The rare Salmonella enterica serovar Isangi: genomic characterization of the antimicrobial resistance, virulence potential and epidemiology of Brazilian strains in comparison to global isolates

Abstract

Introduction. Salmonella enterica serovar Isangi (S. Isangi) is a rare non-typhoidal serovar, related to invasive nosocomial infections in various countries and to increasing antimicrobial resistance rates. Gap statement. Despite existing reports on S. Isangi, there is a lack of information of specific traits regarding this serovar, which could be improved through genomic analyses. Aim. Our goals were to characterize the antimicrobial resistance, virulence potential and genomic relatedness of 11 S. Isangi strains from Brazil in comparison to 185 genomes of global isolates using whole-genome sequencing (WGS) data. Methodology. Phenotypic resistance was determined by disc-diffusion. The search for resistance genes, plasmids, prophages, Salmonella pathogenicity islands (SPIs) and virulence genes, plus multi-locus sequence typing (MLST) and core-genome MLST (cgMLST) were performed using WGS. Results. Brazilian S. Isangi strains showed phenotypic resistance to nalidixic acid, ciprofloxacin and streptomycin, and harboured antimicrobial resistance [qnrB19, aac(6’)-Iaa, mdsAB] and heavy metal tolerance (arsD, golST) genes. Col(pHAD28) and IncFII(S) plasmids, virulence genes related to adherence, macrophage induction, magnesium uptake, regulation and type III secretion systems, 12 SPIs and eight prophages were detected. The 185 additional global genomes analysed harboured resistance genes against 11 classes of antimicrobial compounds, 22 types of plasmids, 32 prophages, 14 SPIs, and additional virulence genes related to serum resistance, stress adaptation and toxins. Sequence type (ST)216 was assigned to genomes from Brazil and other countries, while ST335 was the most frequent ST, especially among South African genomes. cgMLST showed that Brazilian genomes were more closely related to genomes from European and African countries, the USA and Taiwan, while the majority of South African genomes were more closely related among each other. Conclusion. The presence of S. Isangi strains from Brazil and different countries showing a close genomic correlation, antimicrobial resistance profiles to drugs used in human therapy and a large number of virulence determinants reinforced the need for stronger initiatives to monitor rare non-typhoidal Salmonella serovars such as S. Isangi in order to prevent its dissemination among human and non-human sources.

Rare serovars of non-typhoidal Salmonella enterica isolated from humans, beef cattle and abattoir environments in Nigeria

“…This is not surprising, as quinolones, which are medically important antimicrobials in human health, have been reported to be used as growth promoters in the livestock industry in Nigeria and may have contributed to the emergence of NTS resistant to ciprofloxacin [ 39 ]. Chromosomal mutations in the QRDR of parC (T57S) reported to cause clinical resistance in Salmonella species was observed in all 22 NTS isolates and this is in agreement with reports of other related studies conducted in Nigeria [ 17 , 37 , 38 ] and other locations [ 9 , 34 ]. This is a known mutation conferring resistance in Salmonella spp isolates exhibiting low ciprofloxacin minimum inhibition concentrations as reported by other studies in recent times [ 40 , 41 ].…”

“…enterica (NTS) isolated from food animals, especially beef cattle, are frequently resistant to antimicrobials [ 12 , 14 , 17 , 28 ]. Cattle have been implicated as a likely source in the transmission of NTS to humans via the food chain [ 9 , 10 , 13 ]. The hazards of people working in proximity with these food animals and the possibility of being colonized with NTS have however, not been adequately explained.…”

“…In Nigeria, as in many emerging economies, many families rely on beef cattle rearing as a source of income as well as a major supply of animal protein, resulting in increased beef consumption [ 8 ]. Non-typhoidal Salmonella (NTS) are transmitted to humans mostly through the ingestion of contaminated raw or undercooked meat or other animal products [ 9 , 10 ]. NTS is the leading cause of diarrhea, infecting 550 million people annually, including 220 million in young children under five years of age [ 10 ].…”

Antimicrobial resistance, virulence potential and genomic epidemiology of global genomes of the rare Salmonella enterica serovar Orion

“…In South Korea, rare NTS serovars London and Othmarschen have been responsible for foodborne outbreaks in 2006-2007(Kim, 2010. Moreover, the spread of antimicrobial resistance also affected rare serovars, which have been displaying increasing phenotypic and genotypic resistance levels to diverse antimicrobials of clinical and veterinary use (Aworh et al, 2024;Monte et al, 2021;Vilela, Rodrigues, et al, 2023;Yong et al, 2005).…”