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Qiu J, Shi Y, Zhao F, Xu Y, Xu H, Dai Y, Cao Y. The Pan-Genomic Analysis of Corynebacterium striatum Revealed its Genetic Characteristics as an Emerging Multidrug-Resistant Pathogen. Evol Bioinform Online 2023; 19:11769343231191481. [PMID: 37576785 PMCID: PMC10422898 DOI: 10.1177/11769343231191481] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 07/03/2023] [Indexed: 08/15/2023] Open
Abstract
Corynebacterium striatum is a Gram-positive bacterium that is straight or slightly curved and non-spore-forming. Although it was originally believed to be a part of the normal microbiome of human skin, a growing number of studies have identified it as a cause of various chronic diseases, bacteremia, and respiratory infections. However, despite its increasing importance as a pathogen, the genetic characteristics of the pathogen population, such as genomic characteristics and differences, the types of resistance genes and virulence factors carried by the pathogen and their distribution in the population are poorly understood. To address these knowledge gaps, we conducted a pan-genomic analysis of 314 strains of C. striatum isolated from various tissues and geographic locations. Our analysis revealed that C. striatum has an open pan-genome, comprising 5692 gene families, including 1845 core gene families, 2362 accessory gene families, and 1485 unique gene families. We also found that C. striatum exhibits a high degree of diversity across different sources, but strains isolated from skin tissue are more conserved. Furthermore, we identified 53 drug resistance genes and 42 virulence factors by comparing the strains to the drug resistance gene database (CARD) and the pathogen virulence factor database (VFDB), respectively. We found that these genes and factors are widely distributed among C. striatum, with 77.7% of strains carrying 2 or more resistance genes and displaying primary resistance to aminoglycosides, tetracyclines, lincomycin, macrolides, and streptomycin. The virulence factors are primarily associated with pathogen survival within the host, iron uptake, pili, and early biofilm formation. In summary, our study provides insights into the population diversity, resistance genes, and virulence factors ofC. striatum from different sources. Our findings could inform future research and clinical practices in the diagnosis, prevention, and treatment of C. striatum-associated diseases.
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Affiliation(s)
- Junhui Qiu
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Provence, College of Life Science, Sichuan University, Chengdu, Sichuan, China
| | - Yulan Shi
- Wound Treatment Center of West China Hospital of Sichuan University, West China College of Nursing, Sichuan University, Chengdu, Sichuan, China
| | - Fei Zhao
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Provence, College of Life Science, Sichuan University, Chengdu, Sichuan, China
| | - Yi Xu
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Provence, College of Life Science, Sichuan University, Chengdu, Sichuan, China
| | - Hui Xu
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Provence, College of Life Science, Sichuan University, Chengdu, Sichuan, China
| | - Yan Dai
- Wound Treatment Center of West China Hospital of Sichuan University, West China College of Nursing, Sichuan University, Chengdu, Sichuan, China
| | - Yi Cao
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Provence, College of Life Science, Sichuan University, Chengdu, Sichuan, China
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Mycobacterium Time-Series Genome Analysis Identifies AAC2′ as a Potential Drug Target with Naloxone Showing Potential Bait Drug Synergism. Molecules 2022; 27:molecules27196150. [PMID: 36234683 PMCID: PMC9571707 DOI: 10.3390/molecules27196150] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/15/2022] [Accepted: 09/15/2022] [Indexed: 11/16/2022] Open
Abstract
The World Health Organization has put drug resistance in tuberculosis on its list of significant threats, with a critical emphasis on resolving the genetic differences in Mycobacterium tuberculosis. This provides an opportunity for a better understanding of the evolutionary progression leading to anti-microbial resistance. Anti-microbial resistance has a great impact on the economic stability of the global healthcare sector. We performed a timeline genomic analysis from 2003 to 2021 of 578 mycobacterium genomes to understand the pattern underlying genomic variations. Potential drug targets based on functional annotation was subjected to pharmacophore-based screening of FDA-approved phyto-actives. Reaction search, MD simulations, and metadynamics studies were performed. A total of 4,76,063 mutations with a transition/transversion ratio of 0.448 was observed. The top 10 proteins with the least number of mutations were high-confidence drug targets. Aminoglycoside 2′-N-acetyltransferase protein (AAC2′), conferring resistance to aminoglycosides, was shortlisted as a potential drug target based on its function and role in bait drug synergism. Gentamicin-AAC2′ binding pose was used as a pharmacophore template to screen 10,570 phyto-actives. A total of 66 potential hits were docked to obtain naloxone as a lead—active with a docking score of −6.317. Naloxone is an FDA-approved drug that rapidly reverses opioid overdose. This is a classic case of a repurposed phyto-active. Naloxone consists of an amine group, but the addition of the acetyl group is unfavorable, with a reaction energy of 612.248 kcal/mol. With gentamicin as a positive control, molecular dynamic simulation studies were performed for 200 ns to check the stability of binding. Metadynamics-based studies were carried out to compare unbinding energy with gentamicin. The unbinding energies were found to be −68 and −74 kcal/mol for naloxone and gentamycin, respectively. This study identifies naloxone as a potential drug candidate for a bait drug synergistic approach against Mycobacterium tuberculosis.
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Wang S, Wei L, Gao Y, Rong Y, Zha Z, Lv Y, Feng Z. Novel amikacin resistance genes identified from human gut microbiota by functional metagenomics. J Appl Microbiol 2022; 133:898-907. [PMID: 35543338 DOI: 10.1111/jam.15615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/10/2022] [Accepted: 03/30/2022] [Indexed: 11/30/2022]
Abstract
AIMS The aim of this study was to evaluate the diversity and potential for horizontal transfer of amikacin resistance genes from the human gut. METHODS AND RESULTS A library of human fecal microbiota was constructed and subjected to functional screening for amikacin resistance. In total, five amikacin resistance genes that conferred relatively high amikacin resistance, with minimum inhibitory concentrations (MICs) ranging from 64 to >512, were identified from the library, including a novel aminoglycoside acetyltransferase gene and a 16S rRNA methyltransferase (MTase) gene, labeled aac(6')-Iao and rmtI respectively. AAC(6')-Iao showed the highest identity of 48% to AAC(6')-Ian from a clinical isolate Serratia marcescens, whereas RmtI shared the closest amino acid identity of 32% with ArmA from Klebsiella pneumonia. The MICs of these five subclones to six commonly used aminoglycosides were determined. Susceptibility analysis indicated that RmtI was associated with high resistance phenotype to 4,6-disubstituted 2-DOS aminoglycosides, whereas AAC(6')-Iao conferred resistance to amikacin and kanamycin. In addition, kinetic parameters of AAC(6')-Iao were determined, suggesting a strong catalytic effect on amikacin and kanamycin. CONCLUSIONS Antibiotic resistance genes with low identity to known sequences can be uncovered by functional metagenomics. In addition, the diversity and prevalence of amikacin resistance genes merit further investigation in extended habitats, especially the 16S rRNA MTase gene that might have been underestimated in previous cognition. SIGNIFICANCE AND IMPACT OF STUDY Two novel amikacin resistance genes were identified in this study, including a 16S rRNA methyltransferase gene rmtI and an aminoglycoside acetyltransferase gene aac(6')-Iao. This work would contribute to the in-depth study of the diversity and horizontal transfer potential of amikacin resistance genes in the microbiome of the human gut.
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Affiliation(s)
- Shaochen Wang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Lin Wei
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yuejiao Gao
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yufeng Rong
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Zhengqi Zha
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Yunbin Lv
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Zhiyang Feng
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
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Tarek N, El-Gendy AO, Khairalla AS, Abdel-Fattah M, Tawfik E, Azmy AF. Genomic analysis of Enterococcus durans NT21, a putative bacteriocin-producing isolate. MOLECULAR BIOLOGY RESEARCH COMMUNICATIONS 2022; 11:143-153. [PMID: 36718242 PMCID: PMC9661671 DOI: 10.22099/mbrc.2022.44088.1760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Enterococcus species are a long-standing and non-pathogenic commensal bacterium, representing an important part of the normal. Enterococcus durans is a rarely isolated species from animals and humans, and it was a tiny constituent of human oral cavity and animal intestinal flora, as well as animal-derived foods, particularly dairy products. This study evaluated the security of our strain E. durans NT21 by using whole-genome sequencing (WGS), physicochemical features, and antimicrobial activity. The complete genomic of our strain Enterococcus durans NT21was sequenced and analyzed by using several bioinformatics tools to identify bacteriocin genes, virulence genes, antibiotic resistance genes, Crispr-Cas and pathogenicity islands. The results showed that our strain NT21 lacks the presence of virulence genes, pathogenicity islands, plasmids and has only two antibiotic resistance genes. On the other hand, it produces three bacteriocin-like inhibitory substances (Enterolysin A, P and L50a). It has six gene-encoded Crisper-Cas and one cluster Crispr-Cas gene. According to our findings, E. durans NT21 is a possible probiotic strain that is safe for both human and animal use.
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Affiliation(s)
- Nashwa Tarek
- Department of Botany and Microbiology, Faculty of Science, Beni-Suef University, Egypt,Basic Science Department, Faculty of Oral and Dental medicine, Nahda University Beni-Suef (NUB), Beni
| | - Ahmed O. El-Gendy
- Microbiology and Immunology Department, Faculty of Pharmacy, Beni-Suef University
| | - Ahmed S. Khairalla
- Microbiology and Immunology Department, Faculty of Pharmacy, Beni-Suef University ,Department of Biology, University of Regina, Saskatchewan, Canada
| | - Medhat Abdel-Fattah
- Department of Botany and Microbiology, Faculty of Science, Beni-Suef University, Egypt
| | - Eman Tawfik
- Department of Botany and Microbiology,Faculty of Science, Helwan University, Egypt, Eman Tawfik and Ahmed F. Azmy contributed equally to the project.,Corresponding Author: Lecturer of Genetics and Genetic Engineering, Botany and Microbiology Department, Faculty of Science, Helwan University, Egypt, Tel: +2 01119383526; Fax: +2 0225552468; E. mail:
| | - Ahmed F. Azmy
- Microbiology and Immunology Department, Faculty of Pharmacy, Beni-Suef University , Eman Tawfik and Ahmed F. Azmy contributed equally to the project.,Corresponding Author: Lecturer of Genetics and Genetic Engineering, Botany and Microbiology Department, Faculty of Science, Helwan University, Egypt, Tel: +2 01119383526; Fax: +2 0225552468; E. mail:
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El-Far A, Samir S, El-Gebaly E, Omar M, Dahroug H, El-Shenawy A, Soliman NS, Gamal D. High Rates of Aminoglycoside Methyltransferases Associated with Metallo-Beta-Lactamases in Multidrug-Resistant and Extensively Drug-Resistant Pseudomonas aeruginosa Clinical Isolates from a Tertiary Care Hospital in Egypt. Infect Drug Resist 2021; 14:4849-4858. [PMID: 34848977 PMCID: PMC8613939 DOI: 10.2147/idr.s335582] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 10/22/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains of Pseudomonas aeruginosa are the leading cause of healthcare-associated infections worldwide. OBJECTIVE The aim was to identify the resistant phenotypes among P. aeruginosa and to characterize different aminoglycosides and carbapenem resistance genes as major mechanisms of resistance in these isolates, in Theodor Bilharz Research Institute (TBRI), a tertiary care hospital in Cairo, Egypt. METHODS During a period of 11 months, 42 P. aeruginosa clinical isolates were collected from the microbiology laboratory by routine culture. Antimicrobial sensitivity testing to the aminoglycosides gentamicin and amikacin, and other classes of antibiotics, was performed by a disk diffusion method. Isolates were tested for aminoglycoside resistance genes, aac(6')-lb, aac-(3)-lla, rmtB, rmtC, armA, rmtD, and rmtF, and carbapenemase resistance genes bla NDM, bla VIM, and bla IMP, using conventional PCR. RESULTS Thirty-three (78.5%) of the clinical P. aeruginosa isolates showed MDR and XDR phenotypes at 42.4% and 57.65%, respectively, and these were included in the study. Aminoglycoside resistance was found in 97%, whereas carbapenem resistance was found in 81% of the isolates phenotypically. Only 59.4% (19/26) of the aminoglycoside-resistant isolates harbored resistance genes; none of the amikacin-susceptible isolates harbored any of the tested aminoglycoside resistance genes. Aminoglycoside resistance genes rmtB, armA, aac(6')-lb, and rmtF were found at rates of 17/33 (51.5%), 3/33 (9%), 2/33 (6%), and 2/33 (6%), respectively, whereas rmtD, acc(3)-II, and rmtC were not detected. Only 40.7% (11/27) of the carbapenem-resistant isolates harbored resistance genes. Carbapenem resistance genes, bla NDM andbla VIM, were found at rates of 7/33 (21.2%) and 6/33 (18.1%), respectively, and bla IMP was not detected. CONCLUSION Rates of MDR and XDR P. aeruginosa and resistance to aminoglycosides and carbapenems in our setting are high. Methyltransferases and metallo-beta-lactamases are the main mechanisms of resistance to aminoglycosides and carbapenems, respectively. The presence of bla NDM and rmtF in the strains confirms their rapid dissemination in the Egyptian environment.
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Affiliation(s)
- Amira El-Far
- Microbiology Department, Theodor Bilharz Research Institute (TBRI), Cairo, Egypt
| | - Safia Samir
- Biochemistry and Molecular Biology Department, Theodor Bilharz Research Institute (TBRI), Cairo, Egypt
| | - Eman El-Gebaly
- Microbiology and Immunology Department, Faculty of Pharmacy, Beni-Suif University, Beni-Suif, Egypt
- Department of Microbiology and Immunology, Faculty of Pharmacy, October 6 University, Beni-Suef, 12585, Egypt
| | - Maysa Omar
- Microbiology Department, Theodor Bilharz Research Institute (TBRI), Cairo, Egypt
| | - Heba Dahroug
- Microbiology Department, Theodor Bilharz Research Institute (TBRI), Cairo, Egypt
| | - Ahmed El-Shenawy
- Microbiology Department, Theodor Bilharz Research Institute (TBRI), Cairo, Egypt
| | - Noha Salah Soliman
- Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Doaa Gamal
- Microbiology Department, Theodor Bilharz Research Institute (TBRI), Cairo, Egypt
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Herrera-Sánchez MP, Castro-Vargas RE, Fandiño-de-Rubio LC, Rodríguez-Hernández R, Rondón-Barragán IS. Molecular identification of fluoroquinolone resistance in Salmonella spp. isolated from broiler farms and human samples obtained from two regions in Colombia. Vet World 2021; 14:1767-1773. [PMID: 34475696 PMCID: PMC8404129 DOI: 10.14202/vetworld.2021.1767-1773] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 05/24/2021] [Indexed: 11/30/2022] Open
Abstract
Background and Aim: Salmonella is one of the most common foodborne pathogens, the emergence of antibiotic-resistant strains of which is increasing. The aim of this study was to phenotypically and genotypically characterize the fluoroquinolone resistance of Salmonella isolates from broiler and humans in two regions of Colombia. Materials and Methods: Salmonella strains (n=49) were evaluated. The phenotype of antibiotic resistance was assessed by an automated method and agar diffusion method, as well as the presence of the quinolone resistance genes qnrA, qnrB, qnrC, qnrD, qnrS, and aac(6’)-Ib as determined by polymerase chain reaction. Results: Strains were resistant to ciprofloxacin (75%), levofloxacin (57.1%), and enrofloxacin (38.8%). Molecular identification showed that 24 out of 49 strains possessed the qnrB gene (48.9%), while only one isolate from the Santander region possessed the aac(6’)-Ib gene. Regarding Class 1 integron, it was present in 11 out of the 49 strains (22.44%). Conclusion: This study reports the presence of the gene qnrB as well the presence of Class 1 integrons in broiler Salmonella isolates, which may contribute to the resistance to fluoroquinolones.
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Affiliation(s)
- María Paula Herrera-Sánchez
- Research Group in Immunobiology and Pathogenesis, Laboratory of Immunology and Molecular Biology, Faculty of Veterinary Medicine and Zootechnics, University of Tolima, Santa Helena Highs, Ibagué 730006299, Tolima, Colombia
| | - Rafael Enrique Castro-Vargas
- Research Group in Immunobiology and Pathogenesis, Laboratory of Immunology and Molecular Biology, Faculty of Veterinary Medicine and Zootechnics, University of Tolima, Santa Helena Highs, Ibagué 730006299, Tolima, Colombia.,Poultry Research Group, Laboratory of Immunology and Molecular Biology, Faculty of Veterinary Medicine and Zootechnics, University of Tolima, Santa Helena Highs, Ibagué 730006299, Tolima, Colombia
| | - Luz Clemencia Fandiño-de-Rubio
- Poultry Research Group, Laboratory of Immunology and Molecular Biology, Faculty of Veterinary Medicine and Zootechnics, University of Tolima, Santa Helena Highs, Ibagué 730006299, Tolima, Colombia
| | - Roy Rodríguez-Hernández
- Poultry Research Group, Laboratory of Immunology and Molecular Biology, Faculty of Veterinary Medicine and Zootechnics, University of Tolima, Santa Helena Highs, Ibagué 730006299, Tolima, Colombia
| | - Iang Schroniltgen Rondón-Barragán
- Research Group in Immunobiology and Pathogenesis, Laboratory of Immunology and Molecular Biology, Faculty of Veterinary Medicine and Zootechnics, University of Tolima, Santa Helena Highs, Ibagué 730006299, Tolima, Colombia.,Poultry Research Group, Laboratory of Immunology and Molecular Biology, Faculty of Veterinary Medicine and Zootechnics, University of Tolima, Santa Helena Highs, Ibagué 730006299, Tolima, Colombia
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Azam M, Bitu MNA, Mohapatra RK, Al-Resayes SI, Pintilie L, Wabaidur SM, Alqahtani FF, Islam MS, Sarangi AK, Kudrat-E-Zahan M. Synthesis, characterization of Uranyl(VI), Th(IV), Zr(IV) mixed-ligand complexes with S-methyl-2-(4-methoxybenzylidine)dithiocarbazate and N-donor co-ligand, and their evaluation as antimicrobial agent. JOURNAL OF SAUDI CHEMICAL SOCIETY 2021. [DOI: 10.1016/j.jscs.2021.101207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Aminoglycoside antibiotic resistance conferred by Hpa2 of MDR Acinetobacter baumannii: an unusual adaptation of a common histone acetyltransferase. Biochem J 2019; 476:795-808. [PMID: 30573651 DOI: 10.1042/bcj20180791] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 12/18/2018] [Accepted: 12/20/2018] [Indexed: 12/20/2022]
Abstract
Antibiotic-resistant bacteria pose the greatest threat to human health. Among the list of such bacteria released by WHO, carbapenem-resistant Acinetobacter baumannii, for which almost no treatment exists, tops the list. A. baumannii is one of the most troublesome ESKAPE pathogens and mechanisms that have facilitated its rise as a successful pathogen are not well studied. Efforts in this direction have resulted in the identification of Hpa2-Ab, an uncharacterized histone acetyltransferase enzyme of GNAT superfamily. Here, we show that Hpa2-Ab confers resistance against aminoglycoside antibiotics using Escherichia coli DH5α strains in which Hpa2 gene is expressed. Resistivity for aminoglycoside antibiotics is demonstrated with the help of CLSI-2010 and KB tests. Isothermal titration calorimetry, MALDI and acetylation assays indicate that conferred resistance is an outcome of evolved antibiotic acetylation capacity in this. Hpa2 is known to acetylate nuclear molecules; however, here it is found to cross its boundary and participate in other functions. An array of biochemical and biophysical techniques were also used to study this protein, which demonstrates that Hpa2-Ab is intrinsically oligomeric in nature, exists primarily as a dimer and its interface is mainly stabilized by hydrophobic interactions. Our work demonstrates an evolved survival strategy by A. baumannii and provides insights into the mechanism that facilitates it to rise as a successful pathogen.
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