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Meidaninikjeh S, Mohammadi P, Elikaei A. Bacteriophages and bacterial extracellular vesicles, threat or opportunity? Life Sci 2024; 350:122749. [PMID: 38821215 DOI: 10.1016/j.lfs.2024.122749] [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: 12/04/2023] [Revised: 03/25/2024] [Accepted: 05/23/2024] [Indexed: 06/02/2024]
Abstract
Emergence of antimicrobial-resistant bacteria (AMR) is one of the health major problems worldwide. The scientists are looking for a novel method to treat infectious diseases. Phage therapy is considered a suitable approach for treating infectious diseases. However, there are different challenges in this way. Some biological aspects can probably influence on therapeutic results and further investigations are necessary to reach a successful phage therapy. Bacteriophage activity can influence by bacterial defense system. Bacterial extracellular vesicles (BEVs) are one of the bacterial defense mechanisms which can modify the results of bacteriophage activity. BEVs have the significant roles in the gene transferring, invasion, escape, and spreading of bacteriophages. In this review, the defense mechanisms of bacteria against bacteriophages, especially BEVs secretion, the hidden linkage of BEVs and bacteriophages, and its possible consequences on the bacteriophage activity as well phage therapy will be discussed.
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Affiliation(s)
- Sepideh Meidaninikjeh
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran.
| | - Parisa Mohammadi
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran; Research Center for Applied Microbiology and Microbial Biotechnology, Alzahra University, Tehran, Iran.
| | - Ameneh Elikaei
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran; Research Center for Applied Microbiology and Microbial Biotechnology, Alzahra University, Tehran, Iran.
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2
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Huang D, Xia R, Chen C, Liao J, Chen L, Wang D, Alvarez PJJ, Yu P. Adaptive strategies and ecological roles of phages in habitats under physicochemical stress. Trends Microbiol 2024:S0966-842X(24)00042-8. [PMID: 38433027 DOI: 10.1016/j.tim.2024.02.002] [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: 12/04/2023] [Revised: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 03/05/2024]
Abstract
Bacteriophages (phages) play a vital role in ecosystem functions by influencing the composition, genetic exchange, metabolism, and environmental adaptation of microbial communities. With recent advances in sequencing technologies and bioinformatics, our understanding of the ecology and evolution of phages in stressful environments has substantially expanded. Here, we review the impact of physicochemical environmental stress on the physiological state and community dynamics of phages, the adaptive strategies that phages employ to cope with environmental stress, and the ecological effects of phage-host interactions in stressful environments. Specifically, we highlight the contributions of phages to the adaptive evolution and functioning of microbiomes and suggest that phages and their hosts can maintain a mutualistic relationship in response to environmental stress. In addition, we discuss the ecological consequences caused by phages in stressful environments, encompassing biogeochemical cycling. Overall, this review advances an understanding of phage ecology in stressful environments, which could inform phage-based strategies to improve microbiome performance and ecosystem resilience and resistance in natural and engineering systems.
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Affiliation(s)
- Dan Huang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Rong Xia
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Chengyi Chen
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jingqiu Liao
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Linxing Chen
- Department of Earth and Planetary Sciences, University of California Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California Berkeley, Berkeley, CA 94720, USA
| | - Dongsheng Wang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Pedro J J Alvarez
- Department of Civil and Environmental Engineering, Rice University, Houston, TX 77005, USA
| | - Pingfeng Yu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, 314100, China.
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3
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Aitken JM, Aitken JE, Agrawal G. Mycobacterium avium ssp. paratuberculosis and Crohn's Disease-Diagnostic Microbiological Investigations Can Inform New Therapeutic Approaches. Antibiotics (Basel) 2024; 13:158. [PMID: 38391544 PMCID: PMC10886072 DOI: 10.3390/antibiotics13020158] [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: 12/04/2023] [Revised: 01/24/2024] [Accepted: 02/03/2024] [Indexed: 02/24/2024] Open
Abstract
Mycobacterium avium ssp. paratuberculosis (MAP) is the cause of Johne's disease (JD), which is a chronic infectious gastrointestinal disease of ruminants and is often fatal. In humans, MAP has been associated with Crohn's disease (CD) for over a century, without conclusive evidence of pathogenicity. Numerous researchers have contributed to the subject, but there is still a need for evidence of the causation of CD by MAP. An infectious aetiology in CD that is attributable to MAP can only be proven by bacteriological investigations. There is an urgency in resolving this question due to the rising global incidence rates of CD. Recent papers have indicated the "therapeutic ceiling" may be close in the development of new biologics. Clinical trial outcomes have demonstrated mild or inconsistent improvements in therapeutic interventions over the last decades when compared with placebo. The necessity to revisit therapeutic options for CD is becoming more urgent and a renewed focus on causation is essential for progress in identifying new treatment options. This manuscript discusses newer interventions, such as vaccination, FMT, dietary remediation and gut microbiome regulation, that will become more relevant as existing therapeutic options expire. Revisiting the MAP theory as a potential infectious cause of CD, rather than the prevailing concept of an "aberrant immune response" will require expanding the current therapeutic programme to include potential new alternatives, and combinations of existing treatments. To advance research on MAP in humans, it is essential for microbiologists and medical scientists to microscopically detect CWDM and to biologically amplify the growth by directed culture.
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Affiliation(s)
- John M Aitken
- Otakaro Pathways Ltd., Innovation Park, Christchurch 7675, New Zealand
| | - Jack E Aitken
- Otakaro Pathways Ltd., Innovation Park, Christchurch 7675, New Zealand
| | - Gaurav Agrawal
- Division of Diabetes & Nutritional Sciences, Franklin-Wilkins Building, King's College London, London SE1 9NH, UK
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Field CJ, Bowerman KL, Hugenholtz P. Multiple independent losses of sporulation and peptidoglycan in the Mycoplasmatales and related orders of the class Bacilli. Microb Genom 2024; 10:001176. [PMID: 38189216 PMCID: PMC10868615 DOI: 10.1099/mgen.0.001176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 12/19/2023] [Indexed: 01/09/2024] Open
Abstract
Many peptidoglycan-deficient bacteria such as the Mycoplasmatales are known host-associated lineages, lacking the environmental resistance mechanisms and metabolic capabilities necessary for a free-living lifestyle. Several peptidoglycan-deficient and non-sporulating orders of interest are thought to be descended from Gram-positive sporulating Bacilli through reductive evolution. Here we annotate 2650 genomes belonging to the class Bacilli, according to the Genome Taxonomy Database, to predict the peptidoglycan and sporulation phenotypes of three novel orders, RFN20, RF39 and ML615J-28, known only through environmental sequence surveys. These lineages are interspersed between peptidoglycan-deficient non-sporulating orders including the Mycoplasmatales and Acholeplasmatales, and more typical Gram-positive orders such as the Erysipelotrichales and Staphylococcales. We use the extant genotypes to perform ancestral state reconstructions. The novel orders are predicted to have small genomes with minimal metabolic capabilities and to comprise a mix of peptidoglycan-deficient and/or non-sporulating species. In contrast to expectations based on cultured representatives, the order Erysipelotrichales lacks many of the genes involved in peptidoglycan and endospore formation. The reconstructed evolutionary history of these traits suggests multiple independent whole-genome reductions and loss of phenotype via intermediate transition states that continue into the present. We suggest that the evolutionary history of the reduced-genome lineages within the class Bacilli is one driven by multiple independent transitions to host-associated lifestyles, with the degree of reduction in environmental resistance and metabolic capabilities correlated with degree of host association.
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Affiliation(s)
- Christian J. Field
- School of Chemistry and Molecular Biosciences, The Australian Centre for Ecogenomics, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Kate L. Bowerman
- School of Chemistry and Molecular Biosciences, The Australian Centre for Ecogenomics, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Philip Hugenholtz
- School of Chemistry and Molecular Biosciences, The Australian Centre for Ecogenomics, The University of Queensland, St Lucia, QLD 4072, Australia
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Lim JS, Chai YY, Ser WX, Haeren AV, Lim YH, Raja T, Foo JB, Hamzah S, Sellappans R, Yow HY. Novel drug candidates against antibiotic-resistant microorganisms: A review. IRANIAN JOURNAL OF BASIC MEDICAL SCIENCES 2024; 27:134-150. [PMID: 38234674 PMCID: PMC10790292 DOI: 10.22038/ijbms.2023.71672.15593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 08/12/2023] [Indexed: 01/19/2024]
Abstract
Antibiotic resistance is fast spreading globally, leading to treatment failures and adverse clinical outcomes. This review focuses on the resistance mechanisms of the top five threatening pathogens identified by the World Health Organization's global priority pathogens list: carbapenem-resistant Acinetobacter baumannii, carbapenem-resistant Pseudomonas aeruginosa, carbapenem-resistant, extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae, vancomycin-resistant Enterococcus faecium and methicillin, vancomycin-resistant Staphylococcus aureus. Several novel drug candidates have shown promising results from in vitro and in vivo studies, as well as clinical trials. The novel drugs against carbapenem-resistant bacteria include LCB10-0200, apramycin, and eravacycline, while for Enterobacteriaceae, the drug candidates are LysSAP-26, DDS-04, SPR-206, nitroxoline, cefiderocol, and plazomicin. TNP-209, KBP-7072, and CRS3123 are agents against E. faecium, while Debio 1450, gepotidacin, delafloxacin, and dalbavancin are drugs against antibiotic-resistant S. aureus. In addition to these identified drug candidates, continued in vitro and in vivo studies are required to investigate small molecules with potential antibacterial effects screened by computational receptor docking. As drug discovery progresses, preclinical and clinical studies should also be extensively conducted on the currently available therapeutic agents to unravel their potential antibacterial effect and spectrum of activity, as well as safety and efficacy profiles.
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Affiliation(s)
- Jing-Sheng Lim
- School of Pharmacy, Faculty of Health and Medical Sciences, Taylor’s University, Subang Jaya, Malaysia
| | - Yoke-Yen Chai
- School of Pharmacy, Faculty of Health and Medical Sciences, Taylor’s University, Subang Jaya, Malaysia
| | - Wei-Xin Ser
- School of Pharmacy, Faculty of Health and Medical Sciences, Taylor’s University, Subang Jaya, Malaysia
| | - Aniqah Van Haeren
- School of Pharmacy, Faculty of Health and Medical Sciences, Taylor’s University, Subang Jaya, Malaysia
| | - Yan-Hong Lim
- School of Pharmacy, Faculty of Health and Medical Sciences, Taylor’s University, Subang Jaya, Malaysia
| | - Tarshiiny Raja
- School of Pharmacy, Faculty of Health and Medical Sciences, Taylor’s University, Subang Jaya, Malaysia
| | - Jhi-Biau Foo
- School of Pharmacy, Faculty of Health and Medical Sciences, Taylor’s University, Subang Jaya, Malaysia
- Medical Advancement for Better Quality of Life Impact Lab, Taylor’s University, 47500 Selangor, Malaysia
| | - Sharina Hamzah
- School of Pharmacy, Faculty of Health and Medical Sciences, Taylor’s University, Subang Jaya, Malaysia
- Medical Advancement for Better Quality of Life Impact Lab, Taylor’s University, 47500 Selangor, Malaysia
| | - Renukha Sellappans
- School of Pharmacy, Faculty of Health and Medical Sciences, Taylor’s University, Subang Jaya, Malaysia
| | - Hui Yin Yow
- School of Pharmacy, Faculty of Health and Medical Sciences, Taylor’s University, Subang Jaya, Malaysia
- Department of Pharmaceutical Life Sciences, Faculty of Pharmacy, Universiti Malaya, Kuala Lumpur, Malaysia
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Bratkovič T, Zahirović A, Bizjak M, Rupnik M, Štrukelj B, Berlec A. New treatment approaches for Clostridioides difficile infections: alternatives to antibiotics and fecal microbiota transplantation. Gut Microbes 2024; 16:2337312. [PMID: 38591915 PMCID: PMC11005816 DOI: 10.1080/19490976.2024.2337312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 03/27/2024] [Indexed: 04/10/2024] Open
Abstract
Clostridioides difficile causes a range of debilitating intestinal symptoms that may be fatal. It is particularly problematic as a hospital-acquired infection, causing significant costs to the health care system. Antibiotics, such as vancomycin and fidaxomicin, are still the drugs of choice for C. difficile infections, but their effectiveness is limited, and microbial interventions are emerging as a new treatment option. This paper focuses on alternative treatment approaches, which are currently in various stages of development and can be divided into four therapeutic strategies. Direct killing of C. difficile (i) includes beside established antibiotics, less studied bacteriophages, and their derivatives, such as endolysins and tailocins. Restoration of microbiota composition and function (ii) is achieved with fecal microbiota transplantation, which has recently been approved, with standardized defined microbial mixtures, and with probiotics, which have been administered with moderate success. Prevention of deleterious effects of antibiotics on microbiota is achieved with agents for the neutralization of antibiotics that act in the gut and are nearing regulatory approval. Neutralization of C. difficile toxins (iii) which are crucial virulence factors is achieved with antibodies/antibody fragments or alternative binding proteins. Of these, the monoclonal antibody bezlotoxumab is already in clinical use. Immunomodulation (iv) can help eliminate or prevent C. difficile infection by interfering with cytokine signaling. Small-molecule agents without bacteriolytic activity are usually selected by drug repurposing and can act via a variety of mechanisms. The multiple treatment options described in this article provide optimism for the future treatment of C. difficile infection.
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Affiliation(s)
- Tomaž Bratkovič
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Abida Zahirović
- Department of Biotechnology, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Maruša Bizjak
- Department of Biotechnology, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Maja Rupnik
- National Laboratory for Health, Environment and Food, Prvomajska 1, Maribor, Slovenia
- Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Borut Štrukelj
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
- Department of Biotechnology, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Aleš Berlec
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
- Department of Biotechnology, Jožef Stefan Institute, Ljubljana, Slovenia
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Unveil the Secret of the Bacteria and Phage Arms Race. Int J Mol Sci 2023; 24:ijms24054363. [PMID: 36901793 PMCID: PMC10002423 DOI: 10.3390/ijms24054363] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 02/25/2023] Open
Abstract
Bacteria have developed different mechanisms to defend against phages, such as preventing phages from being adsorbed on the surface of host bacteria; through the superinfection exclusion (Sie) block of phage's nucleic acid injection; by restricting modification (R-M) systems, CRISPR-Cas, aborting infection (Abi) and other defense systems to interfere with the replication of phage genes in the host; through the quorum sensing (QS) enhancement of phage's resistant effect. At the same time, phages have also evolved a variety of counter-defense strategies, such as degrading extracellular polymeric substances (EPS) that mask receptors or recognize new receptors, thereby regaining the ability to adsorb host cells; modifying its own genes to prevent the R-M systems from recognizing phage genes or evolving proteins that can inhibit the R-M complex; through the gene mutation itself, building nucleus-like compartments or evolving anti-CRISPR (Acr) proteins to resist CRISPR-Cas systems; and by producing antirepressors or blocking the combination of autoinducers (AIs) and its receptors to suppress the QS. The arms race between bacteria and phages is conducive to the coevolution between bacteria and phages. This review details bacterial anti-phage strategies and anti-defense strategies of phages and will provide basic theoretical support for phage therapy while deeply understanding the interaction mechanism between bacteria and phages.
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A Flexible and Efficient Microfluidics Platform for the Characterization and Isolation of Novel Bacteriophages. Appl Environ Microbiol 2023; 89:e0159622. [PMID: 36602353 PMCID: PMC9888219 DOI: 10.1128/aem.01596-22] [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] [Indexed: 01/06/2023] Open
Abstract
Bacteriophages are viruses that infect bacteria. This property makes them highly suitable for varied uses in industry or in the development of the treatment of bacterial infections. However, the conventional methods that are used to isolate and analyze these bacteriophages from the environment are generally cumbersome and time consuming. Here, we adapted a high-throughput microfluidic setup for long-term analysis of bacteriophage-bacteria interaction and demonstrate isolation of phages from environmental samples. IMPORTANCE Bacteriophages are gaining increased attention for their potential application as agents to combat antibiotic-resistant infections. However, isolation and characterization of new phages are time consuming and limited by currently used methods. The microfluidics platform presented here allows the isolation and long-term analysis of phages and their effect on host cells with fluorescent light microscopy imaging. Furthermore, this new workflow allows high-throughput characterization of environmental samples for the identification of phages alongside gaining detailed insight into the host response. Taken together, this microfluidics platform will be a valuable tool for phage research, enabling faster and more efficient screening and characterization of host-phage interactions.
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Rastmanesh R. Microbial Repercussion on Hemodialysis Catheter-Related Bloodstream Infection Outcome: A 2-Year Retrospective Study: An Escape Mechanism Comment [Letter]. Infect Drug Resist 2021; 14:4361-4362. [PMID: 34707379 PMCID: PMC8542588 DOI: 10.2147/idr.s342637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 10/12/2021] [Indexed: 11/23/2022] Open
Affiliation(s)
- Reza Rastmanesh
- Independent Researcher, Private Clinic, Tehran, Iran.,The Nutrition Society, London, UK.,American Physical Society, College Park, MD, USA
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