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Xiahou ZY, Wambulwa MC, Xu ZC, Ye LJ, Fan PZ, Magige EA, Luo YH, Liu J. A Multiplex PCR System of Novel Microsatellite Loci for Population Genetic Application in Walnuts. PLANTS (BASEL, SWITZERLAND) 2023; 12:4101. [PMID: 38140428 PMCID: PMC10747719 DOI: 10.3390/plants12244101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023]
Abstract
Multiplex polymerase chain reaction (PCR) of microsatellite loci allows for simultaneous amplification of two or more pairs of primers in a single PCR reaction; hence, it is cost and time effective. However, very few attempts have been reported in non-model species. In this study, by combining a genome-based de novo development and cross-species application approach, a multiplex PCR system comprising 5 PCR reactions of 33 microsatellites consisting of 26 novel genomic and 7 literature-sourced loci was tested for polymorphisms, cross-species transferability, and the ability to assess genetic diversity and population structure of three walnut species (Juglans spp.). We found that the genome-based approach is more efficient than other methods. An allelic ladder was developed for each locus to enhance consistent genotyping among laboratories. The population genetic analysis results showed that all 33 loci were successfully transferred across the three species, showing high polymorphism and a strong genetic structure. Hence, the multiplex PCR system is highly applicable in walnut species. Furthermore, we propose an efficient pipeline to characterize and genotype polymorphic microsatellite loci. The novel toolbox developed here will aid future ecology and evolution studies in walnut and could serve as a model for other plant species.
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Affiliation(s)
- Zuo-Ying Xiahou
- CAS Key Laboratory for Plant and Biodiversity of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (Z.-Y.X.); (M.C.W.)
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Moses C. Wambulwa
- CAS Key Laboratory for Plant and Biodiversity of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (Z.-Y.X.); (M.C.W.)
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Department of Life Sciences, School of Science and Computing, South Eastern Kenya University, Kitui 170-90200, Kenya
| | - Zu-Chang Xu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Lin-Jiang Ye
- CAS Key Laboratory for Plant and Biodiversity of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (Z.-Y.X.); (M.C.W.)
- Key Laboratory of Plant Resources and Biodiversity of Jiangxi Province, Jingdezhen University, Jingdezhen 333400, China
| | - Peng-Zhen Fan
- CAS Key Laboratory for Plant and Biodiversity of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (Z.-Y.X.); (M.C.W.)
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Ephie A. Magige
- CAS Key Laboratory for Plant and Biodiversity of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (Z.-Y.X.); (M.C.W.)
| | - Ya-Huang Luo
- CAS Key Laboratory for Plant and Biodiversity of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (Z.-Y.X.); (M.C.W.)
| | - Jie Liu
- CAS Key Laboratory for Plant and Biodiversity of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (Z.-Y.X.); (M.C.W.)
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
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Ghalavand Z, Taheri M, Eslami G, Karimi-Yazdi M, Sadredinamin M. Invasion of HeLa Cells by Shigella Species Clinical Isolates Recovered from Pediatric Diarrhea. Foodborne Pathog Dis 2023; 20:509-513. [PMID: 37738332 DOI: 10.1089/fpd.2023.0066] [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] [Indexed: 09/24/2023] Open
Abstract
Shigella is considered a major public health concern, especially for children younger than 5 years of age in developing countries. The pathogenicity of Shigella is a complex process that involves the interplay of multiple genes located on a large, unstable virulence plasmid as well as chromosomal pathogenicity islands. Since various factors (including virulence and antibiotic resistance genes) are associated with the severity and duration of shigellosis, in this article, we aim to evaluate whether the invasion of HeLa cells is affected by Shigella spp. isolates with different characteristics (including serogroups, virulence gene profiles, and antibiotic resistance patterns) recovered from pediatric patients in Tehran, Iran. Cell invasion ability of 10 Shigella isolates with different serogroups (Shigella flexneri and Shigella sonnei), gene profiling (virA, sen, ipgD, ipaD, ipaC, ipaB, and ipaH), and antibiotic resistance phenotyping (ampicillin, azithromycin, ciprofloxacin, nalidixic acid, trimethoprim-sulfamethoxazole, cefixime, cefotaxime, minocycline, and levofloxacin) were measured by plaque-forming assay in HeLa cell lines. The results show that all the selected Shigella spp. isolates recovered from pediatric patients were able to invade HeLa cells, but the total number and average size of plaques were different between the isolates. The higher invasion ability of S. flexneri isolates in HeLa cells compared to S. sonnei isolates was attributed to the presence of particular virulence genes; however, the role of each of these virulence factors remains to be determined.
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Affiliation(s)
- Zohreh Ghalavand
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Marzieh Taheri
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Faculty of Paramedical Sciences, Mazandaran University of Medical Sciences, Sari, Iran
| | - Gita Eslami
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Mehrzad Sadredinamin
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Sheydai F, Tukmechi A. Cell wall disruption, membrane damage, and decrease in the expression of Yrp1 virulence factor in Yersinia ruckeri by propolis ethanol extract. IRANIAN JOURNAL OF MICROBIOLOGY 2023; 15:533-540. [PMID: 38045706 PMCID: PMC10692965 DOI: 10.18502/ijm.v15i4.13507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Background and Objectives Instead of antibiotics, propolis is a promising alternative for treating bacterial diseases. The aim of this study was to evaluate the effect of propolis ethanol extract (PEE) on Yersinia ruckeri (Y. ruckeri), a fish pathogen, by examining its impact on the cell wall, cytoplasmic membrane, and gene expression. Materials and Methods The effect of propolis on the bacterial cell wall, membrane, and DNA using scanning electron microscopy (SEM) was investigated. Its effect on the NAD+/NADH ratio, reactive oxygen species (ROS) production, as well as the expression of a virulence factor (yrp1) was also determined. Results It was demonstrated that PEE has multiple antibacterial mechanisms against Y. ruckeri involving cell wall damage, membrane lysis, and a decrease in gene expression. Conclusion The obtained results indicated that the mode of propolis action against Y. ruckeri is both structural and functional, while others showed propolis only could inactivate bacteria in a structural way.
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Affiliation(s)
- Fardin Sheydai
- Department of Microbiology, Faculty of Veterinary Medicine, Urmia University, Urmia, Iran
| | - Amir Tukmechi
- Department of Microbiology, Faculty of Veterinary Medicine, Urmia University, Urmia, Iran
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Shahnaij M, Amin MB, Hoque MM, Mondol AS, Rana KJ, Azmi IJ, Talukder KA. Characterization of Shigella flexneri Serotype 6 Strains Isolated from Bangladesh and Identification of a New Phylogenetic Cluster. J Bacteriol 2023; 205:e0040622. [PMID: 36927058 PMCID: PMC10127597 DOI: 10.1128/jb.00406-22] [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: 11/01/2022] [Accepted: 02/16/2023] [Indexed: 03/18/2023] Open
Abstract
A significant cause of shigellosis in Bangladesh and other developing countries is Shigella flexneri serotype 6. This serotype has been subtyped, on the basis of the absence or presence of a group-specific antigen, E1037, into S. flexneri 6a and 6b, respectively. Here, we provided rationales for the subclassification, using several phenotypic and molecular tools. A set of S. flexneri 6a and 6b strains isolated between 1997 and 2015 were characterized by analyzing their biochemical properties, plasmid profiles, virulence markers, pulsed-field gel electrophoresis (PFGE) results, and ribotype. Additionally, the genomic relatedness of these subserotypes was investigated with global isolates of serotype 6 using publicly available genomes. Both subserotypes of S. flexneri 6 agglutinated with monoclonal antiserum against S. flexneri (MASF) B and type VI-specific antiserum (MASF VI) and were PCR positive for O-antigen flippase-specific genes and virulence markers (ipaH, ial, sen, and sigA). Unlike S. flexneri 6a strains, S. flexneri 6b strains seroagglutinated with anti-E1037 antibodies, MASF IV-I. Notably, these two antigenically distinct subserotypes were clonally diverse, showing two distinct PFGE patterns following the digestion of chromosomal DNA with either XbaI or IceuI. In addition, hybridization of a 16S rRNA gene probe with HindIII-digested genomic DNA yielded two distinguishing ribotypes. Genomic comparison of S. flexneri subserotype 6a and 6b strains from Bangladesh indicated that, although these strains were in genomic synteny, the majority of them formed a unique phylogroup (PG-4) that was missing for the global isolates. This study supports the subserotyping and emphasizes the need for global monitoring of the S. flexneri subserotypes 6a and 6b. IMPORTANCE Shigella flexneri serotype 6 is one of the predominant serotypes among shigellosis cases in Bangladesh. Characterization of a novel subserotype of S. flexneri 6 (VI:E1037), agglutinated with type 6-specific antibody and anti-E1037, indicates a unique evolutionary ancestry. PFGE genotyping supports the finding that these two antigenically distinct subserotypes are clonally diverse. A phylogenetic study based on single-nucleotide polymorphism (SNP) data revealed that these two subserotypes were in genomic synteny, although their genomes were reduced. Interestingly, a majority of the S. flexneri 6 strains isolated from Bangladesh form a novel phylogenetic cluster. Therefore, this report underpins the global monitoring and tracking of the novel subserotype.
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Affiliation(s)
- Mohammad Shahnaij
- Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Mohammed Badrul Amin
- Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - M. Mozammel Hoque
- Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Abdus Salam Mondol
- Department of Public Health Nutrition, Primeasia University, Dhaka, Bangladesh
| | - Kazi Jewel Rana
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Ishrat J. Azmi
- Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Kaisar A. Talukder
- Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Bangladesh
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Delik E, Eroğlu B, Çolak ÇY, Özçelik AT, Tefon Öztürk BE. Alterations of Growth, Biofilm-Forming, and Gene Expression of Bordetella pertussis by Antibiotics at Sub-Minimal Inhibitory Concentrations. Res Microbiol 2023:104058. [PMID: 37044235 DOI: 10.1016/j.resmic.2023.104058] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 03/29/2023] [Accepted: 04/03/2023] [Indexed: 04/14/2023]
Abstract
Bordetella pertussis is the primary agent of the acute respiratory disease pertussis. It has been reported that the disease has recently become more common, especially in adults and adolescents, and adaptation of the pathogen is thought to have an important influence on the recurrence of the disease. This study aims to determine the effect of erythromycin, azithromycin, and trimethoprim-sulfamethoxazole used in the treatment of pertussis on the virulence gene expressions (prn, ptxS1, fhaB), biofilm-forming and growth of B. pertussis. In this study, the minimal inhibitory concentration (MIC) values of azithromycin and erythromycin in B. pertussis local strain Saadet were determined to be 0.09 μg/mL and 0.3 μg/mL, respectively. However, the Tohama-I and Saadet strains were resistant to trimethoprim-sulfamethoxazole (MIC>32 μg/mL). The biofilm-forming of the Saadet strain decreased with the increase in antibiotic doses. It was observed that 1/32MIC erythromycin and 1/32MIC azithromycin upregulated the expression of fhaB in Tohama-I, whereas the expression of ptxS1 and prn significantly decreased in sub-MICs of erythromycin. In the Saadet strain, only ptxS1 was highly expressed at 1/16MIC azithromycin and erythromycin (p>0.05). This is the first study to investigate the effect of sub-MIC antibiotics on the expression of virulence genes and biofilm-forming of B. pertussis.
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Affiliation(s)
- Eda Delik
- Biology Department, Faculty of Science, Akdeniz University, 07058, Antalya, Turkiye.
| | - Berfin Eroğlu
- Biology Department, Faculty of Science, Akdeniz University, 07058, Antalya, Turkiye.
| | - Çiğdem Yılmaz Çolak
- Genetic Engineering and Biotechnology Institute, TUBITAK, 41470, Kocaeli, Turkiye.
| | - Aysun Türkanoğlu Özçelik
- Agricultural Biotechnology Department, Faculty of Agriculture, Akdeniz University, 07058, Antalya, Turkiye.
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Prevalence of Multidrug-Resistant and Extended-Spectrum Beta-Lactamase-Producing Shigella Species in Asia: A Systematic Review and Meta-Analysis. Antibiotics (Basel) 2022; 11:antibiotics11111653. [PMID: 36421297 PMCID: PMC9687025 DOI: 10.3390/antibiotics11111653] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/10/2022] [Accepted: 11/15/2022] [Indexed: 11/22/2022] Open
Abstract
Shigellosis remains one of the leading causes of morbidity and mortality worldwide and is the second leading cause of diarrheal mortality among all age groups. However, the global emergence of antimicrobial-resistant Shigella strains, limiting the choice of effective drugs for shigellosis, has become the major challenge in the treatment of Shigella infections. The aim of this systematic review and meta-analysis was to provide an updated picture of the prevalence of antimicrobial-resistant Shigella species in Asia. A comprehensive and systematic search was performed on three electronic databases (PubMed, ScienceDirect and Scopus), in which 63 eligible studies published between 2010 and 2022 were identified. From our meta-analysis of proportions using a random-effects model, the overall prevalence of Shigella spp. in Asian patients was estimated to be 8.0% (95% CI: 5.5–10.5). The pooled prevalence rates of multidrug-resistant (MDR) and extended-spectrum beta-lactamase (ESBL)-producing Shigella strains were 68.7% (95% CI: 59.9–77.5) and 23.9% (95% CI: 12.9–34.8), respectively. Concerning recommended antimicrobial drugs for Shigella, the prevalence of resistance was highest for ciprofloxacin (29.8%) and azithromycin (29.2%), followed by ceftriaxone (23.8%), in spite of their importance as first- and second-line treatments for shigellosis. In contrast, resistance to carbapenems, such as ertapenem (0.0%), imipenem (0.1%) and meropenem (0.0%), was almost non-existent among the 49 tested antibiotics. The significantly high prevalence estimation suggests that the multidrug-resistant Shigella is a pressing threat to public health worthy of careful and justified interventions. Effective antibiotic treatment strategies, which may lead to better outcomes for the control and treatment of shigellosis in Asia, are essential.
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Teixeira RA, Lima EC, Benetti AD, Thue PS, Lima DR, Sher F, Dos Reis GS, Rabiee N, Seliem MK, Abatal M. Composite of methyl polysiloxane and avocado biochar as adsorbent for removal of ciprofloxacin from waters. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:74823-74840. [PMID: 35641743 DOI: 10.1007/s11356-022-21176-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
Two carbon composite materials were prepared by mixing avocado biochar and methyl polysiloxane (MK). Firstly, MK was dissolved in ethanol, and then the biochar was added at different times. In sample 1 (R1), the time of adding biochar was immediately after dissolving MK in ethanol, and in sample 2 (R2), after 48 h of MK dissolved in ethanol. The samples were characterized by nitrogen adsorption/desorption measurements obtaining specific surface areas (SBET) of 115 m2 g-1 (R1) and 580 m2 g-1 (R2). The adsorbents were further characterized using scanning electron microscopy, FTIR and Raman spectroscopy, adsorption of vapors of n-heptane and water, thermal analysis, Bohem titration, pHpzc, and C H N elemental analysis. R1 and R2 adsorbents were employed as adsorbents to remove the antibiotic ciprofloxacin from the waters. The t1/2 and t0.95 based on the interpolation of Avrami fractional-order were 20.52 and 246.4 min (R1) and 14.00 and 157.6 min (R2), respectively. Maximum adsorption capacities (Qmax) based on the Liu isotherm were 10.77 (R1) and 63.80 mg g-1 (R2) for ciprofloxacin. The thermodynamic studies showed a spontaneous and exothermic process for both samples, and the value of ΔH° is compatible with physical adsorption.
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Affiliation(s)
- Roberta A Teixeira
- Graduate Program in Water Resources and Environmental Sanitation, Hydraulic Research Institute (IPH), Federal University of Rio Grande Do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Eder C Lima
- Institute of Chemistry, Federal University of Rio Grande Do Sul (UFRGS), Av. Bento Goncalves 9500, RS, Postal Box, 15003, Porto Alegre, ZIP 91501-970, Brazil.
- Graduate Program in Science of Materials (PGCIMAT), Institute of Chemistry, Federal University of Rio Grande Do Sul (UFRGS), Av. Bento Gonçalves 9500, Porto Alegre, RS, ZIP 91501-970, Brazil.
- Metallurgical, and Materials Engineering (PPGE3M), School of Engineering, Graduate Program in Mine, Federal University of Rio Grande Do Sul (UFRGS), Av. Bento Gonçalves 9500, Porto Alegre, RS, Brazil.
| | - Antônio D Benetti
- Graduate Program in Water Resources and Environmental Sanitation, Hydraulic Research Institute (IPH), Federal University of Rio Grande Do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Pascal S Thue
- Graduate Program in Science of Materials (PGCIMAT), Institute of Chemistry, Federal University of Rio Grande Do Sul (UFRGS), Av. Bento Gonçalves 9500, Porto Alegre, RS, ZIP 91501-970, Brazil
| | - Diana R Lima
- Metallurgical, and Materials Engineering (PPGE3M), School of Engineering, Graduate Program in Mine, Federal University of Rio Grande Do Sul (UFRGS), Av. Bento Gonçalves 9500, Porto Alegre, RS, Brazil
| | - Farooq Sher
- Department of Engineering, School of Science and Technology, Nottingham Trent University, Nottingham, NG11 8NS, UK
| | - Glaydson S Dos Reis
- Department of Forest Biomaterials and Technology, Swedish University of Agricultural Sciences, Biomass Technology Centre, 901 83, Umeå, Sweden
| | - Navid Rabiee
- Department of Physics, Sharif University of Technology, P.O. Box 11155-9161, Tehran, Iran
- School of Engineering, Macquarie University, Sydney, NSW, 2109, Australia
| | - Moaaz K Seliem
- Faculty of Earth Science, Beni-Suef University, Beni-Suef, Egypt
| | - Mohamed Abatal
- Facultad de Ingeniería, Universidad Autónoma del Carmen, C.P. 24153, Ciudad del Carmen, Mexico
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