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Genomic characterization of invasive typhoidal and non-typhoidal Salmonella in southwestern Nigeria. 2022

Odion O Ikhimiukor, and Anderson O Oaikhena, and Ayorinde O Afolayan, and Abayomi Fadeyi, and Aderemi Kehinde, and Veronica O Ogunleye, and Aaron O Aboderin, and Oyinlola O Oduyebo, and Charles J Elikwu, and Erkison Ewomazino Odih, and Ifeoluwa Komolafe, and Silvia Argimón, and Abiodun Egwuenu, and Ini Adebiyi, and Oluwadamilola A Sadare, and Tochi Okwor, and Mihir Kekre, and Anthony Underwood, and Chikwe Ihekweazu, and David M Aanensen, and Iruka N Okeke
Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria.

Salmonellosis causes significant morbidity and mortality in Africa. Information on lineages of invasive Salmonella circulating in Nigeria is sparse. Salmonella enterica isolated from blood (n = 60) and cerebrospinal fluid (CSF, n = 3) between 2016 and 2020 from five tertiary hospitals in southwest Nigeria were antimicrobial susceptibility-tested and Illumina-sequenced. Genomes were analysed using publicly-available bioinformatic tools. Isolates and sequence types (STs) from blood were S. Typhi [ST1, n = 1 and ST2, n = 43] and invasive non-typhoidal Salmonella (iNTS) (S. Enteritidis [ST11, n = 7], S. Durham [ST10, n = 2], S. Rissen [ST8756, n = 2], S. Chester [ST2063, n = 1], S. Dublin [ST10, n = 1], S. Infantis [ST603, n = 1], S. Telelkebir [ST8757, n = 1] and S. Typhimurium [ST313, n = 1]). S. Typhi ST2 (n = 2) and S. Adabraka ST8757 (n = 1) were recovered from CSF. Most S. Typhi belonged to genotype 3.1.1 (n = 44), carried an IncY plasmid, had several antibiotic resistance genes (ARGs) including blaTEM-1 (n = 38), aph(6)-Id (n = 32), tet(A) (n = 33), sul2 (n = 32), dfrA14 (n = 30) as well as quinolone resistance-conferring gyrA_S83Y single-nucleotide polymorphisms (n = 37). All S. Enteritidis harboured aph(3")-Ib, blaTEM-1, catA1, dfrA7, sul1, sul2, tet(B) genes, and a single ARG, qnrB19, was detected in S. Telelkebir. Typhoidal toxins cdtB, pltA and pltB were detected in S. Typhi, Rissen, Chester, and Telelkebir. Most invasive salmonelloses in southwest Nigeria are vaccine-preventable infections due to multidrug-resistant, West African dominant S. Typhi lineage 3.1.1. Invasive NTS serovars, including some harbouring typhoidal toxin or resistance genes, represented a third of the isolates emphasizing the need for better diagnosis and surveillance.

UI MeSH Term Description Entries
D008826 Microbial Sensitivity Tests Any tests that demonstrate the relative efficacy of different chemotherapeutic agents against specific microorganisms (i.e., bacteria, fungi, viruses). Bacterial Sensitivity Tests,Drug Sensitivity Assay, Microbial,Minimum Inhibitory Concentration,Antibacterial Susceptibility Breakpoint Determination,Antibiogram,Antimicrobial Susceptibility Breakpoint Determination,Bacterial Sensitivity Test,Breakpoint Determination, Antibacterial Susceptibility,Breakpoint Determination, Antimicrobial Susceptibility,Fungal Drug Sensitivity Tests,Fungus Drug Sensitivity Tests,Sensitivity Test, Bacterial,Sensitivity Tests, Bacterial,Test, Bacterial Sensitivity,Tests, Bacterial Sensitivity,Viral Drug Sensitivity Tests,Virus Drug Sensitivity Tests,Antibiograms,Concentration, Minimum Inhibitory,Concentrations, Minimum Inhibitory,Inhibitory Concentration, Minimum,Inhibitory Concentrations, Minimum,Microbial Sensitivity Test,Minimum Inhibitory Concentrations,Sensitivity Test, Microbial,Sensitivity Tests, Microbial,Test, Microbial Sensitivity,Tests, Microbial Sensitivity
D009549 Nigeria A republic in western Africa, south of NIGER between BENIN and CAMEROON. Its capital is Abuja. Federal Republic of Nigeria
D006801 Humans Members of the species Homo sapiens. Homo sapiens,Man (Taxonomy),Human,Man, Modern,Modern Man
D000072179 Interleukin-1 Receptor-Like 1 Protein A receptor for INTERLEUKIN-33 that is related structurally to the interleukin-1 receptor. It contains three extracellular IMMUNOGLOBULIN-LIKE DOMAIN regions and associates with INTERLEUKIN-1 RECEPTOR ACCESSORY PROTEIN upon binding IL-33 to initiate signaling. It may function in the response of HELPER T CELLS to INFLAMMATION. IL1RL1 Protein,Interleukin 1 Receptor-Related Protein,Interleukin-33 Receptor,Interleukin 1 Receptor Like 1 Protein,Interleukin 1 Receptor Related Protein,Interleukin 33 Receptor,Receptor, Interleukin-33
D000900 Anti-Bacterial Agents Substances that inhibit the growth or reproduction of BACTERIA. Anti-Bacterial Agent,Anti-Bacterial Compound,Anti-Mycobacterial Agent,Antibacterial Agent,Antibiotics,Antimycobacterial Agent,Bacteriocidal Agent,Bacteriocide,Anti-Bacterial Compounds,Anti-Mycobacterial Agents,Antibacterial Agents,Antibiotic,Antimycobacterial Agents,Bacteriocidal Agents,Bacteriocides,Agent, Anti-Bacterial,Agent, Anti-Mycobacterial,Agent, Antibacterial,Agent, Antimycobacterial,Agent, Bacteriocidal,Agents, Anti-Bacterial,Agents, Anti-Mycobacterial,Agents, Antibacterial,Agents, Antimycobacterial,Agents, Bacteriocidal,Anti Bacterial Agent,Anti Bacterial Agents,Anti Bacterial Compound,Anti Bacterial Compounds,Anti Mycobacterial Agent,Anti Mycobacterial Agents,Compound, Anti-Bacterial,Compounds, Anti-Bacterial
D012477 Salmonella enteritidis A serotype of Salmonella enterica which is an etiologic agent of gastroenteritis in man and other animals. Salmonella enterica serovar enteritidis
D012480 Salmonella Infections Infections with bacteria of the genus SALMONELLA. Salmonellosis,Infections, Salmonella,Infection, Salmonella,Salmonella Infection,Salmonelloses
D014435 Typhoid Fever An acute systemic febrile infection caused by SALMONELLA TYPHI, a serotype of SALMONELLA ENTERICA. Enteric Fever,Typhus, Abdominal,Salmonella typhi Infection,Typhoid,Abdominal Typhus,Enteric Fevers,Fever, Enteric,Fever, Typhoid,Fevers, Enteric,Fevers, Typhoid,Infection, Salmonella typhi,Infections, Salmonella typhi,Salmonella typhi Infections,Typhoid Fevers,Typhoids
D014436 Typhoid-Paratyphoid Vaccines Vaccines used to prevent TYPHOID FEVER and/or PARATYPHOID FEVER which are caused by various species of SALMONELLA. Attenuated, subunit, and inactivated forms of the vaccines exist. Paratyphoid Vaccine,Typhoid Vaccine,Vaccines, Paratyphoid,Vaccines, Typhoid,Paratyphoid Vaccines,Typhoid Paratyphoid Vaccines,Typhoid Vaccines,Vaccine, Paratyphoid,Vaccine, Typhoid,Vaccines, Typhoid-Paratyphoid
D023281 Genomics The systematic study of the complete DNA sequences (GENOME) of organisms. Included is construction of complete genetic, physical, and transcript maps, and the analysis of this structural genomic information on a global scale such as in GENOME WIDE ASSOCIATION STUDIES. Functional Genomics,Structural Genomics,Comparative Genomics,Genomics, Comparative,Genomics, Functional,Genomics, Structural

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