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Karpenko A, Shelenkov A, Manzeniuk I, Kulikova N, Gevorgyan A, Mikhaylova Y, Akimkin V. Whole genome analysis of multidrug-resistant Escherichia coli isolate collected from drinking water in Armenia revealed the plasmid-borne mcr-1.1-mediated colistin resistance. Microbiol Spectr 2024:e0075124. [PMID: 39166856 DOI: 10.1128/spectrum.00751-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 07/19/2024] [Indexed: 08/23/2024] Open
Abstract
The rate of polymyxin-resistant Enterobacteriaceae, as well as human and animal infections caused by them, is increasing worldwide, posing a high epidemiological threat since colistin represents a last-resort antibiotic to treat complicated infections. The study of environmental niches, in particular, aquatic ecosystems in terms of genome analysis of inhabiting antimicrobial-resistant (AMR) microorganisms as reservoirs of acquired resistance determinants (AMR genes), represents a specific concern from a One Health approach. Here, we present a phenotypic AMR analysis and molecular characterization of Escherichia coli isolate found in municipal drinking water after an accident in the water supply system of a residential building in Armenia in 2021. CrieF1144 E. coli isolate was resistant to ampicillin, ampicillin/sulbactam, cefuroxime, ciprofloxacin, levofloxacin, trimethoprim/sulfamethoxazole, colistin, and tigecycline, whereas whole genome sequencing (WGS) revealed blaTEM-1B, tet(A), and a combination of dfrA14 with sul1 resistance determinants, which corresponds well with phenotypic resistance above. Moreover, the multidrug-resistant isolate studied harbored mcr-1.1 gene on a conjugative 251 Kb IncHI2 plasmid, whose structure was determined using hybrid short- and long-reads assembly. CrieF1141_p1 plasmid carried all antimicrobial resistance genes revealed in the isolate and did not harbor any virulence determinants, so it could contribute to the spread of AMR genes in the bacterial population. Two copies of ISApl1 transposase-encoding element, which is likely to mediate mcr-1.1 gene mobilization, were revealed surrounding this gene in a plasmid. IMPORTANCE Evolutionary patterns of Escherichia coli show that they usually develop into highly pathogenic forms by acquiring fitness advantages such as antimicrobial resistance (AMR) and various virulence factors through horizontal gene transfer mediated by mobile elements. This has led to high prevalence of multidrug-resistant (MDR) strains, which highlights the relevancy of enhanced surveillance to monitor and prevent transmission of the MDR bacteria to human and animal populations. However, the limited number of reports regarding the whole genome sequencing (WGS) investigation of MDR E. coli strains isolated from drinking water and harboring mcr genes hampers the adoption of a comprehensive approach to address the relationship between environmental E. coli populations and human and veterinary infections. Our results highlight the relevance of analyzing the environment, especially water, as a part of the surveillance programs to understand the origins and dissemination of antimicrobial resistance within the One Health concept.
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Affiliation(s)
- Anna Karpenko
- Department of Molecular Diagnostics and Epidemiology, Central Research Institute of Epidemiology, Moscow, Russia
| | - Andrey Shelenkov
- Department of Molecular Diagnostics and Epidemiology, Central Research Institute of Epidemiology, Moscow, Russia
| | - Igor Manzeniuk
- Administrative and Management Department - Directorate, Central Research Institute of Epidemiology, Moscow, Russia
| | - Nina Kulikova
- Department of Molecular Diagnostics and Epidemiology, Central Research Institute of Epidemiology, Moscow, Russia
| | - Arman Gevorgyan
- Republican Veterinary and Phytosanitary Laboratory Services Center, Yerevan, Armenia
| | - Yulia Mikhaylova
- Department of Molecular Diagnostics and Epidemiology, Central Research Institute of Epidemiology, Moscow, Russia
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Che S, Sun C, Yang L, Zhou M, Xia L, Yan J, Jiang M, Wang J, Wang H, Zhao W, Toth I, Hu B, Guo T, Fan J. T6SS and T4SS Redundantly Secrete Effectors to Govern the Virulence and Bacterial Competition in Pectobacterium PccS1. PHYTOPATHOLOGY 2024; 114:1926-1939. [PMID: 38749069 DOI: 10.1094/phyto-11-23-0455-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/06/2024]
Abstract
Previous studies revealed that the type VI secretion system (T6SS) has an essential role in bacterial competition and virulence in many gram-negative bacteria. However, the role of T6SS in virulence in Pectobacterium atrosepticum remains controversial. We examined a closely related strain, PccS1, and discovered that its T6SS comprises a single-copy cluster of 17 core genes with a higher identity to homologs from P. atrosepticum. Through extensive phenotypic and functional analyses of over 220 derivatives of PccS1, we found that three of the five VgrGs could be classified into group I VgrGs. These VgrGs interacted with corresponding DUF4123 domain proteins, which were secreted outside of the membrane and were dependent on either the T6SS or type IV secretion system (T4SS). This interaction directly governed virulence and competition. Meanwhile, supernatant proteomic analyses with strains defective in the T6SS and/or T4SS confirmed that effectors, such as FhaB, were secreted redundantly to control the virulence and suppress host callose deposition in the course of infection. Notably, this redundant secretion mechanism between the T6SS and T4SS is believed to be the first of its kind in bacteria.
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Affiliation(s)
- Shu Che
- Laboratory of Bacteriology, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- Cell and Molecular Science, James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
| | - Chen Sun
- Laboratory of Bacteriology, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Liuke Yang
- Laboratory of Bacteriology, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Min Zhou
- Laboratory of Bacteriology, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Lingyan Xia
- Laboratory of Bacteriology, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jingyuan Yan
- Laboratory of Bacteriology, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Mengyi Jiang
- Laboratory of Bacteriology, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiaju Wang
- Laboratory of Bacteriology, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Huan Wang
- Laboratory of Bacteriology, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- Cell and Molecular Science, James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
- Institute of Agricultural Science of Suzhou, Taihu Lake District, Suzhou 215155, China
| | - Wenjun Zhao
- CAIQ Center for Biosafety, Sanya 572024, China
| | - Ian Toth
- Cell and Molecular Science, James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
| | - Baishi Hu
- Laboratory of Bacteriology, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Tao Guo
- Southern Breeding Administrate Office of Hainan Province, Sanya 572000, China
| | - Jiaqin Fan
- Laboratory of Bacteriology, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
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Gupta S, Biswas P, Das B, Mondal S, Gupta P, Das D, Mallick AI. Selective depletion of Campylobacter jejuni via T6SS dependent functionality: an approach for improving chickens gut health. Gut Pathog 2024; 16:38. [PMID: 38997758 PMCID: PMC11245787 DOI: 10.1186/s13099-024-00628-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 06/28/2024] [Indexed: 07/14/2024] Open
Abstract
The targeted depletion of potential gut pathogens is often challenging because of their intrinsic ability to thrive in harsh gut environments. Earlier, we showed that Campylobacter jejuni (C. jejuni) exclusively uses the Type-VI Secretion System (T6SS) to target its prey such as Escherichia coli (E. coli), and phenotypic differences between T6SS-negative and T6SS-positive C. jejuni isolates toward bile salt sensitivity. However, it remains unclear how the target-driven T6SS functionality prevails in a polymicrobial gut environment. Here, we investigated the fate of microbial competition in an altered gut environment via bacterial T6SS using a T6SS-negative and -positive C. jejuni or its isogenic mutant of the hemolysin-coregulated protein (hcp). We showed that in the presence of bile salt and prey bacteria (E. coli), T6SS-positive C. jejuni experiences enhanced intracellular stress leading to cell death. Intracellular tracking of fluorophore-conjugated bile salts confirmed that T6SS-mediated bile salt influx into C. jejuni can enhance intracellular oxidative stress, affecting C. jejuni viability. We further investigated whether the T6SS activity in the presence of prey (E. coli) perturbs the in vivo colonization of C. jejuni. Using chickens as primary hosts of C. jejuni and non-pathogenic E. coli as prey, we showed a marked reduction of C. jejuni load in chickens cecum when bile salt solution was administered orally. Analysis of local antibody responses and pro-inflammatory gene expression showed a reduced risk of tissue damage, indicating that T6SS activity in the complex gut environment can be exploited as a possible measure to clear the persistent colonization of C. jejuni in chickens.
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Affiliation(s)
- Subhadeep Gupta
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, West Bengal, 741246, India
| | - Prakash Biswas
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, West Bengal, 741246, India
| | - Bishnu Das
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, West Bengal, 741246, India
| | - Samiran Mondal
- Department of Veterinary Pathology, West Bengal University of Animal and Fishery Sciences, Kolkata, West Bengal, 700037, India
| | - Parna Gupta
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, West Bengal, 741246, India
| | - Dipjyoti Das
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, West Bengal, 741246, India.
| | - Amirul Islam Mallick
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, West Bengal, 741246, India.
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Huang Q, Zhang M, Zhang Y, Li X, Luo X, Ji S, Lu R. IcmF2 of the type VI secretion system 2 plays a role in biofilm formation of Vibrio parahaemolyticus. Arch Microbiol 2024; 206:321. [PMID: 38907796 DOI: 10.1007/s00203-024-04060-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 06/24/2024]
Abstract
Vibrio parahaemolyticus possesses two distinct type VI secretion systems (T6SS), namely T6SS1 and T6SS2. T6SS1 is predominantly responsible for adhesion to Caco-2 and HeLa cells and for the antibacterial activity of V. parahaemolyticus, while T6SS2 mainly contributes to HeLa cell adhesion. However, it remains unclear whether the T6SS systems have other physiological roles in V. parahaemolyticus. In this study, we demonstrated that the deletion of icmF2, a structural gene of T6SS2, reduced the biofilm formation capacity of V. parahaemolyticus under low salt conditions, which was also influenced by the incubation time. Nonetheless, the deletion of icmF2 did not affect the biofilm formation capacity in marine-like growth conditions, nor did it impact the flagella-driven swimming and swarming motility of V. parahaemolyticus. IcmF2 was found to promote the production of the main components of the biofilm matrix, including extracellular DNA (eDNA) and extracellular proteins, and cyclic di-GMP (c-di-GMP) in V. parahaemolyticus. Additionally, IcmF2 positively influenced the transcription of cpsA, mfpA, and several genes involved in c-di-GMP metabolism, including scrJ, scrL, vopY, tpdA, gefA, and scrG. Conversely, the transcription of scrA was negatively impacted by IcmF2. Therefore, IcmF2-dependent biofilm formation was mediated through its effects on the production of eDNA, extracellular proteins, and c-di-GMP, as well as its impact on the transcription of cpsA, mfpA, and genes associated with c-di-GMP metabolism. This study confirmed new physiological roles for IcmF2 in promoting biofilm formation and c-di-GMP production in V. parahaemolyticus.
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Affiliation(s)
- Qinglian Huang
- Department of Clinical Laboratory, Qidong People's Hospital, Qidong, Jiangsu, 226200, China
- Department of Clinical Laboratory, Nantong Third People's Hospital, Affiliated Nantong Hospital 3 of Nantong University, Nantong, Jiangsu, 226006, China
| | - Miaomiao Zhang
- Department of Clinical Laboratory, Nantong Third People's Hospital, Affiliated Nantong Hospital 3 of Nantong University, Nantong, Jiangsu, 226006, China
| | - Yiquan Zhang
- Department of Clinical Laboratory, Nantong Third People's Hospital, Affiliated Nantong Hospital 3 of Nantong University, Nantong, Jiangsu, 226006, China.
| | - Xue Li
- Department of Clinical Laboratory, Nantong Third People's Hospital, Affiliated Nantong Hospital 3 of Nantong University, Nantong, Jiangsu, 226006, China
| | - Xi Luo
- Department of Clinical Laboratory, Nantong Third People's Hospital, Affiliated Nantong Hospital 3 of Nantong University, Nantong, Jiangsu, 226006, China
| | - Shenjie Ji
- Department of Clinical Laboratory, Qidong People's Hospital, Qidong, Jiangsu, 226200, China.
| | - Renfei Lu
- Department of Clinical Laboratory, Nantong Third People's Hospital, Affiliated Nantong Hospital 3 of Nantong University, Nantong, Jiangsu, 226006, China.
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Viñes J, Lopera C, Vergara A, Roca I, Vila J, Casals-Pascual C, Martínez JA, García-Vidal C, Soriano A, Pitart C. Emergence of carbapenem-resistant Pseudomonas aeruginosa ST179 producing both IMP-16 and KPC-2: a case study of introduction from Peru to Spain. Microbiol Spectr 2024; 12:e0061424. [PMID: 38727230 PMCID: PMC11237478 DOI: 10.1128/spectrum.00614-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 04/24/2024] [Indexed: 06/06/2024] Open
Abstract
We describe four cases of a novel carbapenem-resistant Pseudomonas aeruginosa ST179 clone carrying the blaKPC-2 or blaKPC-35 gene together with blaIMP-16, imported from Peru to Spain and isolated from leukemia patients. All isolates were multidrug-resistant but remained susceptible to fosfomycin, cefiderocol, and colistin. Whole-genome sequencing revealed that blaKPC-2 and blaKPC-35 were located in an IncP6 plasmid, whereas blaIMP-16 was in a chromosomal type 1 integron. This study highlights the global threat of multidrug-resistant P. aeruginosa clones and underscores the importance of monitoring and early detection of emerging resistance mechanisms to guide appropriate treatment strategies. The importation and spread of such clones emphasize the urgent need to implement strict infection control measures to prevent the dissemination of carbapenem-resistant bacteria. IMPORTANCE This is the first documented case of a Pseudomonas aeruginosa ST179 strain carrying the blaKPC-35 gene, and it represents the first report of a P. aeruginosa co-harboring blaIMP-16 and either blaKPC-2 or blaKPC-35, which wre imported from Peru to Spain, highlighting a threat due to the capacity of spreading carbapenem-resistance via plasmid conjugation.
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Affiliation(s)
- Joaquim Viñes
- Servei de Microbiologia i Parasitologia-CDB, Hospital Clínic de Barcelona, Barcelona, Spain
- Institut de Salut Global (ISGlobal), Barcelona, Spain
- Servei Veterinari de Genètica Molecular (SVGM), Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Carlos Lopera
- Departament de Malalties Infeccioses, Hospital Clínic de Barcelona, Barcelona, Spain
| | - Andrea Vergara
- Servei de Microbiologia i Parasitologia-CDB, Hospital Clínic de Barcelona, Barcelona, Spain
- Institut de Salut Global (ISGlobal), Barcelona, Spain
- Departament de Fonaments Clínics, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Barcelona, Spain
- CIBER Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Ignasi Roca
- Servei de Microbiologia i Parasitologia-CDB, Hospital Clínic de Barcelona, Barcelona, Spain
- Institut de Salut Global (ISGlobal), Barcelona, Spain
- Departament de Fonaments Clínics, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Barcelona, Spain
- CIBER Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Jordi Vila
- Servei de Microbiologia i Parasitologia-CDB, Hospital Clínic de Barcelona, Barcelona, Spain
- Institut de Salut Global (ISGlobal), Barcelona, Spain
- Departament de Fonaments Clínics, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Barcelona, Spain
- CIBER Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Climent Casals-Pascual
- Servei de Microbiologia i Parasitologia-CDB, Hospital Clínic de Barcelona, Barcelona, Spain
- Institut de Salut Global (ISGlobal), Barcelona, Spain
- Departament de Fonaments Clínics, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Barcelona, Spain
- CIBER Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - José Antonio Martínez
- Departament de Malalties Infeccioses, Hospital Clínic de Barcelona, Barcelona, Spain
- Departament de Fonaments Clínics, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Barcelona, Spain
- CIBER Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Carolina García-Vidal
- Departament de Malalties Infeccioses, Hospital Clínic de Barcelona, Barcelona, Spain
- Departament de Fonaments Clínics, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Barcelona, Spain
- CIBER Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Alex Soriano
- Departament de Malalties Infeccioses, Hospital Clínic de Barcelona, Barcelona, Spain
- Departament de Fonaments Clínics, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Barcelona, Spain
- CIBER Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Cristina Pitart
- Servei de Microbiologia i Parasitologia-CDB, Hospital Clínic de Barcelona, Barcelona, Spain
- Institut de Salut Global (ISGlobal), Barcelona, Spain
- Departament de Fonaments Clínics, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Barcelona, Spain
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Yoon JB, Yoon Y, Park JW, Yerke AM, Jaiswal YS, Williams LL, Hwang S, Moon KH. Effect of polystyrene nanoplastics exposure on gene expression and pathogenesis of zoonotic pathogen, Edwardsiella piscicida. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 272:116057. [PMID: 38335574 DOI: 10.1016/j.ecoenv.2024.116057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/15/2024] [Accepted: 01/28/2024] [Indexed: 02/12/2024]
Abstract
A surge in the number of anthropogenic pollutants has been caused by increasing industrial activities. Nanoplastics are spotlighted as a new aquatic pollutant that are a threat to microbes and larger organisms. Our previous study showed that the subinhibitory concentrations of aquatic pollutants such as phenol and formalin act as signaling molecules and modulate global gene expression and metabolism. In this study, we aimed to investigate the impact of a new type of anthropogenic contaminant, polystyrene (PS) nanoplastics, on the expression of key virulence factors in zoonotic pathogen Edwardsiella piscicida and the assessment of potential changes in the susceptibility of zebrafish as a model host. The TEM data indicated a noticeable change in the cell membrane indicating that PS particles were possibly entering the bacterial cells. Transcriptome analyses performed to identify the differentially expressed genes upon PS exposure revealed that the genes involved in major virulence factor type VI secretion system (T6SS) were down-regulated. However, the expression of T6SS-related genes was recovered from the PS adapted E. piscicida when nanoplastics are free. This demonstrated the hypervirulence of pathogen in infection assays with both cell lines and in vivo zebrafish model. Therefore, this study provides experimental evidence elucidating the direct regulatory impact of nanoplastics influx into aquatic ecosystems on fish pathogenic bacteria, notably influencing the expression of virulence factors.
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Affiliation(s)
- Ju Bin Yoon
- Laboratory of Marine Microbiology, Division of Convergence on Marine Science, National Korea Maritime and Ocean University, Busan 49112, South Korea; Department of Convergence Study on the Ocean Science and Technology, Ocean Science and Technology School, National Korea Maritime and Ocean University, Busan 49112, South Korea
| | - Yongjoon Yoon
- Laboratory of Marine Microbiology, Division of Convergence on Marine Science, National Korea Maritime and Ocean University, Busan 49112, South Korea; Department of Marine Bioscience and Environment, National Korea Maritime and Ocean University, Busan 49112, South Korea
| | - Jeong Woo Park
- Laboratory of Marine Microbiology, Division of Convergence on Marine Science, National Korea Maritime and Ocean University, Busan 49112, South Korea; Department of Convergence Study on the Ocean Science and Technology, Ocean Science and Technology School, National Korea Maritime and Ocean University, Busan 49112, South Korea
| | - Aaron M Yerke
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Yogini S Jaiswal
- Center for Excellence in Post Harvest Technologies, North Carolina Agricultural and Technical State University, The North Carolina Research Campus, 500 Laureate Way, Kannapolis, NC 28081, USA
| | - Leonard L Williams
- Center for Excellence in Post Harvest Technologies, North Carolina Agricultural and Technical State University, The North Carolina Research Campus, 500 Laureate Way, Kannapolis, NC 28081, USA
| | - Sungmin Hwang
- Division of Practical Research, Honam National Institute Biological Resources, Mokpo-si 58762, South Korea.
| | - Ki Hwan Moon
- Laboratory of Marine Microbiology, Division of Convergence on Marine Science, National Korea Maritime and Ocean University, Busan 49112, South Korea; Department of Convergence Study on the Ocean Science and Technology, Ocean Science and Technology School, National Korea Maritime and Ocean University, Busan 49112, South Korea; Department of Marine Bioscience and Environment, National Korea Maritime and Ocean University, Busan 49112, South Korea.
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MacGillivray KA, Ng SL, Wiesenfeld S, Guest RL, Jubery T, Silhavy TJ, Ratcliff WC, Hammer BK. Trade-offs constrain adaptive pathways to the type VI secretion system survival. iScience 2023; 26:108332. [PMID: 38025790 PMCID: PMC10679819 DOI: 10.1016/j.isci.2023.108332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 08/25/2023] [Accepted: 10/22/2023] [Indexed: 12/01/2023] Open
Abstract
The Type VI Secretion System (T6SS) is a nano-harpoon used by many bacteria to inject toxins into neighboring cells. While much is understood about mechanisms of T6SS-mediated toxicity, less is known about the ways that competitors can defend themselves against this attack, especially in the absence of their own T6SS. Here we subjected eight replicate populations of Escherichia coli to T6SS attack by Vibrio cholerae. Over ∼500 generations of competition, isolates of the E. coli populations evolved to survive T6SS attack an average of 27-fold better, through two convergently evolved pathways: apaH was mutated in six of the eight replicate populations, while the other two populations each had mutations in both yejM and yjeP. However, the mutations we identified are pleiotropic, reducing cellular growth rates, and increasing susceptibility to antibiotics and elevated pH. These trade-offs help us understand how the T6SS shapes the evolution of bacterial interactions.
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Affiliation(s)
- Kathryn A. MacGillivray
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Parker H. Petit Institute for Bioengineering & Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
| | - Siu Lung Ng
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Parker H. Petit Institute for Bioengineering & Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
| | - Sophia Wiesenfeld
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Parker H. Petit Institute for Bioengineering & Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
| | - Randi L. Guest
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Tahrima Jubery
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Parker H. Petit Institute for Bioengineering & Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
| | - Thomas J. Silhavy
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - William C. Ratcliff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Parker H. Petit Institute for Bioengineering & Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
| | - Brian K. Hammer
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Parker H. Petit Institute for Bioengineering & Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
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Srinivasan A, Sajeevan A, Rajaramon S, David H, Solomon AP. Solving polymicrobial puzzles: evolutionary dynamics and future directions. Front Cell Infect Microbiol 2023; 13:1295063. [PMID: 38145044 PMCID: PMC10748482 DOI: 10.3389/fcimb.2023.1295063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 11/03/2023] [Indexed: 12/26/2023] Open
Abstract
Polymicrobial infections include various microorganisms, often necessitating different treatment methods than a monomicrobial infection. Scientists have been puzzled by the complex interactions within these communities for generations. The presence of specific microorganisms warrants a chronic infection and impacts crucial factors such as virulence and antibiotic susceptibility. Game theory is valuable for scenarios involving multiple decision-makers, but its relevance to polymicrobial infections is limited. Eco-evolutionary dynamics introduce causation for multiple proteomic interactions like metabolic syntropy and niche segregation. The review culminates both these giants to form evolutionary dynamics (ED). There is a significant amount of literature on inter-bacterial interactions that remain unsynchronised. Such raw data can only be moulded by analysing the ED involved. The review culminates the inter-bacterial interactions in multiple clinically relevant polymicrobial infections like chronic wounds, CAUTI, otitis media and dental carries. The data is further moulded with ED to analyse the niche colonisation of two notoriously competitive bacteria: S.aureus and P.aeruginosa. The review attempts to develop a future trajectory for polymicrobial research by following recent innovative strategies incorporating ED to curb polymicrobial infections.
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Affiliation(s)
| | | | | | | | - Adline Princy Solomon
- Quorum Sensing Laboratory, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
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Maurya S, Arya CK, Parmar N, Sathyanarayanan N, Joshi CG, Ramanathan G. Genomic profiling and characteristics of a C1 degrading heterotrophic fresh-water bacterium Paracoccus sp. strain DMF. Arch Microbiol 2023; 206:6. [PMID: 38015256 DOI: 10.1007/s00203-023-03729-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/29/2023]
Abstract
Paracoccus species are metabolically versatile gram-negative, aerobic facultative methylotrophic bacteria showing enormous promise for environmental and bioremediation studies. Here we report, the complete genome analysis of Paracoccus sp. strain DMF (P. DMF) that was isolated from a domestic wastewater treatment plant in Kanpur, India (26.4287 °N, 80.3891 °E) based on its ability to degrade a recalcitrant organic solvent N, N-dimethylformamide (DMF). The results reveal a genome size of 4,202,269 base pairs (bp) with a G + C content of 67.9%. The assembled genome comprises 4141 coding sequences (CDS), 46 RNA sequences, and 2 CRISPRs. Interestingly, catabolic operons related to the conventional marine-based methylated amines (MAs) degradation pathway were functionally annotated within the genome of an obligated aerobic heterotroph that is P. DMF. The genomic data-based characterization presented here for the novel heterotroph P. DMF aims to improve the understanding of the phenotypic gene products, enzymes, and pathways involved with greater emphasis on facultative methylotrophic motility-based latent pathogenicity.
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Affiliation(s)
- Shiwangi Maurya
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India
| | - Chetan Kumar Arya
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India
| | - Nidhi Parmar
- Gujarat Biotechnology Research Centre (GBRC), Gandhinagar, Gujarat, 382 011, India
| | - Nitish Sathyanarayanan
- Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, 560065, India
| | - Chaitanya G Joshi
- Gujarat Biotechnology Research Centre (GBRC), Gandhinagar, Gujarat, 382 011, India
| | - Gurunath Ramanathan
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India.
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10
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Dreyer A, Lenz C, Groß U, Bohne W, Zautner AE. Characterization of Campylobacter jejuni proteome profiles in co-incubation scenarios. Front Microbiol 2023; 14:1247211. [PMID: 38029072 PMCID: PMC10666060 DOI: 10.3389/fmicb.2023.1247211] [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: 06/28/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023] Open
Abstract
In dynamic microbial ecosystems, bacterial communication is a relevant mechanism for interactions between different microbial species. When C. jejuni resides in the intestine of either avian or human hosts, it is exposed to diverse bacteria from the microbiome. This study aimed to reveal the influence of co-incubation with Enterococcus faecalis, Enterococcus faecium, or Staphylococcus aureus on the proteome of C. jejuni 81-176 using data-independent-acquisition mass spectrometry (DIA-MS). We compared the proteome profiles during co-incubation with the proteome profile in response to the bile acid deoxycholate (DCA) and investigated the impact of DCA on proteomic changes during co-incubation, as C. jejuni is exposed to both factors during colonization. We identified 1,375 proteins by DIA-MS, which is notably high, approaching the theoretical maximum of 1,645 proteins. S. aureus had the highest impact on the proteome of C. jejuni with 215 up-regulated and 230 down-regulated proteins. However, these numbers are still markedly lower than the 526 up-regulated and 516 down-regulated proteins during DCA exposure. We identified a subset of 54 significantly differentially expressed proteins that are shared after co-incubation with all three microbial species. These proteins were indicative of a common co-incubation response of C. jejuni. This common proteomic response partly overlapped with the DCA response; however, several proteins were specific to the co-incubation response. In the co-incubation experiment, we identified three membrane-interactive proteins among the top 20 up-regulated proteins. This finding suggests that the presence of other bacteria may contribute to increased adherence, e.g., to other bacteria but eventually also epithelial cells or abiotic surfaces. Furthermore, a conjugative transfer regulon protein was typically up-expressed during co-incubation. Exposure to both, co-incubation and DCA, demonstrated that the two stressors influenced each other, resulting in a unique synergistic proteomic response that differed from the response to each stimulus alone. Data are available via ProteomeXchange with identifier PXD046477.
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Affiliation(s)
- Annika Dreyer
- Institute for Medical Microbiology and Virology, University Medical Center Göttingen, Göttingen, Germany
| | - Christof Lenz
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Department of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Uwe Groß
- Institute for Medical Microbiology and Virology, University Medical Center Göttingen, Göttingen, Germany
| | - Wolfgang Bohne
- Institute for Medical Microbiology and Virology, University Medical Center Göttingen, Göttingen, Germany
| | - Andreas Erich Zautner
- Institute for Medical Microbiology and Virology, University Medical Center Göttingen, Göttingen, Germany
- Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
- Center for Health and Medical Prevention (CHaMP), Otto-von-Guericke University Magdeburg, Magdeburg, Germany
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11
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Bourigault Y, Dupont CA, Desjardins JB, Doan T, Bouteiller M, Le Guenno H, Chevalier S, Barbey C, Latour X, Cascales E, Merieau A. Pseudomonas fluorescens MFE01 delivers a putative type VI secretion amidase that confers biocontrol against the soft-rot pathogen Pectobacterium atrosepticum. Environ Microbiol 2023; 25:2564-2579. [PMID: 37622480 DOI: 10.1111/1462-2920.16492] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 08/15/2023] [Indexed: 08/26/2023]
Abstract
The type VI secretion system (T6SS) is a contractile nanomachine widespread in Gram-negative bacteria. The T6SS injects effectors into target cells including eukaryotic hosts and competitor microbial cells and thus participates in pathogenesis and intermicrobial competition. Pseudomonas fluorescens MFE01 possesses a single T6SS gene cluster that confers biocontrol properties by protecting potato tubers against the phytopathogen Pectobacterium atrosepticum (Pca). Here, we demonstrate that a functional T6SS is essential to protect potato tuber by reducing the pectobacteria population. Fluorescence microscopy experiments showed that MFE01 displays an aggressive behaviour with an offensive T6SS characterized by continuous and intense T6SS firing activity. Interestingly, we observed that T6SS firing is correlated with rounding of Pectobacterium cells, suggesting delivery of a potent cell wall targeting effector. Mutagenesis coupled with functional assays then revealed that a putative T6SS secreted amidase, Tae3Pf , is mainly responsible for MFE01 toxicity towards Pca. Further studies finally demonstrated that Tae3Pf is toxic when produced in the periplasm, and that its toxicity is counteracted by the Tai3Pf inner membrane immunity protein.
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Affiliation(s)
- Yvann Bourigault
- Laboratoire de Communication Bactérienne et Stratégies Anti-infectieuses (CBSA, UR 4312), Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, Rouen, France
- Structure Fédérative de Recherche Normandie Végétale, NORVEGE Fed4277, Mont-Saint-Aignan, France
| | - Charly A Dupont
- Laboratoire de Communication Bactérienne et Stratégies Anti-infectieuses (CBSA, UR 4312), Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, Rouen, France
- Structure Fédérative de Recherche Normandie Végétale, NORVEGE Fed4277, Mont-Saint-Aignan, France
| | - Jonas B Desjardins
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM, UMR 7255), Institut de Microbiologie de la Méditerranée (IMM, FR3479), CNRS-Aix-Marseille Univ, Marseille, France
| | - Thierry Doan
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM, UMR 7255), Institut de Microbiologie de la Méditerranée (IMM, FR3479), CNRS-Aix-Marseille Univ, Marseille, France
| | - Mathilde Bouteiller
- Laboratoire de Communication Bactérienne et Stratégies Anti-infectieuses (CBSA, UR 4312), Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, Rouen, France
- Structure Fédérative de Recherche Normandie Végétale, NORVEGE Fed4277, Mont-Saint-Aignan, France
| | - Hugo Le Guenno
- Plateforme de Microscopie, Institut de Microbiologie de la Méditerranée (IMM, FR3479), CNRS-Aix-Marseille Univ, Marseille, France
| | - Sylvie Chevalier
- Laboratoire de Communication Bactérienne et Stratégies Anti-infectieuses (CBSA, UR 4312), Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, Rouen, France
| | - Corinne Barbey
- Laboratoire de Communication Bactérienne et Stratégies Anti-infectieuses (CBSA, UR 4312), Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, Rouen, France
- Structure Fédérative de Recherche Normandie Végétale, NORVEGE Fed4277, Mont-Saint-Aignan, France
| | - Xavier Latour
- Laboratoire de Communication Bactérienne et Stratégies Anti-infectieuses (CBSA, UR 4312), Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, Rouen, France
- Structure Fédérative de Recherche Normandie Végétale, NORVEGE Fed4277, Mont-Saint-Aignan, France
| | - Eric Cascales
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM, UMR 7255), Institut de Microbiologie de la Méditerranée (IMM, FR3479), CNRS-Aix-Marseille Univ, Marseille, France
| | - Annabelle Merieau
- Laboratoire de Communication Bactérienne et Stratégies Anti-infectieuses (CBSA, UR 4312), Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, Rouen, France
- Structure Fédérative de Recherche Normandie Végétale, NORVEGE Fed4277, Mont-Saint-Aignan, France
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12
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Anand A, Falquet L, Abou-Mansour E, L'Haridon F, Keel C, Weisskopf L. Biological hydrogen cyanide emission globally impacts the physiology of both HCN-emitting and HCN-perceiving Pseudomonas. mBio 2023; 14:e0085723. [PMID: 37650608 PMCID: PMC10653877 DOI: 10.1128/mbio.00857-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 07/11/2023] [Indexed: 09/01/2023] Open
Abstract
IMPORTANCE Bacteria communicate by exchanging chemical signals, some of which are volatile and can remotely reach other organisms. HCN was one of the first volatiles discovered to severely impact exposed organisms by inhibiting their respiration. Using HCN-deficient mutants in two Pseudomonas strains, we demonstrate that HCN's impact goes beyond the sole inhibition of respiration and affects both emitting and receiving bacteria in a global way, modulating their motility, biofilm formation, and production of antimicrobial compounds. Our data suggest that bacteria could use HCN not only to control their own cellular functions, but also to remotely influence the behavior of other bacteria sharing the same environment. Since HCN emission occurs in both clinically and environmentally relevant Pseudomonas, these findings are important to better understand or even modulate the expression of bacterial traits involved in both virulence of opportunistic pathogens and in biocontrol efficacy of plant-beneficial strains.
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Affiliation(s)
- Abhishek Anand
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Laurent Falquet
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | | | - Christoph Keel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Laure Weisskopf
- Department of Biology, University of Fribourg, Fribourg, Switzerland
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13
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Goodyear MC, Seidel L, Krieger JR, Geddes-McAlister J, Levesque RC, Khursigara CM. Quantitative proteomics reveals unique responses to antimicrobial treatments in clinical Pseudomonas aeruginosa isolates. mSystems 2023; 8:e0049123. [PMID: 37623324 PMCID: PMC10654054 DOI: 10.1128/msystems.00491-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 07/05/2023] [Indexed: 08/26/2023] Open
Abstract
IMPORTANCE Pseudomonas aeruginosa is an important pathogen often associated with hospital-acquired infections and chronic lung infections in people with cystic fibrosis. P. aeruginosa possesses a wide array of intrinsic and adaptive mechanisms of antibiotic resistance, and the regulation of these mechanisms is complex. Label-free quantitative proteomics is a powerful tool to compare susceptible and resistant strains of bacteria and their responses to antibiotic treatments. Here we compare the proteomes of three isolates of P. aeruginosa with different antibiotic resistance profiles in response to five challenge conditions. We uncover unique and shared proteome changes for the widely used laboratory strain PAO1 and two isolates of the Liverpool epidemic strain of P. aeruginosa, LESlike1 and LESB58. Our data set provides insight into antibiotic resistance in clinically relevant Pseudomonas isolates and highlights proteins, including those with uncharacterized functions, which can be further investigated for their role in adaptive responses to antibiotic treatments.
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Affiliation(s)
- Mara C. Goodyear
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Laura Seidel
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | | | | | - Roger C. Levesque
- Institut de biologie integrative et des systems (IBIS), Département de microbiologie-infectiologie et d'immunologie, Université Laval, Laval, Quebec, Canada
| | - Cezar M. Khursigara
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
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14
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Dupont CA, Bourigault Y, Osmond T, Nier M, Barbey C, Latour X, Konto-Ghiorghi Y, Verdon J, Merieau A. Pseudomonas fluorescens MFE01 uses 1-undecene as aerial communication molecule. Front Microbiol 2023; 14:1264801. [PMID: 37908545 PMCID: PMC10614000 DOI: 10.3389/fmicb.2023.1264801] [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: 07/21/2023] [Accepted: 09/27/2023] [Indexed: 11/02/2023] Open
Abstract
Bacterial communication is a fundamental process used to synchronize gene expression and collective behavior among the bacterial population. The most studied bacterial communication system is quorum sensing, a cell density system, in which the concentration of inductors increases to a threshold level allowing detection by specific receptors. As a result, bacteria can change their behavior in a coordinated way. While in Pseudomonas quorum sensing based on the synthesis of N-acyl homoserine lactone molecules is well studied, volatile organic compounds, although considered to be communication signals in the rhizosphere, are understudied. The Pseudomonas fluorescens MFE01 strain has a very active type six secretion system that can kill some competitive bacteria. Furthermore, MFE01 emits numerous volatile organic compounds, including 1-undecene, which contributes to the aerial inhibition of Legionella pneumophila growth. Finally, MFE01 appears to be deprived of N-acyl homoserine lactone synthase. The main objective of this study was to explore the role of 1-undecene in the communication of MFE01. We constructed a mutant affected in undA gene encoding the enzyme responsible for 1-undecene synthesis to provide further insight into the role of 1-undecene in MFE01. First, we studied the impacts of this mutation both on volatile organic compounds emission, using headspace solid-phase microextraction combined with gas chromatography-mass spectrometry and on L. pneumophila long-range inhibition. Then, we analyzed influence of 1-undecene on MFE01 coordinated phenotypes, including type six secretion system activity and biofilm formation. Next, to test the ability of MFE01 to synthesize N-acyl homoserine lactones in our conditions, we investigated in silico the presence of corresponding genes across the MFE01 genome and we exposed its biofilms to an N-acyl homoserine lactone-degrading enzyme. Finally, we examined the effects of 1-undecene emission on MFE01 biofilm maturation and aerial communication using an original experimental set-up. This study demonstrated that the ΔundA mutant is impaired in biofilm maturation. An exposure of the ΔundA mutant to the volatile compounds emitted by MFE01 during the biofilm development restored the biofilm maturation process. These findings indicate that P. fluorescens MFE01 uses 1-undecene emission for aerial communication, reporting for the first time this volatile organic compound as bacterial intraspecific communication signal.
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Affiliation(s)
- Charly A. Dupont
- Laboratoire de Communication Bactérienne et Stratégies Anti-infectieuses (CBSA UR), Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, Rouen, France
- Structure Fédérative de Recherche Normandie Végétale and Entente Franco-Québécoise NOR-SEVE, NORVEGE, Rouen, France
| | - Yvann Bourigault
- Laboratoire de Communication Bactérienne et Stratégies Anti-infectieuses (CBSA UR), Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, Rouen, France
- Structure Fédérative de Recherche Normandie Végétale and Entente Franco-Québécoise NOR-SEVE, NORVEGE, Rouen, France
| | - Théo Osmond
- Laboratoire de Communication Bactérienne et Stratégies Anti-infectieuses (CBSA UR), Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, Rouen, France
- Structure Fédérative de Recherche Normandie Végétale and Entente Franco-Québécoise NOR-SEVE, NORVEGE, Rouen, France
| | - Maëva Nier
- Laboratoire Ecologie and Biologie des Interactions, Université de Poitiers, Poitiers, France
| | - Corinne Barbey
- Laboratoire de Communication Bactérienne et Stratégies Anti-infectieuses (CBSA UR), Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, Rouen, France
- Structure Fédérative de Recherche Normandie Végétale and Entente Franco-Québécoise NOR-SEVE, NORVEGE, Rouen, France
| | - Xavier Latour
- Laboratoire de Communication Bactérienne et Stratégies Anti-infectieuses (CBSA UR), Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, Rouen, France
- Structure Fédérative de Recherche Normandie Végétale and Entente Franco-Québécoise NOR-SEVE, NORVEGE, Rouen, France
| | - Yoan Konto-Ghiorghi
- Laboratoire de Communication Bactérienne et Stratégies Anti-infectieuses (CBSA UR), Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, Rouen, France
- Structure Fédérative de Recherche Normandie Végétale and Entente Franco-Québécoise NOR-SEVE, NORVEGE, Rouen, France
| | - Julien Verdon
- Laboratoire Ecologie and Biologie des Interactions, Université de Poitiers, Poitiers, France
| | - Annabelle Merieau
- Laboratoire de Communication Bactérienne et Stratégies Anti-infectieuses (CBSA UR), Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, Rouen, France
- Structure Fédérative de Recherche Normandie Végétale and Entente Franco-Québécoise NOR-SEVE, NORVEGE, Rouen, France
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15
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Riediger M, Hoffmann K, Isberner R, Dreyer A, Tersteegen A, Marquardt P, Kaasch AJ, Zautner AE. Chimaeribacter arupi a new member of the Yersineacea family has the characteristics of a human pathogen. Front Cell Infect Microbiol 2023; 13:1277522. [PMID: 37868348 PMCID: PMC10587679 DOI: 10.3389/fcimb.2023.1277522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 09/14/2023] [Indexed: 10/24/2023] Open
Abstract
Chimaeribacter arupi (heterotypic synonym: "Nissabacter archeti") is a facultative anaerobic, newly described Gram-negative rod and belongs to the Yersineacea family. Here, we report the case of a 19-month-old female infant patient who presented to the emergency unit with somnolence and fever. C. arupi was isolated from a positive blood culture, taken via an implanted Broviac catheter, proving a bloodstream infection by the pathogen. The objective of this study was to utilize whole genome sequencing to assess the genes encoding potential virulence associated factors, which may play a role in host tropism, tissue invasion and the subsequent stages in the pathogenesis of a bloodstream infection with C. arupi. The genome of the isolate was completely sequenced employing Illumina MiSeq and Nanopore MinION sequencing and the presumptive virulence associated factors and antimicrobial resistance genes were investigated in more detail. Additionally, we performed metabolic profiling and susceptibility testing by microdilution. The presence of predicted TcfC-like α-Pili suggests that C. arupi is highly adapted to humans as a host. It utilizes flagellar and type IV pili-mediated motility, as well as a number of γ1-pili and a σ-pilus, which may be used to facilitate biofilm formation and adherence to host epithelia. Additionally, long polar fimbriae may aid in tissue invasion. The bacterium possesses antioxidant factors, which may enable temporary survival in phagolysosomes, and a capsule that potentially provides protection from phagocytosis. It may acquire iron ions from erythrocytes through the type 6 secretion system and hemolysins. Furthermore, the isolate exhibits beta-lactamase-mediated penicillin and aminopenicillin resistance. Based on the analysis of the whole genome, we conclude that C. arupi possesses virulence factors associated with tissue invasion and may thus be a potential opportunistic pathogen of bloodstream infections.
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Affiliation(s)
- Matthias Riediger
- Institut für Medizinische Mikrobiologie und Krankenhaushygiene, Medizinische Fakultät der Otto-von-Guericke Universität Magdeburg, Magdeburg, Germany
| | - Katharina Hoffmann
- Institut für Medizinische Mikrobiologie und Krankenhaushygiene, Medizinische Fakultät der Otto-von-Guericke Universität Magdeburg, Magdeburg, Germany
| | - Riekje Isberner
- Universitätskinderklinik, Medizinische Fakultät der Otto-von-Guericke Universität Magdeburg, Magdeburg, Germany
| | - Annika Dreyer
- Institut für Medizinische Mikrobiologie und Virologie, Universitätsmedizin Göttingen, Göttingen, Germany
| | - Aljoscha Tersteegen
- Institut für Medizinische Mikrobiologie und Krankenhaushygiene, Medizinische Fakultät der Otto-von-Guericke Universität Magdeburg, Magdeburg, Germany
| | - Pauline Marquardt
- Institut für Medizinische Mikrobiologie und Krankenhaushygiene, Medizinische Fakultät der Otto-von-Guericke Universität Magdeburg, Magdeburg, Germany
| | - Achim J. Kaasch
- Institut für Medizinische Mikrobiologie und Krankenhaushygiene, Medizinische Fakultät der Otto-von-Guericke Universität Magdeburg, Magdeburg, Germany
- Center for Health and Medical Prevention (CHaMP), Center for Health and Medical Prevention, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
| | - Andreas E. Zautner
- Institut für Medizinische Mikrobiologie und Krankenhaushygiene, Medizinische Fakultät der Otto-von-Guericke Universität Magdeburg, Magdeburg, Germany
- Center for Health and Medical Prevention (CHaMP), Center for Health and Medical Prevention, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany
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16
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Smith JA, Holmes DE, Woodard TL, Li Y, Liu X, Wang LY, Meier D, Schwarz IA, Lovley DR. Detrimental impact of the Geobacter metallireducens type VI secretion system on direct interspecies electron transfer. Microbiol Spectr 2023; 11:e0094123. [PMID: 37650614 PMCID: PMC10580878 DOI: 10.1128/spectrum.00941-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 07/02/2023] [Indexed: 09/01/2023] Open
Abstract
Direct interspecies electron transfer (DIET) is important in anaerobic communities of environmental and practical significance. Other than the need for close physical contact for electrical connections, the interactions of DIET partners are poorly understood. Type VI secretion systems (T6SSs) typically kill competitive microbes. Surprisingly, Geobacter metallireducens highly expressed T6SS genes when DIET-based co-cultures were initiated with Geobacter sulfurreducens. T6SS gene expression was lower when the electron shuttle anthraquinone-2,6-disulfonate was added to alleviate the need for interspecies contact. Disruption of hcp, the G. metallireducens gene for the main T6SS needle-tube protein subunit, and the most highly upregulated gene in DIET-grown cells eliminated the long lag periods required for the initiation of DIET. The mutation did not aid DIET in the presence of granular-activated carbon (GAC), consistent with the fact that DIET partners do not make physical contact when electrically connected through conductive materials. The hcp-deficient mutant also established DIET quicker with Methanosarcina barkeri. However, the mutant also reduced Fe(III) oxide faster than the wild-type strain, a phenotype not expected from the loss of the T6SS. Quantitative PCR revealed greater gene transcript abundance for key components of extracellular electron transfer in the hcp-deficient mutant versus the wild-type strain, potentially accounting for the faster Fe(III) oxide reduction and impact on DIET. The results highlight that interspecies interactions beyond electrical connections may influence DIET effectiveness. The unexpected increase in the expression of genes for extracellular electron transport components when hcp was deleted emphasizes the complexities in evaluating the electromicrobiology of highly adaptable Geobacter species. IMPORTANCE Direct interspecies electron transfer is an alternative to the much more intensively studied process of interspecies H2 transfer as a mechanism for microbes to share electrons during the cooperative metabolism of energy sources. DIET is an important process in anaerobic soils and sediments generating methane, a significant greenhouse gas. Facilitating DIET can accelerate and stabilize the conversion of organic wastes to methane biofuel in anaerobic digesters. Therefore, a better understanding of the factors controlling how fast DIET partnerships are established is expected to lead to new strategies for promoting this bioenergy process. The finding that when co-cultured with G. sulfurreducens, G. metallireducens initially expressed a type VI secretion system, a behavior not conducive to interspecies cooperation, illustrates the complexity of establishing syntrophic relationships.
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Affiliation(s)
- Jessica A. Smith
- Department of Microbiology, University of Massachusetts Amherst, Morrill IV N Science Center, Amherst, Massachusetts, USA
- Department of Biomolecular Sciences, Central Connecticut State University, New Britain, Connecticut, USA
| | - Dawn E. Holmes
- Department of Microbiology, University of Massachusetts Amherst, Morrill IV N Science Center, Amherst, Massachusetts, USA
- Department of Physical and Biological Sciences, Western New England University, Springfield, Massachusetts, USA
| | - Trevor L. Woodard
- Department of Microbiology, University of Massachusetts Amherst, Morrill IV N Science Center, Amherst, Massachusetts, USA
| | - Yang Li
- Department of Microbiology, University of Massachusetts Amherst, Morrill IV N Science Center, Amherst, Massachusetts, USA
- School of Ocean Science and Technology, Dalian University of Technology, Panjin, Liaoning, China
| | - Xinying Liu
- Department of Microbiology, University of Massachusetts Amherst, Morrill IV N Science Center, Amherst, Massachusetts, USA
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing, China
| | - Li-Ying Wang
- Department of Microbiology, University of Massachusetts Amherst, Morrill IV N Science Center, Amherst, Massachusetts, USA
| | - David Meier
- Department of Microbiology, University of Massachusetts Amherst, Morrill IV N Science Center, Amherst, Massachusetts, USA
| | - Ingrid A. Schwarz
- Department of Biomolecular Sciences, Central Connecticut State University, New Britain, Connecticut, USA
| | - Derek R. Lovley
- Department of Microbiology, University of Massachusetts Amherst, Morrill IV N Science Center, Amherst, Massachusetts, USA
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Doering T, Tandon K, Topa SH, Pidot SJ, Blackall LL, van Oppen MJH. Genomic exploration of coral-associated bacteria: identifying probiotic candidates to increase coral bleaching resilience in Galaxea fascicularis. MICROBIOME 2023; 11:185. [PMID: 37596630 PMCID: PMC10439622 DOI: 10.1186/s40168-023-01622-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 07/14/2023] [Indexed: 08/20/2023]
Abstract
BACKGROUND Reef-building corals are acutely threatened by ocean warming, calling for active interventions to reduce coral bleaching and mortality. Corals associate with a wide diversity of bacteria which can influence coral health, but knowledge of specific functions that may be beneficial for corals under thermal stress is scant. Under the oxidative stress theory of coral bleaching, bacteria that scavenge reactive oxygen (ROS) or nitrogen species (RNS) are expected to enhance coral thermal resilience. Further, bacterial carbon export might substitute the carbon supply from algal photosymbionts, enhance thermal resilience and facilitate bleaching recovery. To identify probiotic bacterial candidates, we sequenced the genomes of 82 pure-cultured bacteria that were isolated from the emerging coral model Galaxea fascicularis. RESULTS Genomic analyses showed bacterial isolates were affiliated with 37 genera. Isolates such as Ruegeria, Muricauda and Roseovarius were found to encode genes for the synthesis of the antioxidants mannitol, glutathione, dimethylsulfide, dimethylsulfoniopropionate, zeaxanthin and/or β-carotene. Genes involved in RNS-scavenging were found in many G. fascicularis-associated bacteria, which represents a novel finding for several genera (including Pseudophaeobacter). Transporters that are suggested to export carbon (semiSWEET) were detected in seven isolates, including Pseudovibrio and Roseibium. Further, a range of bacterial strains, including strains of Roseibium and Roseovarius, revealed genomic features that may enhance colonisation and association of bacteria with the coral host, such as secretion systems and eukaryote-like repeat proteins. CONCLUSIONS Our work provides an in-depth genomic analysis of the functional potential of G. fascicularis-associated bacteria and identifies novel combinations of traits that may enhance the coral's ability to withstand coral bleaching. Identifying and characterising bacteria that are beneficial for corals is critical for the development of effective probiotics that boost coral climate resilience. Video Abstract.
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Affiliation(s)
- Talisa Doering
- School of BioSciences, The University of Melbourne, Parkville, VIC Australia
| | - Kshitij Tandon
- School of BioSciences, The University of Melbourne, Parkville, VIC Australia
| | - Sanjida H. Topa
- School of BioSciences, The University of Melbourne, Parkville, VIC Australia
| | - Sacha J. Pidot
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, VIC Australia
| | - Linda L. Blackall
- School of BioSciences, The University of Melbourne, Parkville, VIC Australia
| | - Madeleine J. H. van Oppen
- School of BioSciences, The University of Melbourne, Parkville, VIC Australia
- Australian Institute of Marine Science, Townsville, QLD Australia
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Kim M, Park SJ. Complete genome sequence of Halomonas alkaliantarctica MSP3 isolated from marine sediment, Jeju Island. Mar Genomics 2023; 70:101046. [PMID: 37355294 DOI: 10.1016/j.margen.2023.101046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 05/24/2023] [Indexed: 06/26/2023]
Abstract
As a moderate halophilic-heterotrophic bacterium, Halomonas alkaliantarctica MSP3 was isolated from marine sediment located in Jeju island, South Korea. The complete genome of strain MSP3 was sequenced and analyzed to reveal its genetic features and metabolic potential. The genome size of MSP3 was about 4.23 Mbp with 54.7% G + C content, and it contained 3811 protein-coding sequences and 79 RNA genes (61 tRNA and 18 rRNA). According to the genome annotation, it was revealed that the strain MSP3 harbors genes encoding for urease and urea transporters, which play a crucial role in the process of urea degradation and utilization. In addition, it is noteworthy that the MSP3 strain possesses genes encoding for both cytochrome c oxidase and cytochrome bd oxidase, thereby conferring upon it the ability to adapt to various levels of oxygen (oxic to microoxic) and to execute denitrification processes in the absence of oxygen. Moreover, it was observed that strain MSP3 had genes for the glyoxylate cycle, which is an alternative pathway to the TCA cycle. Furthermore, it was observed that the MSP3 strain exhibited the ability to thrive across a diverse spectrum of NaCl concentrations, ranging from 2% to 10% (w/v). Collectively, strain MSP3 may possess an advantage over competitors within the marine ecosystem, particularly in conditions where carbon substrates are restricted. The genomic-based assumption could potentially be substantiated by the presence of a multitude of transporter genes within the genome.
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Affiliation(s)
- Minji Kim
- Department of Biology, Jeju National University, Jeju 63243, South Korea
| | - Soo-Je Park
- Department of Biology, Jeju National University, Jeju 63243, South Korea.
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Azam MW, Zarrilli R, Khan AU. Updates on the Virulence Factors Produced by Multidrug-Resistant Enterobacterales and Strategies to Control Their Infections. Microorganisms 2023; 11:1901. [PMID: 37630461 PMCID: PMC10456890 DOI: 10.3390/microorganisms11081901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 07/06/2023] [Accepted: 07/25/2023] [Indexed: 08/27/2023] Open
Abstract
The Enterobacterales order is a massive group of Gram-negative bacteria comprised of pathogenic and nonpathogenic members, including beneficial commensal gut microbiota. The pathogenic members produce several pathogenic or virulence factors that enhance their pathogenic properties and increase the severity of the infection. The members of Enterobacterales can also develop resistance against the common antimicrobial agents, a phenomenon called antimicrobial resistance (AMR). Many pathogenic Enterobacterales members are known to possess antimicrobial resistance. This review discusses the virulence factors, pathogenicity, and infections caused by multidrug-resistant Enterobacterales, especially E. coli and some other bacterial species sharing similarities with the Enterobacterales members. We also discuss both conventional and modern approaches used to combat the infections caused by them. Understanding the virulence factors produced by the pathogenic bacteria will help develop novel strategies and methods to treat infections caused by them.
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Affiliation(s)
- Mohd W. Azam
- Medical Microbiology and Molecular Biology Laboratory, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Raffaele Zarrilli
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy
| | - Asad U. Khan
- Medical Microbiology and Molecular Biology Laboratory, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
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González Espinosa J, Hernández Gómez YF, Javier Martínez Y, Flores Gallardo FJ, Pacheco Aguilar JR, Ramos López MÁ, Arvizu Gómez JL, Saldaña Gutierrez C, Rodríguez Morales JA, García Gutiérrez MC, Amaro Reyes A, Álvarez Hidalgo E, Nuñez Ramírez J, Hernández Flores JL, Campos Guillén J. Kosakonia cowanii Ch1 Isolated from Mexican Chili Powder Reveals Growth Inhibition of Phytopathogenic Fungi. Microorganisms 2023; 11:1758. [PMID: 37512930 PMCID: PMC10384288 DOI: 10.3390/microorganisms11071758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/03/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023] Open
Abstract
Kosakonia cowanii strain Ch1 was isolated from Mexican chili powder, and the genome was sequenced. The genome was 4,765,544 bp in length, with an average G + C content of 56.22%, and a plasmid (pCh1) of 128,063 bp with an average G + C content of 52.50%. A phylogenetic analysis revealed a close relation with pathogenic strains; nevertheless, some virulence-related genes were absent, and this genetic characteristic may explain the fact that K. cowanii Ch1 behaved as a non-pathogenic strain when infection assays were performed on the leaves and fruits of Capsicum annuum L. Surprisingly, we observed that this bacterial strain had the ability to spread throughout serrano pepper seeds. Furthermore, K. cowanii Ch1 was evaluated for the production of volatile organic compounds (VOCs) against fungal pathogens, and the results showed that Alternaria alternata and Sclerotium rolfsii were inhibited in a radial mycelial growth assay by a mean rate of 70% and 64%, while Fusarium oxysporum was inhibited by only approximately 10%. Based on the headspace solid-phase microextraction combined with the gas chromatography mass spectrometry (HS-SPME-GC-MS), 67 potential VOCs were identified during the fermentation of K. cowanii Ch1 in TSA medium. From these VOCs, nine main compounds were identified based on relative peak area: dodecanoic acid; 3-hydroxy ethanol; 1-butanol-3-methyl; acetaldehyde; butanoic acid, butyl ester; cyclodecane; 2-butanone, 3-hydroxy; disulfide, dimethyl and pyrazine-2,5-dimethyl. Our findings show the potential of K. cowanii Ch1 for the biocontrol of fungal pathogens through VOCs production and reveal additional abilities and metabolic features as beneficial bacterial specie.
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Affiliation(s)
- Jacqueline González Espinosa
- Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, Av. De las Ciencias S/N, Querétaro 76220, Mexico
| | | | - Yomaiko Javier Martínez
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, Querétaro 76010, Mexico
| | | | | | - Miguel Ángel Ramos López
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, Querétaro 76010, Mexico
| | - Jackeline Lizzeta Arvizu Gómez
- Secretaría de Investigación y Posgrado, Centro Nayarita de Innovación y Transferencia de Tecnología (CENITT), Universidad Autónoma de Nayarit, Tepic 63173, Mexico
| | - Carlos Saldaña Gutierrez
- Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, Av. De las Ciencias S/N, Querétaro 76220, Mexico
| | | | | | - Aldo Amaro Reyes
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, Querétaro 76010, Mexico
| | - Erika Álvarez Hidalgo
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, Querétaro 76010, Mexico
| | - Jorge Nuñez Ramírez
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, Querétaro 76010, Mexico
| | | | - Juan Campos Guillén
- Facultad de Química, Universidad Autónoma de Querétaro, Cerro de las Campanas S/N, Querétaro 76010, Mexico
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21
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Ugochukwu ICI, Rhimi W, Chebil W, Rizzo A, Tempesta M, Giusiano G, Tábora RFM, Otranto D, Cafarchia C. Part 2: Understanding the role of Malassezia spp. in skin disorders: pathogenesis of Malassezia associated skin infections. Expert Rev Anti Infect Ther 2023; 21:1245-1257. [PMID: 37883035 DOI: 10.1080/14787210.2023.2274500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 10/19/2023] [Indexed: 10/27/2023]
Abstract
INTRODUCTION Malassezia is a major component of the skin microbiome, a lipophilic symbiotic organism of the mammalian skin, which can switch to opportunistic pathogens triggering multiple dermatological disorders in humans and animals. This phenomenon is favored by endogenous and exogenous host predisposing factors, which may switch Malassezia from a commensal to a pathogenic phenotype. AREA COVERED This review summarizes and discusses the most recent literature on the pathogenesis of Malassezia yeasts, which ultimately results in skin disorders with different clinical presentation. A literature search of Malassezia pathogenesis was performed via PubMed and Google scholar (up to May 2023), using the following keywords: Pathogenesis and Malassezia;host risk factors and Malassezia, Malassezia and skin disorders; Malassezia and virulence factors: Malassezia and metabolite production; Immunology and Malassezia. EXPERT OPINION Malassezia yeasts can maintain skin homeostasis being part of the cutaneous mycobiota; however, when the environmental or host conditions change, these yeasts are endowed with a remarkable plasticity and adaptation by modifying their metabolism and thus contributing to the appearance or aggravation of human and animal skin disorders.
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Affiliation(s)
- Iniobong Chukwuebuka Ikenna Ugochukwu
- Department of Veterinary Medicine, University of Bari Aldo Moro, Valenzano, Italy
- Department of Veterinary Pathology and Microbiology, University of Nigeria, Nsukka, Nigeria
| | - Wafa Rhimi
- Department of Veterinary Medicine, University of Bari Aldo Moro, Valenzano, Italy
| | - Wissal Chebil
- Laboratory of Medical and Molecular Parasitology-Mycology, Department of Clinical Biology, Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
| | - Antonio Rizzo
- Department of Veterinary Medicine, University of Bari Aldo Moro, Valenzano, Italy
| | - Maria Tempesta
- Department of Veterinary Medicine, University of Bari Aldo Moro, Valenzano, Italy
| | - Gustavo Giusiano
- Departamento de Micología, Instituto de Medicina Regional, Facultad de Medicina, Universidad Nacional del Nordeste, Resistencia, Argentina
| | | | - Domenico Otranto
- Department of Veterinary Medicine, University of Bari Aldo Moro, Valenzano, Italy
- Faculty of Veterinary Sciences, Bu-Ali Sina University, Hamedan, Iran
| | - Claudia Cafarchia
- Department of Veterinary Medicine, University of Bari Aldo Moro, Valenzano, Italy
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22
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de Sousa T, Hébraud M, Alves O, Costa E, Maltez L, Pereira JE, Martins Â, Igrejas G, Poeta P. Study of Antimicrobial Resistance, Biofilm Formation, and Motility of Pseudomonas aeruginosa Derived from Urine Samples. Microorganisms 2023; 11:1345. [PMID: 37317319 DOI: 10.3390/microorganisms11051345] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 04/28/2023] [Accepted: 05/17/2023] [Indexed: 06/16/2023] Open
Abstract
Pseudomonas aeruginosa causes urinary tract infections associated with catheters by forming biofilms on the surface of indwelling catheters. Therefore, controlling the spread of the bacteria is crucial to preventing its transmission in hospitals and the environment. Thus, our objective was to determine the antibiotic susceptibility profiles of twenty-five P. aeruginosa isolates from UTIs at the Medical Center of Trás-os-Montes and Alto Douro (CHTMAD). Biofilm formation and motility are also virulence factors studied in this work. Out of the twenty-five P. aeruginosa isolates, 16% exhibited multidrug resistance, being resistant to at least three classes of antibiotics. However, the isolates showed a high prevalence of susceptibility to amikacin and tobramycin. Resistance to carbapenem antibiotics, essential for treating infections when other antibiotics fail, was low in this study, Notably, 92% of the isolates demonstrated intermediate sensitivity to ciprofloxacin, raising concerns about its efficacy in controlling the disease. Genotypic analysis revealed the presence of various β-lactamase genes, with class B metallo-β-lactamases (MBLs) being the most common. The blaNDM, blaSPM, and blaVIM-VIM2 genes were detected in 16%, 60%, and 12% of the strains, respectively. The presence of these genes highlights the emerging threat of MBL-mediated resistance. Additionally, virulence gene analysis showed varying prevalence rates among the strains. The exoU gene, associated with cytotoxicity, was found in only one isolate, while other genes such as exoS, exoA, exoY, and exoT had a high prevalence. The toxA and lasB genes were present in all isolates, whereas the lasA gene was absent. The presence of various virulence genes suggests the potential of these strains to cause severe infections. This pathogen demonstrated proficiency in producing biofilms, as 92% of the isolates were found to be capable of doing so. Currently, antibiotic resistance is one of the most serious public health problems, as options become inadequate with the continued emergence and spread of multidrug-resistant strains, combined with the high rate of biofilm production and the ease of dissemination. In conclusion, this study provides insights into the antibiotic resistance and virulence profiles of P. aeruginosa strains isolated from human urine infections, highlighting the need for continued surveillance and appropriate therapeutic approaches.
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Affiliation(s)
- Telma de Sousa
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associate Laboratory for Green Chemistry (LAQV), Chemistry Department, Faculty of Science and Technology, University Nova of Lisbon, 2829-516 Lisbon, Portugal
| | - Michel Hébraud
- Université Clermont Auvergne, INRAE, UMR Microbiologie Environnement Digestif Santé (MEDiS), 60122 Saint-Genès-Champanelle, France
| | - Olimpia Alves
- Medical Centre of Trás-os-Montes and Alto Douro, Clinical Pathology Department, 5000-801 Vila Real, Portugal
| | - Eliana Costa
- Medical Centre of Trás-os-Montes and Alto Douro, Clinical Pathology Department, 5000-801 Vila Real, Portugal
| | - Luís Maltez
- Veterinary and Animal Research Centre (CECAV), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - José Eduardo Pereira
- Veterinary and Animal Research Centre (CECAV), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Ângela Martins
- Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Department of Zootechnics, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Gilberto Igrejas
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associate Laboratory for Green Chemistry (LAQV), Chemistry Department, Faculty of Science and Technology, University Nova of Lisbon, 2829-516 Lisbon, Portugal
| | - Patricia Poeta
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associate Laboratory for Green Chemistry (LAQV), Chemistry Department, Faculty of Science and Technology, University Nova of Lisbon, 2829-516 Lisbon, Portugal
- Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
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Pothula R, Lee MW, Patricia Stock S. Type 6 Secretion System components hcp and vgrG support mutualistic partnership between Xenorhabdus bovienii symbiont and Steinernema jollieti host. J Invertebr Pathol 2023; 198:107925. [PMID: 37087093 DOI: 10.1016/j.jip.2023.107925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 04/11/2023] [Accepted: 04/16/2023] [Indexed: 04/24/2023]
Abstract
Xenorhabdus, like other Gram-negative bacteria, possesses a Type 6 Secretion System (T6SS) which acts as a contact-dependent molecular syringe, delivering diverse proteins (effectors) directly into other cells. The number of T6SS loci encoded in Xenorhabdus genomes are variable both at the inter and intraspecific level. Some environmental isolates of Xenorhabdus bovienii, encode at least one T6SS locus while others possess two loci. Previous work conducted by our team demonstrated that X. bovienii [Jollieti strain SS-2004], which has two T6SSs (T6SS-1 and T6SS-2), hcp genes are required for biofilm formation. Additionally, while T6SS-1 hcp gene plays a role in the antibacterial competition, T6SS-2 hcp does not. In this study, we tested the hypothesis that vgrG genes are also involved in mutualistic and pathogenic interactions. For this purpose, targeted mutagenesis together with wet lab experiments including colonization, competition, biofilm, and virulence experiments, were carried out to assess the role of vgrG in the mutualistic and antagonistic interactions in the life cycle of XBJ. Our results revealed that vgrG genes are not required for biofilm formation but play a role in outcompeting other Xenorhabdus bacteria. Additionally, both vgrG and hcp genes are required to fully colonize the nematode host. We also demonstrated that hcp and vgrG genes in both T6SS clusters are needed to support the reproductive fitness of the nematodes. Overall, results from this study revealed that in X. bovieni jollieti strain, the twoT6SS clusters play an important role in the fitness of the nematodes in relation to colonization and reproduction. These results lay a foundation for further investigations on the functional significance of T6SSs in the mutualistic and pathogenic lifecycle of Xenorhabdus spp.
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Affiliation(s)
- Ratnasri Pothula
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, United States
| | - Min-Woo Lee
- Corn, Soybean, and Wheat Quality Research Lab, USDA-ARS Wooster, OH, United States
| | - S Patricia Stock
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, United States; College of Agriculture, California State University, Chico, CA, United States.
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The Anti-Listeria Activity of Pseudomonas fluorescens Isolated from the Horticultural Environment in New Zealand. Pathogens 2023; 12:pathogens12020349. [PMID: 36839621 PMCID: PMC9960311 DOI: 10.3390/pathogens12020349] [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: 01/09/2023] [Revised: 02/12/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
Beneficial bacteria with antibacterial properties are attractive alternatives to chemical-based antibacterial or bactericidal agents. Our study sourced such bacteria from horticultural produce and environments to explore the mechanisms of their antimicrobial properties. Five strains of Pseudomonas fluorescens were studied that possessed antibacterial activity against the pathogen Listeria monocytogenes. The vegetative culture of these strains (Pseudomonas fluorescens-PFR46I06, Pseudomonas fluorescens-PFR46H06, Pseudomonas fluorescens-PFR46H07, Pseudomonas fluorescens-PFR46H08 and Pseudomonas fluorescens-PFR46H09) were tested against Listeria monocytogenes (n = 31), Listeria seeligeri (n = 1) and Listeria innocua (n = 1) isolated from seafood and horticultural sources and from clinical cases (n = 2) using solid media coculture and liquid media coculture. All Listeria strains were inhibited by all strains of P. fluorescens; however, P. fluorescens-PFR46H07, P. fluorescens-PFR46H08 and P. fluorescens-PFR46H09 on solid media showed good inhibition, with average zones of inhibition of 14.8 mm, 15.1 mm and 18.2 mm, respectively, and the other two strains and P. fluorescens-PFR46H09 had a significantly greater zone of inhibition than the others (p < 0.05). There was no inhibition observed in liquid media coculture or in P. fluorescens culture supernatants against Listeria spp. by any of the P. fluorescens strains. Therefore, we hypothesized that the structural apparatus that causes cell-to-cell contact may play a role in the ejection of ant-listeria molecules on solid media to inhibit Listeria isolates, and we investigated the structural protein differences using whole-cell lysate proteomics. We paid special attention to the type VI secretion system (TSS-T6SS) for the transfer of effector proteins or bacteriocins. We found significant differences in the peptide profiles and protein summaries between these isolates' lysates, and PFR46H06 and PFR46H07 possessed the fewest secretion system structural proteins (12 and 11, respectively), while PFR46H08 and PFR46H09 had 18 each. P. fluorescens-PFR46H09, which showed the highest antimicrobial effect, had nine tss-T6SS structural proteins compared to only four in the other three strains.
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Wen J, Liao L, Duan Z, Su S, Zhang J, Chen B. Identification and Regulatory Roles of a New Csr Small RNA from Arctic Pseudoalteromonas fuliginea BSW20308 in Temperature Responses. Microbiol Spectr 2023; 11:e0409422. [PMID: 36625662 PMCID: PMC9927453 DOI: 10.1128/spectrum.04094-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 12/15/2022] [Indexed: 01/11/2023] Open
Abstract
Small RNAs (sRNAs) play a very important role in gene regulation at the posttranscriptional level. However, sRNAs from nonmodel microorganisms, extremophiles in particular, have been rarely explored. We discovered a putative sRNA, termed Pf1 sRNA, in Pseudoalteromonas fuliginea BSW20308 isolated from the polar regions in our previous work. In this study, we identified the sRNA and investigated its regulatory role in gene expression under different temperatures. Pf1 sRNA was confirmed to be a new member of the CsrB family but has little sequence similarity with Escherichia coli CsrB. However, Pf1 sRNA was able to bind to CsrA from E. coli and P. fuliginea BSW20308 to regulate glycogen synthesis. The Pf1 sRNA knockout strain (ΔPf1) affected motility, fitness, and global gene expression in transcriptomes and proteomes at 4°C and 32°C. Genes related to carbon metabolism, amino acid metabolism, salinity tolerance, antibiotic resistance, oxidative stress, motility, chemotaxis, biofilm, and secretion systems were differentially expressed in the wild-type strain and the ΔPf1 mutant. Our study suggested that Pf1 sRNA might play an important role in response to environmental changes by regulating global gene expression. Specific targets of the Pf1 sRNA-CsrA system were tentatively proposed, such as genes involved in the type VI secretion system, TonB-dependent receptors, and response regulators, but most of them have an unknown function. Since this is the first study of CsrB family sRNA in Pseudoalteromonas and microbes from the polar regions, it provides a novel insight at the posttranscriptional level into the responses and adaptation to temperature changes in bacteria from extreme environments. This study also sheds light on the evolution of sRNA in extreme environments and expands the bacterial sRNA database. IMPORTANCE Previous research on microbial temperature adaptation has focused primarily on functional genes, with little attention paid to posttranscriptional regulation. Small RNAs, the major posttranscriptional modulators of gene expression, are greatly underexplored, especially in nonpathogenic and nonmodel microorganisms. In this study, we verified the first Csr sRNA, named Pf1 sRNA, from Pseudoalteromonas, a model genus for studying cold adaptation. We revealed that Pf1 sRNA played an important role in global regulation and was indispensable in improving fitness. This study provided us a comprehensive view of sRNAs from Pseudoalteromonas and expanded our understanding of bacterial sRNAs from extreme environments.
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Affiliation(s)
- Jiao Wen
- Key Laboratory for Polar Science, Ministry of Natural Resources, Polar Research Institute of China, Shanghai, China
| | - Li Liao
- Key Laboratory for Polar Science, Ministry of Natural Resources, Polar Research Institute of China, Shanghai, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
- Southern Laboratory of Ocean Science and Engineering (Guangdong, Zhuhai), Zhuhai, China
| | - Zedong Duan
- Key Laboratory for Polar Science, Ministry of Natural Resources, Polar Research Institute of China, Shanghai, China
| | - Shiyuan Su
- Key Laboratory for Polar Science, Ministry of Natural Resources, Polar Research Institute of China, Shanghai, China
| | - Jin Zhang
- Key Laboratory for Polar Science, Ministry of Natural Resources, Polar Research Institute of China, Shanghai, China
| | - Bo Chen
- Key Laboratory for Polar Science, Ministry of Natural Resources, Polar Research Institute of China, Shanghai, China
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Chhetri G, Kim I, Kim J, So Y, Park S, Jung Y, Seo T. Paraburkholderia tagetis sp. nov., a novel species isolated from roots of Tagetes patula enhances the growth and yield of Solanum lycopersicum L. (tomato). Front Microbiol 2023; 14:1140484. [PMID: 37082173 PMCID: PMC10110911 DOI: 10.3389/fmicb.2023.1140484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/21/2023] [Indexed: 04/22/2023] Open
Abstract
A multifunctional, Gram-stain-negative, aerobic, motile by flagella, short-rod shaped bacteria, designated strain RG36T was isolated from roots of marigold plant (Tagetes patula) sampled at Dongguk University, Republic of Korea. A 16S rRNA sequences indicated that the closest phylogenetic neighbors were Paraburkholderia acidiphila 7Q-K02T (99.0%) and Paraburkholderia sacchari IPT101T (98.9%) of the family Burkholderiaceae. The draft genome size was 8.52 Mb (63.7% GC). The genome contained 7,381 coding sequences. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values of strain RG36T with its most closely related species were only 83.1-88.7 and 27.6-36.7%, respectively. Strain RG36T contained Q-8 as the major respiratory quinone and its main fatty acids (>10%) were C16:0, C17:0 cyclo, C19:0 cyclo ω8c, and summed feature 8 (comprising C18:1 ω7c and/or C18:1 ω6c). Strain RG36T accumulates polyhydroxybutyrates (PHB) and exhibits multiple plant growth-promoting properties including production of indole-3-acetic acid (IAA), siderophores, protease, phosphate solubilization, and harboring gene clusters for its multifunctional properties. A pot experiment was conducted to evaluate the effect of PGPR on the growth of Solanum lycopersicum L. (Tomato). Result also confirmed the ability of strain RG36T to promote tomato plant growth, especially it increases the yield of tomatoes. Structural assessment of the bioplastic by Fourier transform infrared (FTIR), nuclear magnetic resonance (NMR), and GC-MS spectroscopy, which confirmed the structure of the polymer as PHB. Our study revealed the potential of strain RG36T to promote the growth of tomato plant and fruit yield by stimulating the various phytohormones, which could be use as bio-fertilizers to reduce the use of chemical fertilizers and promotes sustainable agricultural production. The phenotypic, chemotaxonomic and phylogenetic data, and genome analysis showed that strain RG36T represents a novel species of the genus Paraburkholderia, for which the name Paraburkholderia tagetis sp. nov. is proposed. The type strain is RG36T (=KACC 22685T = TBRC 15696T).
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Idosa AW, Wozniak DJ, Hall-Stoodley L. Surface Dependent Inhibition of Mycobacterium abscessus by Diverse Pseudomonas aeruginosa Strains. Microbiol Spectr 2022; 10:e0247122. [PMID: 36394312 PMCID: PMC9769778 DOI: 10.1128/spectrum.02471-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 10/25/2022] [Indexed: 11/19/2022] Open
Abstract
Both Pseudomonas aeruginosa and Mycobacterium abscessus are bacteria that cause pulmonary infection in people with inflammatory lung disease, including individuals with cystic fibrosis (CF). These bacterial species inhabit the same environmental reservoirs (soil and water) and can be coisolated in the lungs of people with CF. We investigated the interaction of these bacteria and found an antagonistic interaction favoring P. aeruginosa that was observed in biofilms but not in planktonic cultures. This antagonism extended to multiple P. aeruginosa strains and against Mycobacterium smegmatis. We tested known P. aeruginosa mutants for genes that can play roles in interbacterial contact-dependent (type III and type VI secretion systems) and contact-independent (quorum sensing, type II secretion) antagonism pathways to interrogate the mechanism of action. Our results indicate that well-known mechanisms of interbacterial competition are not responsible for the antagonism of P. aeruginosa toward M. abscessus, suggesting a novel antibacterial strategy. IMPORTANCE The biofilm lifestyle is favored by many organisms, and understanding interbacterial interactions that occur between coisolated bacterial species can provide new information regarding bacterial defense mechanisms and antibacterial targets. This may also provide insights into possible interbacterial interactions impacting host immunity during coinfection. Here, we investigate an antagonistic interaction favoring P. aeruginosa over M. abscessus exclusively in dual-species biofilms and not in liquid coculture.
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Affiliation(s)
- Ayantu W. Idosa
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
| | - Daniel J. Wozniak
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Luanne Hall-Stoodley
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
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Kiel A, Creutz I, Rückert C, Kaltschmidt BP, Hütten A, Niehaus K, Busche T, Kaltschmidt B, Kaltschmidt C. Genome-Based Analysis of Virulence Factors and Biofilm Formation in Novel P. aeruginosa Strains Isolated from Household Appliances. Microorganisms 2022; 10:microorganisms10122508. [PMID: 36557761 PMCID: PMC9781345 DOI: 10.3390/microorganisms10122508] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/09/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
In household washing machines, opportunistic pathogens such as Pseudomonas aeruginosa are present, which represent the household as a possible reservoir for clinical pathogens. Here, four novel P. aeruginosa strains, isolated from different sites of household appliances, were investigated regarding their biofilm formation. Only two isolates showed strong surface-adhered biofilm formation. In consequence of these phenotypic differences, we performed whole genome sequencing using Oxford Nanopore Technology together with Illumina MiSeq. Whole genome data were screened for the prevalence of 285 virulence- and biofilm-associated genes as well as for prophages. Linking biofilm phenotypes and parallelly appearing gene compositions, we assume a relevancy of the las quorum sensing system and the phage-encoded bacteriophage control infection gene bci, which was found on integrated phi297 DNA in all biofilm-forming isolates. Additionally, only the isolates revealing strong biofilm formation harbored the ϕCTX-like prophage Dobby, implicating a role of this prophage on biofilm formation. Investigations on clinically relevant pathogens within household appliances emphasize their adaptability to harsh environments, with high concentrations of detergents, providing greater insights into pathogenicity and underlying mechanisms. This in turn opens the possibility to map and characterize potentially relevant strains even before they appear as pathogens in society.
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Affiliation(s)
- Annika Kiel
- Department of Cell Biology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
- Correspondence:
| | - Ines Creutz
- Proteome and Metabolome Research, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
| | - Christian Rückert
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
| | - Bernhard Peter Kaltschmidt
- Department of Thin Films and Physics of Nanostructures, Center of Spinelectronic Materials and Devices, Faculty of Physics, Bielefeld University, 33615 Bielefeld, Germany
| | - Andreas Hütten
- Department of Thin Films and Physics of Nanostructures, Center of Spinelectronic Materials and Devices, Faculty of Physics, Bielefeld University, 33615 Bielefeld, Germany
| | - Karsten Niehaus
- Proteome and Metabolome Research, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
| | - Tobias Busche
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
| | - Barbara Kaltschmidt
- Department of Cell Biology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
| | - Christian Kaltschmidt
- Department of Cell Biology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
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Eigentler L, Davidson FA, Stanley-Wall NR. Mechanisms driving spatial distribution of residents in colony biofilms: an interdisciplinary perspective. Open Biol 2022; 12:220194. [PMID: 36514980 PMCID: PMC9748781 DOI: 10.1098/rsob.220194] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Biofilms are consortia of microorganisms that form collectives through the excretion of extracellular matrix compounds. The importance of biofilms in biological, industrial and medical settings has long been recognized due to their emergent properties and impact on surrounding environments. In laboratory situations, one commonly used approach to study biofilm formation mechanisms is the colony biofilm assay, in which cell communities grow on solid-gas interfaces on agar plates after the deposition of a population of founder cells. The residents of a colony biofilm can self-organize to form intricate spatial distributions. The assay is ideally suited to coupling with mathematical modelling due to the ability to extract a wide range of metrics. In this review, we highlight how interdisciplinary approaches have provided deep insights into mechanisms causing the emergence of these spatial distributions from well-mixed inocula.
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Affiliation(s)
- Lukas Eigentler
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK,Mathematics, School of Science and Engineering, University of Dundee, Dundee DD1 4HN, UK
| | - Fordyce A. Davidson
- Mathematics, School of Science and Engineering, University of Dundee, Dundee DD1 4HN, UK
| | - Nicola R. Stanley-Wall
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
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Cai H, Yu J, Qiao Y, Ma Y, Zheng J, Lin M, Yan Q, Huang L. Effect of the Type VI Secretion System Secreted Protein Hcp on the Virulence of Aeromonas salmonicida. Microorganisms 2022; 10:microorganisms10122307. [PMID: 36557560 PMCID: PMC9784854 DOI: 10.3390/microorganisms10122307] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/16/2022] [Accepted: 11/19/2022] [Indexed: 11/23/2022] Open
Abstract
Aeromonas salmonicida, a psychrophilic bacterial pathogen, is widely distributed in marine freshwater, causing serious economic losses to major salmon farming areas in the world. At present, it is still one of the most important pathogens threatening salmon farming. Hcp (haemolysin-coregulated protein) is an effector protein in the type-VI secretion system (T6SS), which is secreted by T6SS and functions as its structural component. The results of our previous genomic sequencing showed that hcp existed in the mesophilic A. salmonicida SRW-OG1 isolated from naturally infected Epinephelus coioides. To further explore the role of Hcp in A. salmonicida SRW-OG1, we constructed an hcp-RNAi strain and verified its effect on the virulence of A. salmonicida. The results showed that compared with the wild strain, the hcp-RNAi strain suffered from different degrees of decreased adhesion, growth, biofilm formation, extracellular product secretion, and virulence. It was suggested that hcp may be an important virulence gene of A. salmonicida SRW-OG1.
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Affiliation(s)
- Hongyan Cai
- Key Laboratory of Healthy Mariculture for the East China Sea, Fisheries College, Ministry of Agriculture, Jimei University, Xiamen 361021, China
| | - Jiaying Yu
- Key Laboratory of Healthy Mariculture for the East China Sea, Fisheries College, Ministry of Agriculture, Jimei University, Xiamen 361021, China
| | - Ying Qiao
- Fourth Institute of Oceanography, Ministry of Natural Resources, No. 26, New Century Avenue, Beihai 536000, China
| | - Ying Ma
- Key Laboratory of Healthy Mariculture for the East China Sea, Fisheries College, Ministry of Agriculture, Jimei University, Xiamen 361021, China
| | - Jiang Zheng
- Key Laboratory of Healthy Mariculture for the East China Sea, Fisheries College, Ministry of Agriculture, Jimei University, Xiamen 361021, China
| | - Mao Lin
- Key Laboratory of Healthy Mariculture for the East China Sea, Fisheries College, Ministry of Agriculture, Jimei University, Xiamen 361021, China
| | - Qingpi Yan
- Key Laboratory of Healthy Mariculture for the East China Sea, Fisheries College, Ministry of Agriculture, Jimei University, Xiamen 361021, China
- Correspondence: (Q.Y.); (L.H.)
| | - Lixing Huang
- Key Laboratory of Healthy Mariculture for the East China Sea, Fisheries College, Ministry of Agriculture, Jimei University, Xiamen 361021, China
- Correspondence: (Q.Y.); (L.H.)
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Zhu J, Chen Y, Yang X. Antibiotic Resistance, Molecular Characteristics and Risk Factors of Carbapenem-Resistant Klebsiella pneumoniae in Clinical Isolates. Infect Drug Resist 2022; 15:6671-6680. [PMID: 36411757 PMCID: PMC9675329 DOI: 10.2147/idr.s383010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 10/20/2022] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND The global epidemic of carbapenem-resistant Klebsiella pneumonia (CRKP) has become a significant public health challenge. This study aimed to investigate the antibiotic resistance and molecular characteristics of CRKP and the clinical characteristics of infected patients. METHODS Sixty-two clinically isolated CRKP strains were collected for the first time from the First Affiliated Hospital of Zhejiang Chinese Medical University in Zhejiang Province. The carbapenemase gene, virulence-associated gene, capsular serotype gene and fenestra protein gene were detected by PCR. Univariate logistic regression and multivariate logistic regression analyses were performed to predict the risk factors for the prognosis of CRKP infection. RESULTS All CRKP isolates were resistant to meropenem, piperacillin-tazobactam, and ceftazidime (100%, 62/62), and all but one CRKP isolate was resistant to imipenem and cefepime (96.8%, 61/62). The rate of colistin resistance was the lowest (11.9%, 8/62). For CRKP in the ICU, the rates of resistance to various antibiotics were significantly higher than those in general ward patients. Fifty strains carried the carbapenemase gene bla KPC, and 3 strains carried both the bla KPC and bla NDM genes. The virulence genes uge, wabG, ycf, entB, ureA and fimH were detected in more than 90% of the 62 CRKP strains. Two strains had Ompk35, Ompk36 and Hcp gene deletions. The bla KPC, rmpA and rmpA2 genes had the highest positive rate in blood samples, and bla NDM had the highest positive rate in stool samples. Multivariate analysis showed that pulmonary disease affected the prognosis of CRKP infection. CONCLUSION The prevalence and molecular characteristics of CRKP clinical isolates in Zhengjiang Province in China were described, and the antibiotic resistance rate was higher. Additionally, relevant genes of CRKP strains and clinical characteristics of patients are related to the progression and prognosis of CRKP infection.
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Affiliation(s)
- Jingxuan Zhu
- The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine), Hangzhou, Zhejiang, 310006, People’s Republic of China
| | - Ye Chen
- The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine), Hangzhou, Zhejiang, 310006, People’s Republic of China
| | - Xuejing Yang
- The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine), Hangzhou, Zhejiang, 310006, People’s Republic of China
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Transcriptomic Analysis of Vibrio parahaemolyticus Underlying the Wrinkly and Smooth Phenotypes. Microbiol Spectr 2022; 10:e0218822. [PMID: 36098555 PMCID: PMC9604176 DOI: 10.1128/spectrum.02188-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Vibrio parahaemolyticus, a causative agent of seafood-associated gastroenteritis, undergoes opaque-translucent (OP-TR) colony switching associated with capsular polysaccharide (CPS) production. Here, we showed that V. parahaemolyticus was also able to naturally and reversibly switch between wrinkly and smooth phenotypes. More than 1,000 genes were significantly differentially expressed during colony morphology switching, including the major virulence gene loci and key biofilm-related genes. The genes responsible for type III secretion system 1 (T3SS1), type VI secretion systems (T6SS1 and T6SS2), and flagellar synthesis were downregulated in the wrinkly spreader phenotype, whereas genes located on the pathogenicity island Vp-PAI and those responsible for chitin-regulated pili (ChiRP) and Syp exopolysaccharide synthesis were upregulated. In addition, we showed that the wrinkly spreader grew faster, had greater motility and biofilm capacities, and produced more c-di-GMP than the smooth type. A dozen genes potentially associated with c-di-GMP metabolism were shown to be significantly differentially expressed, which may account for the differences in c-di-GMP levels between the two phenotypes. Most importantly, dozens of putative regulators were significantly differentially expressed, and hundreds of noncoding RNAs were detected during colony morphology switching, indicating that phenotype switching is strictly regulated by a complex molecular regulatory network in V. parahaemolyticus. Taken together, the presented work highlighted the gene expression profiles related to wrinkly-smooth switching, showing that the significantly differentially expressed genes were involved in various biological behaviors, including virulence factor production, biofilm formation, metabolism, adaptation, and colonization. IMPORTANCE We showed that Vibrio parahaemolyticus was able to naturally and reversibly switch between wrinkly and smooth phenotypes and disclosed the gene expression profiles related to wrinkly-smooth switching, showing that the significantly differentially expressed genes between the two colony morphology phenotypes were involved in various biological behaviors, including virulence factor production, biofilm formation, metabolism, adaptation, and colonization.
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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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Gmiter D, Kaca W. Into the understanding the multicellular lifestyle of Proteus mirabilis on solid surfaces. Front Cell Infect Microbiol 2022; 12:864305. [PMID: 36118021 PMCID: PMC9478170 DOI: 10.3389/fcimb.2022.864305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 08/15/2022] [Indexed: 11/17/2022] Open
Abstract
Indwelling urinary catheterization can lead to the development of catheter-associated urinary tract infections (CAUTIs), an important type of nosocomial infection, as well as other medical issues among institutionalized adults. Recently, Proteus mirabilis was highlighted as the important cause of CAUTIs. The pathogenicity of P. mirabilis is dependent on two multicellular types of surface colonization: the adherence and swarming motility. Adhesion, mostly mediated by fimbrial and nonfimbrial adhesins, is important for the initiation of biofilm formation. Moreover, the production of urease frequently results in biofilm crystallization, which leads to the blockage of catheters. The heterologous polymeric matrix of the biofilm offers protection against antibiotics and the host immune system. P. mirabilis displays remarkable motility abilities. After contact with solid surfaces, hyper-flagellated cells are able to rapidly migrate. The importance of swarming motility in CAUTIs development remains controversial; however, it was indicated that swarming cells were able to co-express other virulence factors. Furthermore, flagella are strong immunomodulating proteins. On the other hand, both biofilm formation and swarming motility implicates multiple inter- and intraspecies interactions, which might contribute to the pathogenicity.
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Cooper B. The Detriment of Salicylic Acid to the Pseudomonas savastanoi pv. phaseolicola Proteome. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:814-824. [PMID: 35612310 DOI: 10.1094/mpmi-05-22-0104-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Salicylic acid (SA), a natural product, is the major hormonal regulator of the plant immune system. SA also has antibacterial activity that is not completely elucidated. To gain a better understanding of this, Pseudomonas savastanoi pv. phaseolicola, a bacterial pathogen of beans, was exposed to sub-inhibitory amounts of SA and was then examined using quantitative mass spectrometry. Among the 2,185 proteins quantified, there were pronounced increases in p-hydroxybenzoic acid efflux pumps and multidrug efflux pumps. By contrast there were significant decreases in porin proteins, high-osmolarity response proteins, and protein components of the type VI secretion system. In addition, there were alterations in enzymes likely affecting the production of alginate, which is needed for infection. Furthermore, there was a decrease in an enzyme needed to detoxify methylglyoxal. Assays confirmed a reduction in alginate production and an increase in cellular methylglyoxal concentrations after SA treatment. Culture assays demonstrated that SA altered bacterial growth curves more so than other hydroxylated benzoic acid isomers. These data reveal that SA is antibiotic and that P. savastanoi pv. phaseolicola significantly alters its proteome in response to SA in vitro. Similar alterations to the bacterial proteome occur in beans during an immune reaction when SA increases at the site of infection. Thus, in beans, SA likely deters bacterial infection by adversely altering the bacterial proteome. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2022.
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Affiliation(s)
- Bret Cooper
- Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, 20705, U.S.A
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Wada N, Hsu MT, Tandon K, Hsiao SSY, Chen HJ, Chen YH, Chiang PW, Yu SP, Lu CY, Chiou YJ, Tu YC, Tian X, Chen BC, Lee DC, Yamashiro H, Bourne DG, Tang SL. High-resolution spatial and genomic characterization of coral-associated microbial aggregates in the coral Stylophora pistillata. SCIENCE ADVANCES 2022; 8:eabo2431. [PMID: 35857470 PMCID: PMC9258956 DOI: 10.1126/sciadv.abo2431] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/13/2022] [Indexed: 05/29/2023]
Abstract
Bacteria commonly form aggregates in a range of coral species [termed coral-associated microbial aggregates (CAMAs)], although these structures remain poorly characterized despite extensive efforts studying the coral microbiome. Here, we comprehensively characterize CAMAs associated with Stylophora pistillata and quantify their cell abundance. Our analysis reveals that multiple Endozoicomonas phylotypes coexist inside a single CAMA. Nanoscale secondary ion mass spectrometry imaging revealed that the Endozoicomonas cells were enriched with phosphorus, with the elemental compositions of CAMAs different from coral tissues and endosymbiotic Symbiodiniaceae, highlighting a role in sequestering and cycling phosphate between coral holobiont partners. Consensus metagenome-assembled genomes of the two dominant Endozoicomonas phylotypes confirmed their metabolic potential for polyphosphate accumulation along with genomic signatures including type VI secretion systems allowing host association. Our findings provide unprecedented insights into Endozoicomonas-dominated CAMAs and the first direct physiological and genomic linked evidence of their biological role in the coral holobiont.
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Affiliation(s)
- Naohisa Wada
- Biodiversity Research Center, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
| | - Ming-Tsung Hsu
- Biodiversity Research Center, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
| | - Kshitij Tandon
- Biodiversity Research Center, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
| | - Silver Sung-Yun Hsiao
- Institute of Astronomy and Astrophysics, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
| | - Hsing-Ju Chen
- Biodiversity Research Center, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
| | - Yu-Hsiang Chen
- Biodiversity Research Center, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
| | - Pei-Wen Chiang
- Biodiversity Research Center, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
| | - Sheng-Ping Yu
- Biodiversity Research Center, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
| | - Chih-Ying Lu
- Biodiversity Research Center, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei 11529, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan
| | - Yu-Jing Chiou
- Biodiversity Research Center, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
| | - Yung-Chi Tu
- Biodiversity Research Center, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
| | - Xuejiao Tian
- Research Center for Applied Sciences, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
| | - Bi-Chang Chen
- Research Center for Applied Sciences, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
| | - Der-Chuen Lee
- Institute of Earth Sciences, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
| | - Hideyuki Yamashiro
- Sesoko Station, Tropical Biosphere Research Center, University of the Ryukyus, 3422 Sesoko, Motobu, Okinawa 905-0227, Japan
| | - David G. Bourne
- College of Science and Engineering, James Cook University, Townsville, 4811 QLD, Australia
- Australian Institute of Marine Science, Townsville, 4810 QLD, Australia
- AIMS@JCU, Townsville, 4811 QLD, Australia
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
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Liao C, Huang X, Wang Q, Yao D, Lu W. Virulence Factors of Pseudomonas Aeruginosa and Antivirulence Strategies to Combat Its Drug Resistance. Front Cell Infect Microbiol 2022; 12:926758. [PMID: 35873152 PMCID: PMC9299443 DOI: 10.3389/fcimb.2022.926758] [Citation(s) in RCA: 86] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 06/09/2022] [Indexed: 11/24/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen causing nosocomial infections in severely ill and immunocompromised patients. Ubiquitously disseminated in the environment, especially in hospitals, it has become a major threat to human health due to the constant emergence of drug-resistant strains. Multiple resistance mechanisms are exploited by P. aeruginosa, which usually result in chronic infections difficult to eradicate. Diverse virulence factors responsible for bacterial adhesion and colonization, host immune suppression, and immune escape, play important roles in the pathogenic process of P. aeruginosa. As such, antivirulence treatment that aims at reducing virulence while sparing the bacterium for its eventual elimination by the immune system, or combination therapies, has significant advantages over traditional antibiotic therapy, as the former imposes minimal selective pressure on P. aeruginosa, thus less likely to induce drug resistance. In this review, we will discuss the virulence factors of P. aeruginosa, their pathogenic roles, and recent advances in antivirulence drug discovery for the treatment of P. aeruginosa infections.
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Affiliation(s)
- Chongbing Liao
- Key Laboratory of Medical Molecular Virology (Ministry of Education (MOE)/National Health Commission (NHC)/Chinese Academy of Medical Sciences (CAMS)), School of Basic Medical Science, Fudan University, Shanghai, China
| | - Xin Huang
- Key Laboratory of Medical Molecular Virology (Ministry of Education (MOE)/National Health Commission (NHC)/Chinese Academy of Medical Sciences (CAMS)), School of Basic Medical Science, Fudan University, Shanghai, China
| | - Qingxia Wang
- Key Laboratory of Medical Molecular Virology (Ministry of Education (MOE)/National Health Commission (NHC)/Chinese Academy of Medical Sciences (CAMS)), School of Basic Medical Science, Fudan University, Shanghai, China
| | - Dan Yao
- Key Laboratory of Medical Molecular Virology (Ministry of Education (MOE)/National Health Commission (NHC)/Chinese Academy of Medical Sciences (CAMS)), School of Basic Medical Science, Fudan University, Shanghai, China
| | - Wuyuan Lu
- Key Laboratory of Medical Molecular Virology (Ministry of Education (MOE)/National Health Commission (NHC)/Chinese Academy of Medical Sciences (CAMS)), School of Basic Medical Science, Fudan University, Shanghai, China
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
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Lee J, Lee DW. Insecticidal Serralysin of Serratia marcescens Is Detoxified in M3 Midgut Region of Riptortus pedestris. Front Microbiol 2022; 13:913113. [PMID: 35711769 PMCID: PMC9197470 DOI: 10.3389/fmicb.2022.913113] [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: 04/05/2022] [Accepted: 05/06/2022] [Indexed: 11/18/2022] Open
Abstract
Riptortus pedestris insect indiscriminately acquires not only the symbiotic bacterium Burkholderia insecticola, but also entomopathogens that are abundant in the soil via feeding. However, it is unclear how the host insect survives oral infections of entomopathogens. A previous study suggested that serralysin, a potent virulence factor produced by Serratia marcescens, suppresses cellular immunity by degrading adhesion molecules, thereby contributing to bacterial pathogenesis. Here, we observed that S. marcescens orally administered to R. pedestris stably colonized the insect midgut, while not exhibiting insecticidal activity. Additionally, oral infection with S. marcescens did not affect the host growth or fitness. When co-incubated with the midgut lysates of R. pedestris, serralysin was remarkably degraded. The detoxification activity against serralysin was enhanced in the midgut extract of gut symbiont-colonizing insects. The mRNA expression levels of serralysin genes were negligible in M3-colonizing S. marcescens. M3-colonizing S. marcescens did not produce serralysin toxin. Immunoblot analyses revealed that serralysin was not detected in the M3 midgut region. The findings of our study suggest that orally infected S. marcescens lose entomopathogenicity through host-derived degrading factors and suppression of serralysin.
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Affiliation(s)
- Junbeom Lee
- Metabolomics Research Center for Functional Materials, Kyungsung University, Busan, South Korea
| | - Dae-Weon Lee
- Metabolomics Research Center for Functional Materials, Kyungsung University, Busan, South Korea.,Department of SmartBio, Kyungsung University, Busan, South Korea
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Muneeswari R, Iyappan S, Swathi KV, Vinu R, Ramani K, Sekaran G. Biocatalytic lipoprotein bioamphiphile induced treatment of recalcitrant hydrocarbons in petroleum refinery oil sludge through transposon technology. JOURNAL OF HAZARDOUS MATERIALS 2022; 431:128520. [PMID: 35228072 DOI: 10.1016/j.jhazmat.2022.128520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/04/2022] [Accepted: 02/17/2022] [Indexed: 06/14/2023]
Abstract
The present investigation employed transposon technology to enhance the degradation of recalcitrant petroleum hydrocarbons present in petroleum oil sludge by using biosurfactant hyper-producing strain Enterobacter xiangfangensis STP-3. Out of 2500 transposon induced mutants, mutants M257E.xiangfangensis and M916E.xiangfangensis hyper-produce biocatalytic lipoprotein biosurfactant by1.98 and 2.34 fold higher than wild-type strain. Transposon induced mutation also modified the amino acid composition which improved the hydrophobicity and thermal stability of the biosurfactants produced by mutants, compared to the wild-type biosurfactant. GC-MS and LC-MS-MS revealed that biosurfactants have pentameric lipid moiety and esterase as protein moiety. Increased biosurfactant hydrophobicity and yield by the mutants resulted in the enhanced bioavailability of petroleum hydrocarbons, thereby mutants M257E.xiangfangensis and M916E.xiangfangensis demonstrated better petroleum oil sludge degradation by 82% and 88% respectively, than wild-type (72%). Disrupted genes vgr G and pgm M in M257E.xiangfangensis and M916E.xiangfangensis respectively hyper-produce biosurfactant by competitive pathway inhibition and increased precursor availability mechanism. Hyper-production of biosurfactant was also validated by comparing the expression of biosynthetic genes ent E, ent F and est using qPCR. This is the first report on the application of transposon technology to hyper-produce biosurfactant for the effective bioremediation of hydrocarbon contaminated environments.
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Affiliation(s)
- R Muneeswari
- Biomolecules and Biocatalysis Laboratory, Department of Biotechnology, SRM Institute of Science and Technology, Kancheepuram District, Kattankulathur 603203, Tamil Nadu, India
| | - S Iyappan
- Department of Genetic Engineering, SRM Institute of Science and Technology, Kancheepuram District, Kattankulathur 603203, Tamil Nadu, India
| | - K V Swathi
- Biomolecules and Biocatalysis Laboratory, Department of Biotechnology, SRM Institute of Science and Technology, Kancheepuram District, Kattankulathur 603203, Tamil Nadu, India
| | - R Vinu
- Department of Chemical Engineering, Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
| | - K Ramani
- Biomolecules and Biocatalysis Laboratory, Department of Biotechnology, SRM Institute of Science and Technology, Kancheepuram District, Kattankulathur 603203, Tamil Nadu, India.
| | - G Sekaran
- SRM Institute of Science and Technology, Ramapuram 600089, Tamil Nadu, India
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40
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Hieu DQ, Hang BTB, Lokesh J, Garigliany MM, Huong DTT, Yen DT, Liem PT, Tam BM, Hai DM, Son VN, Phuong NT, Farnir F, Kestemont P. Salinity significantly affects intestinal microbiota and gene expression in striped catfish juveniles. Appl Microbiol Biotechnol 2022; 106:3245-3264. [PMID: 35366085 DOI: 10.1007/s00253-022-11895-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/08/2022] [Accepted: 03/19/2022] [Indexed: 12/17/2022]
Abstract
In the present study, juvenile striped catfish (Pangasianodon hypophthalmus), a freshwater fish species, have been chronically exposed to a salinity gradient from freshwater to 20 psu (practical salinity unit) and were sampled at the beginning (D20) and the end (D34) of exposure. The results revealed that the intestinal microbial profile of striped catfish reared in freshwater conditions were dominated by the phyla Bacteroidetes, Firmicutes, Proteobacteria, and Verrucomicrobia. Alpha diversity measures (observed OTUs (operational taxonomic units), Shannon and Faith's PD (phylogenetic diversity)) showed a decreasing pattern as the salinities increased, except for the phylogenetic diversity at D34, which was showing an opposite trend. Furthermore, the beta diversity between groups was significantly different. Vibrio and Akkermansia genera were affected differentially with increasing salinity, the former being increased while the latter was decreased. The genus Sulfurospirillium was found predominantly in fish submitted to salinity treatments. Regarding the host response, the fish intestine likely contributed to osmoregulation by modifying the expression of osmoregulatory genes such as nka1a, nka1b, slc12a1, slc12a2, cftr, and aqp1, especially in fish exposed to 15 and 20 psu. The expression of heat shock proteins (hsp) hsp60, hsp70, and hsp90 was significantly increased in fish reared in 15 and 20 psu. On the other hand, the expression of pattern recognition receptors (PRRs) were inhibited in fish exposed to 20 psu at D20. In conclusion, the fish intestinal microbiota was significantly disrupted in salinities higher than 10 psu and these effects were proportional to the exposure time. In addition, the modifications of intestinal gene expression related to ion exchange and stressful responses may help the fish to adapt hyperosmotic environment. KEY POINTS: • It is the first study to provide detailed information on the gut microbiota of fish using the amplicon sequencing method. • Salinity environment significantly modified the intestinal microbiota of striped catfish. • Intestinal responses may help the fish adapt to hyperosmotic environment.
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Affiliation(s)
- Dang Quang Hieu
- Research Unit in Environmental and Evolutionary Biology, Institute of Life Earth & Environment (ILEE), University of Namur, Namur, Belgium.
| | - Bui Thi Bich Hang
- College of Aquaculture and Fisheries, Can Tho University, Can Tho City, Vietnam
| | - Jep Lokesh
- Université de Pau Et Des Pays de L'Adour, Saint-Pee-sur-Nivelle, E2S UPPA, INRAE, NuMéA, France
| | - Mutien-Marie Garigliany
- Department of Pathology, Faculty of Veterinary Medicine, University of Liège, Liege, Belgium
| | - Do Thi Thanh Huong
- College of Aquaculture and Fisheries, Can Tho University, Can Tho City, Vietnam
| | - Duong Thuy Yen
- College of Aquaculture and Fisheries, Can Tho University, Can Tho City, Vietnam
| | - Pham Thanh Liem
- College of Aquaculture and Fisheries, Can Tho University, Can Tho City, Vietnam
| | - Bui Minh Tam
- College of Aquaculture and Fisheries, Can Tho University, Can Tho City, Vietnam
| | - Dao Minh Hai
- College of Aquaculture and Fisheries, Can Tho University, Can Tho City, Vietnam.,Department of Animal Production, Faculty of Veterinary Medicine, University of Liège, Liege, Belgium
| | - Vo Nam Son
- College of Aquaculture and Fisheries, Can Tho University, Can Tho City, Vietnam
| | - Nguyen Thanh Phuong
- College of Aquaculture and Fisheries, Can Tho University, Can Tho City, Vietnam
| | - Frédéric Farnir
- Department of Animal Production, Faculty of Veterinary Medicine, University of Liège, Liege, Belgium
| | - Patrick Kestemont
- Research Unit in Environmental and Evolutionary Biology, Institute of Life Earth & Environment (ILEE), University of Namur, Namur, Belgium.
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41
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Pankratov TA, Nikitin PA, Patutina EO. Genome Analysis of Two Lichen Bacteriobionts, Lichenibacterium ramalinae and Lichenibacterium minor: Toxin‒Antitoxin Systems and Secretion Proteins. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722020096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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42
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Pan X, Tang M, You J, Osire T, Sun C, Fu W, Yi G, Yang T, Yang ST, Rao Z. PsrA is a novel regulator contributes to antibiotic synthesis, bacterial virulence, cell motility and extracellular polysaccharides production in Serratia marcescens. Nucleic Acids Res 2021; 50:127-148. [PMID: 34893884 PMCID: PMC8754645 DOI: 10.1093/nar/gkab1186] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/13/2021] [Accepted: 12/03/2021] [Indexed: 12/23/2022] Open
Abstract
Serratia marcescens is a Gram-negative bacterium of the Enterobacteriaceae family that can produce numbers of biologically active secondary metabolites. However, our understanding of the regulatory mechanisms behind secondary metabolites biosynthesis in S. marcescens remains limited. In this study, we identified an uncharacterized LysR family transcriptional regulator, encoding gene BVG90_12635, here we named psrA, that positively controlled prodigiosin synthesis in S. marcescens. This phenotype corresponded to PsrA positive control of transcriptional of the prodigiosin-associated pig operon by directly binding to a regulatory binding site (RBS) and an activating binding site (ABS) in the promoter region of the pig operon. We demonstrated that L-proline is an effector for the PsrA, which enhances the binding affinity of PsrA to its target promoters. Using transcriptomics and further experiments, we show that PsrA indirectly regulates pleiotropic phenotypes, including serrawettin W1 biosynthesis, extracellular polysaccharide production, biofilm formation, swarming motility and T6SS-mediated antibacterial activity in S. marcescens. Collectively, this study proposes that PsrA is a novel regulator that contributes to antibiotic synthesis, bacterial virulence, cell motility and extracellular polysaccharides production in S. marcescens and provides important clues for future studies exploring the function of the PsrA and PsrA-like proteins which are widely present in many other bacteria.
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Affiliation(s)
- Xuewei Pan
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Mi Tang
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Jiajia You
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Tolbert Osire
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Changhao Sun
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Weilai Fu
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China.,Fujian Dabeinong Aquatic Sci. & Tech. Co., Ltd., Zhangzhou 363500, China
| | - Ganfeng Yi
- Fujian Dabeinong Aquatic Sci. & Tech. Co., Ltd., Zhangzhou 363500, China
| | - Taowei Yang
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Shang-Tian Yang
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Zhiming Rao
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
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43
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Kitao T, Kubori T, Nagai H. Recent advances in structural studies of the Legionella pneumophila Dot/Icm type IV secretion system. Microbiol Immunol 2021; 66:67-74. [PMID: 34807482 PMCID: PMC9302130 DOI: 10.1111/1348-0421.12951] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 11/15/2021] [Indexed: 11/29/2022]
Abstract
The intracellular bacterial pathogen Legionella pneumophila utilizes the Dot/Icm type IV secretion system to translocate approximately 300 effector proteins to establish a replicative niche known as the Legionella‐containing vacuole. The Dot/Icm system is classified as a type IVB secretion system, which is evolutionarily closely related to the I‐type conjugation systems and is distinct from type IVA secretion systems, such as the Agrobacterium VirB/D4 system. Although both type IVA and IVB systems directly transport nucleic acids or proteins into the cytosol of recipient cells, the components and architecture of type IVB systems are much more complex than those of type IVA systems. Taking full advantage of rapidly developing cryo‐electron microscopy techniques, the structural details of the transport apparatus and coupling complexes in the Dot/Icm system have been clarified in the past few years. In this review, we summarize recent progress in the structural studies of the L. pneumophila type IVB secretion system and the insights gained into the mechanisms of substrate recognition and transport.
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Affiliation(s)
- Tomoe Kitao
- Department of Microbiology, Graduate School of Medicine, Gifu University, Gifu, Gifu, 501-1194, Japan
| | - Tomoko Kubori
- Department of Microbiology, Graduate School of Medicine, Gifu University, Gifu, Gifu, 501-1194, Japan.,G-CHAIN, Gifu University, Gifu, Gifu, 501-1194, Japan
| | - Hiroki Nagai
- Department of Microbiology, Graduate School of Medicine, Gifu University, Gifu, Gifu, 501-1194, Japan.,G-CHAIN, Gifu University, Gifu, Gifu, 501-1194, Japan
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44
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Nolan C, Behrends V. Sub-Inhibitory Antibiotic Exposure and Virulence in Pseudomonas aeruginosa. Antibiotics (Basel) 2021; 10:antibiotics10111393. [PMID: 34827331 PMCID: PMC8615142 DOI: 10.3390/antibiotics10111393] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/09/2021] [Accepted: 11/10/2021] [Indexed: 12/20/2022] Open
Abstract
Pseudomonas aeruginosa is a prime opportunistic pathogen, one of the most important causes of hospital-acquired infections and the major cause of morbidity and mortality in cystic fibrosis lung infections. One reason for the bacterium's pathogenic success is the large array of virulence factors that it can employ. Another is its high degree of intrinsic and acquired resistance to antibiotics. In this review, we first summarise the current knowledge about the regulation of virulence factor expression and production. We then look at the impact of sub-MIC antibiotic exposure and find that the virulence-antibiotic interaction for P. aeruginosa is antibiotic-specific, multifaceted, and complex. Most studies undertaken to date have been in vitro assays in batch culture systems, involving short-term (<24 h) antibiotic exposure. Therefore, we discuss the importance of long-term, in vivo-mimicking models for future work, particularly highlighting the need to account for bacterial physiology, which by extension governs both virulence factor expression and antibiotic tolerance/resistance.
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R M, S I, Kv S, Kp S, T R, G S, K R. Genomic characterization of Enterobacter xiangfangensis STP-3: Application to real time petroleum oil sludge bioremediation. Microbiol Res 2021; 253:126882. [PMID: 34619415 DOI: 10.1016/j.micres.2021.126882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/19/2021] [Accepted: 09/24/2021] [Indexed: 10/20/2022]
Abstract
Sustainable treatment of petroleum oil sludge still remains as a major challenge to petroleum refineries. Bioremediation is the promising technology involving bacteria for simultaneous production of biosurfactant and followed by degradation of petroleum compounds. Complete genomic knowledge on such potential microbes could accentuate its successful exploitation. The present study discusses the genomic characteristics of novel biosurfactant producing petrophilic/ petroleum hydrocarbon degrading strain, Enterobacter xiangfangensis STP-3, isolated from petroleum refinery oil sludge contaminated soil. The genome has 4,584,462 bp and 4372 protein coding sequences. Functional analysis using the RAST and KEGG databases revealed the presence of biosynthetic gene clusters linked to glycolipid and lipopeptide production and multiple key candidate genes linked with the degradation pathway of petroleum hydrocarbons. Orthology study revealed diversity in gene clusters associated to membrane transport, carbohydrate, amino acid metabolism, virulence and defence mechanisms, and nucleoside and nucleotide synthesis. The comparative analysis with 27 other genomes predicted that the core genome contributes to its inherent bioremediation potential, whereas the accessory genome influences its environmental adaptability in unconventional environmental conditions. Further, experimental results showed that E. xiangfangensis STP-3 was able to degrade PHCs by 82 % in 14 days during the bioremediation of real time petroleum oil sludge with the concomitant production of biosurfactant and metabolic enzymes, To the best of our knowledge, no comprehensive genomic study has been previously reported on the biotechnological prospective of this species.
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Affiliation(s)
- Muneeswari R
- Biomolecules and Biocatalysis Laboratory, Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, 603203, Kancheepuram District, Tamil Nadu, India
| | - Iyappan S
- Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, 603 203, Kancheepuram District, Tamil Nadu, India
| | - Swathi Kv
- Biomolecules and Biocatalysis Laboratory, Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, 603203, Kancheepuram District, Tamil Nadu, India
| | - Sudheesh Kp
- Nutrition, Genetics and Biotechnology Division, ICAR-Central Institute of Brackishwater Aquaculture, Chennai, 600028, Tamil Nadu, India
| | - Rajesh T
- CSIR-National Environmental Engineering Research Institute, Chennai Zonal Lab, Tamil Nadu, India
| | - Sekaran G
- Biomolecules and Biocatalysis Laboratory, Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, 603203, Kancheepuram District, Tamil Nadu, India
| | - Ramani K
- Biomolecules and Biocatalysis Laboratory, Department of Biotechnology, SRM Institute of Science and Technology, Kattankulathur, 603203, Kancheepuram District, Tamil Nadu, India.
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46
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Defending against the Type Six Secretion System: beyond Immunity Genes. Cell Rep 2021; 33:108259. [PMID: 33053336 DOI: 10.1016/j.celrep.2020.108259] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 07/10/2020] [Accepted: 09/21/2020] [Indexed: 02/07/2023] Open
Abstract
The bacterial type six secretion system (T6SS) delivers toxic effector proteins into neighboring cells, but bacteria must protect themselves against their own T6SS. Immunity genes are the best-characterized defenses, protecting against specific cognate effectors. However, the prevalence of the T6SS and the coexistence of species with heterologous T6SSs suggest evolutionary pressure selecting for additional defenses against it. Here we review defenses against the T6SS beyond self-associated immunity genes, such as diverse stress responses that can recognize T6SS-inflicted damage and coordinate induction of molecular armor, repair pathways, and overall survival. Some of these stress responses are required for full survival even in the presence of immunity genes. Finally, we propose that immunity gene-independent protection is, mechanistically, bacterial innate immunity and that such defenses and the T6SS have co-evolved and continue to shape one another in polymicrobial communities.
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Mendoza-Suárez M, Andersen SU, Poole PS, Sánchez-Cañizares C. Competition, Nodule Occupancy, and Persistence of Inoculant Strains: Key Factors in the Rhizobium-Legume Symbioses. FRONTIERS IN PLANT SCIENCE 2021; 12:690567. [PMID: 34489993 PMCID: PMC8416774 DOI: 10.3389/fpls.2021.690567] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 07/19/2021] [Indexed: 05/06/2023]
Abstract
Biological nitrogen fixation by Rhizobium-legume symbioses represents an environmentally friendly and inexpensive alternative to the use of chemical nitrogen fertilizers in legume crops. Rhizobial inoculants, applied frequently as biofertilizers, play an important role in sustainable agriculture. However, inoculants often fail to compete for nodule occupancy against native rhizobia with inferior nitrogen-fixing abilities, resulting in low yields. Strains with excellent performance under controlled conditions are typically selected as inoculants, but the rates of nodule occupancy compared to native strains are rarely investigated. Lack of persistence in the field after agricultural cycles, usually due to the transfer of symbiotic genes from the inoculant strain to naturalized populations, also limits the suitability of commercial inoculants. When rhizobial inoculants are based on native strains with a high nitrogen fixation ability, they often have superior performance in the field due to their genetic adaptations to the local environment. Therefore, knowledge from laboratory studies assessing competition and understanding how diverse strains of rhizobia behave, together with assays done under field conditions, may allow us to exploit the effectiveness of native populations selected as elite strains and to breed specific host cultivar-rhizobial strain combinations. Here, we review current knowledge at the molecular level on competition for nodulation and the advances in molecular tools for assessing competitiveness. We then describe ongoing approaches for inoculant development based on native strains and emphasize future perspectives and applications using a multidisciplinary approach to ensure optimal performance of both symbiotic partners.
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Affiliation(s)
| | - Stig U. Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Philip S. Poole
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
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48
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Boluk G, Arizala D, Dobhal S, Zhang J, Hu J, Alvarez AM, Arif M. Genomic and Phenotypic Biology of Novel Strains of Dickeya zeae Isolated From Pineapple and Taro in Hawaii: Insights Into Genome Plasticity, Pathogenicity, and Virulence Determinants. FRONTIERS IN PLANT SCIENCE 2021; 12:663851. [PMID: 34456933 PMCID: PMC8386352 DOI: 10.3389/fpls.2021.663851] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 06/30/2021] [Indexed: 05/04/2023]
Abstract
Dickeya zeae, a bacterial plant pathogen of the family Pectobacteriaceae, is responsible for a wide range of diseases on potato, maize, rice, banana, pineapple, taro, and ornamentals and significantly reduces crop production. D. zeae causes the soft rot of taro (Colocasia esculenta) and the heart rot of pineapple (Ananas comosus). In this study, we used Pacific Biosciences single-molecule real-time (SMRT) sequencing to sequence two high-quality complete genomes of novel strains of D. zeae: PL65 (size: 4.74997 MB; depth: 701x; GC: 53.6%) and A5410 (size: 4.7792 MB; depth: 558x; GC: 53.5%) isolated from economically important Hawaiian crops, taro, and pineapple, respectively. Additional complete genomes of D. zeae representing three additional hosts (philodendron, rice, and banana) and other species used for a taxonomic comparison were retrieved from the NCBI GenBank genome database. Genomic analyses indicated the truncated type III and IV secretion systems (T3SS and T4SS) in the taro strain, which only harbored one and two genes of T3SS and T4SS, respectively, and showed high heterogeneity in the type VI secretion system (T6SS). Unlike strain EC1, which was isolated from rice and recently reclassified as D. oryzae, neither the genome PL65 nor A5410 harbors the zeamine biosynthesis gene cluster, which plays a key role in virulence of other Dickeya species. The percentages of average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) between the two genomes were 94.47 and 57.00, respectively. In this study, we compared the major virulence factors [plant cell wall-degrading extracellular enzymes and protease (Prt)] produced by D. zeae strains and evaluated the virulence on taro corms and pineapple leaves. Both strains produced Prts, pectate lyases (Pels), and cellulases but no significant quantitative differences were observed (p > 0.05) between the strains. All the strains produced symptoms on taro corms and pineapple leaves, but the strain PL65 produced symptoms more rapidly than others. Our study highlights the genetic constituents of pathogenicity determinants and genomic heterogeneity that will help to understand the virulence mechanisms and aggressiveness of this plant pathogen.
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Affiliation(s)
- Gamze Boluk
- Department of Plant and Environmental Protection Sciences, University of Hawai’i at Mānoa, Honolulu, HI, United States
| | - Dario Arizala
- Department of Plant and Environmental Protection Sciences, University of Hawai’i at Mānoa, Honolulu, HI, United States
| | - Shefali Dobhal
- Department of Plant and Environmental Protection Sciences, University of Hawai’i at Mānoa, Honolulu, HI, United States
| | - Jingxin Zhang
- Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - John Hu
- Department of Plant and Environmental Protection Sciences, University of Hawai’i at Mānoa, Honolulu, HI, United States
| | - Anne M. Alvarez
- Department of Plant and Environmental Protection Sciences, University of Hawai’i at Mānoa, Honolulu, HI, United States
| | - Mohammad Arif
- Department of Plant and Environmental Protection Sciences, University of Hawai’i at Mānoa, Honolulu, HI, United States
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Abstract
Many bacterial species employ systems for interference competition with other microorganisms. Some systems are effective without contact (e.g., through secretion of toxins), while other systems (e.g., type VI secretion system [T6SS]) require direct contact between cells. Here, we provide the initial characterization of a novel contact-dependent competition system for Proteus mirabilis. In neonatal mice, a commensal P. mirabilis strain apparently eliminated commensal Escherichia coli. We replicated the phenotype in vitro and showed that P. mirabilis efficiently reduced the viability of several Enterobacteriaceae species but not Gram-positive species or yeast cells. Importantly, P. mirabilis strains isolated from humans also killed E. coli. A reduction of viability occurred from early stationary phase to 24 h of culture and was observed in shaking liquid media as well as on solid media. Killing required contact but was independent of T6SS, which is the only contact-dependent killing system described for P. mirabilis. Expression of the killing system was regulated by osmolarity and components secreted into the supernatant. Stationary-phase P. mirabilis culture supernatant itself did not kill but was sufficient to induce killing in an exponentially growing coculture. In contrast, killing was largely prevented in media with low osmolarity. In summary, we provide the initial characterization of a potentially novel interbacterial competition system used by P. mirabilis. IMPORTANCE The study of bacterial competition systems has received significant attention in recent years. These systems are important in a multitude of polymicrobial environments and collectively shape the composition of complex ecosystems like the mammalian gut. They are also being explored as narrow-spectrum alternatives to specifically eliminate problematic pathogenic species. However, only a small fraction of the estimated number of interbacterial competition systems has been identified. We discovered a competition system that is novel for Proteus mirabilis. Inspired by an observation in infant mice, we confirmed in vitro that P. mirabilis was able to efficiently kill several Enterobacteriaceae species. This killing system might represent a new function of a known competition system or even a novel system, as the observed characteristics do not fit with described contact-dependent competition systems. Further characterization of this system might help understand how P. mirabilis competes with other Enterobacteriaceae in various niches.
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Extracellular Proteome Analysis Shows the Abundance of Histidine Kinase Sensor Protein, DNA Helicase, Putative Lipoprotein Containing Peptidase M75 Domain and Peptidase C39 Domain Protein in Leptospira interrogans Grown in EMJH Medium. Pathogens 2021; 10:pathogens10070852. [PMID: 34358002 PMCID: PMC8308593 DOI: 10.3390/pathogens10070852] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 07/02/2021] [Accepted: 07/04/2021] [Indexed: 01/01/2023] Open
Abstract
Leptospirosis is a re-emerging form of zoonosis that is caused by the spirochete pathogen Leptospira. Extracellular proteins play critical roles in the pathogenicity and survival of this pathogen in the host and environment. Extraction and analysis of extracellular proteins is a difficult task due to the abundance of enrichments like serum and bovine serum albumin in the culture medium, as is distinguishing them from the cellular proteins that may reach the analyte during extraction. In this study, extracellular proteins were separated as secretory proteins from the culture supernatant and surface proteins were separated during the washing of the cell pellet. The proteins identified were sorted based on the proportion of the cellular fractions and the extracellular fractions. The results showed the identification of 56 extracellular proteins, out of which 19 were exclusively extracellular. For those proteins, the difference in quantity with respect to their presence within the cell was found to be up to 1770-fold. Further, bioinformatics analysis elucidated characteristics and functions of the identified proteins. Orthologs of extracellular proteins in various Leptospira species were found to be closely related among different pathogenic forms. In addition to the identification of extracellular proteins, this study put forward a method for the extraction and identification of extracellular proteins.
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