Genomic Insights into Antimicrobial Resistance in Salmonella typhi: A Bioinformatics-Based Surveillance Model from Public Datasets with Implications for Resource-Limited Settings
Article Sidebar
Page Numbers:
241-261
Published:
Jun 30, 2025
Digital Object Identifier:
10.58578/ajstm.v2i2.6485
Save this to:
Article Metrics:
Viewed: 297 times
Downloaded: 153 times
Article can trace at:
Author Fee:
Free Publication Fees for Foreign Researchers (USD 0.00)
Check for article on SINTA:
LYAS Publisher cordially invites qualified professionals to serve as Editors or Reviewers. Your expertise will make an important contribution to maintaining and strengthening the academic quality of our publications. Interested applicants are kindly requested to complete the application form at the following link: Editors & Reviewers
Connected Papers:
Please feel free to contact us if you need any further information about the submission process or if you have any additional questions.
Authors:
Ehizokhale Jude Usiabulu1, Abel Onolunosen Abhadionmhen2, Husseni Iduku3 
Copyright :
Authors retain copyright and grant the journal right of first publication.
Main Article Content
Abstract
Antimicrobial resistance (AMR) in Salmonella typhi represents an escalating global health challenge, particularly in regions with limited capacity for surveillance and treatment. This study investigates the genetic diversity and AMR mechanisms of S. typhi strains using publicly available genomic data. Twenty genomes were retrieved from GenBank and analyzed to identify resistance genes and genetic variations. The analysis focused on key AMR determinants, including blaTEM (beta-lactam resistance), qnrS (quinolone resistance), and aac(3)-I (aminoglycoside resistance), assessing their distribution across isolates. Phylogenetic analysis revealed substantial genetic diversity and indicated clonal dissemination of strains with similar resistance profiles. Mutation screening of gyrA and parC genes associated with fluoroquinolone resistance identified recurrent mutations, underscoring their role in resistance development. Bioinformatics tools such as BLAST+, Prokka, ResFinder, and iTOL were employed for sequence alignment, gene annotation, AMR gene detection, and phylogenetic reconstruction. The findings demonstrate the effectiveness of bioinformatics approaches in AMR surveillance, especially in resource-constrained settings where direct sample collection is often impractical. This study highlights the pervasive presence of AMR genes in S. typhi and reinforces the value of genomic surveillance in tracking resistance trends and informing targeted public health interventions. The research offers a novel and efficient model for AMR monitoring and provides foundational insights into resistance mechanisms in S. typhi, with implications for regions affected by AMR, such as Northeast Nigeria.
Downloads
Download data is not yet available.
Article Details
How to Cite
Usiabulu, E. J., Abhadionmhen, A. O., & Iduku, H. (2025). Genomic Insights into Antimicrobial Resistance in Salmonella typhi: A Bioinformatics-Based Surveillance Model from Public Datasets with Implications for Resource-Limited Settings. African Journal of Sciences and Traditional Medicine, 2(2), 241-261. https://doi.org/10.58578/ajstm.v2i2.6485
Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.
References
Adesegun, O. A., Adeyemi, O. O., Ehioghae, O., Rabor, D. F., Binuyo, T. O., Alafin, B. A., Nnagha, O. B., Idowu, A. O., & Osonuga, A. (2020). Current trends in the epidemiology and management of enteric fever in Africa: A literature review. Asian Pacific Journal of Tropical Medicine, 13(5), 204-213. https://doi.org/10.4103/1995-7645.283515
Adikwu, P., Ogbonna, I. O., Obande, G. A., Umeh, E. U., Iheukwumere, C. C., & Awodi, P. S. (2023). Chloramphenicol is re-emerging as an effective drug in the treatment of typhoid fever in Southern Benue state, Nigeria. Microbes and Infectious Diseases, 4(2), 601-610. https://doi.org/10.21608/mid.2022.126422.1257
Ajekiigbe, V. O., Ogieuhi, I. J., Odeniyi, T. A., Ogunleke, P. O., Olatunde, J. T., Babalola, A. V., Omoleke, A. A., Omitade, T. F., Olakanmi, D. E., Akingbola, A., & Anthony, C. S. (2025). Understanding Nigeria’s antibiotic resistance crisis among neonates and its future implications. Discover Public Health, 22(1), 28. https://doi.org/10.1186/s12982-025-00422-y
Alenazy, R. (2022). Antibiotic resistance in Salmonella: Targeting multidrug resistance by understanding efflux pumps, regulators, and the inhibitors. Journal of King Saud University-Science, 34(7), 102275. https://doi.org/10.1016/j.jksus.2022.102275
Argimón, S., Yeats, C. A., Goater, R. J., Abudahab, K., Taylor, B., Underwood, A., Sánchez-Busó, L., Wong, V. K., Dyson, Z. A., Nair, S., & Park, S. E. (2021). A global resource for genomic predictions of antimicrobial resistance and surveillance of Salmonella Typhi at Pathogenwatch. Nature Communications, 12(1), 2879. https://doi.org/10.1038/s41467-021-23091-2
Bianconi, I., Aschbacher, R., & Pagani, E. (2023). Current uses and future perspectives of genomic technologies in clinical microbiology. Antibiotics, 12(11), 1580. https://doi.org/10.3390/antibiotics12111580
Bello, A. B., Adesola, O. R., Idris, I., Scott, G. Y., Alfa, S., & Ajibade, F. A. (2024). Combatting extensively drug-resistant Salmonella: A global perspective on outbreaks, impacts, and control strategies. Pathogens and Global Health, 118(7-8), 559-573. https://doi.org/10.1080/20477724.2024.2416864
Bloom, D. E., & Cadarette, D. (2019). Infectious disease threats in the twenty-first century: Strengthening the global response. Frontiers in Immunology, 10, 549. https://doi.org/10.3389/fimmu.2019.00549
Bortolaia, V., Kaas, R. S., Ruppe, E., et al. (2020). ResFinder 4.0 for predictions of phenotypic antimicrobial resistance from whole genome sequencing data. Journal of Antimicrobial Chemotherapy, 75(12), 2785-2798. https://doi.org/10.1093/jac/dkaa345
Collineau, L., Boerlin, P., Carson, C. A., Chapman, B., Fazil, A., Hetman, B., McEwen, S. A., Parmley, E. J., Reid-Smith, R. J., Taboada, E. N., & Smith, B. A. (2019). Integrating whole-genome sequencing data into quantitative risk assessment of foodborne antimicrobial resistance: A review of opportunities and challenges. Frontiers in Microbiology, 10, 1107. https://doi.org/10.3389/fmicb.2019.01107
Coluzzi, C., Piscon, B., Dérozier, S., Chiapello, H., & Gal-Mor, O. (2025). Comparative genomics of Salmonella enterica serovars Paratyphi A, Typhi, and Typhimurium reveals distinct profiles of their pangenome, mobile genetic elements, antimicrobial resistance, and defense systems repertoire. Virulence, 16(1), 2504658. https://doi.org/10.1080/21505594.2025.2504658
Coque, T. M., Cantón, R., Pérez-Cobas, A. E., Fernández-de-Bobadilla, M. D., & Baquero, F. (2023). Antimicrobial resistance in the global health network: Known unknowns and challenges for efficient responses in the 21st century. Microorganisms, 11(4), 1050. https://doi.org/10.3390/microorganisms11041050
da Silva, K. E., Tanmoy, A. M., Pragasam, A. K., Iqbal, J., Sajib, M. S. I., Mutreja, A., Veeraraghavan, B., Tamrakar, D., Qamar, F. N., Dougan, G., & Bogoch, I. (2022). The international and intercontinental spread and expansion of antimicrobial-resistant Salmonella Typhi: A genomic epidemiology study. The Lancet Microbe, 3(8), e567-e577. https://doi.org/10.1016/S2666-5247(22)00093-3
Dadgostar, P. (2019). Antimicrobial resistance: Implications and costs. Infection and Drug Resistance, 12, 3903-3910. https://doi.org/10.2147/IDR.S234610
Davin-Regli, A., Pages, J. M., & Ferrand, A. (2021). Clinical status of efflux resistance mechanisms in gram-negative bacteria. Antibiotics, 10(9), 1117. https://doi.org/10.3390/antibiotics10091117
Djordjevic, S. P., Jarocki, V. M., Seemann, T., Cummins, M. L., Watt, A. E., Drigo, B., Wyrsch, E. R., Reid, C. J., Donner, E., & Howden, B. P. (2024). Genomic surveillance for antimicrobial resistance—a One Health perspective. Nature Reviews Genetics, 25(2), 142-157. https://doi.org/10.1038/s41576-023-00649-y
Dyson, Z. A., Ashton, P. M., Khanam, F., Chunga, A., Shakya, M., Meiring, J., Tonks, S., Karkey, A., Msefula, C., Clemens, J. D., & Dunstan, S. J. (2023). Genomic epidemiology and antimicrobial resistance transmission of Salmonella Typhi and Paratyphi A at three urban sites in Africa and Asia. medRxiv, 2023-03. https://doi.org/10.1101/2023.03.11.23286741
El-Maradny, Y. A., Nortey, M. A., Hakayuwa, C. M., Anyamene, E. L., Mary, J., Engmann, S. T., Tsikata, C. Y., Ahmed, D. A., Onyeaghala, C., Heniedy, A. M., & Gesaka, S. R. (2025). The impact of socioeconomic disparities, climate factors, and antimicrobial stewardship on antimicrobial resistance in Africa. Discover Public Health, 22(1), 1-21. https://doi.org/10.1186/s12982-025-00631-7
Fatima, S., Ishaq, Z., Irfan, M., AlAsmari, A. F., Achakzai, J. K., Zaheer, T., Ali, A., & Akbar, A. (2023). Whole-genome sequencing of multidrug resistance Salmonella Typhi clinical strains isolated from Balochistan, Pakistan. Frontiers in Public Health, 11, 1151805. https://doi.org/10.3389/fpubh.2023.1151805
Feng, Y., Pan, H., Zheng, B., Li, F., Teng, L., Jiang, Z., Feng, M., Zhou, X., Peng, X., Xu, X., & Wang, H. (2023). An integrated nationwide genomics study reveals transmission modes of typhoid fever in China. MBio, 14(5), e01333-23. https://doi.org/10.1128/mbio.01333-23
Hendriksen, R. S., Bortolaia, V., Tate, H., Tyson, G. H., Aarestrup, F. M., & McDermott, P. F. (2019). Using genomics to track global antimicrobial resistance. Frontiers in Public Health, 7, 242. https://doi.org/10.3389/fpubh.2019.00242
Hurtado, R., Barh, D., Weimer, B. C., Viana, M. V. C., Profeta, R., Sousa, T. J., Aburjaile, F. F., Quino, W., Souza, R. P., Mestanza, O., & Gavilán, R. G. (2022). WGS-based lineage and antimicrobial resistance pattern of Salmonella Typhimurium isolated during 2000–2017 in Peru. Antibiotics, 11(9), 1170. https://doi.org/10.3390/microorganisms9102155
Ingle, D. J., Nair, S., Hartman, H., Ashton, P. M., Dyson, Z. A., Day, M., Freedman, J., Chattaway, M. A., Holt, K. E., & Dallman, T. J. (2019). Informal genomic surveillance of regional distribution of Salmonella Typhi genotypes and antimicrobial resistance via returning travellers. PLOS Neglected Tropical Diseases, 13(9), e0007620. https://doi.org/10.1371/journal.pntd.0007620
Katiyar, A., Sharma, P., Dahiya, S., Singh, H., Kapil, A., & Kaur, P. (2020). Genomic profiling of antimicrobial resistance genes in clinical isolates of Salmonella Typhi from patients infected with Typhoid fever in India. Scientific Reports, 10(1), 8299. https://doi.org/10.1038/s41598-020-64934-0
Kavai, S. M., Mutai, W. C., Mbae, C., Kering, K., Ng’etich, R., Muturi, P., Kigen, C., Mugo, M., Imoli, D., Wairimu, C., & Kariuki, S. (2025). Genomic insights into the role of Salmonella Typhi carriers in antimicrobial resistance and typhoid transmission in Urban Kenya. PLOS One, 20(5), e0321879. https://doi.org/10.1371/journal.pone.0321879
Khan, M., & Shamim, S. (2022). Understanding the mechanism of antimicrobial resistance and pathogenesis of Salmonella enterica serovar Typhi. Microorganisms, 10(10), 2006. https://doi.org/10.3390/microorganisms10102006
Kim, C. L., Cruz Espinoza, L. M., Vannice, K. S., Tadesse, B. T., Owusu-Dabo, E., Rakotozandrindrainy, R., Jani, I. V., Teferi, M., Bassiahi Soura, A., Lunguya, O., & Steele, A. D. (2022). The burden of typhoid fever in sub-Saharan Africa: A perspective. Research and Reports in Tropical Medicine, 13, 1-9. https://doi.org/10.2147/RRTM.S282461
Kumar, A., & Kumar, A. (2021). Antibiotic resistome of Salmonella typhi: Molecular determinants for the emergence of drug resistance. Frontiers of Medicine, 15(5), 693-703. https://doi.org/10.1007/s11684-020-0777-6
Kumar, S., Stecher, G., & Tamura, K. (2018). MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, 33(7), 1870-1874. https://doi.org/10.1093/molbev/msw054
Letunic, I., & Bork, P. (2021). iTOL v6: Interactive Tree of Life. Nucleic Acids Research, 49(W1), W293-W296. https://doi.org/10.1093/nar/gkab300
Lima, N. C. B., Tanmoy, A. M., Westeel, E., De Almeida, L. G. P., Rajoharison, A., Islam, M., Endtz, H. P., Saha, S. K., De Vasconcelos, A. T. R., & Komurian-Pradel, F. (2019). Analysis of isolates from Bangladesh highlights multiple ways to carry resistance genes in Salmonella Typhi. BMC Genomics, 20, 1-15. https://doi.org/10.1186/s12864-019-5916-6
Mancuso, G., Midiri, A., Gerace, E., & Biondo, C. (2021). Bacterial antibiotic resistance: The most critical pathogens. Pathogens, 10(10), 1310. https://doi.org/10.3390/pathogens10101310
Musa, K., Okoliegbe, I., Abdalaziz, T., Aboushady, A. T., Stelling, J., & Gould, I. M. (2023). Laboratory surveillance, quality management, and its role in addressing antimicrobial resistance in Africa: A narrative review. Antibiotics, 12(8), 1313. https://doi.org/10.3390/antibiotics12081313
Nafea, A. M., Wang, Y., Wang, D., Salama, A. M., Aziz, M. A., Xu, S., & Tong, Y. (2024). Application of next-generation sequencing to identify different pathogens. Frontiers in Microbiology, 14, 1329330. https://doi.org/10.3389/fmicb.2023.1329330
Nathania, I., Nainggolan, I. M., Yasmon, A., Nusatia, A. C. M., Tjoa, E., Gunardi, W. D., & Moehario, L. H. (2022). Hotspots sequences of gyr A, gyr B, par C, and par E genes encoded for fluoroquinolones resistance from local Salmonella Typhi strains in Jakarta. BMC Microbiology, 22(1), 250. https://doi.org/10.1186/s12866-022-02666-z
Ndagi, U., Falaki, A. A., Abdullahi, M., Lawal, M. M., & Soliman, M. E. (2020). Antibiotic resistance: Bioinformatics-based understanding as a functional strategy for drug design. RSC Advances, 10(31), 18451-18468. https://doi.org/10.1039/D0RA01484B
Nuanmuang, N., Leekitcharoenphon, P., Njage, P. M. K., Thorn, A. V., & Aarestrup, F. M. (2024). The dynamics of bla TEM resistance genes in Salmonella Typhi. Scientific Reports, 14(1), 24311. https://doi.org/10.1038/s41598-024-74321-8
Ostrer, L., Khodursky, R. F., Johnson, J. R., Hiasa, H., & Khodursky, A. (2019). Analysis of mutational patterns in quinolone resistance-determining regions of GyrA and ParC of clinical isolates. International Journal of Antimicrobial Agents, 53(3), 318-324. https://doi.org/10.1016/j.ijantimicag.2018.12.004
R Core Team. (2020). R: A language and environment for statistical computing. R Foundation for Statistical Computing. https://www.R-project.org
Rahman, S. I. A., Dyson, Z. A., Klemm, E. J., Khanam, F., Holt, K. E., Chowdhury, E. K., Dougan, G., & Qadri, F. (2020). Population structure and antimicrobial resistance patterns of Salmonella Typhi isolates in urban Dhaka, Bangladesh from 2004 to 2016. PLOS Neglected Tropical Diseases, 14(2), e0008036. https://doi.org/10.1371/journal.pntd.0008036
Salam, M. A., Al-Amin, M. Y., Salam, M. T., Pawar, J. S., Akhter, N., Rabaan, A. A., & Alqumber, M. A. (2023, January). Antimicrobial resistance: A growing serious threat for global public health. Healthcare, 11(13), 1946. https://doi.org/10.3390/healthcare11131946
Samantray, D., Tanwar, A. S., Murali, T. S., Brand, A., Satyamoorthy, K., & Paul, B. (2023). A comprehensive bioinformatics resource guide for genome-based antimicrobial resistance studies. OMICS: A Journal of Integrative Biology, 27(10), 445-460. https://doi.org/10.1089/omi.2023.0140
Sayers, E. W., Cavanaugh, M., Clark, K., Ostell, J., Pruitt, K. D., & Karsch-Mizrachi, I. (2020). GenBank. Nucleic Acids Research, 48(D1), D84-D86. https://doi.org/10.1093/nar/gkz956
Seemann, T. (2014). Prokka: Rapid prokaryotic genome annotation. Bioinformatics, 30(14), 2068-2069. https://doi.org/10.1093/bioinformatics/btu153
Shepherd, M. J., Fu, T., Harrington, N. E., Kottara, A., Cagney, K., Chalmers, J. D., Paterson, S., Fothergill, J. L., & Brockhurst, M. A. (2024). Ecological and evolutionary mechanisms driving within-patient emergence of antimicrobial resistance. Nature Reviews Microbiology, 22(10), 650-665. https://doi.org/10.1038/s41579-024-01041-1
Struelens, M. J., Ludden, C., Werner, G., Sintchenko, V., Jokelainen, P., & Ip, M. (2024). Real-time genomic surveillance for enhanced control of infectious diseases and antimicrobial resistance. Frontiers in Science, 2, 1298248. https://doi.org/10.3389/fsci.2024.1298248
Tang, K. W. K., Millar, B. C., & Moore, J. E. (2023). Antimicrobial resistance (AMR). British Journal of Biomedical Science, 80, 11387. https://doi.org/10.3389/bjbs.2023.11387
Thakur, V., Uniyal, A., & Tiwari, V. (2021). A comprehensive review on pharmacology of efflux pumps and their inhibitors in antibiotic resistance. European Journal of Pharmacology, 903, 174151. https://doi.org/10.1016/j.ejphar.2021.174151
Usiabulu, E. J., Abhadionmhen, O. A., & Iduku, H. (2025). ML-powered privacy preservation in biomedical data sharing. African Journal of Medicine, Surgery and Public Health Research, 2(3), 389-407. https://doi.org/10.58578/AJMSPHR.v2i3.6143
Van Camp, P. J., Haslam, D. B., & Porollo, A. (2020). Bioinformatics approaches to the understanding of molecular mechanisms in antimicrobial resistance. International Journal of Molecular Sciences, 21(4), 1363. https://doi.org/10.3390/ijms21041363
Waskom, M. L., et al. (2020). Seaborn: Statistical data visualization. Journal of Open Source Software, 5(49), 3021. https://doi.org/10.21105/joss.03021
Yusof, N. Y., Norazzman, N. I. I., Zaidi, N. F. M., Azlan, M. M., Ghazali, B., Najib, M. A., Malik, A. H. A., Halim, M. A. H. A., Sanusi, M. N. S. M., Zainal, A. A., & Aziah, I. (2022). Prevalence of antimicrobial resistance genes in Salmonella Typhi: A systematic review and meta-analysis. Tropical Medicine and Infectious Disease, 7(10), 271. https://doi.org/10.3390/tropicalmed7100271
Adikwu, P., Ogbonna, I. O., Obande, G. A., Umeh, E. U., Iheukwumere, C. C., & Awodi, P. S. (2023). Chloramphenicol is re-emerging as an effective drug in the treatment of typhoid fever in Southern Benue state, Nigeria. Microbes and Infectious Diseases, 4(2), 601-610. https://doi.org/10.21608/mid.2022.126422.1257
Ajekiigbe, V. O., Ogieuhi, I. J., Odeniyi, T. A., Ogunleke, P. O., Olatunde, J. T., Babalola, A. V., Omoleke, A. A., Omitade, T. F., Olakanmi, D. E., Akingbola, A., & Anthony, C. S. (2025). Understanding Nigeria’s antibiotic resistance crisis among neonates and its future implications. Discover Public Health, 22(1), 28. https://doi.org/10.1186/s12982-025-00422-y
Alenazy, R. (2022). Antibiotic resistance in Salmonella: Targeting multidrug resistance by understanding efflux pumps, regulators, and the inhibitors. Journal of King Saud University-Science, 34(7), 102275. https://doi.org/10.1016/j.jksus.2022.102275
Argimón, S., Yeats, C. A., Goater, R. J., Abudahab, K., Taylor, B., Underwood, A., Sánchez-Busó, L., Wong, V. K., Dyson, Z. A., Nair, S., & Park, S. E. (2021). A global resource for genomic predictions of antimicrobial resistance and surveillance of Salmonella Typhi at Pathogenwatch. Nature Communications, 12(1), 2879. https://doi.org/10.1038/s41467-021-23091-2
Bianconi, I., Aschbacher, R., & Pagani, E. (2023). Current uses and future perspectives of genomic technologies in clinical microbiology. Antibiotics, 12(11), 1580. https://doi.org/10.3390/antibiotics12111580
Bello, A. B., Adesola, O. R., Idris, I., Scott, G. Y., Alfa, S., & Ajibade, F. A. (2024). Combatting extensively drug-resistant Salmonella: A global perspective on outbreaks, impacts, and control strategies. Pathogens and Global Health, 118(7-8), 559-573. https://doi.org/10.1080/20477724.2024.2416864
Bloom, D. E., & Cadarette, D. (2019). Infectious disease threats in the twenty-first century: Strengthening the global response. Frontiers in Immunology, 10, 549. https://doi.org/10.3389/fimmu.2019.00549
Bortolaia, V., Kaas, R. S., Ruppe, E., et al. (2020). ResFinder 4.0 for predictions of phenotypic antimicrobial resistance from whole genome sequencing data. Journal of Antimicrobial Chemotherapy, 75(12), 2785-2798. https://doi.org/10.1093/jac/dkaa345
Collineau, L., Boerlin, P., Carson, C. A., Chapman, B., Fazil, A., Hetman, B., McEwen, S. A., Parmley, E. J., Reid-Smith, R. J., Taboada, E. N., & Smith, B. A. (2019). Integrating whole-genome sequencing data into quantitative risk assessment of foodborne antimicrobial resistance: A review of opportunities and challenges. Frontiers in Microbiology, 10, 1107. https://doi.org/10.3389/fmicb.2019.01107
Coluzzi, C., Piscon, B., Dérozier, S., Chiapello, H., & Gal-Mor, O. (2025). Comparative genomics of Salmonella enterica serovars Paratyphi A, Typhi, and Typhimurium reveals distinct profiles of their pangenome, mobile genetic elements, antimicrobial resistance, and defense systems repertoire. Virulence, 16(1), 2504658. https://doi.org/10.1080/21505594.2025.2504658
Coque, T. M., Cantón, R., Pérez-Cobas, A. E., Fernández-de-Bobadilla, M. D., & Baquero, F. (2023). Antimicrobial resistance in the global health network: Known unknowns and challenges for efficient responses in the 21st century. Microorganisms, 11(4), 1050. https://doi.org/10.3390/microorganisms11041050
da Silva, K. E., Tanmoy, A. M., Pragasam, A. K., Iqbal, J., Sajib, M. S. I., Mutreja, A., Veeraraghavan, B., Tamrakar, D., Qamar, F. N., Dougan, G., & Bogoch, I. (2022). The international and intercontinental spread and expansion of antimicrobial-resistant Salmonella Typhi: A genomic epidemiology study. The Lancet Microbe, 3(8), e567-e577. https://doi.org/10.1016/S2666-5247(22)00093-3
Dadgostar, P. (2019). Antimicrobial resistance: Implications and costs. Infection and Drug Resistance, 12, 3903-3910. https://doi.org/10.2147/IDR.S234610
Davin-Regli, A., Pages, J. M., & Ferrand, A. (2021). Clinical status of efflux resistance mechanisms in gram-negative bacteria. Antibiotics, 10(9), 1117. https://doi.org/10.3390/antibiotics10091117
Djordjevic, S. P., Jarocki, V. M., Seemann, T., Cummins, M. L., Watt, A. E., Drigo, B., Wyrsch, E. R., Reid, C. J., Donner, E., & Howden, B. P. (2024). Genomic surveillance for antimicrobial resistance—a One Health perspective. Nature Reviews Genetics, 25(2), 142-157. https://doi.org/10.1038/s41576-023-00649-y
Dyson, Z. A., Ashton, P. M., Khanam, F., Chunga, A., Shakya, M., Meiring, J., Tonks, S., Karkey, A., Msefula, C., Clemens, J. D., & Dunstan, S. J. (2023). Genomic epidemiology and antimicrobial resistance transmission of Salmonella Typhi and Paratyphi A at three urban sites in Africa and Asia. medRxiv, 2023-03. https://doi.org/10.1101/2023.03.11.23286741
El-Maradny, Y. A., Nortey, M. A., Hakayuwa, C. M., Anyamene, E. L., Mary, J., Engmann, S. T., Tsikata, C. Y., Ahmed, D. A., Onyeaghala, C., Heniedy, A. M., & Gesaka, S. R. (2025). The impact of socioeconomic disparities, climate factors, and antimicrobial stewardship on antimicrobial resistance in Africa. Discover Public Health, 22(1), 1-21. https://doi.org/10.1186/s12982-025-00631-7
Fatima, S., Ishaq, Z., Irfan, M., AlAsmari, A. F., Achakzai, J. K., Zaheer, T., Ali, A., & Akbar, A. (2023). Whole-genome sequencing of multidrug resistance Salmonella Typhi clinical strains isolated from Balochistan, Pakistan. Frontiers in Public Health, 11, 1151805. https://doi.org/10.3389/fpubh.2023.1151805
Feng, Y., Pan, H., Zheng, B., Li, F., Teng, L., Jiang, Z., Feng, M., Zhou, X., Peng, X., Xu, X., & Wang, H. (2023). An integrated nationwide genomics study reveals transmission modes of typhoid fever in China. MBio, 14(5), e01333-23. https://doi.org/10.1128/mbio.01333-23
Hendriksen, R. S., Bortolaia, V., Tate, H., Tyson, G. H., Aarestrup, F. M., & McDermott, P. F. (2019). Using genomics to track global antimicrobial resistance. Frontiers in Public Health, 7, 242. https://doi.org/10.3389/fpubh.2019.00242
Hurtado, R., Barh, D., Weimer, B. C., Viana, M. V. C., Profeta, R., Sousa, T. J., Aburjaile, F. F., Quino, W., Souza, R. P., Mestanza, O., & Gavilán, R. G. (2022). WGS-based lineage and antimicrobial resistance pattern of Salmonella Typhimurium isolated during 2000–2017 in Peru. Antibiotics, 11(9), 1170. https://doi.org/10.3390/microorganisms9102155
Ingle, D. J., Nair, S., Hartman, H., Ashton, P. M., Dyson, Z. A., Day, M., Freedman, J., Chattaway, M. A., Holt, K. E., & Dallman, T. J. (2019). Informal genomic surveillance of regional distribution of Salmonella Typhi genotypes and antimicrobial resistance via returning travellers. PLOS Neglected Tropical Diseases, 13(9), e0007620. https://doi.org/10.1371/journal.pntd.0007620
Katiyar, A., Sharma, P., Dahiya, S., Singh, H., Kapil, A., & Kaur, P. (2020). Genomic profiling of antimicrobial resistance genes in clinical isolates of Salmonella Typhi from patients infected with Typhoid fever in India. Scientific Reports, 10(1), 8299. https://doi.org/10.1038/s41598-020-64934-0
Kavai, S. M., Mutai, W. C., Mbae, C., Kering, K., Ng’etich, R., Muturi, P., Kigen, C., Mugo, M., Imoli, D., Wairimu, C., & Kariuki, S. (2025). Genomic insights into the role of Salmonella Typhi carriers in antimicrobial resistance and typhoid transmission in Urban Kenya. PLOS One, 20(5), e0321879. https://doi.org/10.1371/journal.pone.0321879
Khan, M., & Shamim, S. (2022). Understanding the mechanism of antimicrobial resistance and pathogenesis of Salmonella enterica serovar Typhi. Microorganisms, 10(10), 2006. https://doi.org/10.3390/microorganisms10102006
Kim, C. L., Cruz Espinoza, L. M., Vannice, K. S., Tadesse, B. T., Owusu-Dabo, E., Rakotozandrindrainy, R., Jani, I. V., Teferi, M., Bassiahi Soura, A., Lunguya, O., & Steele, A. D. (2022). The burden of typhoid fever in sub-Saharan Africa: A perspective. Research and Reports in Tropical Medicine, 13, 1-9. https://doi.org/10.2147/RRTM.S282461
Kumar, A., & Kumar, A. (2021). Antibiotic resistome of Salmonella typhi: Molecular determinants for the emergence of drug resistance. Frontiers of Medicine, 15(5), 693-703. https://doi.org/10.1007/s11684-020-0777-6
Kumar, S., Stecher, G., & Tamura, K. (2018). MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, 33(7), 1870-1874. https://doi.org/10.1093/molbev/msw054
Letunic, I., & Bork, P. (2021). iTOL v6: Interactive Tree of Life. Nucleic Acids Research, 49(W1), W293-W296. https://doi.org/10.1093/nar/gkab300
Lima, N. C. B., Tanmoy, A. M., Westeel, E., De Almeida, L. G. P., Rajoharison, A., Islam, M., Endtz, H. P., Saha, S. K., De Vasconcelos, A. T. R., & Komurian-Pradel, F. (2019). Analysis of isolates from Bangladesh highlights multiple ways to carry resistance genes in Salmonella Typhi. BMC Genomics, 20, 1-15. https://doi.org/10.1186/s12864-019-5916-6
Mancuso, G., Midiri, A., Gerace, E., & Biondo, C. (2021). Bacterial antibiotic resistance: The most critical pathogens. Pathogens, 10(10), 1310. https://doi.org/10.3390/pathogens10101310
Musa, K., Okoliegbe, I., Abdalaziz, T., Aboushady, A. T., Stelling, J., & Gould, I. M. (2023). Laboratory surveillance, quality management, and its role in addressing antimicrobial resistance in Africa: A narrative review. Antibiotics, 12(8), 1313. https://doi.org/10.3390/antibiotics12081313
Nafea, A. M., Wang, Y., Wang, D., Salama, A. M., Aziz, M. A., Xu, S., & Tong, Y. (2024). Application of next-generation sequencing to identify different pathogens. Frontiers in Microbiology, 14, 1329330. https://doi.org/10.3389/fmicb.2023.1329330
Nathania, I., Nainggolan, I. M., Yasmon, A., Nusatia, A. C. M., Tjoa, E., Gunardi, W. D., & Moehario, L. H. (2022). Hotspots sequences of gyr A, gyr B, par C, and par E genes encoded for fluoroquinolones resistance from local Salmonella Typhi strains in Jakarta. BMC Microbiology, 22(1), 250. https://doi.org/10.1186/s12866-022-02666-z
Ndagi, U., Falaki, A. A., Abdullahi, M., Lawal, M. M., & Soliman, M. E. (2020). Antibiotic resistance: Bioinformatics-based understanding as a functional strategy for drug design. RSC Advances, 10(31), 18451-18468. https://doi.org/10.1039/D0RA01484B
Nuanmuang, N., Leekitcharoenphon, P., Njage, P. M. K., Thorn, A. V., & Aarestrup, F. M. (2024). The dynamics of bla TEM resistance genes in Salmonella Typhi. Scientific Reports, 14(1), 24311. https://doi.org/10.1038/s41598-024-74321-8
Ostrer, L., Khodursky, R. F., Johnson, J. R., Hiasa, H., & Khodursky, A. (2019). Analysis of mutational patterns in quinolone resistance-determining regions of GyrA and ParC of clinical isolates. International Journal of Antimicrobial Agents, 53(3), 318-324. https://doi.org/10.1016/j.ijantimicag.2018.12.004
R Core Team. (2020). R: A language and environment for statistical computing. R Foundation for Statistical Computing. https://www.R-project.org
Rahman, S. I. A., Dyson, Z. A., Klemm, E. J., Khanam, F., Holt, K. E., Chowdhury, E. K., Dougan, G., & Qadri, F. (2020). Population structure and antimicrobial resistance patterns of Salmonella Typhi isolates in urban Dhaka, Bangladesh from 2004 to 2016. PLOS Neglected Tropical Diseases, 14(2), e0008036. https://doi.org/10.1371/journal.pntd.0008036
Salam, M. A., Al-Amin, M. Y., Salam, M. T., Pawar, J. S., Akhter, N., Rabaan, A. A., & Alqumber, M. A. (2023, January). Antimicrobial resistance: A growing serious threat for global public health. Healthcare, 11(13), 1946. https://doi.org/10.3390/healthcare11131946
Samantray, D., Tanwar, A. S., Murali, T. S., Brand, A., Satyamoorthy, K., & Paul, B. (2023). A comprehensive bioinformatics resource guide for genome-based antimicrobial resistance studies. OMICS: A Journal of Integrative Biology, 27(10), 445-460. https://doi.org/10.1089/omi.2023.0140
Sayers, E. W., Cavanaugh, M., Clark, K., Ostell, J., Pruitt, K. D., & Karsch-Mizrachi, I. (2020). GenBank. Nucleic Acids Research, 48(D1), D84-D86. https://doi.org/10.1093/nar/gkz956
Seemann, T. (2014). Prokka: Rapid prokaryotic genome annotation. Bioinformatics, 30(14), 2068-2069. https://doi.org/10.1093/bioinformatics/btu153
Shepherd, M. J., Fu, T., Harrington, N. E., Kottara, A., Cagney, K., Chalmers, J. D., Paterson, S., Fothergill, J. L., & Brockhurst, M. A. (2024). Ecological and evolutionary mechanisms driving within-patient emergence of antimicrobial resistance. Nature Reviews Microbiology, 22(10), 650-665. https://doi.org/10.1038/s41579-024-01041-1
Struelens, M. J., Ludden, C., Werner, G., Sintchenko, V., Jokelainen, P., & Ip, M. (2024). Real-time genomic surveillance for enhanced control of infectious diseases and antimicrobial resistance. Frontiers in Science, 2, 1298248. https://doi.org/10.3389/fsci.2024.1298248
Tang, K. W. K., Millar, B. C., & Moore, J. E. (2023). Antimicrobial resistance (AMR). British Journal of Biomedical Science, 80, 11387. https://doi.org/10.3389/bjbs.2023.11387
Thakur, V., Uniyal, A., & Tiwari, V. (2021). A comprehensive review on pharmacology of efflux pumps and their inhibitors in antibiotic resistance. European Journal of Pharmacology, 903, 174151. https://doi.org/10.1016/j.ejphar.2021.174151
Usiabulu, E. J., Abhadionmhen, O. A., & Iduku, H. (2025). ML-powered privacy preservation in biomedical data sharing. African Journal of Medicine, Surgery and Public Health Research, 2(3), 389-407. https://doi.org/10.58578/AJMSPHR.v2i3.6143
Van Camp, P. J., Haslam, D. B., & Porollo, A. (2020). Bioinformatics approaches to the understanding of molecular mechanisms in antimicrobial resistance. International Journal of Molecular Sciences, 21(4), 1363. https://doi.org/10.3390/ijms21041363
Waskom, M. L., et al. (2020). Seaborn: Statistical data visualization. Journal of Open Source Software, 5(49), 3021. https://doi.org/10.21105/joss.03021
Yusof, N. Y., Norazzman, N. I. I., Zaidi, N. F. M., Azlan, M. M., Ghazali, B., Najib, M. A., Malik, A. H. A., Halim, M. A. H. A., Sanusi, M. N. S. M., Zainal, A. A., & Aziah, I. (2022). Prevalence of antimicrobial resistance genes in Salmonella Typhi: A systematic review and meta-analysis. Tropical Medicine and Infectious Disease, 7(10), 271. https://doi.org/10.3390/tropicalmed7100271