Genome analysis of antimicrobial resistance, virulence, and plasmid presence in Turkish Salmonella serovar Infantis isolates

Acar, Sinem
Bulut, Ece
Stasiewicz, Matthew J.
Soyer, Yeşim
Salmonella enterica subsp. enterica serovar Infantis (S. Infantis) isolates were found to have a multi-drug resistance profile (kanamycin, streptomycin, nalidixic acid, tetracycline, sulfonamide, and sometimes to ampicillin) and high prevalence (91%) in Turkish poultry in our previous studies. To investigate the mechanism behind multi-drug antimicrobial resistance (AMR) and high prevalence in Turkish poultry, 23 of the isolates were sequenced for comparative genomic analyses including: SNP-based comparison to S. Infantis from other countries, comparison of antimicrobial resistance genes (AMGs) with AMR phenotypes, and plasmid identification and annotation. Whole-genome SNP-based phylogenetic analysis found that all 23 Turkish S. Infantis isolates formed a distinct, well-supported Glade, separate from 243 comparison S. Infantis genomes in GenomeTrakr identified as from the US and EU; the isolates most closely related to the cluster of these Turkish isolates were from Israel and Egypt. AMGs identified by bioinformatic analysis, without differentiating chromosomal or plasmid located genes, implied AMR phenotypes with 94% similarity overall to wet lab data, which was performed by phenotypic and conventional PCR methods. Most of the S. Infantis (21/23) isolates had identifiable plasmids, with 76% (16/21) larger than 100 kb and 48% (10/21) larger than 200 kb. A plasmid larger than 200 kb, with the incompatibility type of IncX1, similar to United States S. Infantis plasmid N55391 (99% query coverage and 99% identity overall), which itself is similar to Italian and Hungarian S. Infantis plasmids. Turkish S. Infantis plasmids had different beta-lactam resistance genes (bla(TEM-70), bla(TEM-148) and bla(TEM-198)) than the gene bla(CTX-M-)(65 )found in S. Infantis plasmids from other countries. This is the first observation of these three genes in S. Infantis isolates, The plasmids larger than 200 kb had two distinct regions of interest: Site 1 and Site 2. Site 1 (around 130 kb) had virulence- and bacteriocin- associated genes such as bacteriocin secretion system and type II toxin-antitoxin system genes (vagC, ccdA, ccdB, mchE, cvaB) and an aminoglycoside resistance gene (str). Site 2 (around 75-110 kb) had the antimicrobial resistance genes (aadA, sulI, tetA, tetR) and mercury (mer) resistance gene on tranposons Tn552 and Tn501. Presence of these AMR and virulence genes suggests they may have a role in the emergence of S. Infantis in poultry and support treating this serotype as a an important human health hazard.


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Salmonella enterica subsp. enteric serovars are responsible for causing the highest number of bacterial foodborne infections in the world. Antimicrobial resistance (AR) and virulence of Salmonella isolates play a critical role in systemic infections and they impose great concern to human health in severe salmonellosis cases when multidrug resistance interferes with treatment. Also, antimicrobial resistance genes might be shared with closely related human pathogens. Therefore, antimicrobial susceptibility mo...
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Gültekin, Güzin Candan; Ogel, Z. B.; Oren, N. G. (Elsevier BV, 2008-06-01)
Salmonella enterica ssp. enterica serovar Typhimurium and Salmonella enterica ssp. enterica serovar Enteritidis are the major dominating serotypes of Salmonella in poultry and poultry products. Infection by Salmonella Typhimurium is an important cause of morbidity and mortality in poultry. Rapid differentiation of Salmonella Typhimurium from other Salmonella serotypes including Salmonella Enteritidis can be very crutial for public health and for epidemiologists and for the poultry industry. Ten arbitrarily ...
Emergence, Distribution, and Molecular and Phenotypic Characteristics of Salmonella enterica Serotype 4,5,12:i:-
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Salmonella spp. represent one of the most common causes of bacterial foodborne illnesses around the world. The species Salmonella enterica contains more than 2500 serotypes, and emergence of new human pathogenic Salmonella strains and serotypes represents a major public health issue. Salmonella enterica subsp. enterica serotype 4,5,12:i:- represents a monophasic variant of Salmonella Typhimurium, which has rarely been identified before the mid-1990s. The prevalence of this serotype among human salmonellosis...
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Polat Kılıç, Özlem Gözde; Alpas, Hami; Soyer, Yeşim; Department of Food Engineering (2014)
The main objective of this study was to investigate distribution of Salmonella in fresh peppers in Turkey. To serve this purpose, a total of 255 fresh pepper samples (green, kapya, bell, mazamort and charleston) were collected from 3 districts within 9 supermarkets and 3 bazaars in Ankara, Turkey. Salmonella suspected colonies was confirmed by using polymerase chain reaction (PCR) of Salmonella specific gene, invA. One of isolate was assigned as Salmonella, which was isolated from kapya pepper. Confirmed Sa...
Investigation of class 1 integrons and virulence genes in the emergent Salmonella serovar Infantis in Turkey
Namli, Sahin; Soyer, Yeşim (2021-09-01)
The emerging situation of Salmonella enterica subsp. enterica serovar Infantis (S. Infantis) in Turkey was investigated in terms of virulence genes and mobile genetic elements such as Salmonella genomic island 1 (SGI1) and class 1 (C1) integron to see whether increased multidrug resistance (MDR) and ability to cause human cases is a consequence of their possession. Screening of SGI1 (and its variants) and C1 integrons was done with conventional PCR, while screening of gene cassettes and virulence genes was ...
Citation Formats
S. Acar, E. Bulut, M. J. Stasiewicz, and Y. Soyer, “Genome analysis of antimicrobial resistance, virulence, and plasmid presence in Turkish Salmonella serovar Infantis isolates,” INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY, pp. 0–0, 2019, Accessed: 00, 2020. [Online]. Available: