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Tadesse BT, Gu L, Solem C, Mijakovic I, Jers C. The Probiotic Enterococcus Lactis SF68 as a Potential Food Fermentation Microorganism for Safe Food Production. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:18089-18099. [PMID: 39102436 DOI: 10.1021/acs.jafc.4c03644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/07/2024]
Abstract
Due to the reports describing virulent and multidrug resistant enterococci, their use has become a topic of controversy despite most of them being safe and commonly used in traditionally fermented foods worldwide. We have characterized Enterococcus lactis SF68, a probiotic strain approved by the European Food Safety Authority (EFSA) for use in food and feed, and find that it has a remarkable potential in food fermentations. Genome analysis revealed the potential of SF68 to metabolize a multitude of carbohydrates, including lactose and sucrose, which was substantiated experimentally. Bacteriocin biosynthesis clusters were identified and SF68 was found to display a strong inhibitory effect against Listeria monocytogenes. Fermentation-wise, E. lactis SF68 was remarkably like Lactococcus lactis and displayed a clear mixed-acid shift on slowly fermented sugars. SF68 could produce the butter aroma compounds, acetoin and diacetyl, the production of which was enhanced under aerated conditions in a strain deficient in lactate dehydrogenase activity. Overall, E. lactis SF68 was found to be versatile, with a broad carbohydrate utilization capacity, a capacity for producing bacteriocins, and an ability to grow at elevated temperatures. This is key to eliminating pathogenic and spoilage microorganisms that are frequently associated with fermented foods.
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Affiliation(s)
- Belay Tilahun Tadesse
- National Food Institute, Research Group for Microbial Biotechnology and Biorefining, Technical University of Denmark, Lyngby 2800, Denmark
- Novo Nordisk Foundation Center for Biosustainability, Lyngby 2800, Denmark
| | - Liuyan Gu
- Department of Bio- and Chemical Engineering, Aarhus University, Gustav Wieds vej 10, Aarhus 8000, Denmark
| | - Christian Solem
- National Food Institute, Research Group for Microbial Biotechnology and Biorefining, Technical University of Denmark, Lyngby 2800, Denmark
| | - Ivan Mijakovic
- Novo Nordisk Foundation Center for Biosustainability, Lyngby 2800, Denmark
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg 412 96, Sweden
| | - Carsten Jers
- Novo Nordisk Foundation Center for Biosustainability, Lyngby 2800, Denmark
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El-Saadony MT, Yang T, Saad AM, Alkafaas SS, Elkafas SS, Eldeeb GS, Mohammed DM, Salem HM, Korma SA, Loutfy SA, Alshahran MY, Ahmed AE, Mosa WFA, Abd El-Mageed TA, Ahmed AF, Fahmy MA, El-Tarabily MK, Mahmoud RM, AbuQamar SF, El-Tarabily KA, Lorenzo JM. Polyphenols: Chemistry, bioavailability, bioactivity, nutritional aspects and human health benefits: A review. Int J Biol Macromol 2024; 277:134223. [PMID: 39084416 DOI: 10.1016/j.ijbiomac.2024.134223] [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: 09/10/2022] [Revised: 06/17/2024] [Accepted: 07/26/2024] [Indexed: 08/02/2024]
Abstract
Polyphenols, including phenolics, alkaloids, and terpenes, are secondary metabolites that are commonly found in fruits, vegetables, and beverages, such as tea, coffee, wine, chocolate, and beer. These compounds have gained considerable attention and market demand because of their potential health benefits. However, their application is limited due to their low absorption rates and reduced tissue distribution efficiency. Engineering polyphenol-protein complexes or conjugates can enhance the antioxidant properties, bioavailability, and stability of polyphenols and improve digestive enzyme hydrolysis, target-specific delivery, and overall biological functions. Complex polyphenols, such as melanin, tannins, and ellagitannins, can promote gut microbiota balance, bolster antioxidant defense, and improve overall human health. Despite these benefits, the safety of polyphenol complexes must be thoroughly evaluated before their use as functional food additives or supplements. This review provides a detailed overview of the types of macromolecular polyphenols, their chemical composition, and their role in food enrichment. The mechanisms by which complex polyphenols act as antioxidative, anti-inflammatory, and anticancer agents have also been discussed.
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Affiliation(s)
- Mohamed T El-Saadony
- Department of Agricultural Microbiology, Faculty of Agriculture, Zagazig University, Zagazig, 44511, Egypt
| | - Tao Yang
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, School of Pharmacy, Hainan Medical University, Haikou, 571199, China
| | - Ahmed M Saad
- Department of Biochemistry, Faculty of Agriculture, Zagazig University, Zagazig, 44511, Egypt
| | - Samar Sami Alkafaas
- Molecular Cell Biology Unit, Division of Biochemistry, Department of Chemistry, Faculty of Science, Tanta University, Tanta, 31527, Egypt
| | - Sara Samy Elkafas
- Production Engineering and Mechanical Design Department, Faculty of Engineering, Menofia University, Shebin El Kom, 32511, Egypt; Faculty of Control System and Robotics, Information Technologies, Mechanics and Optics (ITMO) University, Saint-Petersburg, Russia
| | - Gehad S Eldeeb
- Department of Food Technology, Faculty of Agriculture, Suez Canal University, Ismailia, 41522, Egypt
| | - Dina Mostafa Mohammed
- Nutrition and Food Sciences Department, National Research Centre, Dokki, Giza, 12622, Egypt
| | - Heba M Salem
- Department of Poultry Diseases, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt
| | - Sameh A Korma
- Department of Food Science, Faculty of Agriculture, Zagazig University, Zagazig, 44511, Egypt
| | - Samah A Loutfy
- Virology and Immunology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, 12211, Egypt
| | - Mohammad Y Alshahran
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, 9088, Saudi Arabia
| | - Ahmed Ezzat Ahmed
- Department of Biology, College of Science, King Khalid University, Abha, 61421, Saudi Arabia
| | - Walid F A Mosa
- Plant Production Department (Horticulture-Pomology), Faculty of Agriculture, Saba Basha, Alexandria University, Alexandria, 21531, Egypt
| | - Taia A Abd El-Mageed
- Soil and Water Department, Faculty of Agriculture, Fayoum University, Fayoum, 63514, Egypt
| | - Atef F Ahmed
- Department of Biology, College of Science, Taif University, Taif, 21944, Saudi Arabia
| | - Mohamed A Fahmy
- Department of Agricultural Microbiology, Faculty of Agriculture, Zagazig University, Zagazig, 44511, Egypt
| | | | - Reda M Mahmoud
- Dr Nutrition Pharmaceuticals (DNP), Dubai, 48685, United Arab Emirates
| | - Synan F AbuQamar
- Department of Biology, United Arab Emirates University, Al Ain, 15551, United Arab Emirates.
| | - Khaled A El-Tarabily
- Department of Biology, United Arab Emirates University, Al Ain, 15551, United Arab Emirates; Harry Butler Institute, Murdoch University, Murdoch, 6150, W.A., Australia
| | - José M Lorenzo
- Centro Tecnologico´ de La Carne de Galicia, Rúa Galicia No. 4, Parque Tecnologico de Galicia, San Cibrao das Vinas, Ourense, 32900, Spain; Universidad de Vigo, Area´ de Tecnología de Los Alimentos, Facultad de Ciencias de Ourense, Ourense, 32004, Spain
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Obaid Hasson S, Kamil Hasan H, Abdul Kadhem Salman S, Judi HK, Akrami S, Saki M, Adil Hasan M, Fares Hashem D. In vivo and in vitro efficacy of the ithmid kohl/zinc-oxide nanoparticles, ithmid kohl/Aloe vera, and zinc-oxide nanoparticles/Aloe vera for the treatment of bacterial endophthalmitis. Sci Rep 2024; 14:15746. [PMID: 38977762 PMCID: PMC11231241 DOI: 10.1038/s41598-024-66341-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 07/01/2024] [Indexed: 07/10/2024] Open
Abstract
The aim of this study was to investigate the efficacy of the ithmid kohl/zinc-oxide nanoparticles (ZnONPs), ithmid kohl/Aloe vera, and ZnONPs/Aloe vera in the treatment of bacterial endophthalmitis. The endophthalmitis model was prepared by contaminating both eyes of 24 healthy adult male albino rabbits with a clinical isolate of Klebsiella pneumoniae. The animals were randomly divided into eight groups (A-H) according to the treatment. Group A received 1 ml of ithmid kohl/ZnONPs ointment, group B received 1 ml of ithmid kohl/Aloe vera gel ointment, group C received 1 ml of ZnONPs/Aloe vera gel ointment, and groups D, E, and F were treated with 1 ml of ithmid kohl solution (0.5 g/ml in distilled water), 1 ml of ZnONPs (0.5 g/ml) colloidal dispersion, and 1 ml of Aloe vera gel, respectively. Group G received 100 μl of a tetracycline antibiotic solution (final concentration: 16 µg/ml), and group H received sterile distilled water (no treatment). In vitro antibacterial activity was evaluated against K. pneumoniae using the agar well diffusion. The combination of ithmid kohl/ZnONPs was the most effective formulation for treating endophthalmitis model in infected rabbits within 2 days. In vitro antibacterial assay confirmed the potential of the ithmid kohl/ZnONPs formulation, which had the largest zone of inhibition (31 mm) among the compounds tested. The preparation of the ithmid kohl/ZnONPs formulation and its in vivo experiment in albino rabbits for the treatment of bacterial endophthalmitis was an innovative approach that has shown promise and may potentially serve as a viable alternative in clinical practice.
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Affiliation(s)
- Shaimaa Obaid Hasson
- Medical Biotechnology Department, College of Biotechnology, Al-Qasim Green University, Babylon, 51013, Iraq
| | | | - Sumod Abdul Kadhem Salman
- Microbiology Department, College of Veterinary Medicine, Al-Qasim Green University, Babylon, 51013, Iraq
| | - Hawraa K Judi
- Department of Medical Physics, Hilla University College, Babylon, Iraq
| | - Sousan Akrami
- Students' Scientific Research Center (SSRC), Tehran University of Medical Sciences, Tehran, Iran.
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
| | - Morteza Saki
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
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Owaid HA, Al-Ouqaili MT. Molecular and bacteriological investigations for the co-existence CRISPR/Cas system and β-lactamases of types extended-spectrum and carbapenemases in Multidrug, extensive drug and Pandrug-Resistant Klebsiella pneumoniae. Saudi J Biol Sci 2024; 31:104022. [PMID: 38817398 PMCID: PMC11137337 DOI: 10.1016/j.sjbs.2024.104022] [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: 03/17/2024] [Revised: 05/05/2024] [Accepted: 05/10/2024] [Indexed: 06/01/2024] Open
Abstract
The recent approach towards combating the antimicrobial resistance has led to the use of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and associated sequence to overcome the challenges of antimicrobial resistance. Thus, this study aimed to detect the underlying resistance mechanisms such as ESBLs and carbapenemases and whether there is a correlation between multidrug, extensive drug and pan drug resistance and the occurrence of CRISPR loci. A total of one hundred study isolates were subjected to antimicrobial susceptibility testing using the AST card of the Vitek technique to detect resistance patterns involving ESBLs and carbapenemase (CRE). An investigation of the genes encoding CRISPR/Cas systems using PCR was achieved. Out of 81 (81.0%) resistant Klebsiella pneumoniae isolates, 71 (71%) and 21 (21.0%) produced ESBLs and carbapenemases, respectively. Also, 53 (53.0%), 19 (19.0%) and 9 (9.0%) were MDR, XDR, and PDR respectively. It was noted that Cas1, Cas3, CRISPR1, CRISPR2 and CRISPR3 were positive in 38 (38.0%) of the isolates, while CRISPR1 for incomplete CRISPR1-Cas systems alone was detected in 78 (78.0%). Further, the number of intact CRISPR1, intact CRISPR2 and intact CRISPR3 types were 7 (27.0%), 34 (34%) and 18 (18.0%) respectively. It is concluded that antibiotic resistance levels were inversely correlated with the existence of CRISPR/Cas systems. The absence of the CRISPR/Cas system increases the prevalence of MDR, XDR and PDR in ESBL and carbapenem-producing Klebsiella pneumoniae. With the increase in the degree of antibiotic resistance (MDR, XDR to PDR), the occurrence ratio of the (CRISPR)/CRISPR-associated sequence decreased.
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Affiliation(s)
- Hekmat A. Owaid
- Department of Biology, College of Science, University of Anbar, Ramadi, Iraq
| | - Mushtak T.S. Al-Ouqaili
- Department of Microbiology, College of Medicine, University of Anbar, Al-Anbar Governorate, Ramadi, Iraq
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Khazani Asforooshani M, Elikaei A, Abed S, Shafiei M, Barzi SM, Solgi H, Badmasti F, Sohrabi A. A novel Enterococcus faecium phage EF-M80: unveiling the effects of hydrogel-encapsulated phage on wound infection healing. Front Microbiol 2024; 15:1416971. [PMID: 39006751 PMCID: PMC11239553 DOI: 10.3389/fmicb.2024.1416971] [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: 04/13/2024] [Accepted: 06/13/2024] [Indexed: 07/16/2024] Open
Abstract
Background Enterococcus faecium is one of the members of ESKAPE pathogens. Due to its resistance to antimicrobial agents, treating this bacterium has become challenging. The development of innovative approaches to combat antibiotic resistance is necessary. Phage therapy has emerged as a promising method for curing antibiotic-resistant bacteria. Methods In this study, E. faecium phages were isolated from wastewater. Phage properties were characterized through in vitro assays (e.g. morphological studies, and physicochemical properties). In addition, whole genome sequencing was performed. A hydrogel-based encapsulated phage was obtained and its structure characteristics were evaluated. Wound healing activity of the hydrogel-based phage was assessed in a wound mice model. Results The purified phage showed remarkable properties including broad host range, tolerance to high temperature and pH and biofilm degradation feature as a stable and reliable therapeutic agent. Whole genome sequencing revealed that the genome of the EF-M80 phage had a length of 40,434 bp and harbored 65 open reading frames (ORFs) with a GC content of 34.9% (GenBank accession number is OR767211). Hydrogel-based encapsulated phage represented an optimized structure. Phage-loaded hydrogel-treated mice showed that the counting of neutrophils, fibroblasts, blood vessels, hair follicles and percentage of collagen growth were in favor of the wound healing process in the mice model. Conclusion These findings collectively suggest the promising capability of this phage-based therapeutic strategy for the treatment of infections associated with the antibiotic-resistant E. faecium. In the near future, we hope to expect the presence of bacteriophages in the list of antibacterial compounds used in the clinical settings.
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Affiliation(s)
- Mahshid Khazani Asforooshani
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | - Ameneh Elikaei
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
| | - Sahar Abed
- Department of Microbial Biotechnology, Faculty of Basic Sciences and Advanced Technologies in Biology, University of Science and Culture, Tehran, Iran
| | - Morvarid Shafiei
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | | | - Hamid Solgi
- Isfahan Endocrine and Metabolism Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Farzad Badmasti
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | - Aria Sohrabi
- Department of Epidemiology and Biostatistics, Research Center for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
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Kadkhoda H, Gholizadeh P, Ghotaslou R, Pirzadeh T, Ahangarzadeh Rezaee M, Nabizadeh E, Feizi H, Samadi Kafil H, Aghazadeh M. Prevalence of the CRISPR-cas system and its association with antibiotic resistance in clinical Klebsiella pneumoniae isolates. BMC Infect Dis 2024; 24:554. [PMID: 38831286 PMCID: PMC11149351 DOI: 10.1186/s12879-024-09451-5] [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: 02/04/2024] [Accepted: 05/30/2024] [Indexed: 06/05/2024] Open
Abstract
BACKGROUND AND OBJECTIVE(S) CRISPR-Cas is a prokaryotic adaptive immune system that protects bacteria and archaea against mobile genetic elements (MGEs) such as bacteriophages plasmids, and transposons. In this study, we aimed to assess the prevalence of the CRISPR-Cas systems and their association with antibiotic resistance in one of the most challenging bacterial pathogens, Klebsiella pneumoniae. MATERIALS AND METHODS A total of 105 K. pneumoniae isolates were collected from various clinical infections. Extended-spectrum β-lactamases (ESBLs) phenotypically were detected and the presence of ESBL, aminoglycoside-modifying enzymes (AME), and CRISPR-Cas system subtype genes were identified using PCR. Moreover, the diversity of the isolates was determined by enterobacterial repetitive intergenic consensus (ERIC)-PCR. RESULTS Phenotypically, 41.9% (44/105) of the isolates were found to be ESBL producers. A significant inverse correlation existed between the subtype I-E CRISPR-Cas system's presence and ESBL production in K. pneumoniae isolates. Additionally, the frequency of the ESBL genes blaCTX-M1 (3%), blaCTX-M9 (12.1%), blaSHV (51.5%), and blaTEM (33.3%), as well as some AME genes such as aac(3)-Iva (21.2%) and ant(2'')-Ia (3%) was significantly lower in the isolates with the subtype I-E CRISPR-Cas system in comparison to CRISPR-negative isolates. There was a significant inverse correlation between the presence of ESBL and some AME genes with subtype I-E CRISPR-Cas system. CONCLUSION The presence of the subtype I-E CRISPR-Cas system was correlated with the antibiotic-resistant gene (ARGs). The isolates with subtype I-E CRISPR-Cas system had a lower frequency of ESBL genes and some AME genes than CRISPR-negative isolates.
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Affiliation(s)
- Hiva Kadkhoda
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Medical Microbiology, Faculty of Medicine, 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
| | - Reza Ghotaslou
- Department of Medical Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
- Infectious and Tropical Diseases 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
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Edris Nabizadeh
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Medical Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hadi Feizi
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Medical Microbiology, Aalinasab Hospital, Social Security Organization, Tabriz, Iran
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Mohammad Aghazadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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Abed S, Sholeh M, Khazani Asforooshani M, Shafiei M, Hashemi Shahraki A, Nasr S. Insights into the novel Enterococcus faecalis phage: A comprehensive genome analysis. PLoS One 2024; 19:e0301292. [PMID: 38743671 PMCID: PMC11093359 DOI: 10.1371/journal.pone.0301292] [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: 01/30/2024] [Accepted: 03/12/2024] [Indexed: 05/16/2024] Open
Abstract
Enterococcus faecalis, a Gram-positive bacterium, poses a significant clinical challenge owing to its intrinsic resistance to a broad spectrum of antibiotics, warranting urgent exploration of innovative therapeutic strategies. This study investigated the viability of phage therapy as an alternative intervention for antibiotic-resistant E. faecalis, with a specific emphasis on the comprehensive genomic analysis of bacteriophage SAM-E.f 12. The investigation involved whole-genome sequencing of SAM-E.f 12 using Illumina technology, resulting in a robust dataset for detailed genomic characterization. Bioinformatics analyses were employed to predict genes and assign functional annotations. The bacteriophage SAM-E.f 12, which belongs to the Siphoviridae family, exhibited substantial potential, with a burst size of 5.7 PFU/infected cells and a latent period of 20 min. Host range determination experiments demonstrated its effectiveness against clinical E. faecalis strains, positioning SAM-E.f 12 as a precise therapeutic agent. Stability assays underscore resilience across diverse environmental conditions. This study provides a comprehensive understanding of SAM-E.f 12 genomic composition, lytic lifecycle parameters, and practical applications, particularly its efficacy in murine wound models. These results emphasize the promising role of phage therapy, specifically its targeted approach against antibiotic-resistant E. faecalis strains. The nuanced insights derived from this research will contribute to the ongoing pursuit of efficacious phage therapies and offer valuable implications for addressing the clinical challenges associated with E. faecalis infections.
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Affiliation(s)
- Sahar Abed
- Department of Microbial Biotechnology, Faculty of Basic Sciences and Advanced Technologies in Biology, University of Science and Culture, Tehran, Iran
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | - Mohammad Sholeh
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | | | - Morvarid Shafiei
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | - Abdolrazagh Hashemi Shahraki
- Division of Pulmonary, Critical Care and Sleep, College of Medicine-Jacksonville, University of Florida, Gainesville, Florida, United States of America
| | - Shaghayegh Nasr
- Department of Microbial Biotechnology, Faculty of Basic Sciences and Advanced Technologies in Biology, University of Science and Culture, Tehran, Iran
- Microorganisms Bank, Iranian Biological Resource Center (IBRC), ACECR, Tehran, Iran
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Rafiq MS, Shabbir MA, Raza A, Irshad S, Asghar A, Maan MK, Gondal MA, Hao H. CRISPR-Cas System: A New Dawn to Combat Antibiotic Resistance. BioDrugs 2024; 38:387-404. [PMID: 38605260 DOI: 10.1007/s40259-024-00656-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/08/2024] [Indexed: 04/13/2024]
Abstract
Antimicrobial resistance (AMR) can potentially harm global public health. Horizontal gene transfer (HGT), which speeds up the emergence of AMR and increases the burden of drug resistance in mobile genetic elements (MGEs), is the primary method by which AMR genes are transferred across bacterial pathogens. New approaches are urgently needed to halt the spread of bacterial diseases and antibiotic resistance. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), an RNA-guided adaptive immune system, protects prokaryotes from foreign DNA like plasmids and phages. This approach may be essential in limiting horizontal gene transfer and halting the spread of antibiotic resistance. The CRISPR-Cas system has been crucial in identifying and understanding resistance mechanisms and developing novel therapeutic approaches. This review article investigates the CRISPR-Cas system's potential as a tool to combat bacterial AMR. Antibiotic-resistant bacteria can be targeted and eliminated by the CRISPR-Cas system. It has been proven to be an efficient method for removing carbapenem-resistant plasmids and regaining antibiotic susceptibility. The CRISPR-Cas system has enormous potential as a weapon against bacterial AMR. It precisely targets and eliminates antibiotic-resistant bacteria, facilitates resistance mechanism identification, and offers new possibilities in diagnostics and therapeutics.
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Affiliation(s)
- Muhammad Shahzad Rafiq
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, 430070, China
| | | | - Ahmed Raza
- Livestock and Dairy Development Department, Punjab, Pakistan
| | - Shoaib Irshad
- Livestock and Dairy Development Department, Punjab, Pakistan
| | - Andleeb Asghar
- Institute of Pharmaceutical Sciences, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Muhammad Kashif Maan
- Department of Veterinary Surgery and Pet Sciences, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Mushtaq Ahmed Gondal
- Institute of Continuing Education and Extension, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, Pakistan
| | - Haihong Hao
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, 430070, China.
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Velazquez-Meza ME, Galarde-López M, Cornejo-Juárez P, Carrillo-Quiroz BA, Velázquez-Acosta C, Bobadilla-del-Valle M, Ponce-de-León A, Alpuche-Aranda CM. Multidrug-Resistant Staphylococcus sp. and Enterococcus sp. in Municipal and Hospital Wastewater: A Longitudinal Study. Microorganisms 2024; 12:645. [PMID: 38674590 PMCID: PMC11051902 DOI: 10.3390/microorganisms12040645] [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: 02/26/2024] [Revised: 03/12/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
The objective of the study was to detect multidrug-resistant Staphylococcus sp. and Enterococcus sp. isolates in municipal and hospital wastewater and to determine their elimination or persistence after wastewater treatment. Between August 2021 and September 2022, raw and treated wastewater samples were collected at two hospital and two community wastewater treatment plants (WWTPs). In each season of the year, two treated and two raw wastewater samples were collected in duplicate at each of the WWTPs studied. Screening and presumptive identification of staphylococci and enterococci was performed using chromoagars, and identification was performed with the Matrix Assisted Laser Desorption Ionization Time of Flight mass spectrometry (MALDI-TOF MS®). Antimicrobial susceptibility was performed using VITEK 2® automated system. There were 56 wastewater samples obtained during the study period. A total of 182 Staphylococcus sp. and 248 Enterococcus sp. were identified. The highest frequency of Staphylococcus sp. isolation was in spring and summer (n = 129, 70.8%), and for Enterococcus sp. it was in autumn and winter (n = 143, 57.7%). Sixteen isolates of Staphylococcus sp. and sixty-three of Enterococcus sp. persisted during WWTP treatments. Thirteen species of staphylococci and seven species of enterococci were identified. Thirty-one isolates of Staphylococcus sp. and ninety-four of Enterococcus sp. were multidrug-resistant. Resistance to vancomycin (1.1%), linezolid (2.7%), and daptomycin (8.2%/10.9%%), and a lower susceptibility to tigecycline (2.7%), was observed. This study evidences the presence of Staphylococcus sp. and Enterococcus sp. resistant to antibiotics of last choice of clinical treatment, in community and hospital wastewater and their ability to survive WWTP treatment systems.
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Affiliation(s)
- Maria Elena Velazquez-Meza
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca City 62100, Mexico; (M.E.V.-M.); (M.G.-L.); (B.A.C.-Q.)
| | - Miguel Galarde-López
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca City 62100, Mexico; (M.E.V.-M.); (M.G.-L.); (B.A.C.-Q.)
| | - Patricia Cornejo-Juárez
- Departamento de Infectología, Instituto Nacional de Cancerología, Mexico City 14080, Mexico; (P.C.-J.); (C.V.-A.)
| | - Berta Alicia Carrillo-Quiroz
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca City 62100, Mexico; (M.E.V.-M.); (M.G.-L.); (B.A.C.-Q.)
| | - Consuelo Velázquez-Acosta
- Departamento de Infectología, Instituto Nacional de Cancerología, Mexico City 14080, Mexico; (P.C.-J.); (C.V.-A.)
| | - Miriam Bobadilla-del-Valle
- Laboratorio Nacional de Máxima Seguridad para el Estudio de Tuberculosis y Enfermedades Emergentes, Instituto Nacional de Ciencias Médicas y Nutrición “Salvador Zubirán”, Mexico City 14080, Mexico; (M.B.-d.-V.); (A.P.-d.-L.)
| | - Alfredo Ponce-de-León
- Laboratorio Nacional de Máxima Seguridad para el Estudio de Tuberculosis y Enfermedades Emergentes, Instituto Nacional de Ciencias Médicas y Nutrición “Salvador Zubirán”, Mexico City 14080, Mexico; (M.B.-d.-V.); (A.P.-d.-L.)
| | - Celia Mercedes Alpuche-Aranda
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca City 62100, Mexico; (M.E.V.-M.); (M.G.-L.); (B.A.C.-Q.)
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10
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Kang Y, Wang J, Li Z. Meta-analysis addressing the characterization of antibiotic resistome in global hospital wastewater. JOURNAL OF HAZARDOUS MATERIALS 2024; 466:133577. [PMID: 38281357 DOI: 10.1016/j.jhazmat.2024.133577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 12/07/2023] [Accepted: 01/18/2024] [Indexed: 01/30/2024]
Abstract
Hospital wastewater (HWW) is a significant environmental reservoir of antibiotic resistance genes (ARGs). However, currently, no comprehensive understanding exists of the antibiotic resistome in global HWW. In this study, we attempted to address this knowledge gap through an in silico reanalysis of publicly accessible global HWW metagenomic data. We reanalyzed ARGs in 338 HWW samples from 13 countries in Africa, Asia, and Europe. In total, 2420 ARG subtypes belonging to 30 ARG types were detected, dominated by multidrug, beta-lactam, and aminoglycoside resistance genes. ARG composition in Europe differed from that in Asia and Africa. Notably, the ARGs presented co-occurrence with mobile genetic elements (MGEs), metal resistance genes (MRGs), and human bacterial pathogens (HBP), indicating a potential dissemination risk of ARGs in the HWW. Multidrug resistance genes presented co-occurrence with MGEs, MRGs, and HBP, is particularly pronounced. The abundance of contigs that contained ARG, contigs that contained ARG and HBP, contigs that contained ARG and MGE, contigs that contained ARG and MRG were used for health and transmission risk assessment of antibiotic resistome and screened out 40 high risk ARGs in the global HWW. This study first provides a comprehensive characterization and risk of the antibiotic resistome in global HWW.
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Affiliation(s)
- Yutong Kang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102200, China
| | - Jie Wang
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Zhenjun Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102200, China.
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11
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Rodriguez VJ, Pan Y, Salazar AS, Nogueira NF, Raccamarich P, Klatt NR, Jones DL, Alcaide ML. Using unsupervised machine learning to classify behavioral risk markers of bacterial vaginosis. Arch Gynecol Obstet 2024; 309:1053-1063. [PMID: 38310145 DOI: 10.1007/s00404-023-07360-7] [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: 07/06/2023] [Accepted: 12/21/2023] [Indexed: 02/05/2024]
Abstract
INTRODUCTION This study used an unsupervised machine learning algorithm, sidClustering and random forests, to identify clusters of risk behaviors of Bacterial Vaginosis (BV), the most common cause of abnormal vaginal discharge linked to STI and HIV acquisition. METHODS: Participants were 391 cisgender women in Miami, Florida, with a mean of 30.8 (SD = 7.81) years of age; 41.7% identified as Hispanic; 41.7% as Black and 44.8% as White. Participants completed measures of demographics, risk behaviors [sexual, medical, and reproductive history, substance use, and intravaginal practices (IVP)], and underwent collection of vaginal samples; 135 behavioral variables were analyzed. BV was diagnosed using Nugent criteria. RESULTS We identified four clusters, and variables were ranked by importance in distinguishing clusters: Cluster 1: nulliparous women who engaged in IVPs to clean themselves and please sexual partners, and used substances frequently [n = 118 (30.2%)]; Cluster 2: primiparous women who engaged in IVPs using vaginal douches to clean themselves (n = 112 (28.6%)]; Cluster 3: primiparous women who did not use IVPs or substances [n = 87 (22.3%)]; and Cluster 4: nulliparous women who did not use IVPs but used substances [n = 74 (18.9%)]. Clusters were related to BV (p < 0.001). Cluster 2, the cluster of women who used vaginal douches as IVPs, had the highest prevalence of BV (52.7%). CONCLUSIONS Machine learning methods may be particularly useful in identifying specific clusters of high-risk behaviors, in developing interventions intended to reduce BV and IVP, and ultimately in reducing the risk of HIV infection among women.
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Affiliation(s)
- Violeta J Rodriguez
- Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, Miami, USA
- Department of Psychology, University of Georgia, Athens, USA
| | - Yue Pan
- Division of Biostatistics, Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, USA
| | - Ana S Salazar
- Division of Infectious Diseases, Department of Medicine, University of Miami Miller School of Medicine, 1951 NW 10th Avenue, Suite 2300, Miami, FL, 33136, USA
| | - Nicholas Fonseca Nogueira
- Division of Infectious Diseases, Department of Medicine, University of Miami Miller School of Medicine, 1951 NW 10th Avenue, Suite 2300, Miami, FL, 33136, USA
| | - Patricia Raccamarich
- Division of Infectious Diseases, Department of Medicine, University of Miami Miller School of Medicine, 1951 NW 10th Avenue, Suite 2300, Miami, FL, 33136, USA
| | - Nichole R Klatt
- Surgical Outcomes and Precision Medicine Research Division, Department of Surgery, University of Minnesota, Minneapolis, USA
| | - Deborah L Jones
- Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, Miami, USA
| | - Maria L Alcaide
- Division of Infectious Diseases, Department of Medicine, University of Miami Miller School of Medicine, 1951 NW 10th Avenue, Suite 2300, Miami, FL, 33136, USA.
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12
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Acero-Pimentel D, Romero-Sánchez DI, Fuentes-Curiel SN, Quirasco M. Study of an Enterococcus faecium strain isolated from an artisanal Mexican cheese, whole-genome sequencing, comparative genomics, and bacteriocin expression. Antonie Van Leeuwenhoek 2024; 117:40. [PMID: 38393447 PMCID: PMC10891205 DOI: 10.1007/s10482-024-01938-0] [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: 07/28/2023] [Accepted: 01/28/2024] [Indexed: 02/25/2024]
Abstract
Enterococci are ubiquitous microorganisms in almost all environments, from the soil we step on to the food we eat. They are frequently found in naturally fermented foods, contributing to ripening through protein, lipid, and sugar metabolism. On the other hand, these organisms are also leading the current antibiotic resistance crisis. In this study, we performed whole-genome sequencing and comparative genomics of an Enterococcus faecium strain isolated from an artisanal Mexican Cotija cheese, namely QD-2. We found clear genomic differences between commensal and pathogenic strains, particularly in their carbohydrate metabolic pathways, resistance to vancomycin and other antibiotics, bacteriocin production, and bacteriophage and CRISPR content. Furthermore, a bacteriocin transcription analysis performed by RT-qPCR revealed that, at the end of the log phase, besides enterocins A and X, two putative bacteriocins not reported previously are also transcribed as a bicistronic operon in E. faecium QD-2, and are expressed 1.5 times higher than enterocin A when cultured in MRS broth.
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Affiliation(s)
- Daniel Acero-Pimentel
- Departamento de Alimentos y Biotecnología, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico City, Mexico
| | - Diana I Romero-Sánchez
- Departamento de Alimentos y Biotecnología, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico City, Mexico
| | - Sac Nicté Fuentes-Curiel
- Departamento de Alimentos y Biotecnología, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico City, Mexico
| | - Maricarmen Quirasco
- Departamento de Alimentos y Biotecnología, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Mexico City, Mexico.
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13
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Allemailem KS. Recent Advances in Understanding the Molecular Mechanisms of Multidrug Resistance and Novel Approaches of CRISPR/Cas9-Based Genome-Editing to Combat This Health Emergency. Int J Nanomedicine 2024; 19:1125-1143. [PMID: 38344439 PMCID: PMC10859101 DOI: 10.2147/ijn.s453566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 01/26/2024] [Indexed: 02/15/2024] Open
Abstract
The rapid spread of multidrug resistance (MDR), due to abusive use of antibiotics has led to global health emergency, causing substantial morbidity and mortality. Bacteria attain MDR by different means such as antibiotic modification/degradation, target protection/modification/bypass, and enhanced efflux mechanisms. The classical approaches of counteracting MDR bacteria are expensive and time-consuming, thus, it is highly significant to understand the molecular mechanisms of this resistance to curb the problem from core level. The revolutionary approach of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated sequence 9 (CRISPR/Cas9), considered as a next-generation genome-editing tool presents an innovative opportunity to precisely target and edit bacterial genome to alter their MDR strategy. Different bacteria possessing antibiotic resistance genes such as mecA, ermB, ramR, tetA, mqrB and blaKPC that have been targeted by CRISPR/Cas9 to re-sensitize these pathogens against antibiotics, such as methicillin, erythromycin, tigecycline, colistin and carbapenem, respectively. The CRISPR/Cas9 from S. pyogenes is the most widely studied genome-editing tool, consisting of a Cas9 DNA endonuclease associated with tracrRNA and crRNA, which can be systematically coupled as sgRNA. The targeting strategies of CRISPR/Cas9 to bacterial cells is mediated through phage, plasmids, vesicles and nanoparticles. However, the targeting approaches of this genome-editing tool to specific bacteria is a challenging task and still remains at a very preliminary stage due to numerous obstacles awaiting to be solved. This review elaborates some recent updates about the molecular mechanisms of antibiotic resistance and the innovative role of CRISPR/Cas9 system in modulating these resistance mechanisms. Furthermore, the delivery approaches of this genome-editing system in bacterial cells are discussed. In addition, some challenges and future prospects are also described.
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Affiliation(s)
- Khaled S Allemailem
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah51452, Saudi Arabia
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14
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Alkafaas SS, Abdallah AM, Hassan MH, Hussien AM, Elkafas SS, Loutfy SA, Mikhail A, Murad OG, Elsalahaty MI, Hessien M, Elshazli RM, Alsaeed FA, Ahmed AE, Kamal HK, Hafez W, El-Saadony MT, El-Tarabily KA, Ghosh S. Molecular docking as a tool for the discovery of novel insight about the role of acid sphingomyelinase inhibitors in SARS- CoV-2 infectivity. BMC Public Health 2024; 24:395. [PMID: 38321448 PMCID: PMC10848368 DOI: 10.1186/s12889-024-17747-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 01/11/2024] [Indexed: 02/08/2024] Open
Abstract
Recently, COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants, caused > 6 million deaths. Symptoms included respiratory strain and complications, leading to severe pneumonia. SARS-CoV-2 attaches to the ACE-2 receptor of the host cell membrane to enter. Targeting the SARS-CoV-2 entry may effectively inhibit infection. Acid sphingomyelinase (ASMase) is a lysosomal protein that catalyzes the conversion of sphingolipid (sphingomyelin) to ceramide. Ceramide molecules aggregate/assemble on the plasma membrane to form "platforms" that facilitate the viral intake into the cell. Impairing the ASMase activity will eventually disrupt viral entry into the cell. In this review, we identified the metabolism of sphingolipids, sphingolipids' role in cell signal transduction cascades, and viral infection mechanisms. Also, we outlined ASMase structure and underlying mechanisms inhibiting viral entry 40 with the aid of inhibitors of acid sphingomyelinase (FIASMAs). In silico molecular docking analyses of FIASMAs with inhibitors revealed that dilazep (S = - 12.58 kcal/mol), emetine (S = - 11.65 kcal/mol), pimozide (S = - 11.29 kcal/mol), carvedilol (S = - 11.28 kcal/mol), mebeverine (S = - 11.14 kcal/mol), cepharanthine (S = - 11.06 kcal/mol), hydroxyzin (S = - 10.96 kcal/mol), astemizole (S = - 10.81 kcal/mol), sertindole (S = - 10.55 kcal/mol), and bepridil (S = - 10.47 kcal/mol) have higher inhibition activity than the candidate drug amiodarone (S = - 10.43 kcal/mol), making them better options for inhibition.
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Affiliation(s)
- Samar Sami Alkafaas
- Molecular Cell Biology Unit, Division of Biochemistry, Department of Chemistry, Faculty of Science, Tanta University, Tanta, 31527, Egypt.
| | - Abanoub Mosaad Abdallah
- Narcotic Research Department, National Center for Social and Criminological Research (NCSCR), Giza, 11561, Egypt
| | - Mai H Hassan
- Molecular Cell Biology Unit, Division of Biochemistry, Department of Chemistry, Faculty of Science, Tanta University, Tanta, 31527, Egypt
| | - Aya Misbah Hussien
- Biotechnology department at Institute of Graduate Studies and Research, Alexandria University, Alexandria, Egypt
| | - Sara Samy Elkafas
- Production Engineering and Mechanical Design Department, Faculty of Engineering, Menofia University, Menofia, Egypt
- Faculty of Control System and Robotics, ITMO University, Saint-Petersburg, 197101, Russia
| | - Samah A Loutfy
- Virology and Immunology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt
- Nanotechnology Research Center, British University, Cairo, Egypt
| | - Abanoub Mikhail
- Department of Physics, Faculty of Science, Minia University, Minia, Egypt
- Faculty of Physics, ITMO University, Saint Petersburg, Russia
| | - Omnia G Murad
- Division of Biochemistry, Department of Chemistry, Faculty of Science, Tanta University, Tanta, 31527, Egypt
| | - Mohamed I Elsalahaty
- Division of Biochemistry, Department of Chemistry, Faculty of Science, Tanta University, Tanta, 31527, Egypt
| | - Mohamed Hessien
- Molecular Cell Biology Unit, Division of Biochemistry, Department of Chemistry, Faculty of Science, Tanta University, Tanta, 31527, Egypt
| | - Rami M Elshazli
- Biochemistry and Molecular Genetics Unit, Department of Basic Sciences, Faculty of Physical Therapy, Horus University - Egypt, New Damietta, 34517, Egypt
| | - Fatimah A Alsaeed
- Department of Biology, College of Science, King Khalid University, Muhayl, Saudi Arabia
| | - Ahmed Ezzat Ahmed
- Biology Department, College of Science, King Khalid University, Abha, 61413, Saudi Arabia
| | - Hani K Kamal
- Anatomy and Histology, Faculty of Pharmacy, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Wael Hafez
- NMC Royal Hospital, 16Th Street, 35233, Khalifa City, Abu Dhabi, United Arab Emirates
- Medical Research Division, Department of Internal Medicine, The National Research Centre, 12622, 33 El Buhouth St, Ad Doqi, Dokki, Cairo Governorate, Egypt
| | - Mohamed T El-Saadony
- Department of Agricultural Microbiology, Faculty of Agriculture, Zagazig University, Zagazig, 44511, Egypt
| | - Khaled A El-Tarabily
- Department of Biology, College of Science, United Arab Emirates University, Al-Ain, 15551, United Arab Emirates
| | - Soumya Ghosh
- Department of Genetics, Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein, 9301, South Africa
- Natural & Medical Science Research Center, University of Nizwa, Nizwa, Oman
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15
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Ahn Y, Jin S, Park G, Lee HY, Lee H, Shin E, Kim J, Yoo J, Kim Y. Epidemiological analysis and prevention strategies in response to a shigellosis cluster outbreak: a retrospective case series in an alternative school in the Republic of Korea, 2023. Osong Public Health Res Perspect 2024; 15:68-76. [PMID: 38481051 PMCID: PMC10982656 DOI: 10.24171/j.phrp.2023.0298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 12/05/2023] [Accepted: 12/07/2023] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND In March 2023, an alternative school in the Republic of Korea reported 12 cases of shigellosis. This study aims to analyze the epidemiological characteristics in order to determine the cause of the cluster outbreak of shigellosis and to develop prevention strategies. METHODS This study focused on 12 patients with confirmed Shigella infection and investigated their demographics, clinical features, epidemiology, diagnostics, and antimicrobial susceptibility. Following the identification of Shigella, we conducted follow-up rectal smear cultures to manage patients, implementing isolation and control measures. RESULTS This study investigated the emergence of multidrug-resistant Shigella following missionary activities in Cambodia, documenting a cluster infection within an alternative school in Daejeon, the Republic of Korea. The outbreak affected 56 participants, resulting in the confirmation of 12 cases. The incidence rates varied by gender and occupation, with higher rates among males and teachers. All 12 cases demonstrated multidrug resistance. Challenges included delayed pathogen confirmation and suboptimal adherence to isolation criteria. The incident prompted revisions in the criteria for isolation release, focusing on symptom resolution. The study underscores the necessity for strengthened surveillance, educational initiatives focusing on prevention in endemic areas, and improved oversight of unlicensed educational establishments. CONCLUSION Successful response strategies included swift situation assessment, collaborative efforts, effective infection control measures, and modified criteria for isolation release. Continued surveillance of multidrug-resistant strains is recommended, especially in regions with a high prevalence.
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Affiliation(s)
- Yeongseo Ahn
- Division of Infectious Disease Response, Chungcheong Reginal Center for Disease Control and Prevention, Daejeon, Republic of Korea
| | - Sunmi Jin
- Yuseong-gu Health Center, Daejeon, Republic of Korea
| | - Gemma Park
- Division of Infectious Disease Response, Chungcheong Reginal Center for Disease Control and Prevention, Daejeon, Republic of Korea
| | - Hye Young Lee
- Division of Infectious Disease Response, Chungcheong Reginal Center for Disease Control and Prevention, Daejeon, Republic of Korea
| | - Hyungyong Lee
- Division of Infectious Disease Response, Chungcheong Reginal Center for Disease Control and Prevention, Daejeon, Republic of Korea
| | - Eunkyung Shin
- Division of Bacterial Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Junyoung Kim
- Division of Bacterial Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Jaeil Yoo
- Division of Bacterial Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju, Republic of Korea
| | - Yuna Kim
- Division of Infectious Disease Response, Chungcheong Reginal Center for Disease Control and Prevention, Daejeon, Republic of Korea
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16
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Chatupheeraphat C, Peamchai J, Kaewsai N, Anuwongcharoen N, Eiamphungporn W. Enhancing the activity of β-lactamase inhibitory protein-II with cell-penetrating peptide against KPC-2-carrying Klebsiella pneumoniae. PLoS One 2024; 19:e0296727. [PMID: 38277388 PMCID: PMC10817188 DOI: 10.1371/journal.pone.0296727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 12/16/2023] [Indexed: 01/28/2024] Open
Abstract
Carbapenem-resistant Enterobacterales (CRE) is considered a paramount threat due to its rapid spread and high mortality rate. Klebsiella pneumoniae carbapenemases (KPCs), specifically KPC-2, are prevalent enzymes responsible for carbapenem resistance in many countries. While combinations of antibiotics are commonly used, they must be tailored to match the remaining susceptibility of the infecting strains. Therefore, there is a need to develop the β-lactamase inhibitor to effectively address this issue. β-lactamase inhibitor protein (BLIP) and its variants, BLIP-I and BLIP-II, have demonstrated the ability to inhibit class A β-lactamases. In particular, BLIP-II shows strong binding to the KPC-2 carbapenemase, making it a potential candidate for inhibition. To improve the intracellular penetration of BLIP-II, a cell-penetrating peptide (CPP) was employed. In this study, a KRK-rich peptide was introduced at either the N-terminal or C-terminal region of tBLIP-II, excluding the signal sequence of the BLIP-II protein. tBLIP-II, tBLIP-II-CPP, and CPP-BLIP-II were successfully expressed, and the chimeric proteins retained inhibitory activity compared to tBLIP-II alone. It is apparent that homology modeling demonstrated neither the poly-histidine tag nor the CPP interfered with the essential interaction residues of tBLIP-II. Interestingly, BLIP-II-CPP exhibited the highest inhibitory activity, reducing the minimal inhibitory concentration (MIC) of meropenem by 8 folds. Moreover, the combination of tBLIP-CPP with meropenem significantly decreased the viable bacterial cell count compared to the combination of tBLIP-II with meropenem or meropenem alone. These findings suggest that tBLIP-CPP is a promising candidate for restoring carbapenem susceptibility against CRE and provides a valuable therapeutic option for infections caused by CRE.
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Affiliation(s)
- Chawalit Chatupheeraphat
- Center for Research Innovation and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Salaya, Nakhon Pathom, Thailand
| | - Jiratchaya Peamchai
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Noramon Kaewsai
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Nuttapat Anuwongcharoen
- Department of Community Medical Technology, Faculty of Medical Technology, Mahidol University, Salaya, Nakhon Pathom, Thailand
| | - Warawan Eiamphungporn
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
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17
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Martínez-Trejo A, Ruiz-Ruiz JM, Gonzalez-Avila LU, Saldaña-Padilla A, Hernández-Cortez C, de Jesús Colmenero-Solís R, Bello-López JM, Castro-Escarpulli G. The CRISPR-Cas system in clinical strains of Acinetobacter baumannii: an in-silico analysis. Lett Appl Microbiol 2024; 77:ovae003. [PMID: 38211976 DOI: 10.1093/lambio/ovae003] [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: 10/21/2023] [Revised: 12/29/2023] [Accepted: 01/10/2024] [Indexed: 01/13/2024]
Abstract
Acinetobacter baumannii is a relevant bacterium due to its high-resistance profile. It is well known that antimicrobial resistance is primarily linked to mutations and the acquisition of external genomic material, such as plasmids or phages, to which the Clustered Regularly Interspaced Short Palindromic Repeats associated with Cas proteins, or CRISPR-Cas, system is related. It is known that the system can influence the acquisition of foreign genetic material and play a role in various physiological pathways. In this study, we conducted an in-silico analysis using 91 fully assembled genomes of clinical strains obtained from the NCBI database. Among the analyzed genomes, the I-F1 subtype of the CRISPR-Cas system was detected showcasing variations in architecture and phylogeny. Using bioinformatic tools, we determined the presence, distribution, and specific characteristics of the CRISPR-Cas system. We found a possible association of the system with resistance genes but not with virulence determinants. Analysis of the system's components, including spacer sequences, suggests its potential role in protecting against phage infections, highlighting its protective function.
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Affiliation(s)
- Arturo Martínez-Trejo
- Laboratorio de Investigación Clínica y Ambiental, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | - Juan Manuel Ruiz-Ruiz
- Laboratorio Clínico, Unidad Médica de Alta Especialidad, Hospital de Pediatría Dr. Silvestre Frenk Freud, Instituto Mexicano del Seguro Social, Mexico City 06720, Mexico
| | - Luis Uriel Gonzalez-Avila
- Laboratorio de Investigación Clínica y Ambiental, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | - Andres Saldaña-Padilla
- Laboratorio de Investigación Clínica y Ambiental, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico
- Laboratorio de Bioquímica Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | - Cecilia Hernández-Cortez
- Laboratorio de Bioquímica Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | - Raúl de Jesús Colmenero-Solís
- Laboratorio de Investigación Clínica y Ambiental, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | | | - Graciela Castro-Escarpulli
- Laboratorio de Investigación Clínica y Ambiental, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico
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18
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Al-Ouqaili MT, Hussein RA, Majeed YH, Al-Marzooq F. Study of vacuolating cytotoxin A (vacA) genotypes of ulcerogenic and non-ulcerogenic strains of Helicobacter pylori and its association with gastric disease. Saudi J Biol Sci 2023; 30:103867. [PMID: 38020230 PMCID: PMC10663908 DOI: 10.1016/j.sjbs.2023.103867] [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: 09/17/2023] [Revised: 10/24/2023] [Accepted: 11/02/2023] [Indexed: 12/01/2023] Open
Abstract
Globally, Helicobacter pylori (H. pylori), a stomach pathogen, is present in around 50 % of the population. This bacterial infection produces persistent inflammation, which significantly raises the risk of duodenal, gastric ulcer, and stomach cancer. The goal of this study is to identify the vacA genotypes in H. pylori and analyze how they relate to medical conditions brought on by the bacteria and clarithromycin resistance. PCR was used to describe 115 endoscopic stomach samples from infected patients and identify vacA gene. Of the 115 research participants, H. pylori was found in 81 (70.4 %) of them. Of the isolated cultures, only 38 (69.1 %) were resistant to clarithromycin. VacA was discovered in 55 (67.9 %) of the samples that had H. pylori in them. Patients with gastritis were more likely to have s2m2 strains of infection (66.7 %), while those with gastric and duodenal ulcers were more likely to have s1m1 strains (64.7 %). VacA-positive H. pylori strains (60 % n = 33) were more resistant to clarithromycin versus (19.2 % n = 5) for vacA-negative bacteria. Clarithromycin resistance was significantly linked to vacA s2m2 in H. pylori isolates (75.9 %). According to the study's results, the vacA variants s1m1 and s2m2 have a strong connection with the emergence of H. pylori infections that cause peptic ulcer disease in the population of Iraq. Genetic testing is essential in predicting both the course of treatment and the outcome of H. pylori disease.
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Affiliation(s)
- Mushtak T.S. Al-Ouqaili
- Department of Microbiology, College of Medicine, University of Anbar, Al-Anbar Governorate, Ramadi, Iraq
| | - Rawaa A. Hussein
- Department of Clinical Laboratory Sciences, College of Pharmacy, University of Anbar, Al-Anbar Governorate, Ramadi, Iraq
| | - Yasin H. Majeed
- Department of Internal Medicine, College of Medicine, University of Anbar, Al-Anbar Governorate, Ramadi, Iraq
| | - Farah Al-Marzooq
- Department of Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
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Alkompoz AK, Hamed SM, Zaid ASA, Almangour TA, Al-Agamy MH, Aboshanab KM. Correlation of CRISPR/Cas and Antimicrobial Resistance in Klebsiella pneumoniae Clinical Isolates Recovered from Patients in Egypt Compared to Global Strains. Microorganisms 2023; 11:1948. [PMID: 37630508 PMCID: PMC10459600 DOI: 10.3390/microorganisms11081948] [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: 07/17/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/27/2023] Open
Abstract
The CRISPR/Cas system has been long known to interfere with the acquisition of foreign genetic elements and was recommended as a tool for fighting antimicrobial resistance. The current study aimed to explore the prevalence of the CRISPR/Cas system in Klebsiella pneumoniae isolates recovered from patients in Egypt in comparison to global strains and correlate the CRISPR/Cas to susceptibility to antimicrobial agents. A total of 181 clinical isolates were PCR-screened for cas and selected antimicrobial resistance genes (ARGs). In parallel, 888 complete genome sequences were retrieved from the NCBI database for in silico analysis. CRISPR/Cas was found in 46 (25.4%) isolates, comprising 18.8% type I-E and 6.6% type I-E*. Multidrug resistance (MDR) and extensive drug resistance (XDR) were found in 73.5% and 25.4% of the isolates, respectively. More than 95% of the CRISPR/Cas-bearing isolates were MDR (65.2%) or XDR (32.6%). No significant difference was found in the susceptibility to the tested antimicrobial agents among the CRISPR/Cas-positive and -negative isolates. The same finding was obtained for the majority of the screened ARGs. Among the published genomes, 23.2% carried CRISPR/Cas, with a higher share of I-E* (12.8%). They were confined to specific sequence types (STs), most commonly ST147, ST23, ST15, and ST14. More plasmids and ARGs were carried by the CRISPR/Cas-negative group than others, but their distribution in the two groups was not significantly different. The prevalence of some ARGs, such as blaKPC, blaTEM, and rmtB, was significantly higher among the genomes of the CRISPR/Cas-negative strains. A weak, nonsignificant positive correlation was found between the number of spacers and the number of resistance plasmids and ARGs. In conclusion, the correlation between CRISPR/Cas and susceptibility to antimicrobial agents or bearing resistance plasmids and ARGs was found to be nonsignificant. Plasmid-targeting spacers might not be naturally captured by CRISPR/Cas. Spacer match analysis is recommended to provide a clearer image of the exact behavior of CRISPR/Cas towards resistance plasmids.
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Affiliation(s)
| | - Samira M. Hamed
- Department of Microbiology and Immunology, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), 6th of October, Giza 12451, Egypt;
| | - Ahmed S. Abu Zaid
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Cairo 11566, Egypt;
| | - Thamer A. Almangour
- Department of Clinical Pharmacy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Mohamed H. Al-Agamy
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia;
- Department of Microbiology and Immunology, Faculty of Pharmacy, Al-Azhar University, Cairo 11651, Egypt
| | - Khaled M. Aboshanab
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Cairo 11566, Egypt;
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Monteiro Marques J, Coelho M, Santana AR, Pinto D, Semedo-Lemsaddek T. Dissemination of Enterococcal Genetic Lineages: A One Health Perspective. Antibiotics (Basel) 2023; 12:1140. [PMID: 37508236 PMCID: PMC10376465 DOI: 10.3390/antibiotics12071140] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/22/2023] [Accepted: 06/29/2023] [Indexed: 07/30/2023] Open
Abstract
Enterococcus spp. are commensals of the gastrointestinal tracts of humans and animals and colonize a variety of niches such as water, soil, and food. Over the last three decades, enterococci have evolved as opportunistic pathogens, being considered ESKAPE pathogens responsible for hospital-associated infections. Enterococci's ubiquitous nature, excellent adaptative capacity, and ability to acquire virulence and resistance genes make them excellent sentinel proxies for assessing the presence/spread of pathogenic and virulent clones and hazardous determinants across settings of the human-animal-environment triad, allowing for a more comprehensive analysis of the One Health continuum. This review provides an overview of enterococcal fitness and pathogenic traits; the most common clonal complexes identified in clinical, veterinary, food, and environmental sources; as well as the dissemination of pathogenic genomic traits (virulome, resistome, and mobilome) found in high-risk clones worldwide, across the One Health continuum.
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Affiliation(s)
- Joana Monteiro Marques
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Av. da Universidade Técnica de Lisboa, 1300-477 Lisbon, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisbon, Portugal
| | - Mariana Coelho
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Av. da Universidade Técnica de Lisboa, 1300-477 Lisbon, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisbon, Portugal
| | - Andressa Rodrigues Santana
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Av. da Universidade Técnica de Lisboa, 1300-477 Lisbon, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisbon, Portugal
| | - Daniel Pinto
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Av. da Universidade Técnica de Lisboa, 1300-477 Lisbon, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisbon, Portugal
| | - Teresa Semedo-Lemsaddek
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Av. da Universidade Técnica de Lisboa, 1300-477 Lisbon, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisbon, Portugal
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21
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Nazari Moghadam M, Rahimi E, Shakerian A, Momtaz H. Prevalence of Salmonella Typhimurium and Salmonella Enteritidis isolated from poultry meat: virulence and antimicrobial-resistant genes. BMC Microbiol 2023; 23:168. [PMID: 37322421 PMCID: PMC10268442 DOI: 10.1186/s12866-023-02908-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 05/23/2023] [Indexed: 06/17/2023] Open
Abstract
Salmonellosis, a zoonotic disease, is one of the leading causes of foodborne illness worldwide. It is responsible for most infections caused by consumption of contaminated food. In recent years, a significant increase in the resistance of these bacteria to common antibiotics has been observed, posing a serious threat to global public health. The aim of this study was to investigate the prevalence of virulent antibiotic-resistant Salmonella spp. strains in Iranian poultry markets. A total of 440 chicken meat samples were randomly selected from meat supply and distribution facilities in Shahrekord and tested for bacteriological contamination. After culturing and isolating the strains, identification was performed using the classical bacteriological method and PCR. To determine antibiotic resistance, a disc diffusion test was performed according to the recommendations of the French Society of Microbiology. PCR was used to detect resistance and virulence genes. Only 9% of the samples were positive for Salmonella. These were Salmonella typhimurium isolates. All Salmonella typhimurium serotypes tested positive for the rfbJ, fljB, invA and fliC genes. Resistance to TET, cotrimoxazole, NA, NIT, piperacillin/tazobactam and other antibiotics was found in 26 (72.2%), 24 (66.7%), 22 (61.1%) and 21 (58.3%) isolates, respectively. The sul1, sul2 and sul3 genes were present in 20, 12 and 4 of 24 cotrimoxazole-resistant bacteria, respectively. Chloramphenicol resistance was found in six isolates, but more isolates tested positive for the floR and cat two genes. In contrast, 2 (33%) of the cat three genes, 3 (50%) of the cmlA genes and 2 (34%) of the cmlB genes were all positive. The results of this investigation showed that Salmonella typhimurium is the most common serotype of the bacterium. This means that most of the antibiotics commonly used in the livestock and poultry industries are ineffective against most Salmonella isolates, which is important for public health.
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Affiliation(s)
- Marziye Nazari Moghadam
- Research Center of Nutrition and Organic Products, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Ebrahim Rahimi
- Research Center of Nutrition and Organic Products, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran.
| | - Amir Shakerian
- Research Center of Nutrition and Organic Products, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Hassan Momtaz
- Department of Microbiology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
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22
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Jwair NA, Al-Ouqaili MTS, Al-Marzooq F. Inverse Association between the Existence of CRISPR/Cas Systems with Antibiotic Resistance, Extended Spectrum β-Lactamase and Carbapenemase Production in Multidrug, Extensive Drug and Pandrug-Resistant Klebsiella pneumoniae. Antibiotics (Basel) 2023; 12:980. [PMID: 37370299 DOI: 10.3390/antibiotics12060980] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/19/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
Antimicrobial resistance, with the production of extended-spectrum β-lactamases (ESBL) and carbapenemases, is common in the opportunistic pathogen, Klebsiella pneumoniae. This organism has a genome that can contain clustered regularly interspaced short palindromic repeats (CRISPRs), which operate as a defense mechanism against external invaders such as plasmids and viruses. This study aims to determine the association of the CRISPR/Cas systems with antibiotic resistance in K. pneumoniae isolates from Iraqi patients. A total of 100 K. pneumoniae isolates were collected and characterized according to their susceptibility to different antimicrobial agents. The CRISPR/Cas systems were detected via PCR. The phenotypic detection of ESBLs and carbapenemases was performed. The production of ESBL was detected in 71% of the isolates. Carbapenem-resistance was detected in 15% of the isolates, while only 14% were susceptible to all antimicrobial agents. Furthermore, the bacteria were classified into multidrug (77%), extensively drug-resistant (11.0%) and pandrug-resistant (4.0%). There was an inverse association between the presence of the CRISPR/Cas systems and antibiotic resistance, as resistance was higher in the absence of the CRISPR/Cas system. Multidrug resistance in ESBL-producing and carbapenem-resistant K. pneumoniae occurred more frequently in strains negative for the CRISPR/Cas system. Thus, we conclude that genes for exogenous antibiotic resistance can be acquired in the absence of the CRISPR/Cas modules that can protect the bacteria against acquiring foreign DNA.
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Affiliation(s)
- Noor A Jwair
- Department of Microbiology, College of Medicine, University of Anbar, Ramadi P.O. Box 55431, Iraq
| | - Mushtak T S Al-Ouqaili
- Department of Microbiology, College of Medicine, University of Anbar, Ramadi P.O. Box 55431, Iraq
| | - Farah Al-Marzooq
- Department of Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain P.O. Box 15551, United Arab Emirates
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Chen P, An L, Zhang Z. Sequential Therapy of Linezolid and Contezolid to Treat Vancomycin-Resistant Enterococcus faecium Pneumonia in a Centenarian Patient: Case Report. Infect Drug Resist 2023; 16:1573-1578. [PMID: 36969942 PMCID: PMC10032165 DOI: 10.2147/idr.s401533] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 03/06/2023] [Indexed: 03/19/2023] Open
Abstract
Enterococcus faecium (E. faecium) is one of the core components of enterococci and causes serious illnesses in the elderly and immunocompromised patients. Due to its adaptive traits and antibiotic resistance, E. faecium has evolved as a worldwide hospital-associated pathogen, especially vancomsycin-resistant Enterococcus faecium (VREfm). Pneumonia caused by VREfm is quite rare in clinical settings, and optimal treatment has not yet been determined. Here, we present a case of nosocomial VREfm pneumonia with lung cavitation following adenovirus infection, which was successfully treated with linezolid and contezolid.
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Affiliation(s)
- Pengzhi Chen
- Department of Respiratory and Critical Care Medicine, The Second Medical Center & National Clinical Research Center for Geriatric Disease, Chinese PLA General Hospital, Beijing, People’s Republic of China
| | - Li An
- Department of Respiratory and Critical Care Medicine, The Second Medical Center & National Clinical Research Center for Geriatric Disease, Chinese PLA General Hospital, Beijing, People’s Republic of China
| | - Zhijian Zhang
- Department of Respiratory and Critical Care Medicine, The Second Medical Center & National Clinical Research Center for Geriatric Disease, Chinese PLA General Hospital, Beijing, People’s Republic of China
- Correspondence: Zhijian Zhang, Department of Respiratory and Critical Care Medicine, The Second Medical Center & National Clinical Research Center for Geriatric Disease, Chinese PLA General Hospital, Beijing, People’s Republic of China, Tel +86 17701090515, Email
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24
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Antimicrobial Resistance and Recent Alternatives to Antibiotics for the Control of Bacterial Pathogens with an Emphasis on Foodborne Pathogens. Antibiotics (Basel) 2023; 12:antibiotics12020274. [PMID: 36830185 PMCID: PMC9952301 DOI: 10.3390/antibiotics12020274] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 01/21/2023] [Accepted: 01/27/2023] [Indexed: 01/31/2023] Open
Abstract
Antimicrobial resistance (AMR) is one of the most important global public health problems. The imprudent use of antibiotics in humans and animals has resulted in the emergence of antibiotic-resistant bacteria. The dissemination of these strains and their resistant determinants could endanger antibiotic efficacy. Therefore, there is an urgent need to identify and develop novel strategies to combat antibiotic resistance. This review provides insights into the evolution and the mechanisms of AMR. Additionally, it discusses alternative approaches that might be used to control AMR, including probiotics, prebiotics, antimicrobial peptides, small molecules, organic acids, essential oils, bacteriophage, fecal transplants, and nanoparticles.
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25
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Ouédraogo GA, Cissé H, Ouédraogo HS, Kaboré B, Traoré R, Traoré Y, Bassolé IHN, Tchoumbougnang F, Savadogo A. Research of Antibiotic Residues and Bacterial Strain's Antibiotic Resistance Profile in the Liquid Effluents Evacuated in Nature by Two CHUs and a Mixed WWTP of Ouagadougou (Burkina Faso). Infect Drug Resist 2023; 16:2537-2547. [PMID: 37138834 PMCID: PMC10150758 DOI: 10.2147/idr.s408315] [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: 02/12/2023] [Accepted: 04/19/2023] [Indexed: 05/05/2023] Open
Abstract
Background In Burkina Faso, suspicions have been raised that hospital liquid effluents are a source of microbiological contaminants in surface waters of urban and peri-urban areas. This study aimed to determine the antibiotic residues and the antibiotic resistance phenotype of potential pathogenic bacteria in the hospital liquid effluents discharged into nature by the CHUs Bogodogo, Yalgado Ouédraogo and the WWTS of Kossodo. Methods Fifteen samples of liquid effluents discharged into nature were collected. Antibiotic residues were identified by HPLC. A wavelength of 254 nm for the UV detector was set. Antibiotic testing was realized according to CASFM 2019 recommendations. Results Three molecules including Amoxicillin, Chloramphenicol and Ceftriaxone were detected in 13 samples. The strains characterized were 06 E. coli, 09 Pseudomonas spp, 05 Staphylococcus aureus and 04 Salmonella spp. Thus, none of the strains was resistant to Imipenem, but they were resistant to Amoxiclav with rates of 83.33% (E. coli), 88.88% (Pseudomonas spp) and 100% (Staphylococcus aureus and Salmonella spp). Conclusion Ouagadougou hospital liquid effluents discharged into nature are contaminated with antibiotic residues and potential pathogenic bacteria.
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Affiliation(s)
- Ganamé Abasse Ouédraogo
- Laboratoire de Biochimie et Immunologie Appliquées (LaBIA), Université Joseph KI-ZERBO, Ouagadougou, Burkina Faso
- Institut des Sciences Halieutiques (ISH) à Yabassi, Université de Douala, Douala, Cameroun
| | - Hama Cissé
- Laboratoire de Biochimie et Immunologie Appliquées (LaBIA), Université Joseph KI-ZERBO, Ouagadougou, Burkina Faso
| | - Henri Sidabéwindin Ouédraogo
- Laboratoire de Biochimie et Immunologie Appliquées (LaBIA), Université Joseph KI-ZERBO, Ouagadougou, Burkina Faso
| | - Boukaré Kaboré
- Laboratoire de Biochimie et Immunologie Appliquées (LaBIA), Université Joseph KI-ZERBO, Ouagadougou, Burkina Faso
| | - Roukiatou Traoré
- Laboratoire de Biochimie et Immunologie Appliquées (LaBIA), Université Joseph KI-ZERBO, Ouagadougou, Burkina Faso
| | - Yves Traoré
- Laboratoire de Biochimie et Immunologie Appliquées (LaBIA), Université Joseph KI-ZERBO, Ouagadougou, Burkina Faso
| | - Ismael Henri Nestor Bassolé
- Laboratoire de biologie moléculaire, d’épidémiologie et de surveillance des bactéries et virus transmis par les aliments (LaBESTA), Université Joseph Ki-ZERBO, Ouagadougou, Burkina Faso
| | | | - Aly Savadogo
- Laboratoire de Biochimie et Immunologie Appliquées (LaBIA), Université Joseph KI-ZERBO, Ouagadougou, Burkina Faso
- Correspondence: Aly Savadogo, Tel +226 70356227, Email
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26
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Onaran Acar B, Cengız G, Goncuoglu M. Vancomycin-variable enterococci in sheep and cattle isolates and whole-genome sequencing analysis of isolates harboring vanM and vanB genes. IRANIAN JOURNAL OF VETERINARY RESEARCH 2023; 24:182-192. [PMID: 38269016 PMCID: PMC10804430 DOI: 10.22099/ijvr.2023.47465.6855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/26/2023] [Accepted: 09/11/2023] [Indexed: 01/26/2024]
Abstract
Background Vancomycin resistance encoded by the vanA/B/M genes in enterococci is clinically important because of the transmission of these genes between bacteria. While vancomycin resistance is determined by detecting only vanA and vanB genes by routine analyses, failure to detect vanM resistance causes vancomycin resistance to be overlooked, and clinically appropriate treatment cannot be provided. Aims The study aimed to examine the presence of vanM-positive enterococcal isolates in Ankara, Turkey, and to have detailed information about them with sequence analyses. Methods Caecal samples were collected from sheep and cattle during slaughter at different slaughterhouses in Ankara, Turkey. Enterococci isolates were identified, confirmed, and analyzed for the presence of vanA/B/M genes. Antibiotic resistance profiles of isolates were determined by the broth microdilution method. A whole genome sequence analysis of the isolates harboring the vanM and vanB genes was performed. Results 13.7% of enterococcal isolates were determined as Enterococcus faecium and Enterococcus faecalis. 15% of these isolates contained vanB, and 40% were vanM-positive. S98b and C32 isolates were determined to contain 16 CRISPR-Cas elements. 80% of the enterococci isolates were resistant to nitrofurantoin and 15% to ciprofloxacin. The first vanM-positive vancomycin-variable enterococci (VVE) isolates from food-producing animals were identified, and the S98b strain has been assigned to Genbank with the accession number CP104083.1. Conclusion Therefore, new studies are needed to facilitate the identification of vanM-resistant enterococci and VVE strains.
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Affiliation(s)
- B. Onaran Acar
- Department of Food Hygiene and Technology, Faculty of Veterinary Medicine, Ankara University, 06110, Altindag, Ankara, Turkey
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27
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Alkafaas SS, Abdallah AM, Ghosh S, Loutfy SA, Elkafas SS, Abdel Fattah NF, Hessien M. Insight into the role of clathrin-mediated endocytosis inhibitors in SARS-CoV-2 infection. Rev Med Virol 2023; 33:e2403. [PMID: 36345157 PMCID: PMC9877911 DOI: 10.1002/rmv.2403] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 10/08/2022] [Accepted: 10/10/2022] [Indexed: 11/10/2022]
Abstract
Emergence of SARS-CoV-2 variants warrants sustainable efforts to upgrade both the diagnostic and therapeutic protocols. Understanding the details of cellular and molecular basis of the virus-host cell interaction is essential for developing variant-independent therapeutic options. The internalization of SARS-CoV-2, into lung epithelial cells, is mediated by endocytosis, especially clathrin-mediated endocytosis (CME). Although vaccination is the gold standard strategy against viral infection, selective inhibition of endocytic proteins, complexes, and associated adaptor proteins may present a variant-independent therapeutic strategy. Although clathrin and/or dynamins are the most important proteins involved in CME, other endocytic mechanisms are clathrin and/or dynamin independent and rely on other proteins. Moreover, endocytosis implicates some subcellular structures, like plasma membrane, actin and lysosomes. Also, physiological conditions, such as pH and ion concentrations, represent an additional factor that mediates these events. Accordingly, endocytosis related proteins are potential targets for small molecules that inhibit endocytosis-mediated viral entry. This review summarizes the potential of using small molecules, targeting key proteins, participating in clathrin-dependent and -independent endocytosis, as variant-independent antiviral drugs against SARS-CoV-2 infection. The review takes two approaches. The first outlines the potential role of endocytic inhibitors in preventing endocytosis-mediated viral entry and its mechanism of action, whereas in the second computational analysis was implemented to investigate the selectivity of common inhibitors against endocytic proteins in SARS-CoV-2 endocytosis. The analysis revealed that remdesivir, methyl-β-cyclodextrin, rottlerin, and Bis-T can effectively inhibit clathrin, HMG-CoA reductase, actin, and dynamin I GTPase and are more potent in inhibiting SARS-CoV-2 than chloroquine. CME inhibitors for SARS-CoV-2 infection remain understudied.
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Affiliation(s)
- Samar Sami Alkafaas
- Molecular Cell Biology UniteDivision of BiochemistryDepartment of ChemistryFaculty of ScienceTanta UniversityTantaEgypt
| | - Abanoub Mosaad Abdallah
- Narcotic Research DepartmentNational Center for Social and Criminological Research (NCSCR)GizaEgypt
| | - Soumya Ghosh
- Department of GeneticsFaculty of Natural and Agricultural SciencesUniversity of the Free StateBloemfonteinSouth Africa
| | - Samah A. Loutfy
- Virology and Immunology UnitCancer Biology DepartmentNational Cancer Institute (NCI)Cairo UniversityCairoEgypt
- Nanotechnology Research CenterBritish UniversityCairoEgypt
| | - Sara Samy Elkafas
- Production Engineering and Mechanical Design DepartmentFaculty of EngineeringMenofia UniversityMenofiaEgypt
| | - Nasra F. Abdel Fattah
- Virology and Immunology UnitCancer Biology DepartmentNational Cancer Institute (NCI)Cairo UniversityCairoEgypt
| | - Mohamed Hessien
- Molecular Cell Biology UniteDivision of BiochemistryDepartment of ChemistryFaculty of ScienceTanta UniversityTantaEgypt
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Tao S, Chen H, Li N, Fang Y, Xu Y, Liang W. Association of CRISPR-Cas System with the Antibiotic Resistance and Virulence Genes in Nosocomial Isolates of Enterococcus. Infect Drug Resist 2022; 15:6939-6949. [PMID: 36474907 PMCID: PMC9719680 DOI: 10.2147/idr.s388354] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 10/26/2022] [Indexed: 04/07/2024] Open
Abstract
PURPOSE This study aimed to investigate the prevalence of the CRISPR-Cas system in nosocomial isolates of Enterococcus and their possible association with antibiotic resistance and virulence genes. MATERIALS AND METHODS Identification and antimicrobial susceptibility of the microorganism were performed by the automatized VITEK 2 Compact system (bioMerieux, France). A total of 100 Enterococcus isolates were collected and identified by VITEK 2 Compact automatic microbial identification drug susceptibility analyzer. The prevalence of various CRISPR-Cas systems, antibiotic resistance genes and virulence genes were investigated by polymerase chain reaction (PCR). The prevalence of CRISPR-Cas systems associated with antibiotic resistance and virulence genes was performed by appropriate statistical tests. RESULTS A total of 100 isolates of Enterococcus were identified and there were 62/100(62.0%) Enterococcus faecalis isolates and 38/100(38.0%) Enterococcus faecalis isolates. In total, 46 (46.0%) of 100 isolates had at least one CRISPR-Cas locus. CRISPR elements were more prevalent in Enterococcus faecalis isolates. The results of PCR demonstrated that CRISPR1-Cas, orphan CRISPR2, and CRISPR3-Cas were present in 23 (23.0%), 42 (42.0%) and 5 (5.0%) Enterococcus isolates, respectively. Compared with CRISPR-Casnegative isolates, the CRISPR-Cas positive isolates showed significant lower resistance rates against ampicillin, erythromycin, levofloxacin, tetracycline, vancomycin, gentamicin, streptomycin, and rifampicin. Presumably consistent with drug susceptibility, fewer CRISPR loci were identified in vanA, tetM, ermB, aac6'-aph(2"), aadE, and ant(6) positive isolates. There was a significant negative correlation between the CRISPR-Cas locus and the enterococcal virulence factors enterococcal surface protein (esp) gene. CONCLUSION In conclusion, the results indicated that the absence of the CRISPR-Cas system was negatively associated with some antibiotic resistance in clinical isolates of Enterococcus faecalis and Enterococcus faecium. Also, there was a negative correlation with the carriage of antibiotic resistance genes. Furthermore, CRISPR-Cas may prevent some isolates from acquiring certain virulence factors.
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Affiliation(s)
- Shuan Tao
- School of Medicine, Jiangsu University, Zhenjiang, People’s Republic of China
- Department of Clinical Laboratory, Ningbo First Hospital, Ningbo, People’s Republic of China
| | - Huimin Chen
- School of Medicine, Jiangsu University, Zhenjiang, People’s Republic of China
| | - Na Li
- Bengbu Medical College, Bengbu, People’s Republic of China
| | - Yewei Fang
- Department of Clinical Laboratory, Ningbo First Hospital, Ningbo, People’s Republic of China
| | - Yao Xu
- School of Medicine, Ningbo University, Ningbo, People’s Republic of China
| | - Wei Liang
- Department of Clinical Laboratory, Ningbo First Hospital, Ningbo, People’s Republic of China
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Abdelsalam IM, Ghosh S, AlKafaas SS, Bedair H, Malloum A, ElKafas SS, Saad-Allah KM. Nanotechnology as a tool for abiotic stress mitigation in horticultural crops. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01251-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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30
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Bedair H, Ghosh S, Abdelsalam IM, Keerio AA, AlKafaas SS. Potential implementation of trees to remediate contaminated soil in Egypt. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:78132-78151. [PMID: 36175731 DOI: 10.1007/s11356-022-22984-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 09/06/2022] [Indexed: 06/16/2023]
Abstract
Soil and water in Egypt have become contaminated with multiple pollutants. These contaminants arise from diverse sources, including misuse of fertilizers, industrial effluent discharged into irrigation water, discharge of wastewater in rural areas, and mining activities discharging wet and dry atmospheric deposits and heavy metal contamination. The pollutants can directly affect the quality of air, water, and food and have an adverse effect on human health. About 33% of the cultivated lands in Egypt are salinized due to extreme conditions like high temperatures and aridity. The presence of elevated salt levels in the soil leads to grave consequences for seed germination, plant biochemical processes, development, and reproduction, all of which result in the output of reactive oxygen species and eventually plant death. Despite the possibility of thermal, chemical, or a combination of the two to remediate contaminated soils, their applications are complicated and costly. Some plants, called hyperaccumulators, exhibit the potential to clean up pollutants safely from the soil and water at a low cost. All the technologies used in soil decontamination are called phytoremediation. Some physiological (e.g., phytoextraction, phytostabilization, phytotransformation, rhizofiltration, phytostimulation, phytovolatilization, phytodegradation, and phytodesalination) and molecular parameters (e.g., genes, peptides, and proteins) are involved in heavy metals accumulation of these plants. Although trees are not classified as hyperaccumulators, they have recently proved higher phytoremediation potential than herbaceous plants due to their deeper root system and greater biomass growth. Indeed, this review sheds the light on the application of trees for the phytoremediation of salts and heavy metals in Egypt.
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Affiliation(s)
- Heba Bedair
- Botany Department, Faculty of Science, Tanta University, Tanta, 31527, Egypt
| | - Soumya Ghosh
- Department of Genetics, Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein, 9301, South Africa.
| | | | - Ayaz Ali Keerio
- Faculty of Crop Production, Sindh Agriculture University Tando Jam, Sindh, Hyderabad, Pakistan
| | - Samar Sami AlKafaas
- Chemistry Department, Division of Biochemistry, Faculty of Science, Tanta University, Tanta, 31527, Egypt
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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] [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
- Correspondence: Wei Liang, Lianyungang Clinical College of Jiangsu University, No. 161. Xingfu Road, Haizhou District, Lianyungang, Jiangsu Province, 222023, People’s Republic of China, Tel/Fax +86-51885213100; Tel/Fax +86 15351883016, Email
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The Spread of Antibiotic Resistance Genes In Vivo Model. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2022; 2022:3348695. [PMID: 35898691 PMCID: PMC9314185 DOI: 10.1155/2022/3348695] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 06/26/2022] [Accepted: 06/30/2022] [Indexed: 12/20/2022]
Abstract
Infections caused by antibiotic-resistant bacteria are a major public health threat. The emergence and spread of antibiotic resistance genes (ARGs) in the environment or clinical setting pose a serious threat to human and animal health worldwide. Horizontal gene transfer (HGT) of ARGs is one of the main reasons for the dissemination of antibiotic resistance in vitro and in vivo environments. There is a consensus on the role of mobile genetic elements (MGEs) in the spread of bacterial resistance. Most drug resistance genes are located on plasmids, and the spread of drug resistance genes among microorganisms through plasmid-mediated conjugation transfer is the most common and effective way for the spread of multidrug resistance. Experimental studies of the processes driving the spread of antibiotic resistance have focused on simple in vitro model systems, but the current in vitro protocols might not correctly reflect the HGT of antibiotic resistance genes in realistic conditions. This calls for better models of how resistance genes transfer and disseminate in vivo. The in vivo model can better mimic the situation that occurs in patients, helping study the situation in more detail. This is crucial to develop innovative strategies to curtail the spread of antibiotic resistance genes in the future. This review aims to give an overview of the mechanisms of the spread of antibiotic resistance genes and then demonstrate the spread of antibiotic resistance genes in the in vivo model. Finally, we discuss the challenges in controlling the spread of antibiotic resistance genes and their potential solutions.
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