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Liu H, Zhuang L, Zeng Q. Complete genome sequence data of Pseudomonas nitroreducens L4, an endophyte isolated from cotton plants. Data Brief 2024; 55:110639. [PMID: 39022698 PMCID: PMC11252606 DOI: 10.1016/j.dib.2024.110639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/24/2024] [Accepted: 06/10/2024] [Indexed: 07/20/2024] Open
Abstract
Pseudomonas nitroreducens L4 was isolated from the interior of cotton plants, which showed strong biocontrol activity against Verticillium dahlia and other fungal pathogens. To elucidate the biocontrol mechanism, the genome sequence of L4 was sequenced using the Illumina and Nanopore sequencing platform. The assembled genome of L4 consisted of a single circular chromosome was 6,229,472 bp, with an average GC content of 64.95 %, 5,629 protein-coding genes, 72 tRNA, 16 rRNA and 1 tm RNA. Six secondary metabolite biosynthetic gene clusters are identified in the genome. The genome sequence provided a theoretical basis for analyzing the biocontrol mechanism of this strain.
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Affiliation(s)
- Haiyang Liu
- Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, China
- MOA Key Lab of Pest Monitoring and Green Management, Department of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Lubo Zhuang
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Qingchao Zeng
- MOA Key Lab of Pest Monitoring and Green Management, Department of Plant Pathology, China Agricultural University, Beijing 100193, China
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2
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Gulati P, Singh A, Patra S, Bhat S, Verma A. Restriction modification systems in archaea: A panoramic outlook. Heliyon 2024; 10:e27382. [PMID: 38644887 PMCID: PMC11033074 DOI: 10.1016/j.heliyon.2024.e27382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 02/19/2024] [Accepted: 02/28/2024] [Indexed: 04/23/2024] Open
Abstract
Restriction modification (RM) systems are one of the ubiquitous yet primitive defense responses employed by bacteria and archaea with the primary role of safeguarding themselves against invading bacteriophages. Protection of the host occurs by the cleavage of the invading foreign DNA via restriction endonucleases with concomitant methylation of host DNA with the aid of a methyltransferase counterpart. RM systems have been extensively studied in bacteria, however, in the case of archaea there are limited reports of RM enzymes that are investigated to date owing to their inhospitable growth demands. This review aims to broaden the knowledge about what is known about the diversity of RM systems in archaea and encapsulate the current knowledge on restriction and modification enzymes characterized in archaea so far and the role of RM systems in the milieu of archaeal biology.
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Affiliation(s)
- Pallavi Gulati
- Department of Microbiology, Ram Lal Anand College, University of Delhi South Campus, New Delhi 110021, India
| | - Ashish Singh
- Department of Microbiology, University of Delhi South Campus, New Delhi 110021, India
| | - Sandeep Patra
- Department of Microbiology, Ram Lal Anand College, University of Delhi South Campus, New Delhi 110021, India
| | - Shreyas Bhat
- Department of Microbiology, Ram Lal Anand College, University of Delhi South Campus, New Delhi 110021, India
| | - Anil Verma
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA-15213, USA
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Aguilar-Rangel EJ, Savin-Gámez A, García-Maldonado JQ, Prado B, Vásquez-Murrieta MS, Siebe C, Alcántara-Hernández RJ. Increases in the soil ammonia oxidizing phylotypes and their rechange due to long-term irrigation with wastewater. PLoS One 2024; 19:e0299518. [PMID: 38603769 PMCID: PMC11008854 DOI: 10.1371/journal.pone.0299518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 02/13/2024] [Indexed: 04/13/2024] Open
Abstract
Wastewater irrigation is a common practice for agricultural systems in arid and semiarid zones, which can help to overcome water scarcity and contribute with nutrient inputs. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are key in the transformation of NH4+-N in soil and can be affected by variations in soil pH, EC, N and C content, or accumulation of pollutants, derived from wastewater irrigation. The objective of this study was to determine the changes in the ammonia oxidizing communities in agricultural soils irrigated with wastewater for different periods of time (25, 50, and 100 years), and in rainfed soils (never irrigated). The amoA gene encoding for the catalytic subunit of the ammonia monooxygenase was used as molecular reporter; it was quantified by qPCR and sequenced by high throughput sequencing, and changes in the community composition were associated with the soil physicochemical characteristics. Soils irrigated with wastewater showed up to five times more the abundance of ammonia oxidizers (based on 16S rRNA gene relative abundance and amoA gene copies) than those under rainfed agriculture. While the amoA-AOA: amoA-AOB ratio decreased from 9.8 in rainfed soils to 1.6 in soils irrigated for 100 years, indicating a favoring environment for AOB rather than AOA. Further, the community structure of both AOA and AOB changed during wastewater irrigation compared to rainfed soils, mainly due to the abundance variation of certain phylotypes. Finally, the significant correlation between soil pH and the ammonia oxidizing community structure was confirmed, mainly for AOB; being the main environmental driver of the ammonia oxidizer community. Also, a calculated toxicity index based on metals concentrations showed a correlation with AOB communities, while the content of carbon and nitrogen was more associated with AOA communities. The results indicate that wastewater irrigation influence ammonia oxidizers communities, manly by the changes in the physicochemical environment.
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Affiliation(s)
- Eduardo J. Aguilar-Rangel
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Unidad de Posgrado, Edificio D, 1° Piso, Circuito de Posgrados, Ciudad Universitaria, Coyoacán, 04510, Ciudad de México, México
| | - Alba Savin-Gámez
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Unidad de Posgrado, Edificio D, 1° Piso, Circuito de Posgrados, Ciudad Universitaria, Coyoacán, 04510, Ciudad de México, México
| | - José Q. García-Maldonado
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Merida 97310, Yucatán, México
| | - Blanca Prado
- Instituto de Geología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Av. Universidad 3000, Del. Coyoacán, 04510, Ciudad de México, México
| | - María Soledad Vásquez-Murrieta
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Del. Miguel Hidalgo, 11340, Ciudad de México, México
| | - Christina Siebe
- Instituto de Geología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Av. Universidad 3000, Del. Coyoacán, 04510, Ciudad de México, México
| | - Rocío J. Alcántara-Hernández
- Instituto de Geología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Av. Universidad 3000, Del. Coyoacán, 04510, Ciudad de México, México
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Gumustop I, Ortakci F. Comparative genomics of Loigolactobacillus coryniformis with an emphasis on L. coryniformis strain FOL-19 isolated from cheese. Comput Struct Biotechnol J 2023; 21:5111-5124. [PMID: 37920811 PMCID: PMC10618118 DOI: 10.1016/j.csbj.2023.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/04/2023] [Accepted: 10/04/2023] [Indexed: 11/04/2023] Open
Abstract
Loigolactobacillus coryniformis is a member of lactic acid bacteria isolated from various ecological niches. We isolated a novel L. coryniformis strain FOL-19 from artisanal Tulum cheese and performed the whole-genome sequencing for FOL-19. Then, genomic characterization of FOL-19 against ten available whole genome sequences of the same species isolated from kimchi, silage, fermented meat, air of cowshed, dairy, and pheasant chyme was performed to uncover the genetic diversity and biotechnological potential of overall species. The average genome size of 2.93 ± 0.1 Mb, GC content of 42.96% ± 0.002, number of CDS of 2905 ± 165, number of tRNA of 56 ± 10, and number of CRISPR elements of 6.55 ± 1.83 was found. Both Type I and II Cas clusters were observed in L. coryniformis. No bacteriocin biosynthesis gene clusters were found. All strains harbored at least one plasmid except KCTC 3167. All strains were predicted to carry multiple IS elements. The most common origin of the IS elements was belong to Lactiplantibacillus plantarum. Comparative genomic analysis of L. coryniformis revealed hypervariability at the strain level and the presence of CRISPR/Cas suggests that L. coryniformis holds a promising potential for being a reservoir for new CRISPR-based tools. All L. coryniformis strains except PH-1 were predicted to harbor pdu and cbi-cob-hem gene clusters encoding industrially relevant traits of reuterin and cobalamin biosynthesis, respectively. These findings put a step forward for the genomic characterization of L. coryniformis strains for biotechnological applications via genome-guided strain selection to identify industrially relevant traits.
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Affiliation(s)
- Ismail Gumustop
- BioEngineering Department, Faculty of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkey
| | - Fatih Ortakci
- Food Engineering Department, Faculty of Chemical and Metallurgical Engineering, Istanbul Technical University, Istanbul, Turkey
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Jones DC, LaMartina EL, Lewis JR, Dahl AJ, Nadig N, Szabo A, Newton RJ, Skwor TA. One Health and Global Health View of Antimicrobial Susceptibility through the "Eye" of Aeromonas: Systematic Review and Meta-Analysis. Int J Antimicrob Agents 2023; 62:106848. [PMID: 37201798 PMCID: PMC10524465 DOI: 10.1016/j.ijantimicag.2023.106848] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 04/26/2023] [Accepted: 05/09/2023] [Indexed: 05/20/2023]
Abstract
Antimicrobial resistance (AMR) is one of the most pressing public health concerns; therefore, it is imperative to advance our understanding of the factors influencing AMR from Global and One Health perspectives. To address this, Aeromonas populations were identified using 16S rRNA gene libraries among human, agriculture, aquaculture, drinking water, surface water, and wastewater samples, supporting its use as indicator bacteria to study AMR. A systematic review and meta-analysis was then performed from Global and One Health perspectives, including data from 221 articles describing 15 891 isolates from 57 countries. The interconnectedness of different environments was evident as minimal differences were identified between sectors among 21 different antimicrobials. However, resistance to critically important antibiotics (aztreonam and cefepime) was significantly higher among wastewater populations compared with clinical isolates. Additionally, isolates from untreated wastewater typically exhibited increased AMR compared with those from treated wastewater. Furthermore, aquaculture was associated with increased AMR to ciprofloxacin and tetracycline compared with wild-caught seafood. Using the World Health Organization AWaRe classifications, countries with lower consumption of "Access" compared to "Watch" drugs from 2000 to 2015 demonstrated higher AMR levels. The current analysis revealed negative correlations between AMR and anthropogenic factors, such as environmental performance indices and socioeconomic standing. Environmental health and sanitation were two of the environmental factors most strongly correlated with AMR. The current analysis highlights the negative impacts of "Watch" drug overconsumption, anthropogenic activity, absence of wastewater infrastructure, and aquaculture on AMR, thus stressing the need for proper infrastructure and global regulations to combat this growing problem.
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Affiliation(s)
| | - Emily Lou LaMartina
- School of Freshwater Sciences, University of Wisconsin - Milwaukee, Milwaukee, WI, USA
| | - Jenna Rachel Lewis
- Department of Biological Sciences, University of Wisconsin - Milwaukee, Milwaukee, WI, USA
| | - Andrew James Dahl
- Department of Biomedical Sciences, University of Wisconsin - Milwaukee, Milwaukee, WI, USA
| | - Nischala Nadig
- Department of Biomedical Sciences, University of Wisconsin - Milwaukee, Milwaukee, WI, USA
| | - Aniko Szabo
- Division of Biostatistics, Institute for Health & Equity, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Ryan J Newton
- School of Freshwater Sciences, University of Wisconsin - Milwaukee, Milwaukee, WI, USA
| | - Troy A Skwor
- Department of Biomedical Sciences, University of Wisconsin - Milwaukee, Milwaukee, WI, USA.
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Genetic and Environmental Investigation of a Novel Phenylamino Acetamide Inhibitor of the Pseudomonas aeruginosa Type III Secretion System. Appl Environ Microbiol 2023; 89:e0175222. [PMID: 36519869 PMCID: PMC9888221 DOI: 10.1128/aem.01752-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Traditional antibiotics target essential cellular components or metabolic pathways conserved in both pathogenic and nonpathogenic bacteria. Unfortunately, long-term antibiotic use often leads to antibiotic resistance and disruption of the overall microbiota. In this work, we identified a phenylamino acetamide compound, named 187R, that strongly inhibited the expression of the type III secretion system (T3SS) encoding genes and the secretion of the T3SS effector proteins in Pseudomonas aeruginosa. T3SS is an important virulence factor, as T3SS-deficient strains of P. aeruginosa are greatly attenuated in virulence. We further showed that 187R had no effect on bacterial growth, implying a reduced selective pressure for the development of resistance. 187R-mediated repression of T3SS was dependent on ExsA, the master regulator of T3SS in P. aeruginosa. The impact of 187R on the host-associated microbial community was also tested using the Arabidopsis thaliana phyllosphere as a model. Both culture-independent (Illumina sequencing) and culture-dependent (Biolog) methods showed that the application of 187R had little impact on the composition and function of microbial community compared to the antibiotic streptomycin. Together, these results suggested that compounds that target virulence factors could serve as an alternative strategy for disease management caused by bacterial pathogens. IMPORTANCE New antimicrobial therapies are urgently needed, since antibiotic resistance in human pathogens has become one of the world's most urgent public health problems. Antivirulence therapy has been considered a promising alternative for the management of infectious diseases, as antivirulence compounds target only the virulence factors instead of the growth of bacteria, and they are therefore unlikely to affect commensal microorganisms. However, the impacts of antivirulence compounds on the host microbiota are not well understood. We report a potent synthetic inhibitor of the P. aeruginosa T3SS, 187R, and its effect on the host microbiota of Arabidopsis. Both culture-independent (Illumina sequencing) and culture-dependent (Biolog) methods showed that the impacts of the antivirulence compound on the composition and function of host microbiota were limited. These results suggest that antivirulence compounds can be a potential alternative method to antibiotics.
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Holban AM, Gregoire CM, Gestal MC. Conquering the host: Bordetella spp. and Pseudomonas aeruginosa molecular regulators in lung infection. Front Microbiol 2022; 13:983149. [PMID: 36225372 PMCID: PMC9549215 DOI: 10.3389/fmicb.2022.983149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/17/2022] [Indexed: 11/27/2022] Open
Abstract
When bacteria sense cues from the host environment, stress responses are activated. Two component systems, sigma factors, small RNAs, ppGpp stringent response, and chaperones start coordinate the expression of virulence factors or immunomodulators to allow bacteria to respond. Although, some of these are well studied, such as the two-component systems, the contribution of other regulators, such as sigma factors or ppGpp, is increasingly gaining attention. Pseudomonas aeruginosa is the gold standard pathogen for studying the molecular mechanisms to sense and respond to environmental cues. Bordetella spp., on the other hand, is a microbial model for studying host-pathogen interactions at the molecular level. These two pathogens have the ability to colonize the lungs of patients with chronic diseases, suggesting that they have the potential to share a niche and interact. However, the molecular networks that facilitate adaptation of Bordetella spp. to cues are unclear. Here, we offer a side-by-side comparison of what is known about these diverse molecular mechanisms that bacteria utilize to counteract host immune responses, while highlighting the relatively unexplored interactions between them.
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Affiliation(s)
- Alina M. Holban
- Research Institute of the University of Bucharest (ICUB), Bucharest, Romania
- Department of Microbiology and Immunology, Faculty of Biology, University of Bucharest, Bucharest, Romania
| | - Courtney M. Gregoire
- Department of Microbiology and Immunology, Louisiana State University Health Science Center, Shreveport, LA, United States
| | - Monica C. Gestal
- Department of Microbiology and Immunology, Louisiana State University Health Science Center, Shreveport, LA, United States
- *Correspondence: Monica C. Gestal, ;
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Qin S, Xiao W, Zhou C, Pu Q, Deng X, Lan L, Liang H, Song X, Wu M. Pseudomonas aeruginosa: pathogenesis, virulence factors, antibiotic resistance, interaction with host, technology advances and emerging therapeutics. Signal Transduct Target Ther 2022; 7:199. [PMID: 35752612 PMCID: PMC9233671 DOI: 10.1038/s41392-022-01056-1] [Citation(s) in RCA: 281] [Impact Index Per Article: 140.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 06/04/2022] [Accepted: 06/08/2022] [Indexed: 02/05/2023] Open
Abstract
Pseudomonas aeruginosa (P. aeruginosa) is a Gram-negative opportunistic pathogen that infects patients with cystic fibrosis, burn wounds, immunodeficiency, chronic obstructive pulmonary disorder (COPD), cancer, and severe infection requiring ventilation, such as COVID-19. P. aeruginosa is also a widely-used model bacterium for all biological areas. In addition to continued, intense efforts in understanding bacterial pathogenesis of P. aeruginosa including virulence factors (LPS, quorum sensing, two-component systems, 6 type secretion systems, outer membrane vesicles (OMVs), CRISPR-Cas and their regulation), rapid progress has been made in further studying host-pathogen interaction, particularly host immune networks involving autophagy, inflammasome, non-coding RNAs, cGAS, etc. Furthermore, numerous technologic advances, such as bioinformatics, metabolomics, scRNA-seq, nanoparticles, drug screening, and phage therapy, have been used to improve our understanding of P. aeruginosa pathogenesis and host defense. Nevertheless, much remains to be uncovered about interactions between P. aeruginosa and host immune responses, including mechanisms of drug resistance by known or unannotated bacterial virulence factors as well as mammalian cell signaling pathways. The widespread use of antibiotics and the slow development of effective antimicrobials present daunting challenges and necessitate new theoretical and practical platforms to screen and develop mechanism-tested novel drugs to treat intractable infections, especially those caused by multi-drug resistance strains. Benefited from has advancing in research tools and technology, dissecting this pathogen's feature has entered into molecular and mechanistic details as well as dynamic and holistic views. Herein, we comprehensively review the progress and discuss the current status of P. aeruginosa biophysical traits, behaviors, virulence factors, invasive regulators, and host defense patterns against its infection, which point out new directions for future investigation and add to the design of novel and/or alternative therapeutics to combat this clinically significant pathogen.
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Affiliation(s)
- Shugang Qin
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Wen Xiao
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Chuanmin Zhou
- State Key Laboratory of Virology, School of Public Health, Wuhan University, Wuhan, 430071, P.R. China
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND, 58203, USA
| | - Qinqin Pu
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND, 58203, USA
| | - Xin Deng
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, People's Republic of China
| | - Lefu Lan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Haihua Liang
- College of Life Sciences, Northwest University, Xi'an, ShaanXi, 710069, China
| | - Xiangrong Song
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China.
| | - Min Wu
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China.
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND, 58203, USA.
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The Effect of CFTR Modulators on Airway Infection in Cystic Fibrosis. Int J Mol Sci 2022; 23:ijms23073513. [PMID: 35408875 PMCID: PMC8998472 DOI: 10.3390/ijms23073513] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 02/08/2023] Open
Abstract
The advent of Cystic fibrosis transmembrane receptor (CFTR) modulators in 2012 was a critical event in the history of cystic fibrosis (CF) treatment. Unlike traditional therapies that target downstream effects of CFTR dysfunction, CFTR modulators aim to correct the underlying defect at the protein level. These genotype-specific therapies are now available for an increasing number of CF patients, transforming the way we view the condition from a life-limiting disease to one that can be effectively managed. Several studies have demonstrated the vast improvement CFTR modulators have on normalization of sweat chloride, CFTR function, clinical endpoints, and frequency of pulmonary exacerbation. However, their impact on other aspects of the disease, such as pathogenic burden and airway infection, remain under explored. Frequent airway infections as a result of increased susceptibility and impaired innate immune response are a serious problem within CF, often leading to accelerated decline in lung function and disease progression. Current evidence suggests that CFTR modulators are unable to eradicate pathogenic organisms in those with already established lung disease. However, this may not be the case for those with relatively low levels of disease progression and conserved microbial diversity, such as young patients. Furthermore, it remains unknown whether the restorative effects exerted by CFTR modulators extend to immune cells, such as phagocytes, which have the potential to modulate the response of people with CF (pwCF) to infection. Throughout this review, we look at the potential impact of CFTR modulators on airway infection in CF and their ability to shape impaired pulmonary defences to pathogens.
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Oberin M, Badger S, Faverjon C, Cameron A, Bannister-Tyrrell M. Electronic information systems for One Health surveillance of antimicrobial resistance: a systematic scoping review. BMJ Glob Health 2022; 7:e007388. [PMID: 34983786 PMCID: PMC8728452 DOI: 10.1136/bmjgh-2021-007388] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 11/24/2021] [Indexed: 11/24/2022] Open
Abstract
INTRODUCTION Electronic information systems (EIS) that implement a 'One Health' approach by integrating antimicrobial resistance (AMR) data across the human, animal and environmental health sectors, have been identified as a global priority. However, evidence on the availability, technical capacities and effectiveness of such EIS is scarce. METHODS Through a qualitative synthesis of evidence, this systematic scoping review aims to: identify EIS for AMR surveillance that operate across human, animal and environmental health sectors; describe their technical characteristics and capabilities; and assess whether there is evidence for the effectiveness of the various EIS for AMR surveillance. Studies and reports between 1 January 2000 and 21 July 2021 from peer-reviewed and grey literature in the English language were included. RESULTS 26 studies and reports were included in the final review, of which 27 EIS were described. None of the EIS integrated AMR data in a One Health approach across all three sectors. While there was a lack of evidence of thorough evaluations of the effectiveness of the identified EIS, several surveillance system effectiveness indicators were reported for most EIS. Standardised reporting of the effectiveness of EIS is recommended for future publications. The capabilities of the EIS varied in their technical design features, in terms of usability, data display tools and desired outputs. EIS that included interactive features, and geospatial maps are increasingly relevant for future trends in AMR data analytics. CONCLUSION No EIS for AMR surveillance was identified that was designed to integrate a broad range of AMR data from humans, animals and the environment, representing a major gap in global efforts to implement One Health approaches to address AMR.
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Affiliation(s)
- Madalene Oberin
- Ausvet, Fremantle, Western Australia, Australia
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Skye Badger
- Ausvet, Fremantle, Western Australia, Australia
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11
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Affiliation(s)
- Jeremy Hill
- The University of Sydney, Sydney, New South Wales, Australia
| | - Ben Marais
- The University of Sydney, Sydney, New South Wales, Australia
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12
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Valim C, Olatunji YA, Isa YS, Salaudeen R, Golam S, Knol EF, Kanyi S, Jammeh A, Bassat Q, de Jager W, Diaz AA, Wiegand RC, Ramirez J, Moses MA, D'Alessandro U, Hibberd PL, Mackenzie GA. Seeking diagnostic and prognostic biomarkers for childhood bacterial pneumonia in sub-Saharan Africa: study protocol for an observational study. BMJ Open 2021; 11:e046590. [PMID: 34593486 PMCID: PMC8487183 DOI: 10.1136/bmjopen-2020-046590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
INTRODUCTION Clinically diagnosed pneumonia in children is a leading cause of paediatric hospitalisation and mortality. The aetiology is usually bacterial or viral, but malaria can cause a syndrome indistinguishable from clinical pneumonia. There is no method with high sensitivity to detect a bacterial infection in these patients and, as result, antibiotics are frequently overprescribed. Conversely, unrecognised concomitant bacterial infection in patients with malarial infections occur with omission of antibiotic therapy from patients with bacterial infections. Previously, we identified two combinations of blood proteins with 96% sensitivity and 86% specificity for detecting bacterial disease. The current project aimed to validate and improve these combinations by evaluating additional biomarkers in paediatric patients with clinical pneumonia. Our goal was to describe combinations of a limited number of proteins with high sensitivity and specificity for bacterial infection to be incorporated in future point-of-care tests. Furthermore, we seek to explore signatures to prognosticate clinical pneumonia. METHODS AND ANALYSIS Patients (n=900) aged 2-59 months presenting with clinical pneumonia at two Gambian hospitals will be enrolled and classified according to criteria for definitive bacterial aetiology (based on microbiological tests and chest radiographs). We will measure proteins at admission using Luminex-based immunoassays in 90 children with definitive and 160 with probable bacterial aetiology, and 160 children classified according to the prognosis of their disease. Previously identified diagnostic signatures will be assessed through accuracy measures. Moreover, we will seek new diagnostic and prognostic signatures through machine learning methods, including support vector machine, penalised regression and classification trees. ETHICS AND DISSEMINATION Ethics approval has been obtained from the Gambia Government/Medical Research Council Unit The Gambia Joint Ethics Committee (protocol 1616) and the institutional review board of Boston University Medical Centre (STUDY00000958). Study results will be disseminated to the staff of the study hospitals, in scientific seminars and meetings, and in publications. TRIAL REGISTRATION NUMBER H-38462.
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Affiliation(s)
- Clarissa Valim
- Department of Global Health, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Yekin Ajauoi Olatunji
- Medical Research Council Unit, The Gambia at the London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - Yasir Shitu Isa
- Medical Research Council Unit, The Gambia at the London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - Rasheed Salaudeen
- Medical Research Council Unit, The Gambia at the London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - Sarwar Golam
- Medical Research Council Unit, The Gambia at the London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - Edward F Knol
- Center of Translational Immunology, Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | | | - Quique Bassat
- Hospital Clínic, Universitat de Barcelona, ISGlobal, Barcelona, Spain
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Wilco de Jager
- Center of Translational Immunology, Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
- Luminex Corp, Austin, Texas, USA
| | - Alejandro A Diaz
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | | | - Julio Ramirez
- Division of Infectious Diseases, University of Louisville, Louisville, Kentucky, USA
| | - Marsha A Moses
- Vascular Biology Program, Children's Hospital Boston, Boston, Massachusetts, USA
- Department of Surgery, Harvard Medical School, Boston, Massachusetts, USA
| | - Umberto D'Alessandro
- Disease Elimination and Control, Medical Research Council Unit, Fajara, Gambia
- London School of Hygiene & Tropical Medicine, London, UK
| | | | - Grant A Mackenzie
- Medical Research Council Unit, The Gambia at the London School of Hygiene & Tropical Medicine, Fajara, The Gambia
- Department of Disease Control, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
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13
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Desbois AP, Garza M, Eltholth M, Hegazy YM, Mateus A, Adams A, Little DC, Høg E, Mohan CV, Ali SE, Brunton LA. Systems-thinking approach to identify and assess feasibility of potential interventions to reduce antibiotic use in tilapia farming in Egypt. AQUACULTURE (AMSTERDAM, NETHERLANDS) 2021; 540:736735. [PMID: 34276104 PMCID: PMC8164158 DOI: 10.1016/j.aquaculture.2021.736735] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 03/31/2021] [Accepted: 04/03/2021] [Indexed: 06/01/2023]
Abstract
Antibiotics are used in aquaculture to maintain the health and welfare of stocks; however, the emergence and selection of antibiotic resistance in bacteria poses threats to humans, animals and the environment. Mitigation of antibiotic resistance relies on understanding the flow of antibiotics, residues, resistant bacteria and resistance genes through interconnecting systems, so that potential solutions can be identified and issues around their implementation evaluated. Participatory systems-thinking can capture the deep complexity of a system while integrating stakeholder perspectives. In this present study, such an approach was applied to Nile tilapia (Oreochromis niloticus) production in the Nile Delta of Egypt, where disease events caused by antibiotic-resistant pathogens have been reported. A system map was co-produced with aquaculture stakeholders at a workshop in May 2018 and used to identify hotspots of antibiotic use, exposure and fate and to describe approaches that would promote fish health and thus reduce antibiotic use. Antibiotics are introduced into the aquaculture system via direct application for example in medicated feed, but residues may also be introduced into the system through agricultural drainage water, which is the primary source of water for most fish farms in Egypt. A follow-up survey of stakeholders assessed the perceived feasibility, advantages and disadvantages of potential interventions. Interventions that respondents felt could be implemented in the short-term to reduce antibiotic usage effectively included: more frequent water exchanges, regular monitoring of culture water quality parameters, improved storage conditions for feed, use of probiotics and greater access to farmer and service providers training programmes. Other potential interventions included greater access to suitable and rapid diagnostics, high quality feeds, improved biosecurity measures and genetically-improved fish, but these solutions were expected to be achieved as long-term goals, with cost being of one of the noted barriers to implementation. Identifying feasible and sustainable interventions that can be taken to reduce antibiotic use, and understanding implementation barriers, are important for addressing antibiotic resistance and ensuring the continued efficacy of antibiotics. This is vital to ensuring the productivity of the tilapia sector in Egypt. The approach taken in the present study provides a means to identify points in the system where the effectiveness of interventions can be evaluated and thus it may be applied to other food production systems to combat the problem of antibiotic resistance.
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Affiliation(s)
- Andrew P. Desbois
- Institute of Aquaculture, University of Stirling, FK9 4LA, United Kingdom
| | - Maria Garza
- Royal Veterinary College, University of London, AL9 7TA, United Kingdom
| | - Mahmoud Eltholth
- Institute of Aquaculture, University of Stirling, FK9 4LA, United Kingdom
- Department of Hygiene and Preventive Medicine, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh, Egypt
- Global Academy of Agriculture and Food Security, The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Yamen M. Hegazy
- Department of Animal Medicine, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Ana Mateus
- Royal Veterinary College, University of London, AL9 7TA, United Kingdom
| | - Alexandra Adams
- Institute of Aquaculture, University of Stirling, FK9 4LA, United Kingdom
| | - David C. Little
- Institute of Aquaculture, University of Stirling, FK9 4LA, United Kingdom
| | - Erling Høg
- Department of Global Health and Development, London School of Hygiene and Tropical Medicine, United Kingdom
| | | | - Shimaa E. Ali
- WorldFish, Penang, Malaysia
- Department of Hydrobiology, National Research Centre, Egypt
| | - Lucy A. Brunton
- Royal Veterinary College, University of London, AL9 7TA, United Kingdom
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14
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Kirchhelle C, Atkinson P, Broom A, Chuengsatiansup K, Ferreira JP, Fortané N, Frost I, Gradmann C, Hinchliffe S, Hoffman SJ, Lezaun J, Nayiga S, Outterson K, Podolsky SH, Raymond S, Roberts AP, Singer AC, So AD, Sringernyuang L, Tayler E, Rogers Van Katwyk S, Chandler CIR. Setting the standard: multidisciplinary hallmarks for structural, equitable and tracked antibiotic policy. BMJ Glob Health 2020; 5:e003091. [PMID: 32967980 PMCID: PMC7513567 DOI: 10.1136/bmjgh-2020-003091] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/31/2020] [Accepted: 08/03/2020] [Indexed: 01/16/2023] Open
Abstract
There is increasing concern globally about the enormity of the threats posed by antimicrobial resistance (AMR) to human, animal, plant and environmental health. A proliferation of international, national and institutional reports on the problems posed by AMR and the need for antibiotic stewardship have galvanised attention on the global stage. However, the AMR community increasingly laments a lack of action, often identified as an 'implementation gap'. At a policy level, the design of internationally salient solutions that are able to address AMR's interconnected biological and social (historical, political, economic and cultural) dimensions is not straightforward. This multidisciplinary paper responds by asking two basic questions: (A) Is a universal approach to AMR policy and antibiotic stewardship possible? (B) If yes, what hallmarks characterise 'good' antibiotic policy? Our multistage analysis revealed four central challenges facing current international antibiotic policy: metrics, prioritisation, implementation and inequality. In response to this diagnosis, we propose three hallmarks that can support robust international antibiotic policy. Emerging hallmarks for good antibiotic policies are: Structural, Equitable and Tracked. We describe these hallmarks and propose their consideration should aid the design and evaluation of international antibiotic policies with maximal benefit at both local and international scales.
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Affiliation(s)
- Claas Kirchhelle
- School of History, University College Dublin, Dublin, Ireland
- Oxford Martin School, University of Oxford, Oxford, Oxfordshire, UK
| | - Paul Atkinson
- Department of Public Health and Policy/ Institute of Infection and Global Health, University of Liverpool, Liverpool, Merseyside, UK
| | - Alex Broom
- School of Social and Political Sciences, Faculty of Arts and Social Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | | | - Jorge Pinto Ferreira
- Antimicrobial Resistance and Veterinary Products Department, World Organisation for Animal Health, Paris, Île-de-France, France
| | - Nicolas Fortané
- Irisso, Paris-Dauphine University, PSL, INRAE, Paris, Île-de-France, France
| | - Isabel Frost
- Center for Disease Dynamics Economics and Policy, Washington, DC, USA
- Department of Infectious Disease, Imperial College London, London, UK
| | - Christoph Gradmann
- Institute for Health and Society, Dept. of Community Medicine and Global Health, University of Oslo, Oslo, Norway
| | - Stephen Hinchliffe
- Geography, College of Life and Environmental Sciences and Wellcome Centre for Cultures and Environments of Health, University of Exeter, Exeter, Devon, UK
| | - Steven J Hoffman
- Global Strategy Lab, Dahdaleh Institute for Global Health Research, Faculty of Health and Osgoode Hall Law School, York University, Toronto, Ontario, Canada
| | - Javier Lezaun
- Institute for Science, Innovation and Society, School of Anthropology and Museum Ethnography, University of Oxford, Oxford, Oxfordshire, UK
| | - Susan Nayiga
- Infectious Diseases Research Collaboration, Kampala, Central Region, Uganda
| | - Kevin Outterson
- School of Law, Social Innovation on Drug Program, Boston University, Boston, Massachusetts, USA
| | - Scott H Podolsky
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Stephanie Raymond
- School of Social and Political Sciences, Faculty of Arts and Social Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Adam P Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, Liverpool, UK
| | - Andrew C Singer
- Pollution, UK Centre for Ecology & Hydrology, Wallingford, UK
| | - Anthony D So
- Department of International Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
- Innovation + Design Enabling Access (IDEA) Initiative, ReAct - Action on Antibiotic Resistance, Baltimore, Maryland, USA
| | | | - Elizabeth Tayler
- Global Coordination and Partnerships, AMR Division, World Health Organisation, Geneva, Switzerland
| | - Susan Rogers Van Katwyk
- Global Strategy Lab, Dahdaleh Institute for Global Health Research, Faculty of Health and Osgoode Hall Law School, York University, Toronto, Ontario, Canada
- Global Strategy Lab, York University, Toronto, Ontario, Canada
| | - Clare I R Chandler
- Department of Global Health and Development, London School of Hygiene & Tropical Medicine, London, UK
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15
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Soheili V, Taghdisi SM, Abnous K, Ebrahimi M. Point-of-care detection of Escherichia coli O157:H7 in water using AuNPs-based aptasensor. IRANIAN JOURNAL OF BASIC MEDICAL SCIENCES 2020; 23:901-908. [PMID: 32774812 PMCID: PMC7395186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
OBJECTIVES Access to safe drinking and irrigation water has always been one of the major human concerns worldwide. Thus, rapid, sensitive, and inexpensive approaches for pathogenic bacteria detection, such as Escherichia coli O157:H7 (EHEC) that can induce important infectious diseases, are highly on demand. MATERIALS AND METHODS In this study, a sensitive aptamer-based AuNPs bioassay was developed that demonstrated its potential to detect EHEC. In the presence of the target bacterium, the specific adsorbed aptamer, leaves AuNPs surface and interacts with EHEC. The bare nanoparticles aggregate in the presence of NaCl and the color shifts from red to purple and blue depending on the bacterial concentration. RESULTS The proposed aptasensor exhibited a good linear response over a wide concentration range of 876 to 107 CFU/ml and was closely correlated with the line equation of "y=0.0094x+0.0006" (R2= 0.9861). It also showed a low detection limit (LOD) of 263 CFU/ml (Signal/Noise=3). No response was recorded in the presence of other tested bacterial strains including Listeria monocytogenes and Salmonella typhi, indicating the high selectivity of the aptasensor. CONCLUSION This biosensor may be used as a smart device to screen water reservoirs and prevents the outbreak of EHEC-related life-threatening contagious diseases.
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Affiliation(s)
- Vahid Soheili
- Department of Pharmacology and Toxicology, Faculty of Medicine, AJA University of Medical Sciences, Tehran, Iran
| | - Seyed Mohammad Taghdisi
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Khalil Abnous
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohsen Ebrahimi
- Department of Pharmacology and Toxicology, Faculty of Medicine, AJA University of Medical Sciences, Tehran, Iran,Corresponding author: Mohsen Ebrahimi. Department of Pharmacology and Toxicology, Faculty of Medicine, AJA University of Medical Sciences, Tehran, Iran. Tel: +98-21-39954958; Fax: +98-51-38823251;
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16
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Transcriptomic Response in Pseudomonas aeruginosa towards Treatment with a Kaempferol Isolated from Melastoma malabathricum Linn Leaves. Int J Microbiol 2020; 2020:6915483. [PMID: 32089696 PMCID: PMC7023722 DOI: 10.1155/2020/6915483] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 12/20/2019] [Accepted: 01/06/2020] [Indexed: 11/19/2022] Open
Abstract
Pseudomonas aeruginosa is one of the main causes of nosocomial infections and is frequently associated with opportunistic infections among hospitalized patients. Kaempferol-3-O-(2′,6′-di-O-trans-p-coumaroyl)-β-D glucopyranoside (KF) is an antipseudomonal compound isolated from the leaves of the native medicinal plant Melastoma malabathricum. Herein, an RNA-seq transcriptomic approach was employed to study the effect of KF treatment on P. aeruginosa and to elucidate the molecular mechanisms underlying the response to KF at two time points (6 h and 24 h incubation). Quantitative real-time PCR (qRT-PCR) was performed for four genes (uvrD, sodM, fumC1, and rpsL) to assess the reliability of the RNA-seq results. The RNA-seq transcriptomic analysis revealed that KF increases the expression of genes involved in the electron transport chain (NADH-I), resulting in the induction of ATP synthesis. Furthermore, KF also increased the expression of genes associated with ATP-binding cassette transporters, flagella, type III secretion system proteins, and DNA replication and repair, which may further influence nutrient uptake, motility, and growth. The results also revealed that KF decreased the expression of a broad range of virulence factors associated with LPS biosynthesis, iron homeostasis, cytotoxic pigment pyocyanin production, and motility and adhesion that are representative of an acute P. aeruginosa infection profile. In addition, P. aeruginosa pathways for amino acid synthesis and membrane lipid composition were modified to adapt to KF treatment. Overall, the present research provides a detailed view of P. aeruginosa adaptation and behaviour in response to KF and highlights the possible therapeutic approach of using plants to combat P. aeruginosa infections.
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17
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Chen G, Gan J, Yang C, Zuo Y, Peng J, Li M, Huo W, Xie Y, Zhang Y, Wang T, Deng X, Liang H. The SiaA/B/C/D signaling network regulates biofilm formation in Pseudomonas aeruginosa. EMBO J 2020; 39:e103412. [PMID: 32090355 DOI: 10.15252/embj.2019103412] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 01/21/2020] [Accepted: 02/03/2020] [Indexed: 11/09/2022] Open
Abstract
Bacterial cyclic-di-GMP (c-di-GMP) production is associated with biofilm development and the switch from acute to chronic infections. In Pseudomonas aeruginosa, the diguanylate cyclase (DGC) SiaD and phosphatase SiaA, which are co-transcribed as part of a siaABCD operon, are essential for cellular aggregation. However, the detailed functions of this operon and the relationships among its constituent genes are unknown. Here, we demonstrate that the siaABCD operon encodes for a signaling network that regulates SiaD enzymatic activity to control biofilm and aggregates formation. Through protein-protein interaction, SiaC promotes SiaD diguanylate cyclase activity. Biochemical and structural data revealed that SiaB is an unusual protein kinase that phosphorylates SiaC, whereas SiaA phosphatase can dephosphorylate SiaC. The phosphorylation state of SiaC is critical for its interaction with SiaD, which will switch on or off the DGC activity of SiaD and regulate c-di-GMP levels and subsequent virulence phenotypes. Collectively, our data provide insights into the molecular mechanisms underlying the modulation of DGC activity associated with chronic infections, which may facilitate the development of antimicrobial drugs.
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Affiliation(s)
- Gukui Chen
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Jianhua Gan
- State Key Laboratory of Genetic Engineering, Shanghai Public Health Clinical Center, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Chun Yang
- State Key Laboratory of Genetic Engineering, Shanghai Public Health Clinical Center, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Yili Zuo
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Juan Peng
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Meng Li
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Weiping Huo
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Yingpeng Xie
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Yani Zhang
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Tietao Wang
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Xin Deng
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Haihua Liang
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
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18
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Pseudomonas aeruginosa Regulatory Protein AnvM Controls Pathogenicity in Anaerobic Environments and Impacts Host Defense. mBio 2019; 10:mBio.01362-19. [PMID: 31337721 PMCID: PMC6650552 DOI: 10.1128/mbio.01362-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Infections by Pseudomonas aeruginosa, one of the most frequently isolated human pathogens, can create huge financial burdens. However, knowledge of the molecular mechanisms involved in the pathogenesis of P. aeruginosa remains elusive. We identified AnvM as a novel regulator of virulence in P. aeruginosa. Deletion of anvM altered the expression levels of more than 700 genes under aerobic and anaerobic conditions, including quorum sensing system genes and oxidative stress resistance genes. AnvM directly interacted with MvfR and Anr, thus regulating their downstream genes. More importantly, AnvM directly bound to TLR2 and TLR5, which turn on the host immune response. These findings provide insights into the significance of AnvM homologs in pathogenic bacteria and suggest a potential drug target against bacterial infection. Pseudomonas aeruginosa, one of the most common pathogens in hospital-acquired infections, is tightly controlled by a multilayered regulatory network, including the quorum sensing system (QS), the type VI secretion system (T6SS), and resistance to host immunity. We found that the P. aeruginosa 3880 (PA3880) gene, which encodes an unknown protein, acts as a regulator of anaerobic metabolism in response to oxidative stress and virulence in P. aeruginosa. More than 30 PA3880 homologs were found in other bacterial genomes, indicating that PA3880 is widely distributed in the Bacteria kingdom as a highly conserved gene. Deletion of the PA3880 gene changed the expression levels of more than 700 genes, including a group of virulence genes, under both aerobic and anaerobic conditions. To further study the mechanisms of PA3880-mediated regulation in virulence, we utilized a bacterial two-hybrid assay and found that the PA3880 protein interacted directly with QS regulator MvfR and anaerobic regulator Anr. Loss of the PA3880 protein significantly blunted the pathogenicity of P. aeruginosa, resulting in increased host survival, decreased bacterial burdens, reduced inflammatory responses, and fewer lung injuries in challenged mice hosts. Mechanistically, we found that Cys44 was a critical site for the full function of PA3880 in influencing alveolar macrophage phagocytosis and bacterial clearance. We also found that AnvM directly interacted with host receptors Toll-like receptor 2 (TLR2) and TLR5, which might lead to activation of the host immune response. Hence, we gave the name AnvM (anaerobic and virulence modulator) to the PA3880 protein. This characterization of AnvM could help to uncover new targets and strategies to treat P. aeruginosa infections.
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19
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Fitting Pieces into the Puzzle of Pseudomonas aeruginosa Type III Secretion System Gene Expression. J Bacteriol 2019; 201:JB.00209-19. [PMID: 31010903 DOI: 10.1128/jb.00209-19] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Type III secretion systems (T3SS) are widely distributed in Gram-negative microorganisms and critical for host-pathogen and host-symbiont interactions with plants and animals. Central features of the T3SS are a highly conserved set of secretion and translocation genes and contact dependence wherein host-pathogen interactions trigger effector protein delivery and serve as an inducing signal for T3SS gene expression. In addition to these conserved features, there are pathogen-specific properties that include a unique repertoire of effector genes and mechanisms to control T3SS gene expression. The Pseudomonas aeruginosa T3SS serves as a model system to understand transcriptional and posttranscriptional mechanisms involved in the control of T3SS gene expression. The central regulatory feature is a partner-switching system that controls the DNA-binding activity of ExsA, the primary regulator of T3SS gene expression. Superimposed upon the partner-switching mechanism are cyclic AMP and cyclic di-GMP signaling systems, two-component systems, global regulators, and RNA-binding proteins that have positive and negative effects on ExsA transcription and/or synthesis. In the present review, we discuss advances in our understanding of how these regulatory systems orchestrate the activation of T3SS gene expression in the context of acute infections and repression of the T3SS as P. aeruginosa adapts to and colonizes the cystic fibrosis airways.
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20
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Regulatory protein SrpA controls phage infection and core cellular processes in Pseudomonas aeruginosa. Nat Commun 2018; 9:1846. [PMID: 29748556 PMCID: PMC5945682 DOI: 10.1038/s41467-018-04232-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 04/16/2018] [Indexed: 02/06/2023] Open
Abstract
Our understanding of the molecular mechanisms behind bacteria-phage interactions remains limited. Here we report that a small protein, SrpA, controls core cellular processes in response to phage infection and environmental signals in Pseudomonas aeruginosa. We show that SrpA is essential for efficient genome replication of phage K5, and controls transcription by binding to a palindromic sequence upstream of the phage RNA polymerase gene. We identify potential SrpA-binding sites in 66 promoter regions across the P. aeruginosa genome, and experimentally validate direct binding of SrpA to some of these sites. Using transcriptomics and further experiments, we show that SrpA, directly or indirectly, regulates many cellular processes including cell motility, chemotaxis, biofilm formation, pyocyanin synthesis and protein secretion, as well as virulence in a Caenorhabditis elegans model of infection. Further research on SrpA and similar proteins, which are widely present in many other bacteria, is warranted. You et al. show that SrpA, a small protein widely conserved among bacteria, controls core cellular processes in response to phage infection and environmental signals in Pseudomonas aeruginosa, including cell motility, chemotaxis, biofilm formation, and virulence.
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21
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Deng X, Li M, Pan X, Zheng R, Liu C, Chen F, Liu X, Cheng Z, Jin S, Wu W. Fis Regulates Type III Secretion System by Influencing the Transcription of exsA in Pseudomonas aeruginosa Strain PA14. Front Microbiol 2017; 8:669. [PMID: 28469612 PMCID: PMC5395579 DOI: 10.3389/fmicb.2017.00669] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 03/31/2017] [Indexed: 11/21/2022] Open
Abstract
Fis is a versatile DNA binding protein in bacteria. It has been demonstrated in multiple bacteria that Fis plays crucial roles in regulating bacterial virulence factors and optimizing bacterial adaptation to various environments. However, the role of Fis in Pseudomonas aeruginosa virulence as well as gene regulation remains largely unknown. Here, we found that Fis was required for the virulence of P. aeruginosa in a murine acute pneumonia model. Transcriptome analysis revealed that expression of T3SS genes, including master regulator ExsA, was defective in a fis::Tn mutant. We further demonstrate that the continuous transcription of exsC, exsE, exsB, and exsA driven by the exsC promoter was required for the activation of T3SS. Fis was found to specifically bind to the exsB-exsA intergenic region and plays an essential role in the transcription elongation from exsB to exsA. Therefore, we found a novel role of Fis in the regulation of exsA expression.
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Affiliation(s)
- Xuan Deng
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai UniversityTianjin, China
| | - Mei Li
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai UniversityTianjin, China
| | - Xiaolei Pan
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai UniversityTianjin, China
| | - Ruiping Zheng
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai UniversityTianjin, China
| | - Chang Liu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai UniversityTianjin, China
| | - Fei Chen
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai UniversityTianjin, China
| | - Xue Liu
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai UniversityTianjin, China
| | - Zhihui Cheng
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai UniversityTianjin, China
| | - Shouguang Jin
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai UniversityTianjin, China.,Department of Molecular Genetics and Microbiology, College of Medicine, University of FloridaGainesville, FL, USA
| | - Weihui Wu
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai UniversityTianjin, China
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22
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Sadiq FA, Flint S, Li Y, Liu T, Lei Y, Sakandar HA, He G. New mechanistic insights into the motile-to-sessile switch in various bacteria with particular emphasis on Bacillus subtilis and Pseudomonas aeruginosa: a review. BIOFOULING 2017; 33:306-326. [PMID: 28347177 DOI: 10.1080/08927014.2017.1304541] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 03/04/2017] [Indexed: 06/06/2023]
Abstract
A biofilm is a complex assemblage of microbial communities adhered to a biotic or an abiotic surface which is embedded within a self-produced matrix of extracellular polymeric substances. Many transcriptional regulators play a role in triggering a motile-sessile switch and in consequently producing the biofilm matrix. This review is aimed at highlighting the role of two nucleotide signaling molecules (c-di-GMP and c-di-AMP), toxin antitoxin modules and a novel transcriptional regulator BolA in biofilm formation in various bacteria. In addition, it highlights the common themes that have appeared in recent research regarding the key regulatory components and signal transduction pathways that help Bacillus subtilis and Pseudomonas aeruginosa to acquire the biofilm mode of life.
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Affiliation(s)
- Faizan A Sadiq
- a College of Biosystems Engineering and Food Science , Zhejiang University , Hangzhou , PR China
| | - Steve Flint
- b School of Food and Nutrition , Massey University , Palmerston North , New Zealand
| | - Yun Li
- c School of Life Sciences and Food Technology , Hanshan Normal University , Chaozhou , PR China
| | - TongJie Liu
- a College of Biosystems Engineering and Food Science , Zhejiang University , Hangzhou , PR China
| | - Yuan Lei
- a College of Biosystems Engineering and Food Science , Zhejiang University , Hangzhou , PR China
| | | | - GuoQing He
- a College of Biosystems Engineering and Food Science , Zhejiang University , Hangzhou , PR China
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