meropenem (75.0%). K. pneumoniae showed resistance to cephalexin (86.5%), ceftriaxone (75.7%), ceftazidime (73.0%), cefpirome (73.0%) and cefotaxime (67.9%), respectively. CONCLUSIONS Most bacteria isolated from ICU of Fatmawati Hospital Jakarta Indonesia were resistant to the third generation of cephalosporins, and quinolone antibiotics. Regular surveillance of antibiotic susceptibility patterns is very important for setting orders to guide the clinician in choosing empirical or directed therapy of infected patients.
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Affiliation(s)
- Maksum Radji
- Laboratory of Microbiology and Biotechnology, Department of Pharmacy, Faculty of Mathematics and Science, University of Indonesia, Depok, 16424, Indonesia
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40
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Abstract
Reverse vaccinology (RV) is a computational approach that aims to identify putative vaccine candidates in the protein coding genome (proteome) of pathogens. RV has primarily been applied to bacterial pathogens to identify proteins that can be formulated into subunit vaccines, which consist of one or more protein antigens. An RV approach based on a filtering method has already been used to construct a subunit vaccine against Neisseria meningitidis serogroup B that is now registered in several countries (Bexsero). Recently, machine learning methods have been used to improve the ability of RV approaches to identify vaccine candidates. Further improvements related to the incorporation of epitope-binding annotation and gene expression data are discussed. In the future, it is envisaged that RV approaches will facilitate rapid vaccine design with less reliance on conventional animal testing and clinical trials in order to curb the threat of antibiotic resistance or newly emerged outbreaks of bacterial origin.
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Mulatu G, Beyene G, Zeynudin A. Prevalence of Shigella, Salmonella and Campylobacter species and their susceptibility patters among under five children with diarrhea in Hawassa town, south Ethiopia. Ethiop J Health Sci 2015; 24:101-8. [PMID: 24795510 PMCID: PMC4006203 DOI: 10.4314/ejhs.v24i2.1] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Background Diarrhea is the leading cause of morbidity and mortality in under-five children in developing countries including Ethiopia. Therefore, up-to-date data on etiologic agent and susceptibility pattern are important for the management of bacterial diarrhea in under-five children, which was the main objective of this study. Method A cross-sectional study was conducted at Hawassa Adare Hospital and Millennium Health Center from June 6 to October 28, 2011. A total of 158 under-five children with diarrhea were selected using convenient sampling technique. Demographic and clinical data were collected using questionnaire. Fecal samples were collected and processed for bacterial isolation, and antimicrobial susceptibility testing following standard bacteriological techniques. Result A total of 158 fecal samples were collected from 81(51.3%) males and 77(48.7%) females of under-five children with diarrhea. Of the 158 fecal samples, 35(22.2%) bacterial pathogens were isolated. The isolated bacteria were Campylobacter species, 20 (12.7%), Shigella species, 11 (7.0%), and Salmonella species, 4 (2.5%). The majority of the isolates were sensitive to Chloramphenicol, Ciprofloxacin, Nalidixic acid and Cotrimoxazol and high rate of drug resistance was observed against Erythromycin and Amoxicillin. Conclusions The finding of this study indicates that Campylobacter species were the predominant etiologies and the presence of bacterial isolates resistant to the commonly prescribed drugs for treating diarrhea in children. Therefore, periodic monitoring of etiologic agent with their drug resistant pattern is essential in the management of diarrhea in children.
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Affiliation(s)
- Getamesay Mulatu
- Department of Medical Laboratory Technology, Hawassa College of Health Science
| | - Getenet Beyene
- Department of Medical Laboratory and Pathology, Jimma University, Ethiopia
| | - Ahmed Zeynudin
- Department of Medical Laboratory and Pathology, Jimma University, Ethiopia
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Moore JE, Huang J, Yu P, Ma C, Moore PJ, Millar BC, Goldsmith CE, Xu J. High diversity of bacterial pathogens and antibiotic resistance in salmonid fish farm pond water as determined by molecular identification employing 16S rDNA PCR, gene sequencing and total antibiotic susceptibility techniques. Ecotoxicol Environ Saf 2014; 108:281-286. [PMID: 25105488 DOI: 10.1016/j.ecoenv.2014.05.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 05/16/2014] [Accepted: 05/19/2014] [Indexed: 06/03/2023]
Abstract
The aim of this study was to examine the microbiological and related parameters (antibiotic resistance and pathogen identification) of water at two salmonid fish farms in Northern Ireland. Total Bacterial Counts at the Movanagher Fish Farm was 1730 colony forming units (cfu)/ml water (log10 3.24cfu/ml) and 3260cfu/ml (log10 3.51cfu/ml) at the Bushmills Salmon Station. Examination of resulting organisms revealed 10 morphological phenotypes, which were subsequently sequenced to determine their identification. All these organisms were Gram-negative and no Gram-positive organisms were isolated from any water sample. From these phenotypes, eight different genera were identified including Acinetobacter, Aeromonas, Chryseobacterium, Erwinia, Flavobacterium, Pseudomonas and Rheinheimera. One unnamed novel taxon was identified from water at the Movanagher Fish Farm, belonging to the genus Acinetobacter and has been tentatively named Acinetobacter movanagherensis. No other novel taxa were observed. All but one of these environmental organisms (Erwinia) are potential pathogens of fish disease. Total antibiotic resistance was observed to varying degrees in water specimens. The most resistant populations were observed in water taken from the Bushmills Salmon Station inlet, followed by water from the Movanagher Fish Farm. No resistance was observed against tetracycline and there was only one occurrence of resistance against ciprofloxacin. Overall, this study indicates that potential fish pathogens made up the majority of environmental organisms identified, even in the absence of recorded fish disease. There was also relatively high levels of total antibiotic resistance in the bacterial water populations examined, where tetracycline was the only antibiotic with zero resistance. These data indicate that the threat of bacterial disease is relatively close due to the indigenous colonization of farm water and that husbandry standards should be maintained at a high standard to avert bacterial disease outbreaks, rather than relying on the absence of specific pathogens in the immediate farm environment.
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Affiliation(s)
- John E Moore
- Northern Ireland Public Health Laboratory, Department of Bacteriology, Belfast City Hospital, Lisburn Road, Belfast, Northern Ireland, BT9 7AD, UK; School of Biomedical Sciences, University of Ulster, Coleraine, Northern Ireland, BT52 1SA, UK; Centre for Infection & Immunity, School of Medicine, Dentistry and Biomedical Sciences, Queen's University, Health Sciences, Building, 97 Lisburn Road, Belfast, Northern Ireland, BT9 7BL, UK.
| | - Junhua Huang
- Department of Medical Technology, Xi'an Medical College, Xi'an, Shaanxi 710021, China
| | - Pengbo Yu
- Shaanxi Center for Disease Control and Prevention, 3 Jian Dong Street, Xi'an, Shaanxi 710054, China
| | - Chaofeng Ma
- Xi'an Center for Disease Control and Prevention, Xi'an, Shaanxi 710054, China
| | - Peter Ja Moore
- Northern Ireland Public Health Laboratory, Department of Bacteriology, Belfast City Hospital, Lisburn Road, Belfast, Northern Ireland, BT9 7AD, UK; Ballymena Academy, Galgorm Road, Ballymena, Co. Antrim, Northern Ireland, BT42 1AJ, UK
| | - Beverley C Millar
- Northern Ireland Public Health Laboratory, Department of Bacteriology, Belfast City Hospital, Lisburn Road, Belfast, Northern Ireland, BT9 7AD, UK
| | - Colin E Goldsmith
- Northern Ireland Public Health Laboratory, Department of Bacteriology, Belfast City Hospital, Lisburn Road, Belfast, Northern Ireland, BT9 7AD, UK
| | - Jiru Xu
- Department of Pathogenic Biology, Xian Jiatong University, Xi'an, Shaanxi, China
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Levin R, Grinstein S, Schlam D. Phosphoinositides in phagocytosis and macropinocytosis. Biochim Biophys Acta Mol Cell Biol Lipids 2014; 1851:805-23. [PMID: 25238964 DOI: 10.1016/j.bbalip.2014.09.005] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 08/23/2014] [Accepted: 09/08/2014] [Indexed: 01/08/2023]
Abstract
Professional phagocytes provide immunoprotection and aid in the maintenance of tissue homeostasis. They perform these tasks by recognizing, engulfing and eliminating pathogens and endogenous cell debris. Here, we examine the paramount role played by phosphoinositides in phagocytosis and macropinocytosis, two major endocytic routes that mediate the uptake of particulate and fluid matter, respectively. We analyze accumulating literature describing the molecular mechanisms whereby phosphoinositides translate environmental cues into the complex, sophisticated responses that underlie the phagocytic and macropinocytic responses. In addition, we exemplify virulence strategies involving modulation of host cell phosphoinositide signaling that are employed by bacteria to undermine immunity. This article is part of a Special Issue entitled Phosphoinositides.
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Affiliation(s)
- Roni Levin
- Division of Cell Biology, Hospital for Sick Children, 555 University Ave., Toronto M5G1X8, Canada
| | - Sergio Grinstein
- Division of Cell Biology, Hospital for Sick Children, 555 University Ave., Toronto M5G1X8, Canada; Keenan Research Centre of the Li Ka Shing Knowledge Institute, St. Michael's Hospital, 209 Victoria St., Toronto M5C1N8, Canada.
| | - Daniel Schlam
- Division of Cell Biology, Hospital for Sick Children, 555 University Ave., Toronto M5G1X8, Canada
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Luo G, Angelidaki I. Analysis of bacterial communities and bacterial pathogens in a biogas plant by the combination of ethidium monoazide, PCR and Ion Torrent sequencing. Water Res 2014; 60:156-163. [PMID: 24852413 DOI: 10.1016/j.watres.2014.04.047] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 04/22/2014] [Accepted: 04/27/2014] [Indexed: 05/13/2023]
Abstract
The present study investigated the changes of bacterial community composition including bacterial pathogens along a biogas plant, i.e. from the influent, to the biogas reactor and to the post-digester. The effects of post-digestion temperature and time on the changes of bacterial community composition and bacterial pathogens were also studied. Microbial analysis was made by Ion Torrent sequencing of the PCR amplicons from ethidium monoazide treated samples, and ethidium monoazide was used to cleave DNA from dead cells and exclude it from PCR amplification. Both similarity and taxonomic analysis showed that the bacterial community composition in the influent was changed after anaerobic digestion. Firmicutes were dominant in all the samples, while Proteobacteria decreased in the biogas reactor compared with the influent. Variations of bacterial community composition in the biogas reactor with time were also observed. This could be attributed to varying composition of the influent. Batch experiments showed that the methane recovery from the digested residues (obtained from biogas reactor) was mainly related with post-digestion temperature. However, post-digestion time rather than temperature had a significant effect on the changes of bacterial community composition. The changes of bacterial community composition were also reflected in the changes of relative abundance of bacterial pathogens. The richness and relative abundance of bacterial pathogens were reduced after anaerobic digestion in the biogas reactor. It was found in batch experiments that bacterial pathogens showed the highest relative abundance and richness after 30 days' post-digestion. Streptococcus bovis was found in all the samples. Our results showed that special attention should be paid to the post-digestion since the increase in relative abundance of bacterial pathogens after post-digestion might reflect regrowth of bacterial pathogens and limit biosolids disposal vectors.
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Affiliation(s)
- Gang Luo
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, 200433 Shanghai, China; Department of Environmental Engineering, Technical University of Denmark, DK-2800 Kgs Lyngby, Denmark
| | - Irini Angelidaki
- Department of Environmental Engineering, Technical University of Denmark, DK-2800 Kgs Lyngby, Denmark.
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Huang CJ, Knoll W, Sessitsch A, Dostalek J. SPR bacterial pathogen biosensor: the importance of fluidic conditions and probing depth. Talanta 2014; 122:166-71. [PMID: 24720979 DOI: 10.1016/j.talanta.2014.01.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 01/13/2014] [Accepted: 01/20/2014] [Indexed: 11/26/2022]
Abstract
The sensitivity of surface plasmon resonance (SPR) biosensor technology for detection of bacterial analytes is investigated as a function of (a) sample flow conditions and (b) depth of probing electromagnetic field. These parameters are extremely important as such analytes exhibit large (of around micrometer) size which significantly hinders their diffusion-driven transfer from a liquid sample to the sensor and their subsequent specific capture by attached recognition elements. This is due to small diffusion coefficient and strong shear stress that decreases the stability of bonds between the bacterium specific epitope and recognition elements immobilized at the sensor surface. The importance of accurate control of sample flow conditions and probing depth in order to maximize SPR sensor response is experimentally demonstrated and supported by an analytical theory. The tuning of the probing depth of surface plasmon evanescent field to match the size of the target analyte is pursued by using long range surface plasmons.
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Affiliation(s)
- Chun Jen Huang
- Graduate Institute of BioMedical Engineering, National Central University, (32001) No. 300, Jhongda Rd., Jhongli City, Taoyuan County 320, Taiwan
| | - Wolfgang Knoll
- AIT - Austrian Institute of Technology, BioSensor Technologies, Muthgasse 11, 1190 Vienna, Austria
| | - Angela Sessitsch
- AIT Austrian Institute of Technology, Bioresources Unit, Konrad-Lorenz-straße 24, 3430 Tulln, Austria
| | - Jakub Dostalek
- AIT - Austrian Institute of Technology, BioSensor Technologies, Muthgasse 11, 1190 Vienna, Austria.
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Kp P, Arora V, Pp G. Bloodstream Bacterial Pathogens and their Antibiotic Resistance Pattern in Dhahira Region, Oman. Oman Med J 2011; 26:240-79. [PMID: 22043427 DOI: 10.5001/omj.2011.59] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Accepted: 07/06/2011] [Indexed: 11/03/2022] Open
Abstract
OBJECTIVES To describe the epidemiological, clinical, microbiological characteristics and antimicrobial resistance pattern of Bloodstream infections in Dhahira region, Oman. METHODS Clinical data was collected from all patients with positive blood cultures for two years period. Standard laboratory methods were used for blood culture. Antibiotic sensitivity was tested using Kirby-Bauer disc diffusion method. RESULTS Of the 360 bacterial pathogens isolated from 348 patients, 57.8% were gram-positive and 42.2% were gram-negative. The common isolates were: Streptococcus species 76 (21.1%), coagulase-negative Staphylococci 75 (20.8%), Escherichia coli 43 (11.9%), Staphylococcus aureus 41 (11.4%). Overall, mortality was 21.3% (74/348). Staphylococcus species (Staphylococcus aureus and CoNS) were more commonly resistant to Trimethoprim/ Sulphamethoxazole (35.3%) and Penicillin (25.9%). Streptococcus species were resistant to Trimethoprim/Sulphamethoxazole (39.1%) and Erythromycin (19.6%). CONCLUSION Bloodstream infections are important causes of morbidity and mortality in our patients, especially among chronically ill elderly adult males. Prescription of proven resistant antibiotics to suspected bacteremic patients needs attention in Dhahira region.
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