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Yasin N, Rahman H, Sarwar Y, Qasim M, Nisa I, Ikram A, Zaman G, Khan Z, Mirza MR, Khan N, Safi AUR, Alzahrani KJ. Salmonella Typhi from Northwest Pakistan: Molecular Strain Typing and Drug Resistance Signature. Microb Drug Resist 2021; 28:120-126. [PMID: 34357814 DOI: 10.1089/mdr.2020.0304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Objective: To determine the molecular strain typing and drug resistance pattern of Salmonella enterica serovar Typhi prevalent in Northwest Pakistan. Methodology: A total of 2,138 blood samples of suspected typhoid patients from Northwest Pakistan were collected followed by identification of Salmonella Typhi through biochemical, serological, and species-specific fliC-d gene amplification. These isolates were typed by variable-number tandem repeat (VNTR) profiling and investigated for drug resistance. Results: The overall prevalence of Salmonella Typhi was found to be 8.8% (n = 189). Thirty different VNTR strain types of Salmonella Typhi were detected and the most prevalent strain types were T1 and T4, whereas T27 was less prevalent strain. Among the 189 isolates 175 (92.5%) isolates were multidrug resistant, whereas 12 (5.8%) isolates were extensively drug resistant. Resistance to imipenem in Salmonella Typhi was not observed. Most of the isolates have genes encoding for resistance to fluoroquinolones, including gyrA (n = 164), gyrB (n = 160), parC (n = 164), parE (n = 160), ac(6')-ib-cr (n = 163), qnrS (n = 15), and qnrB (n = 3). Similarly, chloramphinicol (cat; n = 147), azithromycin (msrA; n = 3), and co-trimoxazole (dfrA7; n = 145) resistance genes were detected among Salmonella Typhi isolates. Conclusion: In this study, T1 and T4 type Salmonella Typhi strains were predominantly prevalent in Northwest Pakistan. Antibiotic resistance among Salmonella Typhi isolates were observed. Findings of the study would be helpful to devise an appropriate antibiotic policy to control the emergence of drug-resistant Salmonella Typhi in Pakistan.
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Affiliation(s)
- Nusrat Yasin
- Department of Microbiology, Kohat University of Science and Technology, Kohat, Pakistan
| | - Hazir Rahman
- Department of Microbiology, Kohat University of Science and Technology, Kohat, Pakistan.,Department of Microbiology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Yasra Sarwar
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Muhammad Qasim
- Department of Microbiology, Kohat University of Science and Technology, Kohat, Pakistan
| | - Iqbal Nisa
- Department of Microbiology, Kohat University of Science and Technology, Kohat, Pakistan
| | - Aamer Ikram
- Department of Pathology, Armed Forces Institute of Pathology, CMH, Rawalpindi, Pakistan.,National Institute of Health, Islamabad, Pakistan
| | - Gohar Zaman
- Department of Pathology, Armed Forces Institute of Pathology, CMH, Rawalpindi, Pakistan
| | - Zakir Khan
- Institute of Health Sciences, Curkvoa University Adana, Adana, Turkey
| | - Munazza Raza Mirza
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Niamat Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, Pakistan
| | - Aziz-Ur-Rehman Safi
- Department of Microbiology, Kohat University of Science and Technology, Kohat, Pakistan
| | - Khalid J Alzahrani
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia
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Liaquat S, Sarwar Y, Ali A, Haque A, Farooq M, Martinez-Ballesteros I, Laorden L, Garaizar J, Bikandi J. Virulotyping of Salmonella enterica serovar Typhi isolates from Pakistan: Absence of complete SPI-10 in Vi negative isolates. PLoS Negl Trop Dis 2018; 12:e0006839. [PMID: 30500817 PMCID: PMC6267989 DOI: 10.1371/journal.pntd.0006839] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 09/13/2018] [Indexed: 12/30/2022] Open
Abstract
The pathogenesis of Salmonella enterica serovar Typhi (S. Typhi), the cause of typhoid fever in humans, is mainly attributed to the acquisition of horizontally acquired DNA elements. Salmonella pathogenicity islands (SPIs) are indubitably the most important form of horizontally acquired DNA with respect to pathogenesis of this bacterium. The insertion or deletion of any of these transferrable SPIs may have impact on the virulence potential of S. Typhi. In this study, the virulence potential and genetic relatedness of 35 S. Typhi isolates, collected from 2004 to 2013 was determined by identification of SPI and non-SPI virulence factors through a combination of techniques including virulotyping, Whole Genome Sequencing (WGS), and Variable Number of Tandem Repeats (VNTR) profiling. In order to determine the virulence potential of local S. Typhi isolates, 56 virulence related genes were studied by PCR. These genes are located in the core as well as accessory genome (SPIs and plasmid). Major variations among studied virulence determinants were found in case of SPI-7 and SPI-10 associated genes. On the basis of presence of virulence related genes, the studied S. Typhi isolates from Pakistan were clustered into two virulotypes Vi-positive and Vi-negative. Interestingly, SPI-7 and SPI-10 were collectively absent or present in Vi-negative and Vi-positive strains, respectively. Two Vi-negative and 11 Vi-positive S. Typhi strains were also analyzed by whole genome sequencing (WGS) and their results supported the PCR results. Genetic diversity was tested by VNTR-based molecular typing. All 35 isolates were clustered into five groups. Overall, all Vi-negative isolates were placed in a single group (T5) whereas Vi-positive isolates were grouped into four types. Vi-negative and Vi-positive isolates were mutually exclusive. This is the first report on the comparative distribution of SPI and non-SPI related virulence genes in Vi-negative and Vi-positive S. Typhi isolates with an important finding that SPI-10 is absent in all Vi-negative isolates. The distribution of virulence factors in S. Typhi can vary in isolates from different geographical regions and can have significant effect on the disease control. In this study, we have checked the distribution of 56 reported virulence associated factors in 35 local isolates of S. Typhi to identify any variations that can help in designing effective control strategies for typhoid. We have identified four naturally occurring variants which are simultaneously lacking SPI-7 and SPI-10, two adjacently located pathogenicity islands on S. Typhi chromosome. These isolates are not producing Vi capsular antigen hence the Vi based vaccines will not be effective against them. These findings highlight the need to develop typhoid vaccines specifically effective in Pakistan.
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Affiliation(s)
- Sadia Liaquat
- Enteric Pathogen Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan affiliated with Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
- Departments of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Yasra Sarwar
- Enteric Pathogen Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan affiliated with Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
- * E-mail:
| | - Aamir Ali
- Enteric Pathogen Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan affiliated with Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - Abdul Haque
- Akhuwat Faisalabad Institute For Research In Science And Technology, Faisalabad, Pakistan
| | - Muhammad Farooq
- Enteric Pathogen Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan affiliated with Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - Ilargi Martinez-Ballesteros
- Department of Immunology, Microbiology and Parasitology, University of the Basque Country, (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Lorena Laorden
- Department of Immunology, Microbiology and Parasitology, University of the Basque Country, (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Javier Garaizar
- Department of Immunology, Microbiology and Parasitology, University of the Basque Country, (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Joseba Bikandi
- Department of Immunology, Microbiology and Parasitology, University of the Basque Country, (UPV/EHU), Vitoria-Gasteiz, Spain
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Sankar S, Kuppanan S, Nandagopal B, Sridharan G. Diversity of Salmonella enterica serovar Typhi strains collected from india using variable number tandem repeat (VNTR)-PCR analysis. Mol Diagn Ther 2014; 17:257-64. [PMID: 23615945 DOI: 10.1007/s40291-013-0034-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND Typhoid fever is endemic in India, and a seasonal increase of cases is observed annually. In spite of effective therapies and the availability of vaccines, morbidity is widespread owing to the circulation of multiple genetic variants, frequent migration of asymptomatic carriers, unhygienic food practices and the emergence of multidrug resistance and thus continues to be a major public health problem in developing countries, particularly in India. Classical methods of strain typing such as pulsed-field gel electrophoresis, ribotyping, random amplification of polymorphic DNA and amplified fragment length polymorphism are either laborious and technically complicated or less discriminatory. METHODS We investigated the molecular diversity of Indian strains of Salmonella enterica serovar Typhi (S. Typhi) isolated from humans from different parts of India to establish the molecular epidemiology of the organism using the variable number tandem repeat (VNTR)-PCR analysis. The electrophoretic band pattern was analysed using the GelCompar II software program. RESULTS Of the 94 strains tested for three VNTRs loci, 75 VNTR genotypes were obtained. Of the three VNTRs tested in this study, VNTR1 was amplified in all the strains except one and found to be predominant. VNTR2 was amplified only in 57 strains with a Simpson diversity index of 0.93 indicating the high variability of this region within the strains. VNTR3 was amplified in 90 strains. The discriminatory power of this typing tool has been greatly enhanced by this VNTR2 region as the other two regions could not discriminate strains significantly. In our study, about 55 % of the strains amplified all three VNTR regions and 39 % of the strains lacked the VNTR2 region. Among the three VNTR regions tested, the majority of the strains produced similar banding pattern for any two regions grouped into a cluster. The strains grouped as a genotype were from the same geographical location. Strains collected from each geographical region were also highly heterogeneous. CONCLUSION Such analysis is important to identify the genetic clones of the pathogen associated with sporadic infections and disease outbreak to identify the common source and implement public health measures.
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Affiliation(s)
- Sathish Sankar
- Sri Sakthi Amma Institute of Biomedical Research, Sri Narayani Hospital and Research Centre, Sripuram, Vellore 632 055, Tamil Nadu, India.
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