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Chen J, Jia Y, Sun Y, Liu K, Zhou C, Liu C, Li D, Liu G, Zhang C, Yang T, Huang L, Zhuang Y, Wang D, Xu D, Zhong Q, Guo Y, Li A, Seim I, Jiang L, Wang L, Lee SMY, Liu Y, Wang D, Zhang G, Liu S, Wei X, Yue Z, Zheng S, Shen X, Wang S, Qi C, Chen J, Ye C, Zhao F, Wang J, Fan J, Li B, Sun J, Jia X, Xia Z, Zhang H, Liu J, Zheng Y, Liu X, Wang J, Yang H, Kristiansen K, Xu X, Mock T, Li S, Zhang W, Fan G. Global marine microbial diversity and its potential in bioprospecting. Nature 2024; 633:371-379. [PMID: 39232160 DOI: 10.1038/s41586-024-07891-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 07/31/2024] [Indexed: 09/06/2024]
Abstract
The past two decades has witnessed a remarkable increase in the number of microbial genomes retrieved from marine systems1,2. However, it has remained challenging to translate this marine genomic diversity into biotechnological and biomedical applications3,4. Here we recovered 43,191 bacterial and archaeal genomes from publicly available marine metagenomes, encompassing a wide range of diversity with 138 distinct phyla, redefining the upper limit of marine bacterial genome size and revealing complex trade-offs between the occurrence of CRISPR-Cas systems and antibiotic resistance genes. In silico bioprospecting of these marine genomes led to the discovery of a novel CRISPR-Cas9 system, ten antimicrobial peptides, and three enzymes that degrade polyethylene terephthalate. In vitro experiments confirmed their effectiveness and efficacy. This work provides evidence that global-scale sequencing initiatives advance our understanding of how microbial diversity has evolved in the oceans and is maintained, and demonstrates how such initiatives can be sustainably exploited to advance biotechnology and biomedicine.
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Affiliation(s)
- Jianwei Chen
- BGI Research, Qingdao, China
- BGI Research, Shenzhen, China
- Qingdao Key Laboratory of Marine Genomics and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Ying Sun
- BGI Research, Qingdao, China.
- Qingdao Key Laboratory of Marine Genomics and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China.
| | - Kun Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | | | - Chuan Liu
- BGI Research, Shenzhen, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Chengsong Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Tao Yang
- China National GeneBank, BGI Research, Shenzhen, China
- Guangdong Genomics Data Center, BGI Research, Shenzhen, China
| | | | - Yunyun Zhuang
- Key Laboratory of Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, China
| | - Dazhi Wang
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | | | | | - Yang Guo
- BGI Research, Qingdao, China
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | | | - Inge Seim
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Ling Jiang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Simon Ming Yuen Lee
- Department of Food Science and Nutrition, and PolyU-BGI Joint Research Centre for Genomics and Synthetic Biology in Global Deep Ocean Resource, The Hong Kong Polytechnic University, Hong Kong, China
| | - Yujing Liu
- BGI Research, Qingdao, China
- Qingdao Key Laboratory of Marine Genomics and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China
| | | | - Guoqiang Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | | | - Xiaofeng Wei
- China National GeneBank, BGI Research, Shenzhen, China
- Guangdong Genomics Data Center, BGI Research, Shenzhen, China
| | | | - Shanmin Zheng
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | | | - Sen Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Chen Qi
- BGI Research, Shenzhen, China
| | - Jing Chen
- Guangdong Genomics Data Center, BGI Research, Shenzhen, China
| | - Chen Ye
- BGI Research, Shenzhen, China
| | | | | | - Jie Fan
- BGI Research, Qingdao, China
- Qingdao Key Laboratory of Marine Genomics and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China
| | | | | | - Xiaodong Jia
- Joint Laboratory for Translational Medicine Research, Liaocheng People's Hospital, Liaocheng, China
| | - Zhangyong Xia
- Department of Neurology, The Second People's Hospital of Liaocheng, Liaocheng, China
| | - He Zhang
- BGI Research, Qingdao, China
- BGI Research, Shenzhen, China
| | | | | | - Xin Liu
- BGI Research, Qingdao, China
- BGI Research, Shenzhen, China
| | | | | | - Karsten Kristiansen
- BGI Research, Shenzhen, China
- Qingdao Key Laboratory of Marine Genomics and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xun Xu
- BGI Research, Qingdao, China
- BGI Research, Shenzhen, China
- Qingdao Key Laboratory of Marine Genomics and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, China
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK.
| | - Shengying Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China.
| | - Wenwei Zhang
- BGI Research, Shenzhen, China.
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, China.
| | - Guangyi Fan
- BGI Research, Qingdao, China.
- BGI Research, Shenzhen, China.
- Qingdao Key Laboratory of Marine Genomics and Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, China.
- Department of Food Science and Nutrition, and PolyU-BGI Joint Research Centre for Genomics and Synthetic Biology in Global Deep Ocean Resource, The Hong Kong Polytechnic University, Hong Kong, China.
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, China.
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Belay WY, Getachew M, Tegegne BA, Teffera ZH, Dagne A, Zeleke TK, Abebe RB, Gedif AA, Fenta A, Yirdaw G, Tilahun A, Aschale Y. Mechanism of antibacterial resistance, strategies and next-generation antimicrobials to contain antimicrobial resistance: a review. Front Pharmacol 2024; 15:1444781. [PMID: 39221153 PMCID: PMC11362070 DOI: 10.3389/fphar.2024.1444781] [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: 06/06/2024] [Accepted: 08/05/2024] [Indexed: 09/04/2024] Open
Abstract
Antibacterial drug resistance poses a significant challenge to modern healthcare systems, threatening our ability to effectively treat bacterial infections. This review aims to provide a comprehensive overview of the types and mechanisms of antibacterial drug resistance. To achieve this aim, a thorough literature search was conducted to identify key studies and reviews on antibacterial resistance mechanisms, strategies and next-generation antimicrobials to contain antimicrobial resistance. In this review, types of resistance and major mechanisms of antibacterial resistance with examples including target site modifications, decreased influx, increased efflux pumps, and enzymatic inactivation of antibacterials has been discussed. Moreover, biofilm formation, and horizontal gene transfer methods has also been included. Furthermore, measures (interventions) taken to control antimicrobial resistance and next-generation antimicrobials have been discussed in detail. Overall, this review provides valuable insights into the diverse mechanisms employed by bacteria to resist the effects of antibacterial drugs, with the aim of informing future research and guiding antimicrobial stewardship efforts.
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Affiliation(s)
- Wubetu Yihunie Belay
- Department of Pharmacy, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Melese Getachew
- Department of Pharmacy, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Bantayehu Addis Tegegne
- Department of Pharmacy, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Zigale Hibstu Teffera
- Department of Medical Laboratory Science, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Abebe Dagne
- Department of Pharmacy, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Tirsit Ketsela Zeleke
- Department of Pharmacy, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Rahel Belete Abebe
- Department of clinical pharmacy, College of medicine and health sciences, University of Gondar, Gondar, Ethiopia
| | - Abebaw Abie Gedif
- Department of Pharmacy, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Abebe Fenta
- Department of Medical Laboratory Science, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Getasew Yirdaw
- Department of environmental health science, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Adane Tilahun
- Department of Medical Laboratory Science, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Yibeltal Aschale
- Department of Medical Laboratory Science, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
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3
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Kadkhoda H, Gholizadeh P, Samadi Kafil H, Ghotaslou R, Pirzadeh T, Ahangarzadeh Rezaee M, Nabizadeh E, Feizi H, Aghazadeh M. Role of CRISPR-Cas systems and anti-CRISPR proteins in bacterial antibiotic resistance. Heliyon 2024; 10:e34692. [PMID: 39149034 PMCID: PMC11325803 DOI: 10.1016/j.heliyon.2024.e34692] [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: 03/14/2024] [Revised: 07/08/2024] [Accepted: 07/15/2024] [Indexed: 08/17/2024] Open
Abstract
The emergence and development of antibiotic resistance in bacteria is a serious threat to global public health. Antibiotic resistance genes (ARGs) are often located on mobile genetic elements (MGEs). They can be transferred among bacteria by horizontal gene transfer (HGT), leading to the spread of drug-resistant strains and antibiotic treatment failure. CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated genes) is one of the many strategies bacteria have developed under long-term selection pressure to restrict the HGT. CRISPR-Cas systems exist in about half of bacterial genomes and play a significant role in limiting the spread of antibiotic resistance. On the other hand, bacteriophages and other MGEs encode a wide range of anti-CRISPR proteins (Acrs) to counteract the immunity of the CRISPR-Cas system. The Acrs could decrease the CRISPR-Cas system's activity against phages and facilitate the acquisition of ARGs and virulence traits for bacteria. This review aimed to assess the relationship between the CRISPR-Cas systems and Acrs with bacterial antibiotic resistance. We also highlighted the CRISPR technology and Acrs to control and prevent antibacterial resistance. The CRISPR-Cas system can target nucleic acid sequences with high accuracy and reliability; therefore, it has become a novel gene editing and gene therapy tool to prevent the spread of antibiotic resistance. CRISPR-based approaches may pave the way for developing smart antibiotics, which could eliminate multidrug-resistant (MDR) bacteria and distinguish between pathogenic and beneficial microorganisms. Additionally, the engineered anti-CRISPR gene-containing phages in combination with antibiotics could be used as a cutting-edge treatment approach to reduce antibiotic resistance.
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Affiliation(s)
- Hiva Kadkhoda
- Department of Medical Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Pourya Gholizadeh
- Digestive Disease Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
- Zoonoses Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Hossein Samadi Kafil
- Department of Medical Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Reza Ghotaslou
- Department of Medical Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Tahereh Pirzadeh
- Department of Medical Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Ahangarzadeh Rezaee
- Department of Medical Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Edris Nabizadeh
- Department of Medical Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hadi Feizi
- Department of Medical Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Medical Microbiology, Aalinasab Hospital, Social Security Organization, Tabriz, Iran
| | - Mohammad Aghazadeh
- Department of Medical Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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4
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Kogay R, Wolf YI, Koonin EV. Defence systems and horizontal gene transfer in bacteria. Environ Microbiol 2024; 26:e16630. [PMID: 38643972 PMCID: PMC11034907 DOI: 10.1111/1462-2920.16630] [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: 02/09/2024] [Accepted: 04/05/2024] [Indexed: 04/23/2024]
Abstract
Horizontal gene transfer (HGT) is a fundamental process in prokaryotic evolution, contributing significantly to diversification and adaptation. HGT is typically facilitated by mobile genetic elements (MGEs), such as conjugative plasmids and phages, which often impose fitness costs on their hosts. However, a considerable number of bacterial genes are involved in defence mechanisms that limit the propagation of MGEs, suggesting they may actively restrict HGT. In our study, we investigated whether defence systems limit HGT by examining the relationship between the HGT rate and the presence of 73 defence systems across 12 bacterial species. We discovered that only six defence systems, three of which were different CRISPR-Cas subtypes, were associated with a reduced gene gain rate at the species evolution scale. Hosts of these defence systems tend to have a smaller pangenome size and fewer phage-related genes compared to genomes without these systems. This suggests that these defence mechanisms inhibit HGT by limiting prophage integration. We hypothesize that the restriction of HGT by defence systems is species-specific and depends on various ecological and genetic factors, including the burden of MGEs and the fitness effect of HGT in bacterial populations.
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Affiliation(s)
- Roman Kogay
- National Center for Biotechnology Information, National Library of Medicine. National Institutes of Health, Bethesda, MD 20894, USA
| | - Yuri I. Wolf
- National Center for Biotechnology Information, National Library of Medicine. National Institutes of Health, Bethesda, MD 20894, USA
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine. National Institutes of Health, Bethesda, MD 20894, USA
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5
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Yousefi L, Kadkhoda H, Shirmohammadi M, Moaddab SY, Ghotaslou R, Tahereh pirzadeh, Sadeghi J, Somi MH, Ahangarzadeh Rezaee M, Ganbarov K, Samadi Kafil H. CRISPR-like sequences association with antibiotic resistance and biofilm formation in Helicobacter pylori clinical isolates. Heliyon 2024; 10:e26809. [PMID: 38449645 PMCID: PMC10915373 DOI: 10.1016/j.heliyon.2024.e26809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 01/31/2024] [Accepted: 02/20/2024] [Indexed: 03/08/2024] Open
Abstract
Role of clustered regularly interspaced short palindromic repeats (CRISPR)-like sequences in antibiotic resistance and biofilm formation isn't clear. This study investigated association of CRISPR-like sequences with antibiotic resistance and biofilm formation in H. pylori isolates. Thirty-six of H. pylori isolates were studied for existence of CRISPR-like sequences using PCR method and their correlation with biofilm formation and antibiotic resistance. Microtiter-plate technique was utilized for investigating antibiotic resistance profile of isolates against amoxicillin, tetracycline, metronidazole and clarithromycin. Biofilm formation of isolates was analyzed by microtiter-plate-based-method. Out of 23 CRISPR-like positive isolates, 19 had ability of biofilm formation and 7 of 13 CRISPR-like negative isolates were able to form biofilm (Pvalue = 0.445). In CRISPR-like positive isolates, 11 (48%), 18 (78%), 18 (78%) and 23 (100%) were resistant to amoxicillin, tetracycline, metronidazole and clarithromycin, respectively. Since CRISPR-like sequences have role in antibiotic resistance, may be applied as genetic markers of antibiotic resistance. But there was no substantial correlation between biofilm formation and existence of CRISPR-like sequences. These results indicate possible importance of CRISPR-like sequences on acquisition of resistance to antibiotics in this bacterium.
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Affiliation(s)
- Leila Yousefi
- Student Research Committee, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hiva Kadkhoda
- Drug Applied Research center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Masoud Shirmohammadi
- Liver and Gastrointestinal Diseases Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Seyyed Yaghoub Moaddab
- Liver and Gastrointestinal Diseases Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Reza Ghotaslou
- Drug Applied Research center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Tahereh pirzadeh
- Stem Cell Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Javid Sadeghi
- Drug Applied Research center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Hossein Somi
- Liver and Gastrointestinal Diseases Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Khudaverdi Ganbarov
- Research Laboratory of Microbiology and Virology, Baku State University, Z. Khalilov str., 23 AZ1148, Baku, Azerbaijan
| | - Hossein Samadi Kafil
- Drug Applied Research center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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6
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Kogay R, Wolf YI, Koonin EV. Defense systems and horizontal gene transfer in bacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.09.579689. [PMID: 38410456 PMCID: PMC10896350 DOI: 10.1101/2024.02.09.579689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Horizontal gene transfer (HGT) is a fundamental process in the evolution of prokaryotes, making major contributions to diversification and adaptation. Typically, HGT is facilitated by mobile genetic elements (MGEs), such as conjugative plasmids and phages that generally impose fitness costs on their hosts. However, a substantial fraction of bacterial genes is involved in defense mechanisms that limit the propagation of MGEs, raising the possibility that they can actively restrict HGT. Here we examine whether defense systems curb HGT by exploring the connections between HGT rate and the presence of 73 defense systems in 12 bacterial species. We found that only 6 defense systems, 3 of which are different CRISPR-Cas subtypes, are associated with the reduced gene gain rate on the scale of species evolution. The hosts of such defense systems tend to have a smaller pangenome size and harbor fewer phage-related genes compared to genomes lacking these systems, suggesting that these defense mechanisms inhibit HGT by limiting the integration of prophages. We hypothesize that restriction of HGT by defense systems is species-specific and depends on various ecological and genetic factors, including the burden of MGEs and fitness effect of HGT in bacterial populations.
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Affiliation(s)
- Roman Kogay
- National Center for Biotechnology Information, National Library of Medicine. National Institutes of Health, Bethesda, MD 20894, USA
| | - Yuri I. Wolf
- National Center for Biotechnology Information, National Library of Medicine. National Institutes of Health, Bethesda, MD 20894, USA
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine. National Institutes of Health, Bethesda, MD 20894, USA
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Shabbir MAB, Ul-Rahman A, Iftikhar MR, Rasheed M, Maan MK, Sattar A, Ahmad M, Khan FA, Ahmad W, Riaz MI, Aslam HB. Exploring the Interplay of the CRISPR-CAS System with Antibiotic Resistance in Staphylococcus aureus: A Poultry Meat Study from Lahore, Pakistan. MEDICINA (KAUNAS, LITHUANIA) 2024; 60:130. [PMID: 38256391 PMCID: PMC10818619 DOI: 10.3390/medicina60010130] [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: 12/19/2023] [Revised: 01/02/2024] [Accepted: 01/08/2024] [Indexed: 01/24/2024]
Abstract
Staphylococcus aureus is one of the major pathogens responsible for causing food poisoning worldwide. The emergence of antibiotic resistance in this bacterium is influenced by various factors. Among them, bacterial acquired defense systems described as clustered regularly interspaced short palindromic repeats (CRISPR)-cas system might be involved in antibiotic resistance development in bacteria. The current study was designed to assess the prevalence of S. aureus and its antibiotic resistance profile and identify the relationship of the CRISPR-cas system with antimicrobial resistance, followed by phylogenetic analysis. Total samples (n = 188) of poultry meat were collected from the poultry bird market of Lahore, Punjab, Pakistan. We used both phenotypic (antibiotic disc diffusion) and genotypic methods (PCR) to identify multi-drug resistant (MDR) strains of S. aureus. Additionally, the role of the CRISPR-Cas system in the isolated MDR S. aureus was also assessed. In addition, real-time quantitative PCR (qRT-PCR) was used to evaluate the association of the CRISPR-cas system with antimicrobial resistance. All of the S. aureus isolates showed 100% resistance against erythromycin, 97.5% were resistant to tetracycline, and 75% were resistant to methicillin. Eleven isolates were MDR in the current study. The CRISPR system was found in all MDR isolates, and fifteen spacers were identified within the CRISPR locus. Furthermore, MDR S. aureus isolates and the standard strain showed higher expression levels of CRISPR-associated genes. The correlation of said system with MDR isolates points to foreign gene acquisition by horizontal transfer. Current knowledge could be utilized to tackle antibiotic-resistant bacteria, mainly S. aureus.
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Affiliation(s)
- Muhammad Abu Bakr Shabbir
- Institute of Microbiology, Faculty of Veterinary Sciences, University of Veterinary and Animal Sciences, Lahore 54000, Pakistan (F.A.K.)
| | - Aziz Ul-Rahman
- Department of Pathobiology and Biomedical Sciences, Faculty of Veterinary and Animal Sciences, Muhammad Nawaz Shareef (MNS) University of Agriculture, Multan 66000, Pakistan;
| | - Muhammad Rizwan Iftikhar
- Institute of Microbiology, Faculty of Veterinary Sciences, University of Veterinary and Animal Sciences, Lahore 54000, Pakistan (F.A.K.)
| | - Majeeda Rasheed
- Department of life Sciences, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan 64200, Pakistan;
| | - Muhammad Kashif Maan
- Department of Veterinary Surgery, Faculty of Veterinary Sciences, University of Veterinary and Animal Sciences, Lahore 54000, Pakistan
| | - Adeel Sattar
- Department of Pharmacology and Toxicology, Faculty of Biosciences, University of Veterinary and Animal Sciences, Lahore 54000, Pakistan
| | - Mehmood Ahmad
- Department of Pharmacology and Toxicology, Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan;
| | - Farid Ahmed Khan
- Institute of Microbiology, Faculty of Veterinary Sciences, University of Veterinary and Animal Sciences, Lahore 54000, Pakistan (F.A.K.)
| | - Waqas Ahmad
- Department of Pathology, Faculty of Veterinary Sciences, University of Veterinary and Animal Sciences, Lahore 54000, Pakistan;
| | - Muhammad Ilyas Riaz
- Institute of Microbiology, Faculty of Veterinary Sciences, University of Veterinary and Animal Sciences, Lahore 54000, Pakistan (F.A.K.)
| | - Hassaan Bin Aslam
- Institute of Microbiology, Faculty of Veterinary Sciences, University of Veterinary and Animal Sciences, Lahore 54000, Pakistan (F.A.K.)
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8
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Kopf A, Bunk B, Riedel T, Schröttner P. The zoonotic pathogen Wohlfahrtiimonas chitiniclastica - current findings from a clinical and genomic perspective. BMC Microbiol 2024; 24:3. [PMID: 38172653 PMCID: PMC10763324 DOI: 10.1186/s12866-023-03139-7] [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: 08/01/2023] [Accepted: 11/29/2023] [Indexed: 01/05/2024] Open
Abstract
The zoonotic pathogen Wohlfahrtiimonas chitiniclastica can cause several diseases in humans, including sepsis and bacteremia. Although the pathogenesis is not fully understood, the bacterium is thought to enter traumatic skin lesions via fly larvae, resulting in severe myiasis and/or wound contamination. Infections are typically associated with, but not limited to, infestation of an open wound by fly larvae, poor sanitary conditions, cardiovascular disease, substance abuse, and osteomyelitis. W. chitiniclastica is generally sensitive to a broad spectrum of antibiotics with the exception of fosfomycin. However, increasing drug resistance has been observed and its development should be monitored with caution. In this review, we summarize the currently available knowledge and evaluate it from both a clinical and a genomic perspective.
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Affiliation(s)
- Anna Kopf
- Clinic for Cardiology, Sana Heart Center, Leipziger Str. 50, 03048, Cottbus, Germany
- 2nd Medical Clinic for Hematology, Oncology, Pneumology and Nephrology, Carl-Thiem Hospital Cottbus gGmbH, Cottbus, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstrasse 7 B, 38124, Braunschweig, Germany
| | - Thomas Riedel
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstrasse 7 B, 38124, Braunschweig, Germany
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany
| | - Percy Schröttner
- Institute for Medical Microbiology and Virology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.
- Institute for Clinical Chemistry and Laboratory Medicine, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.
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9
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Ramalingam S, Chandrasekar MJN, Krishnan GGN, Nanjan MJ. Plant-based Natural Products as inhibitors for Efflux Pumps to Reverse Multidrug Resistance in Staphylococcus aureus: A Mini Review. Mini Rev Med Chem 2024; 24:272-288. [PMID: 37038687 DOI: 10.2174/1389557523666230406092128] [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: 11/24/2022] [Revised: 02/09/2023] [Accepted: 02/22/2023] [Indexed: 04/12/2023]
Abstract
Wounds provide a favourable site for microbial infection. Wound infection makes the healing more complex and does not proceed in an orchestrated manner leading to the chronic wound. Clinically infected wounds require proper antimicrobial therapy. Broad-spectrum antibiotics are usually prescribed first before going to targeted therapy. The current conventional mode of therapy mainly depends on the use of antibiotics topically or systemically. Repeated and prolonged use of antibiotics, however, leads to multidrug resistance. Staphylococcus aureus is the most common multidrugresistant microorganism found in wounds. It effectively colonizes the wound and produces many toxins, thereby reducing the host immune response and causing recurrent infection, thus making the wound more complex. The overexpression of efflux pumps is one of the major reasons for the emergence of multidrug resistance. Inhibition of efflux pumps is, therefore, a potential strategy to reverse this resistance. The effective therapy to overcome this antibiotic resistance is to use combination therapy, namely the combination of an inhibitor, and a non-antibiotic compound with an antibiotic for their dual function. Many synthetic efflux pump inhibitors to treat wound infections are still under clinical trials. In this connection, several investigations have been carried out on plant-based natural products as multidrug resistance-modifying agents as they are believed to be safe, inexpensive and suitable for chronic wound infections.
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Affiliation(s)
- Shalini Ramalingam
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty, Nilgiris, Tamil Nadu, 643001, India
| | - Moola Joghee Nanjan Chandrasekar
- School of Life Sciences, JSS Academy of Higher Education & Research (Ooty Campus), Longwood, Mysuru Road, Ooty, The Nilgiris, Tamil Nadu, 643001, India
| | - Ganesh G N Krishnan
- Department of Pharmaceutics, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty, Nilgiris, Tamil Nadu, 643001, India
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Kumar V, Yasmeen N, Pandey A, Ahmad Chaudhary A, Alawam AS, Ahmad Rudayni H, Islam A, Lakhawat SS, Sharma PK, Shahid M. Antibiotic adjuvants: synergistic tool to combat multi-drug resistant pathogens. Front Cell Infect Microbiol 2023; 13:1293633. [PMID: 38179424 PMCID: PMC10765517 DOI: 10.3389/fcimb.2023.1293633] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 11/14/2023] [Indexed: 01/06/2024] Open
Abstract
The rise of multi-drug resistant (MDR) pathogens poses a significant challenge to the field of infectious disease treatment. To overcome this problem, novel strategies are being explored to enhance the effectiveness of antibiotics. Antibiotic adjuvants have emerged as a promising approach to combat MDR pathogens by acting synergistically with antibiotics. This review focuses on the role of antibiotic adjuvants as a synergistic tool in the fight against MDR pathogens. Adjuvants refer to compounds or agents that enhance the activity of antibiotics, either by potentiating their effects or by targeting the mechanisms of antibiotic resistance. The utilization of antibiotic adjuvants offers several advantages. Firstly, they can restore the effectiveness of existing antibiotics against resistant strains. Adjuvants can inhibit the mechanisms that confer resistance, making the pathogens susceptible to the action of antibiotics. Secondly, adjuvants can enhance the activity of antibiotics by improving their penetration into bacterial cells, increasing their stability, or inhibiting efflux pumps that expel antibiotics from bacterial cells. Various types of antibiotic adjuvants have been investigated, including efflux pump inhibitors, resistance-modifying agents, and compounds that disrupt bacterial biofilms. These adjuvants can act synergistically with antibiotics, resulting in increased antibacterial activity and overcoming resistance mechanisms. In conclusion, antibiotic adjuvants have the potential to revolutionize the treatment of MDR pathogens. By enhancing the efficacy of antibiotics, adjuvants offer a promising strategy to combat the growing threat of antibiotic resistance. Further research and development in this field are crucial to harness the full potential of antibiotic adjuvants and bring them closer to clinical application.
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Affiliation(s)
- Vikram Kumar
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, Rajasthan, India
- Amity Institute of Pharmacy, Amity University Rajasthan, Jaipur, Rajasthan, India
| | - Nusrath Yasmeen
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, Rajasthan, India
| | - Aishwarya Pandey
- INRS, Eau Terre Environnement Research Centre, Québec, QC, Canada
| | - Anis Ahmad Chaudhary
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Abdullah S. Alawam
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Hassan Ahmad Rudayni
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Asimul Islam
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Sudarshan S. Lakhawat
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, Rajasthan, India
| | - Pushpender K. Sharma
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, Rajasthan, India
| | - Mohammad Shahid
- Department of Basic Medical Sciences, College of Medicine, Prince Sattam bin Abdulaziz University, Al-Kharj, Saudi Arabia
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11
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Ahmed NA, Khattab RA, Ragab YM, Hassan M. Safety assessment of Enterococcus lactis strains complemented with comparative genomics analysis reveals probiotic and safety characteristics of the entire species. BMC Genomics 2023; 24:667. [PMID: 37932698 PMCID: PMC10626658 DOI: 10.1186/s12864-023-09749-9] [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] [Accepted: 10/17/2023] [Indexed: 11/08/2023] Open
Abstract
BACKGROUND The gut microbiota is considered a rich source for potential novel probiotics. Enterococcus genus is a normal component of a healthy gut microbiota, suggesting its vital role. Nosocomial infections caused mainly by E. facalis and E. faecium have been attributed to the plasticity of the Enterococcus genomes. In this study, we assessed the probiotic and safety characteristics of two E. lactis strains isolated from the human gut microbiota using in-vitro and in silico approaches. Additionally, the safety of the E. lactis species was evaluated using comparative genomics analysis. RESULTS The two E. lactis strains 10NA and 50NA showed resistance to bile salts and acid tolerance with antibacterial activity against Escherichia coli, Salmonella typhi, and Clostridioides difficile. For safety assays, the two strains did not display any type of hemolysis on blood agar, and the survival of Caco-2 cells was not significantly different (P-value > 0.05) compared to the control using cell free supernatants at 100% (v/v), 50% (v/v), 10% (v/v), and 5% (v/v) concentrations. Regarding antibiotic susceptibility, both strains were sensitive to vancomycin, tetracycline, and chloramphenicol. Comprehensive whole-genome analysis revealed no concerning associations between virulence or antibiotic resistance genes and any of the identified mobile genetic elements. Comparative genome analysis with closely related E. faecium species genomes revealed the distinctive genomic safety of the E. lactis species. CONCLUSIONS Our two E. lactis strains showed promising probiotic properties in-vitro. Their genomes were devoid of any transferable antibiotic resistance genes. In silico comparative analysis confirmed the safety of the E. lactis species. These results suggest that E. lactis species could be a potential source for safer Enterococcus probiotic supplements.
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Affiliation(s)
- Noha A Ahmed
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo, 11562, Egypt.
| | - Rania Abdelmonem Khattab
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo, 11562, Egypt
| | - Yasser M Ragab
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo, 11562, Egypt
| | - Mariam Hassan
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo, 11562, Egypt.
- Department of Microbiology and Immunology, Faculty of Pharmacy, Galala University, New Galala City, Suez, 43511, Egypt.
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12
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Junaid M, Thirapanmethee K, Khuntayaporn P, Chomnawang MT. CRISPR-Based Gene Editing in Acinetobacter baumannii to Combat Antimicrobial Resistance. Pharmaceuticals (Basel) 2023; 16:920. [PMID: 37513832 PMCID: PMC10384873 DOI: 10.3390/ph16070920] [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: 05/25/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/30/2023] Open
Abstract
Antimicrobial resistance (AMR) poses a significant threat to the health, social, environment, and economic sectors on a global scale and requires serious attention to addressing this issue. Acinetobacter baumannii was given top priority among infectious bacteria because of its extensive resistance to nearly all antibiotic classes and treatment options. Carbapenem-resistant A. baumannii is classified as one of the critical-priority pathogens on the World Health Organization (WHO) priority list of antibiotic-resistant bacteria for effective drug development. Although available genetic manipulation approaches are successful in A. baumannii laboratory strains, they are limited when employed on newly acquired clinical strains since such strains have higher levels of AMR than those used to select them for genetic manipulation. Recently, the CRISPR-Cas (Clustered regularly interspaced short palindromic repeats/CRISPR-associated protein) system has emerged as one of the most effective, efficient, and precise methods of genome editing and offers target-specific gene editing of AMR genes in a specific bacterial strain. CRISPR-based genome editing has been successfully applied in various bacterial strains to combat AMR; however, this strategy has not yet been extensively explored in A. baumannii. This review provides detailed insight into the progress, current scenario, and future potential of CRISPR-Cas usage for AMR-related gene manipulation in A. baumannii.
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Affiliation(s)
- Muhammad Junaid
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
| | - Krit Thirapanmethee
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
| | - Piyatip Khuntayaporn
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
| | - Mullika Traidej Chomnawang
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
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13
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Gómez-Martínez J, Rocha-Gracia RDC, Bello-López E, Cevallos MA, Castañeda-Lucio M, Sáenz Y, Jiménez-Flores G, Cortés-Cortés G, López-García A, Lozano-Zarain P. Comparative Genomics of Pseudomonas aeruginosa Strains Isolated from Different Ecological Niches. Antibiotics (Basel) 2023; 12:antibiotics12050866. [PMID: 37237769 DOI: 10.3390/antibiotics12050866] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/27/2023] [Accepted: 05/04/2023] [Indexed: 05/28/2023] Open
Abstract
The Pseudomonas aeruginosa genome can change to adapt to different ecological niches. We compared four genomes from a Mexican hospital and 59 genomes from GenBank from different niches, such as urine, sputum, and environmental. The ST analysis showed that high-risk STs (ST235, ST773, and ST27) were present in the genomes of the three niches from GenBank, and the STs of Mexican genomes (ST167, ST2731, and ST549) differed from the GenBank genomes. Phylogenetic analysis showed that the genomes were clustering according to their ST and not their niche. When analyzing the genomic content, we observed that environmental genomes had genes involved in adapting to the environment not found in the clinics and that their mechanisms of resistance were mutations in antibiotic resistance-related genes. In contrast, clinical genomes from GenBank had resistance genes, in mobile/mobilizable genetic elements in the chromosome, except for the Mexican genomes that carried them mostly in plasmids. This was related to the presence of CRISPR-Cas and anti-CRISPR; however, Mexican strains only had plasmids and CRISPR-Cas. blaOXA-488 (a variant of blaOXA50) with higher activity against carbapenems was more prevalent in sputum genomes. The virulome analysis showed that exoS was most prevalent in the genomes of urinary samples and exoU and pldA in sputum samples. This study provides evidence regarding the genetic variability among P. aeruginosa isolated from different niches.
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Affiliation(s)
- Jessica Gómez-Martínez
- Posgrado en Microbiología, Centro de Investigaciones de Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico
| | - Rosa Del Carmen Rocha-Gracia
- Posgrado en Microbiología, Centro de Investigaciones de Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico
| | - Elena Bello-López
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - Miguel Angel Cevallos
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - Miguel Castañeda-Lucio
- Posgrado en Microbiología, Centro de Investigaciones de Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico
| | - Yolanda Sáenz
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja (CIBIR), 26006 Logroño, Spain
| | - Guadalupe Jiménez-Flores
- Laboratorio Clínico, Área de Microbiología, Hospital Regional Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado, Puebla 72570, Mexico
| | - Gerardo Cortés-Cortés
- Department of Microbiology and Environmental Toxicology, University of California at Santa Cruz, Santa Cruz, CA 95064, USA
| | - Alma López-García
- Posgrado en Microbiología, Centro de Investigaciones de Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico
| | - Patricia Lozano-Zarain
- Posgrado en Microbiología, Centro de Investigaciones de Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla 72570, Mexico
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14
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Zhang K, Teng D, Mao R, Yang N, Hao Y, Wang J. Thinking on the Construction of Antimicrobial Peptide Databases: Powerful Tools for the Molecular Design and Screening. Int J Mol Sci 2023; 24:ijms24043134. [PMID: 36834553 PMCID: PMC9960615 DOI: 10.3390/ijms24043134] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 01/29/2023] [Accepted: 02/02/2023] [Indexed: 02/08/2023] Open
Abstract
With the accelerating growth of antimicrobial resistance (AMR), there is an urgent need for new antimicrobial agents with low or no AMR. Antimicrobial peptides (AMPs) have been extensively studied as alternatives to antibiotics (ATAs). Coupled with the new generation of high-throughput technology for AMP mining, the number of derivatives has increased dramatically, but manual running is time-consuming and laborious. Therefore, it is necessary to establish databases that combine computer algorithms to summarize, analyze, and design new AMPs. A number of AMP databases have already been established, such as the Antimicrobial Peptides Database (APD), the Collection of Antimicrobial Peptides (CAMP), the Database of Antimicrobial Activity and Structure of Peptides (DBAASP), and the Database of Antimicrobial Peptides (dbAMPs). These four AMP databases are comprehensive and are widely used. This review aims to cover the construction, evolution, characteristic function, prediction, and design of these four AMP databases. It also offers ideas for the improvement and application of these databases based on merging the various advantages of these four peptide libraries. This review promotes research and development into new AMPs and lays their foundation in the fields of druggability and clinical precision treatment.
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Affiliation(s)
- Kun Zhang
- Gene Engineering Laboratory, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Innovative Team of Antimicrobial Peptides and Alternatives to Antibiotics, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing 100081, China
| | - Da Teng
- Gene Engineering Laboratory, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Innovative Team of Antimicrobial Peptides and Alternatives to Antibiotics, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing 100081, China
| | - Ruoyu Mao
- Gene Engineering Laboratory, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Innovative Team of Antimicrobial Peptides and Alternatives to Antibiotics, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing 100081, China
| | - Na Yang
- Gene Engineering Laboratory, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Innovative Team of Antimicrobial Peptides and Alternatives to Antibiotics, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing 100081, China
| | - Ya Hao
- Gene Engineering Laboratory, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Innovative Team of Antimicrobial Peptides and Alternatives to Antibiotics, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing 100081, China
| | - Jianhua Wang
- Gene Engineering Laboratory, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Innovative Team of Antimicrobial Peptides and Alternatives to Antibiotics, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing 100081, China
- Correspondence: ; Tel.: +86-10-82106081 or +86-10-82106079; Fax: +86-10-82106079
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15
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Ateia H, Ogrodzki P, Wilson HV, Ganesan S, Halwani R, Koshy A, Zaher WA. Population Genome Programs across the Middle East and North Africa: Successes, Challenges, and Future Directions. Biomed Hub 2023; 8:60-71. [PMID: 37900972 PMCID: PMC10601860 DOI: 10.1159/000530619] [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: 09/23/2022] [Accepted: 03/29/2023] [Indexed: 10/31/2023] Open
Abstract
In this review, we discuss the current state of population genome programs (PGPs) conducted in the Middle East and North African (MENA) region. This region has high prevalence of genetic diseases and significant health challenges as well as being a significantly underrepresented population in public genetic databases. The majority of ongoing PGPs represent regions in Europe, North and South America, South Asia, Australia, and Africa, with little to no descriptive information highlighted only on the MENA Region when it comes to genome programs databases, outcomes, or the challenges that MENA region countries may face establishing their own national programs. This review has identified 6 PGPs currently underway in the MENA region, namely in the Kingdom of Saudi Arabia, Qatar, Egypt, the United Arab Emirates, Bahrain, and Iran. Due to the rapidly growing involvement of the MENA region in national-scale genomic data collection, an increase in representation in public genetic databases is to be expected to occur in the near future. Whilst significant progress is being made in some MENA countries, future initiatives as well as ongoing programs will be facing several challenges related to collaboration, finance, infrastructure and institutional data access, data analysis, sustainability, health records, and biobanks. The review also reiterates the need for ensuring ethical and regulated genomic initiatives which can drive developments in personalized medicine treatments to improve patient prognosis and quality of life.
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Affiliation(s)
- Hagar Ateia
- G42 Healthcare, Masdar City Abu Dhabi, UAE
- IROS (Insights Research Organization and Solutions), Abu Dhabi, UAE
| | | | - Hannah V. Wilson
- IROS (Insights Research Organization and Solutions), Abu Dhabi, UAE
| | - Subhashini Ganesan
- G42 Healthcare, Masdar City Abu Dhabi, UAE
- IROS (Insights Research Organization and Solutions), Abu Dhabi, UAE
| | | | | | - Walid A. Zaher
- G42 Healthcare, Masdar City Abu Dhabi, UAE
- IROS (Insights Research Organization and Solutions), Abu Dhabi, UAE
- UAE University, Al Ain, UAE
- Khalifa University, Abu Dhabi, UAE
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16
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CRISPR in Modulating Antibiotic Resistance of ESKAPE Pathogens. Mol Biotechnol 2023; 65:1-16. [PMID: 35939207 DOI: 10.1007/s12033-022-00543-8] [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: 12/24/2021] [Accepted: 07/13/2022] [Indexed: 01/11/2023]
Abstract
The ESKAPE (Enterococcus spp., Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) isolates both from the clinical settings and food products are demonstrated to gain resistance to multiple antimicrobials. Therefore, the ESKAPE pathogens pose a serious threat to public health, which warrants specific attention to developing alternative novel therapeutics. The clustered regularly interspaced short palindromic repeats associated (CRISPR-Cas) system is one of the novel methods for managing antibiotic-resistant strains. Specific Cas nucleases can be programmed against bacterial genomic sequences to decrease bacterial resistance to antibiotics. Moreover, a few CRISPR-Cas nucleases have the ability to the sequence-specific killing of bacterial strains. However, some pathogens acquire antibiotic resistance due to the presence of the CRISPR-Cas system. In brief, there is a wide range of functional diversity of CRISPR-Cas systems in bacterial pathogens. Hence, to be an effective and safe infection treatment strategy, a comprehensive understanding of the role of CRISPR-Cas systems in modulating antibiotic resistance in ESKAPE pathogens is essential. The present review summarizes all the mechanisms by which CRISPR confers and prevents antibiotic resistance in ESKAPE. The review also emphasizes the relationship between CRISPR-Cas systems, biofilm formation, and antibiotic resistance in ESKAPE.
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17
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Soliman M, Said HS, El-Mowafy M, Barwa R. Novel PCR detection of CRISPR/Cas systems in Pseudomonas aeruginosa and its correlation with antibiotic resistance. Appl Microbiol Biotechnol 2022; 106:7223-7234. [PMID: 36178514 PMCID: PMC9592639 DOI: 10.1007/s00253-022-12144-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 08/15/2022] [Accepted: 08/24/2022] [Indexed: 12/01/2022]
Abstract
CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated proteins) systems are considered as acquired immune mechanisms in Gram-positive and Gram-negative bacteria and also in archaea. They provide resistance/immunity to attacking bacteriophages or mobile genetic elements as integrative conjugative elements (ICE) as well as plasmid transformation. As an opportunistic pathogen, Pseudomonas aeruginosa has been held responsible for serious infections especially in hospitalized and immunocompromised patients. Three subtypes of type I CRISPR system (I-C, I-E, & I-F1) have been detected in P. aeruginosa genomes. In this work, P. aeruginosa isolates were collected from different clinical sources, and the three CRISPR/Cas subtypes (I-C, I-E, & I-F1) were detected via singleplex and multiplex PCR techniques using novel universal primers that were designed specifically in this study. CRISPR subtypes I-C, I-E, and I-F1 were detected in 10, 9, and 13 isolates, respectively. Furthermore, antimicrobial susceptibility of CRISPR/Cas-positive and negative isolates to different antibiotics and the capacity of biofilm formation were detected using disc diffusion method and tissue culture plate method, respectively. There was a significant correlation between the presence/absence of CRISPR/Cas system and both antimicrobial susceptibility to some antibiotics and biofilm-forming capacity among P. aeruginosa clinical isolates. KEY POINTS: • A novel multiplex-PCR for detection of CRISPR/Cas-positive strains of P. aeruginosa. • Understand the correlation between CRISPR/Cas systems and other characters of P. aeruginosa. • Correlation between antimicrobial susceptibility and CRISPR systems in P. aeruginosa.
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Affiliation(s)
- Mai Soliman
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt
| | - Heba Shehta Said
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt.
| | - Mohammed El-Mowafy
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt.
| | - Rasha Barwa
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt.
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18
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Mikhaylova Y, Shelenkov A, Chernyshkov A, Tyumentseva M, Saenko S, Egorova A, Manzeniuk I, Akimkin V. Whole-Genome Analysis of Staphylococcus aureus Isolates from Ready-to-Eat Food in Russia. Foods 2022; 11:foods11172574. [PMID: 36076759 PMCID: PMC9455289 DOI: 10.3390/foods11172574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/09/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
This study provides a thorough investigation of a diverse set of antimicrobial resistant (AMR) Staphylococcus aureus isolates collected from a broad range of ready-to-eat (RTE) food in various geographic regions of Russia ranging from Pskov to Kamchatka. Thirty-five isolates were characterized using the whole genome sequencing (WGS) analysis in terms of clonal structure, the presence of resistance and virulence determinants, as well as plasmid replicon sequences and CRISPR/Cas systems. To the best of our knowledge, this is the first WGS-based surveillance of Russian RTE food-associated S. aureus isolates. The isolates belonged to fifteen different multilocus sequence typing (MLST)-based types with a predominant being the ones of clonal complex (CC) 22. The isolates studied can pose a threat to public health since about 40% of the isolates carried at least one enterotoxin gene, and 70% of methicillin-resistant (MRSA) isolates carried a tsst1 gene encoding a toxin that may cause severe acute disease. In addition, plasmid analysis revealed some important characteristics, e.g., Rep5 and Rep20 plasmid replicons were a “signature” of MRSA CC22. By analyzing the isolates belonging to the same/single strain based on cgMLST analysis, we were able to identify the differences in their accessory genomes marking their dynamics and plasticity. This data is very important since S. aureus isolates studied and RTE food, in general, represent an important route of transmission and dissemination of multiple pathogenic determinants. We believe that the results obtained will facilitate performing epidemiological surveillance and developing protection measures against this important pathogen in community settings.
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19
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Yadav G, Singh R. In silico analysis reveals the co-existence of CRISPR-Cas type I-F1 and type I-F2 systems and its association with restricted phage invasion in Acinetobacter baumannii. Front Microbiol 2022; 13:909886. [PMID: 36060733 PMCID: PMC9428484 DOI: 10.3389/fmicb.2022.909886] [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: 03/31/2022] [Accepted: 07/25/2022] [Indexed: 11/30/2022] Open
Abstract
Introduction Acinetobacter baumannii, an opportunistic pathogen, rapidly acquires antibiotic resistance, thus compelling researchers to develop alternative treatments at utmost priority. Phage-based therapies are of appreciable benefit; however, CRISPR-Cas systems are a major constraint in this approach. Hence for effective implementation and a promising future of phage-based therapies, a multifaceted understanding of the CRISPR-Cas systems is necessary. Methods This study investigated 4,977 RefSeq genomes of A. baumannii from the NCBI database to comprehend the distribution and association of CRISPR-Cas systems with genomic determinants. Results Approximately 13.84% (n = 689/4,977) isolates were found to carry the CRSIPR-Cas system, and a small fraction of isolates, 1.49% (n = 74/4,977), exhibited degenerated CRISPR-Cas systems. Of these CRISPR-Cas positive (+) isolates, 67.48% (465/689) isolates harbored type I-F1, 28.59% (197/689) had type I-F2, and 3.7% (26/689) had co-existence of both type I-F1 and type I-F2 systems. Co-existing type I-F1 and type I-F2 systems are located distantly (∼1.733 Mb). We found a strong association of CRISPR-Cas systems within STs for type I-F1 and type I-F2, whereas the type I-F1 + F2 was not confined to any particular ST. Isolates with type I-F1 + F2 exhibited a significantly high number of mean spacers (n = 164.58 ± 46.41) per isolate as compared to isolates with type I-F2 (n = 82.87 ± 36.14) and type I-F1 (n = 54.51 ± 26.27) with majority targeting the phages. Isolates with type I-F1 (p < 0.0001) and type I-F2 (p < 0.0115) displayed significantly larger genome sizes than type I-F1 + F2. A significantly reduced number of integrated phages in isolates with co-existence of type I-F1 + F2 compared with other counterparts was observed (p = 0.0041). In addition, the isolates carrying type I-F1 + F2 did not exhibit reduced resistance and virulence genes compared to CRISPR-Cas(-) and CRISPR-Cas (+) type I-F1 and type I-F2, except for bap, abaI, and abaR. Conclusion Our observation suggests that the co-existence of type I-F1 and F2 is more effective in constraining the horizontal gene transfer and phage invasion in A. baumannii than the isolates exhibiting only type I-F1 and only type I-F2 systems.
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Affiliation(s)
- Gulshan Yadav
- Indian Council of Medical Research (ICMR)—National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, India
- Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Ruchi Singh
- Indian Council of Medical Research (ICMR)—National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, India
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Tao S, Chen H, Li N, Liang W. The Application of the CRISPR-Cas System in Antibiotic Resistance. Infect Drug Resist 2022; 15:4155-4168. [PMID: 35942309 PMCID: PMC9356603 DOI: 10.2147/idr.s370869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/17/2022] [Indexed: 11/28/2022] Open
Abstract
The emergence and global epidemic of antimicrobial resistance (AMR) poses a serious threat to global public health in recent years. AMR genes are shared between bacterial pathogens mainly via horizontal gene transfer (HGT) on mobile genetic elements (MGEs), thereby accelerating the spread of antimicrobial resistance (AMR) and increasing the burden of drug resistance. There is an urgent need to develop new strategies to control bacterial infections and the spread of antimicrobial resistance. The clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) are an RNA-guided adaptive immune system in prokaryotes that recognizes and defends against invasive genetic elements such as phages and plasmids. Because of its specifically target and cleave DNA sequences encoding antibiotic resistance genes, CRISPR/Cas system has been developed into a new gene-editing tool for the prevention and control of bacterial drug resistance. CRISPR-Cas plays a potentially important role in controlling horizontal gene transfer and limiting the spread of antibiotic resistance. In this review, we will introduce the structure and working mechanism of CRISPR-Cas systems, followed by delivery strategies, and then focus on the relationship between antimicrobial resistance and CRISPR-Cas. Moreover, the challenges and prospects of this research field are discussed, thereby providing a reference for the prevention and control of the spread of antibiotic resistance.
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Affiliation(s)
- Shuan Tao
- School of Medical, Jiangsu University, Zhenjiang, Jiangsu Province, 212013, People’s Republic of China
- Lianyungang Clinical College of Jiangsu University, Lianyungang, Jiangsu Province, 222023, People’s Republic of China
| | - Huimin Chen
- School of Medical, Jiangsu University, Zhenjiang, Jiangsu Province, 212013, People’s Republic of China
| | - Na Li
- Bengbu Medical College, Bengbu, Anhui Province, 233030, People’s Republic of China
| | - Wei Liang
- Lianyungang Clinical College of Jiangsu University, Lianyungang, Jiangsu Province, 222023, People’s Republic of China
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Zaayman M, Wheatley RM. Fitness costs of CRISPR-Cas systems in bacteria. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35849532 DOI: 10.1099/mic.0.001209] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
CRISPR-Cas systems provide bacteria with both specificity and adaptability in defence against invading genetic elements. From a theoretical perspective, CRISPR-Cas systems confer many benefits. However, they are observed at an unexpectedly low prevalence across the bacterial domain. While these defence systems can be gained horizontally, fitness costs may lead to selection against their carriage. Understanding the source of CRISPR-related fitness costs will help us to understand the evolutionary dynamics of CRISPR-Cas systems and their role in shaping bacterial genome evolution. Here, we review our current understanding of the potential fitness costs associated with CRISPR-Cas systems. In addition to potentially restricting the acquisition of genetic material that could confer fitness benefits, we explore five alternative biological factors that from a theoretical perspective may influence the fitness costs associated with CRISPR-Cas system carriage: (1) the repertoire of defence mechanisms a bacterium has available to it, (2) the potential for a metabolic burden, (3) larger-scale population and environmental factors, (4) the phenomenon of self-targeting spacers, and (5) alternative non-defence roles for CRISPR-Cas.
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Dimitriu T. Evolution of horizontal transmission in antimicrobial resistance plasmids. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35849537 DOI: 10.1099/mic.0.001214] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Mobile genetic elements (MGEs) are one of the main vectors for the spread of antimicrobial resistance (AMR) across bacteria, due to their ability to move horizontally between bacterial lineages. Horizontal transmission of AMR can increase AMR prevalence at multiple scales, from increasing the prevalence of infections by resistant bacteria to pathogen epidemics and worldwide spread of AMR across species. Among MGEs, conjugative plasmids are the main contributors to the spread of AMR. This review discusses the selective pressures acting on MGEs and their hosts to promote or limit the horizontal transmission of MGEs, the mechanisms by which transmission rates can evolve, and their implications for limiting the spread of AMR, with a focus on AMR plasmids.
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Das S, Bombaywala S, Srivastava S, Kapley A, Dhodapkar R, Dafale NA. Genome plasticity as a paradigm of antibiotic resistance spread in ESKAPE pathogens. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:40507-40519. [PMID: 35349073 DOI: 10.1007/s11356-022-19840-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
The major reason behind the spread of antibiotic resistance genes (ARGs) is persistent selective pressure in the environment encountered by bacteria. Genome plasticity plays a crucial role in dissemination of antibiotic resistance among bacterial pathogens. Mobile genetic elements harboring ARGs are reported to dodge bacterial immune system and mediate horizontal gene transfer (HGT) under selective pressure. Residual antibiotic pollutants develop selective pressures that force the bacteria to lose their defense mechanisms (CRISPR-cas) and acquire resistance. The present study targets the ESKAPE organisms (namely, Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp.) causing various nosocomial infections and emerging multidrug-resistant species. The role of CRISPR-cas systems in inhibition of HGT in prokaryotes and its loss due to presence of various stressors in the environment is also focused in the study. IncF and IncH plasmids were identified in all strains of E. faecalis and K. pneumoniae, carrying Beta-lactam and fluoroquinolone resistance genes, whereas sal3, phiCTX, and SEN34 prophages harbored aminoglycoside resistance genes (aadA, aac). Various MGEs present in selected environmental niches that aid the bacterial genome plasticity and transfer of ARGs contributing to its spread are also identified.
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Affiliation(s)
- Sanchita Das
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 4400 20, India
| | - Sakina Bombaywala
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 4400 20, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 2010 20, India
| | - Shweta Srivastava
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 4400 20, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 2010 20, India
| | - Atya Kapley
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 4400 20, India
| | - Rita Dhodapkar
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 4400 20, India
| | - Nishant A Dafale
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, 4400 20, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 2010 20, India.
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Wang Y, Ge H, Wei X, Zhao X. Research progress on antibiotic resistance of Salmonella. FOOD QUALITY AND SAFETY 2022. [DOI: 10.1093/fqsafe/fyac035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Antibiotic abuse results in various antibiotic resistance among a number of foodborne bacteria, posing a severe threat to food safety. Antibiotic resistance genes are commonly detected in foodborne pathogens, which has sparked much interest in finding solutions to these issues. Various strategies against these drug-resistant pathogens have been studied, including new antibiotics and phages. Recently, a powerful tool has been introduced in the fight against drug-resistant pathogens, namely, clustered regularly interspaced short palindromic repeats-CRISPR associated (CRISPR-Cas) system aggregated by a prokaryotic defense mechanism. This review summarized the mechanism of antibiotic resistance in Salmonella and resistance to common antibiotics, analysed the relationship between Salmonella CRISPR-Cas and antibiotic resistance, discussed the changes in antibiotic resistance on the structure and function of CRISPR-Cas, and finally predicted the mechanism of CRISPR-Cas intervention in Salmonella antibiotic resistance. In the future, CRISPR-Cas is expected to become an important tool to reduce the threat of antibiotic-resistant pathogens in food safety.
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Affiliation(s)
- Yizhe Wang
- Research Center for Environmental Ecology and Engineering, Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, China
| | - Hengwei Ge
- Research Center for Environmental Ecology and Engineering, Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, China
| | - Xinyue Wei
- Research Center for Environmental Ecology and Engineering, Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, China
| | - Xihong Zhao
- Research Center for Environmental Ecology and Engineering, Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430205, China
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Liu Y, Wang S, Yang F, Chi W, Ding L, Liu T, Zhu F, Ji D, Zhou J, Fang Y, Zhang J, Xiang P, Zhang Y, Zhao H. Antimicrobial resistance patterns and genetic elements associated with the antibiotic resistance of Helicobacter pylori strains from Shanghai. Gut Pathog 2022; 14:14. [PMID: 35354484 PMCID: PMC8966258 DOI: 10.1186/s13099-022-00488-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 03/21/2022] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Shanghai, in east China, has one of the world's highest burdens of Helicobacter pylori infection. While multidrug regimens can effectively eradicate H. pylori, the increasing prevalence of antibiotic resistance (AR) in H. pylori has been recognized by the WHO as 'high priority' for urgent need of new therapies. Moreover, the genetic characteristics of H. pylori AR in Shanghai is under-reported. The purpose of this study was to determine the resistance prevalence, re-substantiate resistance-conferring mutations, and investigate novel genetic elements associated with H. pylori AR. RESULTS We performed whole genome sequencing and antimicrobial susceptibility testing of 112 H. pylori strains isolated from gastric biopsy specimens from Shanghai patients with different gastric diseases. No strains were resistant to amoxicillin. Levofloxacin, metronidazole and clarithromycin resistance was observed in 39 (34.8%), 73 (65.2%) and 18 (16.1%) strains, respectively. There was no association between gastroscopy diagnosis and resistance phenotypes. We reported the presence or absence of several subsystem protein coding genes including hopE, hofF, spaB, cagY and pflA, and a combination of CRISPRs, which were potentially correlated with resistance phenotypes. The H. pylori strains were also annotated for 80 genome-wide AR genes (ARGs). A genome-wide ARG analysis was performed for the three antibiotics by correlating the phenotypes with the genetic variants, which identified the well-known intrinsic mutations conferring resistance to levofloxacin (N87T/I and/or D91G/Y mutations in gyrA), metronidazole (I38V mutation in fdxB), and clarithromycin (A2143G and/or A2142G mutations in 23S rRNA), and added 174 novel variations, including 23 non-synonymous SNPs and 48 frameshift Indels that were significantly enriched in either the antibiotic-resistant or antibiotic-susceptible bacterial populations. The variant-level linkage disequilibrium analysis highlighted variations in a protease Lon with strong co-occurring correlation with a series of resistance-associated variants. CONCLUSION Our study revealed multidrug antibiotic resistance in H. pylori strains from Shanghai, which was characterized by high metronidazole and moderate levofloxacin resistance, and identified specific genomic characteristics in relation to H. pylori AR. Continued surveillance of H. pylori AR in Shanghai is warranted in order to establish appropriate eradication treatment regimens for this population.
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Affiliation(s)
- Yixin Liu
- Department of Laboratory Medicine, Huadong Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Clinical Geriatric Medicine, Shanghai, China
- Research Center on Aging and Medicine, Fudan University, Shanghai, China
| | - Su Wang
- Department of Laboratory Medicine, Huadong Hospital, Fudan University, Shanghai, China
| | - Feng Yang
- Department of Laboratory Medicine, Huadong Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Clinical Geriatric Medicine, Shanghai, China
- Research Center on Aging and Medicine, Fudan University, Shanghai, China
| | - Wenjing Chi
- Department of Laboratory Medicine, Huadong Hospital, Fudan University, Shanghai, China
| | - Li Ding
- Department of Laboratory Medicine, Huadong Hospital, Fudan University, Shanghai, China
| | - Tao Liu
- Department of Laboratory Medicine, Huadong Hospital, Fudan University, Shanghai, China
| | - Feng Zhu
- Department of Laboratory Medicine, Huadong Hospital, Fudan University, Shanghai, China
| | - Danian Ji
- Department of Endoscopy, Huadong Hospital, Fudan University, Shanghai, China
| | - Jun Zhou
- Department of Endoscopy, Huadong Hospital, Fudan University, Shanghai, China
| | - Yi Fang
- Department of Laboratory Medicine, Huadong Hospital, Fudan University, Shanghai, China
| | - Jinghao Zhang
- Department of Laboratory Medicine, Huadong Hospital, Fudan University, Shanghai, China
| | - Ping Xiang
- Department of Endoscopy, Huadong Hospital, Fudan University, Shanghai, China
| | - Yanmei Zhang
- Department of Laboratory Medicine, Huadong Hospital, Fudan University, Shanghai, China.
- Shanghai Key Laboratory of Clinical Geriatric Medicine, Shanghai, China.
- Research Center on Aging and Medicine, Fudan University, Shanghai, China.
| | - Hu Zhao
- Department of Laboratory Medicine, Huadong Hospital, Fudan University, Shanghai, China.
- Shanghai Key Laboratory of Clinical Geriatric Medicine, Shanghai, China.
- Research Center on Aging and Medicine, Fudan University, Shanghai, China.
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Dong C, Wang X, Ma C, Zeng Z, Pu DK, Liu S, Wu CS, Chen S, Deng Z, Guo FB. Anti-CRISPRdb v2.2: an online repository of anti-CRISPR proteins including information on inhibitory mechanisms, activities and neighbors of curated anti-CRISPR proteins. Database (Oxford) 2022; 2022:6555051. [PMID: 35348649 PMCID: PMC9248852 DOI: 10.1093/database/baac010] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 02/13/2022] [Accepted: 02/21/2022] [Indexed: 12/30/2022]
Abstract
We previously released the Anti-CRISPRdb database hosting anti-CRISPR proteins (Acrs) and associated information. Since then, the number of known Acr families, types, structures and inhibitory activities has accumulated over time, and Acr neighbors can be used as a candidate pool for screening Acrs in further studies. Therefore, we here updated the database to include the new available information. Our newly updated database shows several improvements: (i) it comprises more entries and families because it includes both Acrs reported in the most recent literatures and Acrs obtained via performing homologous alignment; (ii) the prediction of Acr neighbors is integrated into Anti-CRISPRdb v2.2, and users can identify novel Acrs from these candidates; and (iii) this version includes experimental information on the inhibitory strength and stage for Acr-Cas/Acr-CRISPR pairs, motivating the development of tools for predicting specific inhibitory abilities. Additionally, a parameter, the rank of codon usage bias (CUBRank), was proposed and provided in the new version, which showed a positive relationship with predicted result from AcRanker; hence, it can be used as an indicator for proteins to be Acrs. CUBRank can be used to estimate the possibility of genes occurring within genome island-a hotspot hosting potential genes encoding Acrs. Based on CUBRank and Anti-CRISPRdb, we also gave the first glimpse for the emergence of Acr genes (acrs). DATABASE URL http://guolab.whu.edu.cn/anti-CRISPRdb.
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Affiliation(s)
- Chuan Dong
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, No. 185, Donghu Road, Wuchang, Wuhan 430071, China
| | - Xin Wang
- School of Life Science and Technology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu 611731, China
| | - Cong Ma
- School of Life Science and Technology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu 611731, China
| | - Zhi Zeng
- School of Life Science and Technology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu 611731, China
| | - Dong-Kai Pu
- School of Life Science and Technology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu 611731, China
| | - Shuo Liu
- School of Life Science and Technology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu 611731, China
| | - Candy-S Wu
- Thomas Worthington High School, 300 West Granville Road, Worthington, OH 43085, USA
| | - Shixin Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, No. 185, Donghu Road, Wuchang, Wuhan 430071, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, No. 185, Donghu Road, Wuchang, Wuhan 430071, China
| | - Feng-Biao Guo
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, No. 185, Donghu Road, Wuchang, Wuhan 430071, China
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Pursey E, Dimitriu T, Paganelli FL, Westra ER, van Houte S. CRISPR-Cas is associated with fewer antibiotic resistance genes in bacterial pathogens. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200464. [PMID: 34839714 PMCID: PMC8628084 DOI: 10.1098/rstb.2020.0464] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/21/2021] [Indexed: 01/19/2023] Open
Abstract
The acquisition of antibiotic resistance (ABR) genes via horizontal gene transfer (HGT) is a key driver of the rise in multidrug resistance amongst bacterial pathogens. Bacterial defence systems per definition restrict the influx of foreign genetic material, and may therefore limit the acquisition of ABR. CRISPR-Cas adaptive immune systems are one of the most prevalent defences in bacteria, found in roughly half of bacterial genomes, but it has remained unclear if and how much they contribute to restricting the spread of ABR. We analysed approximately 40 000 whole genomes comprising the full RefSeq dataset for 11 species of clinically important genera of human pathogens, including Enterococcus, Staphylococcus, Acinetobacter and Pseudomonas. We modelled the association between CRISPR-Cas and indicators of HGT, and found that pathogens with a CRISPR-Cas system were less likely to carry ABR genes than those lacking this defence system. Analysis of the mobile genetic elements (MGEs) targeted by CRISPR-Cas supports a model where this host defence system blocks important vectors of ABR. These results suggest a potential 'immunocompromised' state for multidrug-resistant strains that may be exploited in tailored interventions that rely on MGEs, such as phages or phagemids, to treat infections caused by bacterial pathogens. This article is part of the theme issue 'The secret lives of microbial mobile genetic elements'.
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Affiliation(s)
- Elizabeth Pursey
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, Cornwall, UK
| | - Tatiana Dimitriu
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, Cornwall, UK
| | - Fernanda L. Paganelli
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Edze R. Westra
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, Cornwall, UK
| | - Stineke van Houte
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, Cornwall, UK
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Tyumentseva M, Mikhaylova Y, Prelovskaya A, Karbyshev K, Tyumentsev A, Petrova L, Mironova A, Zamyatin M, Shelenkov A, Akimkin V. CRISPR Element Patterns vs. Pathoadaptability of Clinical Pseudomonas aeruginosa Isolates from a Medical Center in Moscow, Russia. Antibiotics (Basel) 2021; 10:antibiotics10111301. [PMID: 34827239 PMCID: PMC8615150 DOI: 10.3390/antibiotics10111301] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/15/2021] [Accepted: 10/22/2021] [Indexed: 11/24/2022] Open
Abstract
Pseudomonas aeruginosa is a member of the ESKAPE opportunistic pathogen group, which includes six species of the most dangerous microbes. This pathogen is characterized by the rapid acquisition of antimicrobial resistance, thus causing major healthcare concerns. This study presents a comprehensive analysis of clinical P. aeruginosa isolates based on whole-genome sequencing data. The isolate collection studied was characterized by a variety of clonal lineages with a domination of high-risk epidemic clones and different CRISPR/Cas element patterns. This is the first report on the coexistence of two and even three different types of CRISPR/Cas systems simultaneously in Russian clinical strains of P. aeruginosa. The data include molecular typing and genotypic antibiotic resistance determination, as well as the phylogenetic analysis of the full-length cas gene and anti-CRISPR genes sequences, predicted prophage sequences, and conducted a detailed CRISPR array analysis. The differences between the isolates carrying different types and quantities of CRISPR/Cas systems were investigated. The pattern of virulence factors in P. aeruginosa isolates lacking putative CRISPR/Cas systems significantly differed from that of samples with single or multiple putative CRISPR/Cas systems. We found significant correlations between the numbers of prophage sequences, antibiotic resistance genes, and virulence genes in P. aeruginosa isolates with different patterns of CRISPR/Cas-elements. We believe that the data presented will contribute to further investigations in the field of bacterial pathoadaptability, including antimicrobial resistance and the role of CRISPR/Cas systems in the plasticity of the P. aeruginosa genome.
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Affiliation(s)
- Marina Tyumentseva
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia; (M.T.); (Y.M.); (A.P.); (K.K.); (A.T.); (V.A.)
| | - Yulia Mikhaylova
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia; (M.T.); (Y.M.); (A.P.); (K.K.); (A.T.); (V.A.)
| | - Anna Prelovskaya
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia; (M.T.); (Y.M.); (A.P.); (K.K.); (A.T.); (V.A.)
| | - Konstantin Karbyshev
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia; (M.T.); (Y.M.); (A.P.); (K.K.); (A.T.); (V.A.)
| | - Aleksandr Tyumentsev
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia; (M.T.); (Y.M.); (A.P.); (K.K.); (A.T.); (V.A.)
| | - Lyudmila Petrova
- National Medical and Surgical Center Named after N.I. Pirogov, Nizhnyaya Pervomayskaya Str., 70, 105203 Moscow, Russia; (L.P.); (A.M.); (M.Z.)
| | - Anna Mironova
- National Medical and Surgical Center Named after N.I. Pirogov, Nizhnyaya Pervomayskaya Str., 70, 105203 Moscow, Russia; (L.P.); (A.M.); (M.Z.)
| | - Mikhail Zamyatin
- National Medical and Surgical Center Named after N.I. Pirogov, Nizhnyaya Pervomayskaya Str., 70, 105203 Moscow, Russia; (L.P.); (A.M.); (M.Z.)
| | - Andrey Shelenkov
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia; (M.T.); (Y.M.); (A.P.); (K.K.); (A.T.); (V.A.)
- Correspondence: or
| | - Vasiliy Akimkin
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia; (M.T.); (Y.M.); (A.P.); (K.K.); (A.T.); (V.A.)
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Li C, Wang Y, Gao Y, Li C, Ma B, Wang H. Antimicrobial Resistance and CRISPR Typing Among Salmonella Isolates From Poultry Farms in China. Front Microbiol 2021; 12:730046. [PMID: 34603259 PMCID: PMC8481896 DOI: 10.3389/fmicb.2021.730046] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 08/18/2021] [Indexed: 11/13/2022] Open
Abstract
Although knowledge of the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas system has been applied in many research areas, comprehensive studies of this system in Salmonella, particularly in analysis of antibiotic resistance, have not been reported. In this work, 75 Salmonella isolates obtained from broilers or broilers products were characterized to determine their antimicrobial susceptibilities, antibiotic resistance gene profiles, and CRISPR array diversities, and genotyping was explored. In total, 80.00% (60/75) of the strains were multidrug resistant, and the main pattern observed in the isolates was CN-AZM-AMP-AMC-CAZ-CIP-ATM-TE-SXT-FOS-C. The resistance genes of streptomycin (aadA), phenicol (floR-like and catB3-like), β-lactams (bla TEM, bla OXA, and bla CTX), tetracycline [tet(A)-like], and sulfonamides (sul1 and sul2) appeared at higher frequencies among the corresponding resistant isolates. Subsequently, we analyzed the CRISPR arrays and found 517 unique spacer sequences and 31 unique direct repeat sequences. Based on the CRISPR spacer sequences, we developed a novel typing method, CRISPR locus three spacer sequences typing (CLTSST), to help identify sources of Salmonella outbreaks especially correlated with epidemiological data. Compared with multi-locus sequence typing (MLST), conventional CRISPR typing (CCT), and CRISPR locus spacer pair typing (CLSPT), discrimination using CLTSST was weaker than that using CCT but stronger than that using MLST and CLSPT. In addition, we also found that there were no close correlations between CRISPR loci and antibiotics but had close correlations between CRISPR loci and antibiotic resistance genes in Salmonella isolates.
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Affiliation(s)
- Cui Li
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yulong Wang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yufeng Gao
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Chao Li
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Boheng Ma
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Hongning Wang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
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Dimitriu T, Szczelkun MD, Westra ER. Evolutionary Ecology and Interplay of Prokaryotic Innate and Adaptive Immune Systems. Curr Biol 2021; 30:R1189-R1202. [PMID: 33022264 DOI: 10.1016/j.cub.2020.08.028] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Like many organisms, bacteria and archaea have both innate and adaptive immune systems to defend against infection by viruses and other parasites. Innate immunity most commonly relies on the endonuclease-mediated cleavage of any incoming DNA that lacks a specific epigenetic modification, through a system known as restriction-modification. CRISPR-Cas-mediated adaptive immunity relies on the insertion of short DNA sequences from parasite genomes into CRISPR arrays on the host genome to provide sequence-specific protection. The discovery of each of these systems has revolutionised our ability to carry out genetic manipulations, and, as a consequence, the enzymes involved have been characterised in exquisite detail. In comparison, much less is known about the importance of these two arms of the defence for the ecology and evolution of prokaryotes and their parasites. Here, we review our current ecological and evolutionary understanding of these systems in isolation, and discuss the need to study how innate and adaptive immune responses are integrated when they coexist in the same cell.
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Affiliation(s)
- Tatiana Dimitriu
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn TR10 9FE, UK.
| | - Mark D Szczelkun
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK.
| | - Edze R Westra
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn TR10 9FE, UK.
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31
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Zemmour A, Dali-Yahia R, Maatallah M, Saidi-Ouahrani N, Rahmani B, Benhamouche N, Al-Farsi HM, Giske CG. High-risk clones of extended-spectrum β-lactamase-producing Klebsiella pneumoniae isolated from the University Hospital Establishment of Oran, Algeria (2011-2012). PLoS One 2021; 16:e0254805. [PMID: 34310625 PMCID: PMC8312963 DOI: 10.1371/journal.pone.0254805] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 07/05/2021] [Indexed: 11/18/2022] Open
Abstract
The purpose of the study was to characterize the resistome, virulome, mobilome and Clustered Regularly Interspaced Short Palindromic Repeats-associated (CRISPR-Cas) system of extended-spectrum β-lactamase producing Klebsiella pneumoniae (ESBL-KP) clinical isolates and to determine their phylogenetic relatedness. The isolates were from Algeria, isolated at the University Hospital Establishment of Oran, between 2011 and 2012. ESBL-KP isolates (n = 193) were screened for several antibiotic resistance genes (ARGs) using qPCR followed by Pulsed-Field Gel Electrophoresis (PFGE). Representative isolates were selected from PFGE clusters and subjected to whole-genome sequencing (WGS). Genomic characterization of the WGS data by studying prophages, CRISPR-Cas systems, Multi-Locus Sequence Typing (MLST), serotype, ARGs, virulence genes, plasmid replicons, and their pMLST. Phylogenetic and comparative genomic were done using core genome MLST and SNP-Based analysis. Generally, the ESBL-KP isolates were polyclonal. The whole genome sequences of nineteen isolates were taken of main PFGE clusters. Sixteen sequence types (ST) were found including high-risk clones ST14, ST23, ST37, and ST147. Serotypes K1 (n = 1), K2 (n = 2), K3 (n = 1), K31 (n = 1), K62 (n = 1), and K151 (n = 1) are associated with hyper-virulence. CRISPR-Cas system was found in 47.4%, typed I-E and I-E*. About ARGs, from 193 ESBL-KP, the majority of strains were multidrug-resistant, the CTX-M-1 enzyme was predominant (99%) and the prevalence of plasmid-mediated quinolone resistance (PMQR) genes was high with aac(6')-lb-cr (72.5%) and qnr's (65.8%). From 19 sequenced isolates we identified ESBL, AmpC, and carbapenemase genes: blaCTX-M-15 (n = 19), blaOXA-48 (n = 1), blaCMY-2 (n = 2), and blaCMY-16 (n = 2), as well as non-ESBL genes: qnrB1 (n = 12), qnrS1 (n = 1) and armA (n = 2). We found IncF, IncN, IncL/M, IncA/C2, and Col replicon types, at least once per isolate. This study is the first to report qnrS in ESBL-KP in Algeria. Our analysis shows the concerning co-existence of virulence and resistance genes and would support that genomic surveillance should be a high priority in the hospital environment.
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Affiliation(s)
- Assia Zemmour
- Faculté de Sciences de la Nature et la Vie, Département de Génétique Moléculaire Appliquée, Université des Sciences et la Technologie d’Oran Mohamed-Boudiaf USTOMB, Oran, Algérie
- Laboratoire de Génétique Médicale Appliquée à l’Ophtalmologie, Université d’Oran 1, Oran, Algérie
| | - Radia Dali-Yahia
- Service de bactériologie, Etablissement Hospitalo-Universitaire 1er Novembre 1954, Oran, Algérie
- Faculté de médicine, Université d’Oran 1, Oran, Algérie
| | - Makaoui Maatallah
- Faculté de pharmacie de Monastir, Laboratoire d’Analyse, Traitement et Valorisation des Polluants de l’Environnement et des Produits (LATVPEP: LR01ES16), Université de Monastir, Monastir, Tunisie
| | - Nadjia Saidi-Ouahrani
- Faculté de Sciences de la Nature et la Vie, Département de Génétique Moléculaire Appliquée, Université des Sciences et la Technologie d’Oran Mohamed-Boudiaf USTOMB, Oran, Algérie
| | - Bouabdallah Rahmani
- Faculté de Génie Electrique, Département d’Electronique, Université des Sciences et la Technologie d’Oran Mohamed-Boudiaf USTOMB, Oran, Algérie
| | - Nora Benhamouche
- Faculté de Sciences de la Nature et la Vie, Département de Génétique Moléculaire Appliquée, Université des Sciences et la Technologie d’Oran Mohamed-Boudiaf USTOMB, Oran, Algérie
| | - Hissa M. Al-Farsi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- Central Public Health Laboratories, Ministry of Health, Muscat, Sultanate of Oman
| | - Christian G. Giske
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- Clinical Microbiology, Karolinska University Hospital Solna, Stockholm, Sweden
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Wheatley RM, MacLean RC. CRISPR-Cas systems restrict horizontal gene transfer in Pseudomonas aeruginosa. THE ISME JOURNAL 2021; 15:1420-1433. [PMID: 33349652 PMCID: PMC8105352 DOI: 10.1038/s41396-020-00860-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 11/06/2020] [Accepted: 11/26/2020] [Indexed: 11/29/2022]
Abstract
CRISPR-Cas systems provide bacteria and archaea with an adaptive immune system that targets foreign DNA. However, the xenogenic nature of immunity provided by CRISPR-Cas raises the possibility that these systems may constrain horizontal gene transfer. Here we test this hypothesis in the opportunistic pathogen Pseudomonas aeruginosa, which has emerged as an important model system for understanding CRISPR-Cas function. Across the diversity of P. aeruginosa, active CRISPR-Cas systems are associated with smaller genomes and higher GC content, suggesting that CRISPR-Cas inhibits the acquisition of foreign DNA. Although phage is the major target of CRISPR-Cas spacers, more than 80% of isolates with an active CRISPR-Cas system have spacers that target integrative conjugative elements (ICE) or the conserved conjugative transfer machinery used by plasmids and ICE. Consistent with these results, genomes containing active CRISPR-Cas systems harbour a lower abundance of both prophage and ICE. Crucially, spacers in genomes with active CRISPR-Cas systems map to ICE and phage that are integrated into the chromosomes of closely related genomes lacking CRISPR-Cas immunity. We propose that CRISPR-Cas acts as an important constraint to horizontal gene transfer, and the evolutionary mechanisms that ensure its maintenance or drive its loss are key to the ability of this pathogen to adapt to new niches and stressors.
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Affiliation(s)
| | - R Craig MacLean
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK
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33
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Raza S, Matuła K, Karoń S, Paczesny J. Resistance and Adaptation of Bacteria to Non-Antibiotic Antibacterial Agents: Physical Stressors, Nanoparticles, and Bacteriophages. Antibiotics (Basel) 2021; 10:435. [PMID: 33924618 PMCID: PMC8070485 DOI: 10.3390/antibiotics10040435] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/02/2021] [Accepted: 04/08/2021] [Indexed: 12/14/2022] Open
Abstract
Antimicrobial resistance is a significant threat to human health worldwide, forcing scientists to explore non-traditional antibacterial agents to support rapid interventions and combat the emergence and spread of drug resistant bacteria. Many new antibiotic-free approaches are being developed while the old ones are being revised, resulting in creating unique solutions that arise at the interface of physics, nanotechnology, and microbiology. Specifically, physical factors (e.g., pressure, temperature, UV light) are increasingly used for industrial sterilization. Nanoparticles (unmodified or in combination with toxic compounds) are also applied to circumvent in vivo drug resistance mechanisms in bacteria. Recently, bacteriophage-based treatments are also gaining momentum due to their high bactericidal activity and specificity. Although the number of novel approaches for tackling the antimicrobial resistance crisis is snowballing, it is still unclear if any proposed solutions would provide a long-term remedy. This review aims to provide a detailed overview of how bacteria acquire resistance against these non-antibiotic factors. We also discuss innate bacterial defense systems and how bacteriophages have evolved to tackle them.
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Affiliation(s)
| | | | | | - Jan Paczesny
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland; (S.R.); (K.M.); (S.K.)
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34
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Tartari DC, Zamparette CP, Martini G, Christakis S, Costa LH, Silveira ACDO, Sincero TCM. Genomic analysis of an extensively drug-resistant Pseudomonas aeruginosa ST312 harbouring IncU plasmid-mediated bla KPC-2 isolated from ascitic fluid. J Glob Antimicrob Resist 2021; 25:151-153. [PMID: 33789205 DOI: 10.1016/j.jgar.2021.03.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 11/17/2020] [Accepted: 03/13/2021] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVES The Klebsiella pneumoniae carbapenemase (KPC) is disseminated worldwide mostly by plasmids. However, in Pseudomonas aeruginosa chromosomal mutations are more frequently responsible for resistance to carbapenems than the acquisition of mobile elements harbouring carbapenemases genes. Indeed, although uncommon, KPC-2-producing P. aeruginosa has appeared more frequently, including in Brazil. Here we report the first genomic analysis of a plasmid-mediated KPC-2 in an extensively drug-resistant (XDR) P. aeruginosa isolated in Santa Catarina, Brazil. METHODS Antimicrobial susceptibility testing was performed according to CLSI 2020 guidelines. The genome was sequenced using an Illumina MiSeq platform and the data were analysed using SPAdes and Prokka. In silico predictions were fulfilled using curated bioinformatics tools. RESULTS Pseudomonas aeruginosa strain MIMA_PA2.1 (JACGTM000000000) was classified as XDR, belongs to sequence type 312 (ST312) and harbours the blaKPC-2 gene located on a small (7975 bp) IncU plasmid. This plasmid showed 86.3% identity with a non-conjugative plasmid (KC609322) carrying the blaKPC-2 gene from a multidrug-resistant P. aeruginosa (ST1006) from Colombia isolated in 2006. Besides the blaKPC-2 gene, other resistance genes to β-lactams, aminoglycosides, phenicol, fosfomycin and quinolones were detected, the last two also associated with mobile genetic elements other than the IncU plasmid described here. CONCLUSION This is the first genomic report of the presence of the blaKPC-2 gene carried by Pseudomonas in Southern Brazil and highlights the adaptability of blaKPC-2 to different mobile elements. This draft genome might be useful for comparative genomic analyses to monitor the spread of plasmid-mediated blaKPC in P. aeruginosa in Latin America.
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Affiliation(s)
- Daniela Cristina Tartari
- Departamento de Análises Clínicas, Centro de Ciências da Saúde, Universidade Federal de Santa Catarina (UFSC), Setor E, Bloco K, Florianópolis, Santa Catarina 88040-970, Brazil
| | - Caetana Paes Zamparette
- Departamento de Análises Clínicas, Centro de Ciências da Saúde, Universidade Federal de Santa Catarina (UFSC), Setor E, Bloco K, Florianópolis, Santa Catarina 88040-970, Brazil
| | - Graciele Martini
- Laboratório Central de Saúde Pública de Santa Catarina (LACEN/SC), Florianópolis, Santa Catarina, Brazil
| | - Sandra Christakis
- Laboratório Central de Saúde Pública de Santa Catarina (LACEN/SC), Florianópolis, Santa Catarina, Brazil
| | - Luiz Henrique Costa
- Departamento de Ciências Farmacêuticas, Universidade Regional de Blumenau (FURB), Blumenau, Santa Catarina, Brazil
| | | | - Thaís Cristine Marques Sincero
- Departamento de Análises Clínicas, Centro de Ciências da Saúde, Universidade Federal de Santa Catarina (UFSC), Setor E, Bloco K, Florianópolis, Santa Catarina 88040-970, Brazil.
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35
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Mulkerrins KB, Lyons C, Shiaris MP. Draft Genome Sequence of Enterococcus faecalis AS003, a Strain Possessing All Three Type II-a CRISPR Loci. Microbiol Resour Announc 2021; 10:e01449-20. [PMID: 33737370 PMCID: PMC7975888 DOI: 10.1128/mra.01449-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/26/2021] [Indexed: 11/20/2022] Open
Abstract
Enterococcus faecalis is a clinically significant member of the human microbiome. Three CRISPR-Cas loci are located in conserved locations. Previous studies provide evidence that E. faecalis strains with functional CRISPR-Cas genes are negatively correlated with antibiotic resistance. Here, we report the genome sequence of an unusual strain possessing all three CRISPR-Cas loci.
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Affiliation(s)
- Kevin B Mulkerrins
- Shiaris Laboratory, Department of Biology, University of Massachusetts Boston, Boston, Massachusetts, USA
| | - Casandra Lyons
- Shiaris Laboratory, Department of Biology, University of Massachusetts Boston, Boston, Massachusetts, USA
| | - Michael P Shiaris
- Shiaris Laboratory, Department of Biology, University of Massachusetts Boston, Boston, Massachusetts, USA
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36
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Novel Strategy to Combat Antibiotic Resistance: A Sight into the Combination of CRISPR/Cas9 and Nanoparticles. Pharmaceutics 2021; 13:pharmaceutics13030352. [PMID: 33800235 PMCID: PMC7998274 DOI: 10.3390/pharmaceutics13030352] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/22/2021] [Accepted: 03/03/2021] [Indexed: 12/14/2022] Open
Abstract
Antibiotic resistance is a significant crisis that threatens human health and safety worldwide. There is an urgent need for new strategies to control multidrug-resistant (MDR) bacterial infections. The latest breakthrough in gene-editing tools based on CRISPR/Cas9 has potential application in combating MDR bacterial infections because of their high targeting ability to specifically disrupt the drug resistance genes that microbes use for infection or to kill the pathogen directly. Despite the potential that CRISPR/Cas9 showed, its further utilization has been hampered by undesirable delivery efficiency in vivo. Nanotechnology offers an alternative way to overcome the shortcomings of traditional delivery methods of therapeutic agents. Advances in nanotechnology can improve the efficacy and safety of CRISPR/Cas9 components by using customized nanoparticle delivery systems. The combination of CRISPR/Cas9 and nanotechnology has the potential to open new avenues in the therapy of MDR bacterial infections. This review describes the recent advances related to CRISPR/Cas9 and nanoparticles for antimicrobial therapy and gene delivery, including the improvement in the packaging and localizing efficiency of the CRISPR/Cas9 components in the NP (nanoparticle)/CRISPR system. We pay particular attention to the strengths and limitations of the nanotechnology-based CRISPR/Cas9 delivery system to fight nosocomial pathogens.We highlight the need for more scientific research to explore the combinatorial efficacy of various nanoparticles and CRISPR technology to control and prevent antimicrobial resistance.
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37
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Pinilla-Redondo R, Shehreen S, Marino ND, Fagerlund RD, Brown CM, Sørensen SJ, Fineran PC, Bondy-Denomy J. Discovery of multiple anti-CRISPRs highlights anti-defense gene clustering in mobile genetic elements. Nat Commun 2020; 11:5652. [PMID: 33159058 PMCID: PMC7648647 DOI: 10.1038/s41467-020-19415-3] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 10/06/2020] [Indexed: 12/14/2022] Open
Abstract
Many prokaryotes employ CRISPR-Cas systems to combat invading mobile genetic elements (MGEs). In response, some MGEs have developed strategies to bypass immunity, including anti-CRISPR (Acr) proteins; yet the diversity, distribution and spectrum of activity of this immune evasion strategy remain largely unknown. Here, we report the discovery of new Acrs by assaying candidate genes adjacent to a conserved Acr-associated (Aca) gene, aca5, against a panel of six type I systems: I-F (Pseudomonas, Pectobacterium, and Serratia), I-E (Pseudomonas and Serratia), and I-C (Pseudomonas). We uncover 11 type I-F and/or I-E anti-CRISPR genes encoded on chromosomal and extrachromosomal MGEs within Enterobacteriaceae and Pseudomonas, and an additional Aca (aca9). The acr genes not only associate with other acr genes, but also with genes encoding inhibitors of distinct bacterial defense systems. Thus, our findings highlight the potential exploitation of acr loci neighborhoods for the identification of previously undescribed anti-defense systems.
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Affiliation(s)
- Rafael Pinilla-Redondo
- Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
- University College Copenhagen, Copenhagen, Denmark
| | - Saadlee Shehreen
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Nicole D Marino
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
| | - Robert D Fagerlund
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Genetics Otago, University of Otago, Dunedin, New Zealand
| | - Chris M Brown
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
- Genetics Otago, University of Otago, Dunedin, New Zealand
| | - Søren J Sørensen
- Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.
- Genetics Otago, University of Otago, Dunedin, New Zealand.
- Bio-protection Research Centre, University of Otago, Dunedin, New Zealand.
| | - Joseph Bondy-Denomy
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA.
- Quantitative Biosciences Institute, UCSF, San Francisco, CA, USA.
- Innovative Genomics Institute, Berkeley, CA, USA.
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38
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Yi H, Huang L, Yang B, Gomez J, Zhang H, Yin Y. AcrFinder: genome mining anti-CRISPR operons in prokaryotes and their viruses. Nucleic Acids Res 2020; 48:W358-W365. [PMID: 32402073 PMCID: PMC7319584 DOI: 10.1093/nar/gkaa351] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/09/2020] [Accepted: 05/11/2020] [Indexed: 12/12/2022] Open
Abstract
Anti-CRISPR (Acr) proteins encoded by (pro)phages/(pro)viruses have a great potential to enable a more controllable genome editing. However, genome mining new Acr proteins is challenging due to the lack of a conserved functional domain and the low sequence similarity among experimentally characterized Acr proteins. We introduce here AcrFinder, a web server (http://bcb.unl.edu/AcrFinder) that combines three well-accepted ideas used by previous experimental studies to pre-screen genomic data for Acr candidates. These ideas include homology search, guilt-by-association (GBA), and CRISPR-Cas self-targeting spacers. Compared to existing bioinformatics tools, AcrFinder has the following unique functions: (i) it is the first online server specifically mining genomes for Acr-Aca operons; (ii) it provides a most comprehensive Acr and Aca (Acr-associated regulator) database (populated by GBA-based Acr and Aca datasets); (iii) it combines homology-based, GBA-based, and self-targeting approaches in one software package; and (iv) it provides a user-friendly web interface to take both nucleotide and protein sequence files as inputs, and output a result page with graphic representation of the genomic contexts of Acr-Aca operons. The leave-one-out cross-validation on experimentally characterized Acr-Aca operons showed that AcrFinder had a 100% recall. AcrFinder will be a valuable web resource to help experimental microbiologists discover new Anti-CRISPRs.
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Affiliation(s)
- Haidong Yi
- Department of Computer Science, University of North Carolina at Chapel Hill, NC, USA
- College of Computer Science, Nankai University, Tianjin, China
| | - Le Huang
- College of Computer Science, Nankai University, Tianjin, China
| | - Bowen Yang
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska - Lincoln, Lincoln, NE, USA
| | - Javi Gomez
- Department of Computer Science, Northern Illinois University, DeKalb, IL, USA
| | - Han Zhang
- College of Artificial Intelligence, Nankai University, Tianjin, China
| | - Yanbin Yin
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska - Lincoln, Lincoln, NE, USA
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39
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Westra ER, van Houte S, Gandon S, Whitaker R. The ecology and evolution of microbial CRISPR-Cas adaptive immune systems. Philos Trans R Soc Lond B Biol Sci 2020; 374:20190101. [PMID: 30905294 DOI: 10.1098/rstb.2019.0101] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Edze R Westra
- 1 ESI and CEC, Biosciences, University of Exeter , Cornwall Campus, Penryn TR10 9EZ , UK
| | - Stineke van Houte
- 1 ESI and CEC, Biosciences, University of Exeter , Cornwall Campus, Penryn TR10 9EZ , UK
| | - Sylvain Gandon
- 2 CEFE UMR 5175, CNRS Université de Montpellier Université Paul-Valéry Montpellier EPHE , 34293 Montpellier Cedex 5 , France
| | - Rachel Whitaker
- 3 Department of Microbiology, University of Illinois , Urbana-Champaign, 601 S. Goodwin Avenue, Urbana, IL 61801 , USA
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40
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Birkholz N, Fagerlund RD, Smith LM, Jackson SA, Fineran PC. The autoregulator Aca2 mediates anti-CRISPR repression. Nucleic Acids Res 2019; 47:9658-9665. [PMID: 31428783 PMCID: PMC6765145 DOI: 10.1093/nar/gkz721] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 08/03/2019] [Accepted: 08/06/2019] [Indexed: 12/20/2022] Open
Abstract
CRISPR-Cas systems are widespread bacterial adaptive defence mechanisms that provide protection against bacteriophages. In response, phages have evolved anti-CRISPR proteins that inactivate CRISPR-Cas systems of their hosts, enabling successful infection. Anti-CRISPR genes are frequently found in operons with genes encoding putative transcriptional regulators. The role, if any, of these anti-CRISPR-associated (aca) genes in anti-CRISPR regulation is unclear. Here, we show that Aca2, encoded by the Pectobacterium carotovorum temperate phage ZF40, is an autoregulator that represses the anti-CRISPR–aca2 operon. Aca2 is a helix-turn-helix domain protein that forms a homodimer and interacts with two inverted repeats in the anti-CRISPR promoter. The inverted repeats are similar in sequence but differ in their Aca2 affinity, and we propose that they have evolved to fine-tune, and downregulate, anti-CRISPR production at different stages of the phage life cycle. Specific, high-affinity binding of Aca2 to the first inverted repeat blocks the promoter and induces DNA bending. The second inverted repeat only contributes to repression at high Aca2 concentrations in vivo, and no DNA binding was detectable in vitro. Our investigation reveals the mechanism by which an Aca protein regulates expression of its associated anti-CRISPR.
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Affiliation(s)
- Nils Birkholz
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Robert D Fagerlund
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
- Genetics Otago, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Leah M Smith
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Simon A Jackson
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
- Genetics Otago, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
- Genetics Otago, University of Otago, PO Box 56, Dunedin 9054, New Zealand
- Bio-Protection Research Centre, University of Otago, PO Box 56, Dunedin 9054, New Zealand
- To whom correspondence should be addressed. Tel: +64 3 479 7735;
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Fineran PC. Resistance is not futile: bacterial 'innate' and CRISPR-Cas 'adaptive' immune systems. MICROBIOLOGY-SGM 2019; 165:834-841. [PMID: 30958259 DOI: 10.1099/mic.0.000802] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Bacteria are under a constant pressure from their viruses (phages) and other mobile genetic elements. They protect themselves through a range of defence strategies, which can be broadly classified as 'innate' and 'adaptive'. The bacterial innate immune systems include defences provided by restriction modification and abortive infection, among others. Bacterial adaptive immunity is elicited by a diverse range of CRISPR-Cas systems. Here, I discuss our research on both innate and adaptive phage resistance mechanisms and some of the evasion strategies employed by phages.
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Affiliation(s)
- Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
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