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Shrestha P, Karmacharya J, Han SR, Park H, Oh TJ. In silico analysis and a comparative genomics approach to predict pathogenic trehalase genes in the complete genome of Antarctica Shigella sp. PAMC28760. Virulence 2022; 13:1502-1514. [PMID: 36040103 PMCID: PMC9450901 DOI: 10.1080/21505594.2022.2117679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Although four Shigella species (S. flexneri, S. sonnei, S. dysenteriae, and S. boydii) have been reported, S. sp. PAMC 28760, an Antarctica isolate, is the only one with a complete genome deposited in NCBI database as an uncharacterized isolate. Because it is the world’s driest, windiest, and coldest continent, Antarctica provides an unfavourable environment for microorganisms. Computational analysis of genomic sequences of four Shigella species and our uncategorized Antarctica isolates Shigella sp. PAMC28760 was performed using MP3 (offline version) program to predict trehalase encoding genes as a pathogenic or non-pathogenic form. Additionally, we employed RAST and Prokka (offline version) annotation programs to determine locations of periplasmic (treA) and cytoplasmic (treF) trehalase genes in studied genomes. Our results showed that only 56 out of 134 Shigella strains had two different trehalase genes (treF and treA). It was revealed that the treF gene tends to be prevalent in Shigella species. In addition, both treA and treF genes were present in our strain S. sp. PAMC28760. The main objective of this study was to predict the prevalence of two different trehalase genes (treF and treA) in the complete genome of Shigella sp. PAMC28760 and other complete genomes of Shigella species. Till date, it is the first study to show that two types of trehalase genes are involved in Shigella species, which could offer insight on how the bacteria use accessible carbohydrate like glucose produced from the trehalose degradation pathway, and importance of periplasmic trehalase involvement in bacterial virulence.
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Affiliation(s)
- Prasansah Shrestha
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, Korea
| | - Jayram Karmacharya
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, Korea
| | - So-Ra Han
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, Korea
| | - Hyun Park
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Korea
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, Korea.,Department of Life Science and Biochemical Engineering, SunMoon Univesity, Genome-based BioIT Convergence Institute, Asan, Korea.,Department of Pharmaceutical Engineering and Biotechnology, SunMoon University, Asan, Korea
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Akshay SD, Anupama KP, Deekshit VK, Rohit A, Maiti B. Effect of sub-minimum inhibitory concentration of ceftriaxone on the expression of outer membrane proteins in Salmonella enterica serovar Typhi. World J Microbiol Biotechnol 2022; 38:190. [PMID: 35972699 DOI: 10.1007/s11274-022-03383-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/09/2022] [Indexed: 01/22/2023]
Abstract
Multi-drug resistance (MDR) in Salmonella is one of the major reasons for foodborne outbreaks worldwide. Decreased susceptibility of Salmonella Typhi to first-line drugs such as ceftriaxone, ciprofloxacin, and azithromycin has raised concern. Reduced outer membrane proteins (OMPs) permeability and increased efflux pump transportation are considered to be the main reasons for the emergence of antibiotic resistance in Salmonella. The present study aimed to assess the expression of OMPs at sub-lethal concentrations of ceftriaxone in S. Typhi (Sl5037/BC, and Sl05). The S. Typhi strains were exposed to sub-MIC and half of the sub-MIC concentrations of ceftriaxone at three different time intervals (0 min, 40 min, and 180 min) and analyzed for differential expression of OMPs. Further, the expression variation of OMP encoding genes (yaeT, ompX, lamb, ompA, and ybfM) in response to ceftriaxone was evaluated using real-time PCR. The genes like lamB, ompX, and yaeT showed significant downregulation (p < 0.05) compared to the control without antibiotic exposure, whereas ybfM and ompA showed a moderate downregulation. The expression of omp genes such as lamB, ompA, ompX, ybfM, and yaeT were found to be low in the presence of ceftriaxone, followed by time and dose-dependent. The study provides insights into the possible involvement of OMPs in drug resistance of S. Typhi, which could help develop a therapeutic strategy to combat MDR isolates of S. Typhi.
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Affiliation(s)
- Sadanand Dangari Akshay
- Nitte (Deemed to Be University), Division of Infectious Diseases, Nitte University Centre for Science Education and Research (NUCSER), Paneer Campus, Deralakatte, Mangalore, 575018, India
| | - Karanth Padyana Anupama
- Nitte (Deemed to Be University), Division of Infectious Diseases, Nitte University Centre for Science Education and Research (NUCSER), Paneer Campus, Deralakatte, Mangalore, 575018, India
| | - Vijaya Kumar Deekshit
- Nitte (Deemed to Be University), Division of Infectious Diseases, Nitte University Centre for Science Education and Research (NUCSER), Paneer Campus, Deralakatte, Mangalore, 575018, India
| | - Anusha Rohit
- Nitte (Deemed to Be University), Division of Infectious Diseases, Nitte University Centre for Science Education and Research (NUCSER), Paneer Campus, Deralakatte, Mangalore, 575018, India.,Department of Microbiology, The Madras Medical Mission, 4-A, Dr, Mogappair, Chennai, Tamil Nadu, 600037, India
| | - Biswajit Maiti
- Nitte (Deemed to Be University), Division of Infectious Diseases, Nitte University Centre for Science Education and Research (NUCSER), Paneer Campus, Deralakatte, Mangalore, 575018, India.
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Mohammad Shabani NR, Khairul Hisyam Ismail CM, Anthony AA, Leow CH, Chuah C, Abdul Majeed AB, Nor NM, He Y, Banga Singh KK, Leow CY. Mass spectrometry-based immunopeptidomics and computational vaccinology strategies for the identification of universal Shigella immunogenic candidates. Comput Biol Med 2022; 148:105900. [DOI: 10.1016/j.compbiomed.2022.105900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 06/26/2022] [Accepted: 07/16/2022] [Indexed: 11/16/2022]
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Shabani NRM, Mokhtar M, Leow CH, Lean QY, Chuah C, Singh KKB, Leow CY. Differential expression of cytokine genes in THP-1-derived macrophages infected with mild and virulence strains of Shigella flexneri 2a. INFECTION GENETICS AND EVOLUTION 2020; 85:104532. [PMID: 32911076 DOI: 10.1016/j.meegid.2020.104532] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/25/2020] [Accepted: 09/02/2020] [Indexed: 11/19/2022]
Abstract
Shigella is an intracellular bacterial pathogen that causes bacterial dysentery called shigellosis. The assessment of pro- and anti-inflammatory mediators produced by immune cells against this bacteria are vital in identifying the effectiveness of the immune reaction in protecting the host. In Malaysia, Shigella is ranked as the third most common bacteria causing diarrheal disease among children below 5 years old. In the present study, we aim to examine the differential cytokine gene expressions of macrophages in response to two types of clinical strains of Shigella flexneri 2a (S. flexneri 2a) isolated from patients admitted in Hospital Universiti Sains Malaysia, Kelantan, Malaysia. THP-1-derived macrophages, as the model of human macrophages, were infected separately with S. flexneri 2a mild (SH062) and virulence (SH057) strains for 6, 12, and 24 h, respectively. The gene expression level of inflammatory mediators was identified using real-time quantitative polymerase chain reaction (RT-qPCR). The production of nitric oxide (NO) by the macrophages was measured by using a commercialized NO assay kit. The ability of macrophages to kill the intracellular bacteria was assessed by intracellular killing assay. Induction of tumor necrosis factor-alpha (TNFα), interleukin (IL)-1β, IL-6, IL-12, inducible NO synthase (iNOS), and NO, confirmed the pro-inflammatory reaction of the THP-1-derived macrophages in response to S. flexneri 2a, especially against the SH507 strain. The SH057 also induced a marked increase in the expression levels of the anti-inflammatory cytokine mRNAs at 12 h and 24 h post-infection. In the intracellular killing assay, both strains showed less viable, indicating the generation of pro-inflammatory cytokines in the presence of iNOS and NO was crucial in the stimulation of macrophages for the host defense against shigellosis. Transcription analysis of THP-1-derived macrophages in this study identifies differentially expressed cytokine genes that correlated with the virulence factor of S. flexneri 2a.
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Affiliation(s)
- Nor Raihan Mohammad Shabani
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Health Campus, 16150 Kubang Kerian, Kelantan, Malaysia; Faculty of Health Sciences, Universiti Teknologi MARA, Cawangan Pulau Pinang, Kampus Bertam, 13200 Kepala Batas, Penang, Malaysia
| | - Munirah Mokhtar
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Health Campus, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Chiuan Herng Leow
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Gelugor, Penang, Malaysia
| | - Qi Ying Lean
- Faculty of Pharmacy, Universiti Teknologi MARA, Cawangan Pulau Pinang, Kampus Bertam, 13200 Kepala Batas, Penang, Malaysia
| | - Candy Chuah
- School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150 Kubang Kerian, Kelantan, Malaysia; Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Sungai Long Campus, Jalan Sungai Long, Bandar Sungai Long, 43200 Kajang, Selangor, Malaysia
| | - Kirnpal Kaur Banga Singh
- School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Chiuan Yee Leow
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Health Campus, 16150 Kubang Kerian, Kelantan, Malaysia.
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Differential gene expression profile of Shigella dysenteriae causing bacteremia in an immunocompromised individual. Future Sci OA 2020; 6:FSO456. [PMID: 32257369 PMCID: PMC7117556 DOI: 10.2144/fsoa-2019-0117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
AIM Shigella species has varying levels of virulence gene expression with respect to different sites of infection. In this study, the differential gene expression of S. dysenteriae in response to its site of infection was analyzed by transcriptomics. METHODS This study includes four clinical Shigella isolates. Transcriptomics was done for the stool and blood samples of a single patient. Isolates were screened for the presence of antimicrobial resistance genes. RESULTS The majority of genes involved in invasion were highly expressed in the strain isolated from the primary site of infection. Additionally, antimicrobial resistance (dhfr1A, sulII, bla OXA. bla CTX-M-1 and qnrS) genes were identified. CONCLUSION This study provides a concise view of the transcriptional expression of clinical strains and provides a basis for future functional studies on Shigella spp.
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Harikrishnan H, Banga Singh KK, Ismail A. Outer membrane proteins analysis of Shigella sonnei and evaluation of their antigenicity in Shigella infected individuals. PLoS One 2017; 12:e0182878. [PMID: 28846684 PMCID: PMC5573271 DOI: 10.1371/journal.pone.0182878] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 07/26/2017] [Indexed: 11/22/2022] Open
Abstract
Bacillary dysentery caused by infection with Shigella spp. remains as serious and common health problem throughout the world. It is a highly multi drug resistant organism and rarely identified from the patient at the early stage of infection. S. sonnei is the most frequently isolated species causing shigellosis in industrialized countries. The antigenicity of outer membrane protein of this pathogen expressed during human infection has not been identified to date. We have studied the antigenic outer membrane proteins expressed by S. sonnei, with the aim of identifying presence of specific IgA and IgG in human serum against the candidate protein biomarkers. Three antigenic OMPs sized 33.3, 43.8 and 100.3 kDa were uniquely recognized by IgA and IgG from patients with S. sonnei infection, and did not cross-react with sera from patients with other types of infection. The antigenic proteome data generated in this study are a first for OMPs of S. sonnei, and they provide important insights of human immune responses. Furthermore, numerous prime candidate proteins were identified which will aid the development of new diagnostic tools for the detection of S. sonnei.
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Affiliation(s)
- Hemavathy Harikrishnan
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Kirnpal Kaur Banga Singh
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kelantan, Malaysia
- * E-mail:
| | - Asma Ismail
- Office of the Vice-Chancellor, Universiti Sains Malaysia, Penang, Malaysia
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Kelantan, Malaysia
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Grosso-Becera MV, Servín-González L, Soberón-Chávez G. RNA structures are involved in the thermoregulation of bacterial virulence-associated traits. Trends Microbiol 2015; 23:509-18. [PMID: 25999019 DOI: 10.1016/j.tim.2015.04.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 04/01/2015] [Accepted: 04/16/2015] [Indexed: 11/25/2022]
Abstract
Pathogenic bacteria are exposed to temperature changes during colonization of the human body and during exposure to environmental conditions. Virulence-associated traits are mainly expressed by pathogenic bacteria at 37°C. We review different cases of post-transcriptional regulation of virulence-associated proteins through RNA structures (called RNA thermometers or RNATs) that modulate the translation of mRNAs. The analysis of RNATs in pathogenic bacteria has started to produce a comprehensive picture of the structures involved, and of the genes regulated by this mechanism. However, we are still not able to predict the functionality of putative RNATs predicted by bioinformatics methods, and there is not a global approach to measure the effect of these RNA structures in gene regulation during bacterial infections.
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Affiliation(s)
- María Victoria Grosso-Becera
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones, Biomédicas, Universidad Nacional Autónoma de México, Tercer Circuito Escolar, Apartado Postal 70228, DF, México
| | - Luis Servín-González
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones, Biomédicas, Universidad Nacional Autónoma de México, Tercer Circuito Escolar, Apartado Postal 70228, DF, México
| | - Gloria Soberón-Chávez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones, Biomédicas, Universidad Nacional Autónoma de México, Tercer Circuito Escolar, Apartado Postal 70228, DF, México.
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Abstract
PURPOSE OF REVIEW Shigella spp. are important etiologic agents of diarrhea worldwide. This review summarizes the recent findings on the epidemiology, diagnosis, virulence genes, and pathobiology of Shigella infection. RECENT FINDINGS Shigella flexneri and Shigella sonnei have been identified as the main serogroups circulating in developing and developed countries, respectively. However, a shift in the dominant species from S. flexneri to S. sonnei has been observed in countries that have experienced recent improvements in socioeconomic conditions. Despite the increasing usage of molecular methods in the diagnosis and virulence characterization of Shigella strains, researchers have been unsuccessful in finding a specific target gene for this bacillus. New research has demonstrated the role of proteins whose expressions are temperature-regulated, as well as genes involved in the processes of adhesion, invasion, dissemination, and inflammation, aiding in the clarification of the complex pathobiology of shigellosis. SUMMARY Knowledge about the epidemiologic profile of circulating serogroups of Shigella and an understanding of its pathobiology as well as of the virulence genes is important for the development of preventive measures and interventions to reduce the worldwide spread of shigellosis.
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