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Costache C, Colosi I, Toc DA, Daian K, Damacus D, Botan A, Toc A, Pana AG, Panaitescu P, Neculicioiu V, Schiopu P, Iordache D, Butiuc-Keul A. CRISPR-Cas System, Antimicrobial Resistance, and Enterococcus Genus-A Complicated Relationship. Biomedicines 2024; 12:1625. [PMID: 39062198 PMCID: PMC11274382 DOI: 10.3390/biomedicines12071625] [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: 06/13/2024] [Revised: 07/07/2024] [Accepted: 07/18/2024] [Indexed: 07/28/2024] Open
Abstract
(1) Background: The rise in antibiotic resistant bacteria poses a significant threat to public health worldwide, necessitating innovative solutions. This study explores the role of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) in the context of antibiotic resistance among different species from the Enterococcus genus. (2) Methods: The genomes of Enterococcus included in the study were analyzed using CRISPRCasFinder to distinguish between CRISPR-positive (level 4 CRISPR) and CRISPR-negative genomes. Antibiotic resistance genes were identified, and a comparative analysis explored potential associations between CRISPR presence and antibiotic resistance profiles in Enterococcus species. (3) Results: Out of ten antibiotic resistance genes found in Enterococcus species, only one, the efmA gene, showed a strong association with CRISPR-negative isolates, while the others did not significantly differ between CRISPR-positive and CRISPR-negative Enterococcus genomes. (4) Conclusion: These findings indicate that the efmA gene may be more prevalent in CRISPR-negative Enterococcus genomes, and they may contribute to a better understanding of the molecular mechanisms underlying the acquisition of antibiotic resistance genes in Enterococcus species.
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Affiliation(s)
- Carmen Costache
- Department of Microbiology, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania (I.C.)
- Cluj County Emergency Hospital, 400000 Cluj-Napoca, Romania
| | - Ioana Colosi
- Department of Microbiology, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania (I.C.)
| | - Dan-Alexandru Toc
- Department of Microbiology, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania (I.C.)
- Cluj County Emergency Hospital, 400000 Cluj-Napoca, Romania
| | - Karla Daian
- Faculty of Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
| | - David Damacus
- Faculty of Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
| | - Alexandru Botan
- Faculty of Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
| | - Adelina Toc
- Faculty of Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
| | - Adrian Gabriel Pana
- Faculty of Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
| | - Paul Panaitescu
- Department of Microbiology, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania (I.C.)
| | - Vlad Neculicioiu
- Department of Microbiology, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania (I.C.)
| | - Pavel Schiopu
- Department of Microbiology, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania (I.C.)
| | - Dumitrana Iordache
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeş-Bolyai University, 400084 Cluj-Napoca, Romania
- Centre for Systems Biology, Biodiversity and Bioresources, Babes-Bolyai University, 400006 Cluj-Napoca, Romania
| | - Anca Butiuc-Keul
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeş-Bolyai University, 400084 Cluj-Napoca, Romania
- Centre for Systems Biology, Biodiversity and Bioresources, Babes-Bolyai University, 400006 Cluj-Napoca, Romania
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Yeh HY, Cox NA, Hinton A, Berrang ME. Detection and Distribution of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) in Campylobacter jejuni Isolates from Chicken Livers. J Food Prot 2024; 87:100250. [PMID: 38382707 DOI: 10.1016/j.jfp.2024.100250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 02/12/2024] [Accepted: 02/15/2024] [Indexed: 02/23/2024]
Abstract
Campylobacter jejuni is the leading foodborne bacterial pathogen that causes human gastroenteritis worldwide linked to the consumption of undercooked broiler livers. Application of bacteriophages during poultry production has been used as an alternative approach to reduce contamination of poultry meat by Campylobacter. To make this approach effective, understanding the presence of the bacteriophage sequences in the CRISPR spacers in C. jejuni is critical as they may confer bacterial resistance to bacteriophage treatment. Therefore, in this study, we explored the distribution of the CRISPR arrays from 178 C. jejuni isolated from chicken livers between January and July 2018. Genomic DNA of C. jejuni isolates was extracted, and CRISPR type 1 sequences were amplified by PCR. Amplicons were purified and sequenced by the Sanger dideoxy sequencing method. Direct repeats (DRs) and spacers of CRISPR sequences were identified using the CRISPRFinder program. Further, spacer sequences were submitted to the CRISPRTarget to identify potential homology to bacteriophage types. Even though CRISPR-Cas is reportedly not an active system in Campylobacter, a total of 155 (87%) C. jejuni isolates were found to harbor CRISPR sequences; one type of DR was identified in all 155 isolates. The CRISPR loci lengths ranged from 97 to 431 nucleotides. The numbers of spacers ranged from one to six. A total of 371 spacer sequences were identified in the 155 isolates that could be grouped into 51 distinctive individual sequences. Further comparison of these 51 spacer sequences with those in databases showed that most spacer sequences were homologous to Campylobacter bacteriophage DA10. The results of our study provide important information relative to the development of an effective bacteriophage treatment to mitigate Campylobacter during poultry production.
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Affiliation(s)
- Hung-Yueh Yeh
- U.S. National Poultry Research Center, Agricultural Research Service, United States Department of Agriculture, 950 College Station Road, Athens, GA 30605-2720, USA.
| | - Nelson A Cox
- U.S. National Poultry Research Center, Agricultural Research Service, United States Department of Agriculture, 950 College Station Road, Athens, GA 30605-2720, USA
| | - Arthur Hinton
- U.S. National Poultry Research Center, Agricultural Research Service, United States Department of Agriculture, 950 College Station Road, Athens, GA 30605-2720, USA
| | - Mark E Berrang
- U.S. National Poultry Research Center, Agricultural Research Service, United States Department of Agriculture, 950 College Station Road, Athens, GA 30605-2720, 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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Teixeira IM, Guimarães L, da Silva IT, Fonseca C, Assumpção Y, Lima Dos Santos AL, Antunes M, Pesset C, Ferreira E, Penna B. High prevalence of Panton-Valentine Leucocidin among Staphylococcus coagulans isolated from dogs in Rio de Janeiro. J Appl Microbiol 2023; 134:lxad256. [PMID: 37943996 DOI: 10.1093/jambio/lxad256] [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: 08/14/2023] [Revised: 10/03/2023] [Accepted: 11/03/2023] [Indexed: 11/12/2023]
Abstract
AIMS The purpose of this study was to characterize the capacity for biofilm formation, antimicrobial resistance rates, and search for genetic determinants of resistance and virulence in the species. METHODS AND RESULTS Strains were collected from asymptomatic and infected dogs. Identification was conducted using matrix-assisted laser desorption ionization-time of flight (MALDI-TOF), antimicrobial susceptibility using disk diffusion and PCR targeting mecA. Biofilm formation was evaluated on a microtiter plate assay. A total of 27 strains were selected for whole-genome sequencing. We identified 111 Staphylococcus coagulans. The highest number was obtained from infected dogs. The highest resistance rates were observed for penicillin, gentamicin, and ciprofloxacin/erythromycin. Twelve strains were characterized as resistant to methicillin. All isolates had the ability to form biofilm and were strong producers. Among Methicillin Resistant Staphylococcus coagulans (MRSC), SCCmec types IIIA, and Vc were identified. Acquired resistance genes, such as aac(6')-aph(2''), tet(K), blaZ, qacG, qacJ, and erm(C) were found. Different virulence genes were identified. Of note, Panton-Valentine Leucocidin was highly prevalent among the isolates. CONCLUSION Staphylococcus coagulans had a high isolation rate among infected dogs and demonstrated significant resistance to commonly used antibiotics such as penicillin and gentamicin.
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Affiliation(s)
- Izabel M Teixeira
- Laboratório de Biologia de Anaeróbios, Depto. Microbiologia Médica, IMPG, UFRJ, 21941-902 - Rio de janeiro - Brazil
- Laboratório de Cocos Gram Positivos, Depto. de Microbiologia e Parasitologia, UFF, 24210-130 - Niteroi - Brazil
| | - Luciana Guimarães
- Laboratório de Cocos Gram Positivos, Depto. de Microbiologia e Parasitologia, UFF, 24210-130 - Niteroi - Brazil
| | - Isabella T da Silva
- Laboratório de Cocos Gram Positivos, Depto. de Microbiologia e Parasitologia, UFF, 24210-130 - Niteroi - Brazil
| | - Carolina Fonseca
- Laboratório de Cocos Gram Positivos, Depto. de Microbiologia e Parasitologia, UFF, 24210-130 - Niteroi - Brazil
| | - Yasmim Assumpção
- Laboratório de Cocos Gram Positivos, Depto. de Microbiologia e Parasitologia, UFF, 24210-130 - Niteroi - Brazil
| | - Ana Luiza Lima Dos Santos
- Laboratório de Cocos Gram Positivos, Depto. de Microbiologia e Parasitologia, UFF, 24210-130 - Niteroi - Brazil
| | - Milena Antunes
- Laboratório de Cocos Gram Positivos, Depto. de Microbiologia e Parasitologia, UFF, 24210-130 - Niteroi - Brazil
| | - Camilla Pesset
- Laboratório de Cocos Gram Positivos, Depto. de Microbiologia e Parasitologia, UFF, 24210-130 - Niteroi - Brazil
| | - Eliane Ferreira
- Laboratório de Biologia de Anaeróbios, Depto. Microbiologia Médica, IMPG, UFRJ, 21941-902 - Rio de janeiro - Brazil
| | - Bruno Penna
- Laboratório de Cocos Gram Positivos, Depto. de Microbiologia e Parasitologia, UFF, 24210-130 - Niteroi - Brazil
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