Genomic characterisation of multidrug-resistant Salmonella enterica serovar Kentucky ST198 isolates from various sources in Algeria, North Africa

TL;DR

This study analyzes multidrug-resistant Salmonella Kentucky ST198 isolates from Algeria and finds they are part of a global lineage, emphasizing the need for better antibiotic resistance surveillance.

Contribution

The first comprehensive genomic characterization of S. Kentucky ST198 isolates in Algeria, revealing their global lineage and resistance profiles.

Findings

Algerian S. Kentucky ST198 isolates are closely related to a multidrug-resistant lineage that originated in Egypt and spread globally.

90% of isolates showed resistance to critical antibiotics like ciprofloxacin and azithromycin.

Genomic analysis identified key resistance mutations and plasmid types, including IncI1 and Col156.

Abstract

Salmonella enterica serovar Kentucky (S. Kentucky) sequence type (ST) 198 has emerged as a globally disseminated multidrug-resistant (MDR) lineage posing significant public health challenges. The aim of this study was to characterise 125 S. Kentucky ST198 isolates collected from various sources in Algeria, including humans, animals, food and the environment, or obtained from humans in France (travellers returning from Algeria), between 2015 and 2022. Whole-genome sequencing was performed on 125 isolates to assess their genetic diversity and antimicrobial resistance (AMR) profiles. Phylogenetic analysis revealed that the Algerian S. Kentucky ST198 isolates were closely related to each other and belonged to the MDR lineage that emerged in Egypt before disseminating into Africa, the Middle East, Asia and Europe. These isolates also clustered closely with European and North African isolates carrying the gyrA_D87N mutation. We found that 90% of the isolates had MDR phenotypes, with resistance to critically important antibiotics, including ciprofloxacin, third-generation cephalosporins, azithromycin and chloramphenicol. Genomic analysis revealed that all the isolates had the three known non-synonymous resistance mutations in the quinolone-resistance-determining regions of DNA gyrase (gyrA) and DNA topoisomerase IV (parC). Multiple AMR genes were also identified, including blaCTX-M-15, blaCMY-2, blaCMY-4, qnrB19, mph(A), cmlA1 and floR. The Algerian isolates also contained the main variant of SGI1, SGI1-K, with multiple rearrangements. Plasmid replicon analysis revealed that the most frequent plasmid types were IncI1 (13.6%), Col156 (8.8%) and Col(pVC) (8%). This study provides the first comprehensive genomic insight into S. Kentucky ST198 in Algeria, highlighting the urgent need for a reinforcement of AMR surveillance and control measures in the region. These findings enhance our overall understanding of the epidemiology and evolution of MDR Salmonella and highlight the importance of a One Health approach for combating the spread of resistant pathogens.

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