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AlJindan R, Mahmoud N, AlEraky DM, Almandil NB, AbdulAzeez S, Borgio JF. Phenomics and genomic features of Enterococcus avium IRMC1622a isolated from a clinical sample of hospitalized patient. J Infect Public Health 2024; 17:102463. [PMID: 38833914 DOI: 10.1016/j.jiph.2024.05.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 05/16/2024] [Accepted: 05/26/2024] [Indexed: 06/06/2024] Open
Abstract
BACKGROUND Enterococcus avium (E. avium) is a Gram-positive nosocomial pathogen that is commonly isolated from the alimentary tract. The objective of this functional genomics study was to identify the resistant genes by analyzing the genome of E. avium IRMC1622a, a type of bacteria found in feces collected from a patient at a Saudi Arabian tertiary hospital. METHODS The bacterial strain IRMC1622a was identified by 16 S rRNA sequencing as Enterococcus sp. The resistance phenomics were performed using VITEK® 2, and morphological analysis was achieved using a scanning electron microscope (SEM). Finally, the whole bacterial genome of the bacterial strain IRMC1622a was subjected to sequencing during October 2023 using Oxford Nanopore long-read sequencing technology, and mining for resistant genes. RESULTS The results of antimicrobial resistant phenomics indicated that the IRMC1622a strain was sensitive to all tested antimicrobial agents except for erythromycin, and the same result was confirmed by genomic analysis in addition to other classes of antibiotics. SEM showed E. avium IRMC1622a is ovoid shape, in single cells (L 1.2797 ± 0.1490 µm), in pairs (L 1.7333 ± 0.1054 µm), and in chains (L 2.44033 ± 0.1978 µm). The E. avium IRMC1622a genome has 14 (in CARD) antimicrobial resistance genes that were identified with several mechanisms of antimicrobial resistance, such as the efflux pump and conferring antibiotic resistance. The present study revealed that the E. avium IRMC1622a genome contains a high number of genes associated with virulence factors, and 14 matched pathogenic protein families and predicted as human pathogen (probability score 0.855). We report two (ISEnfa4 and ISEfa5) mobile genetic elements for the first time in the E. avium genome. CONCLUSIONS The study concludes that E. avium IRMC1622a is susceptible to all tested antibacterials except erythromycin. The IRMC1622a has 14 genes encoding antimicrobial resistance mechanisms, including the efflux pump and conferring antibiotic resistance. This could indicate a potential rise in E. avium resistance in healthcare facilities. These observations may raise concerns regarding E. avium resistance in healthcare. We need more research to understand the pathophysiology of E. avium, which leads to hospital-acquired infections.
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Affiliation(s)
- Reem AlJindan
- Department of Microbiology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Nehal Mahmoud
- Department of Microbiology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Doaa M AlEraky
- Department of Biomedical Sciences, College of Medicine, Gulf Medical University, Ajman 4184, United Arab Emirates
| | - Noor B Almandil
- Department of Clinical Pharmacy Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia.
| | - Sayed AbdulAzeez
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - J Francis Borgio
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia.
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Kawamura T, Prah I, Mahazu S, Ablordey A, Saito R. Types A and F Clostridium perfringens in healthcare wastewater from Ghana. Appl Environ Microbiol 2023; 89:e0161923. [PMID: 38051072 PMCID: PMC10734495 DOI: 10.1128/aem.01619-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 10/18/2023] [Indexed: 12/07/2023] Open
Abstract
IMPORTANCE Clostridium perfringens causes gas gangrene and food poisoning in humans, and monitoring this bacterium is important for public health. Although whole-genome sequencing is useful to comprehensively understand the virulence, resistome, and global genetic relatedness of bacteria, limited genomic data from environmental sources and developing countries hamper our understanding of the richness of the intrinsic genomic diversity of this pathogen. Here, we successfully accumulated the genetic data on C. perfringens strains isolated from hospital effluent and provided the first evidence that predicted pathogenic C. perfringens may be disseminated in the clinical environment in Ghana. Our findings suggest the importance of risk assessment in the environment as well as the clinical setting to mitigate the potential outbreak of C. perfringens food poisoning in Ghana.
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Affiliation(s)
- Taira Kawamura
- Department of Molecular Microbiology and Immunology, Graduate School of Medicine and Dental Science, Tokyo Medical and Dental University, Tokyo, Japan
| | - Isaac Prah
- Department of Molecular Microbiology and Immunology, Graduate School of Medicine and Dental Science, Tokyo Medical and Dental University, Tokyo, Japan
| | - Samiratu Mahazu
- Department of Molecular Microbiology and Immunology, Graduate School of Medicine and Dental Science, Tokyo Medical and Dental University, Tokyo, Japan
| | - Anthony Ablordey
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Ryoichi Saito
- Department of Molecular Microbiology and Immunology, Graduate School of Medicine and Dental Science, Tokyo Medical and Dental University, Tokyo, Japan
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Garvey M. Foodborne Clostridioides Species: Pathogenicity, Virulence and Biocontrol Options. Microorganisms 2023; 11:2483. [PMID: 37894141 PMCID: PMC10609181 DOI: 10.3390/microorganisms11102483] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 09/22/2023] [Accepted: 10/02/2023] [Indexed: 10/29/2023] Open
Abstract
Clostridioides species possess many virulence factors and alarming levels of muti-drug resistance which make them a significant risk to public health safety and a causative agent of livestock disease. Clostridioides result in serious systemic and gastrointestinal diseases such as myonecrosis, colitis, food poisoning and gastroenteritis. As foodborne pathogens, Clostridioides species are associated with significant incidences of morbidity and mortality where the application of broad-spectrum antibiotics predisposes patients to virulent Clostridioides colonisation. As part of the One Health approach, there is an urgent need to eliminate the use of antibiotics in food production to safeguard animals, humans and the environment. Alternative options are warranted to control foodborne pathogens at all stages of food production. Antimicrobial peptides and bacteriophages have demonstrated efficacy against Clostridioides species and may offer antimicrobial biocontrol options. The bacteriocin nisin, for example, has been implemented as a biopreservative for the control of Listeria, Staphylococcus and Clostridia species in food. Bacteriophage preparations have also gained recognition for the antibacterial action against highly virulent bacterial species including foodborne pathogens. Studies are warranted to mitigate the formulation and administration limitations associated with the application of such antimicrobials as biocontrol strategies. This review outlines foodborne Clostridioides species, their virulence factors, and potential biocontrol options for application in food production.
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Affiliation(s)
- Mary Garvey
- Department of Life Science, Atlantic Technological University, Ash Lane, F91 YW50 Sligo, Ireland;
- Centre for Precision Engineering, Materials and Manufacturing Research (PEM), Atlantic Technological University, F91 YW50 Sligo, Ireland
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Borgio JF, AlJindan R, Alghourab LH, Alquwaie R, Aldahhan R, Alhur NF, AlEraky DM, Mahmoud N, Almandil NB, AbdulAzeez S. Genomic Landscape of Multidrug Resistance and Virulence in Enterococcus faecalis IRMC827A from a Long-Term Patient. BIOLOGY 2023; 12:1296. [PMID: 37887006 PMCID: PMC10604365 DOI: 10.3390/biology12101296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/25/2023] [Accepted: 09/27/2023] [Indexed: 10/28/2023]
Abstract
We report on a highly virulent, multidrug-resistant strain of Enterococcus faecalis IRMC827A that was found colonizing a long-term male patient at a tertiary hospital in Khobar, Saudi Arabia. The E. faecalis IRMC827A strain carries several antimicrobial drug resistance genes and harbours mobile genetic elements such as Tn6009, which is an integrative conjugative element that can transfer resistance genes between bacteria and ISS1N via an insertion sequence. Whole-genome-sequencing-based antimicrobial susceptibility testing on strains from faecal samples revealed that the isolate E. faecalis IRMC827A is highly resistant to a variety of antibiotics, including tetracycline, doxycycline, minocycline, dalfopristin, virginiamycin, pristinamycin, chloramphenicol, streptomycin, clindamycin, lincomycin, trimethoprim, nalidixic acid and ciprofloxacin. The isolate IRMC827A carries several virulence factors that are significantly associated with adherence, biofilm formation, sortase-assembled pili, manganese uptake, antiphagocytosis, and spreading factor of multidrug resistance. The isolate also encompasses two mutations (G2576T and G2505A) in the 23S rRNA gene associated with linezolid resistance and three more mutations (gyrA p.S83Y, gyrA p.D759N and parC p.S80I) of the antimicrobial resistance phenotype. The findings through next-generation sequencing on the resistome, mobilome and virulome of the isolate in the study highlight the significance of monitoring multidrug-resistant E. faecalis colonization and infection in hospitalized patients. As multidrug-resistant E. faecalis is a serious pathogen, it is particularly difficult to treat and can cause fatal infections. It is important to have quick and accurate diagnostic tests for multidrug-resistant E. faecalis, to track the spread of multidrug-resistant E. faecalis in healthcare settings, and to improve targeted interventions to stop its spread. Further research is necessary to develop novel antibiotics and treatment strategies for multidrug-resistant E. faecalis infections.
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Affiliation(s)
- J. Francis Borgio
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; (J.F.B.); (R.A.); (N.F.A.)
| | - Reem AlJindan
- Department of Microbiology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia;
| | - Lujeen H. Alghourab
- Summer Research Program, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia;
| | - Rahaf Alquwaie
- Master Program of Biotechnology, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia;
| | - Razan Aldahhan
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; (J.F.B.); (R.A.); (N.F.A.)
| | - Norah F. Alhur
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; (J.F.B.); (R.A.); (N.F.A.)
| | - Doaa M. AlEraky
- Department of Biomedical Dental Science, Microbiology and Immunology Division, Collage of Dentistry, Dammam 31441, Saudi Arabia
| | - Nehal Mahmoud
- Department of Microbiology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia;
| | - Noor B. Almandil
- Department of Clinical Pharmacy Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia;
| | - Sayed AbdulAzeez
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; (J.F.B.); (R.A.); (N.F.A.)
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