Large-scale genomic analysis reveals the pESI-like megaplasmid presence in Salmonella Agona, Muenchen, Schwarzengrund, and Senftenberg

Santos, Anamaria M.P. dos; Panzenhagen, Pedro; Ferrari, Rafaela Gomes; Conté-Júnior, Carlos Adam

doi:10.1016/j.fm.2022.104112

Cited by 20 publications

(12 citation statements)

References 54 publications

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“…Furthermore, in this study we found the IncFIB and Incl1-α plasmids in the strains ( Figures 3 and 4 ), which contain a wide variety of resistance elements that have been described and linked to mobile genetic elements ( Partridge et al, 2018 ). These plasmids have been reported in other serotypes, including IncFIB type pESI in Agona and Senftenberg, as well as in isolates that harbor both plasmids ( Cohen et al, 2022 ; dos Santos et al, 2022 ), conferring a severe public health risk. However, there are some discrepancies ( Table 4 ) between the genotype and phenotype of the strains, which could be attributed to several factors, such as promoter regions, secondary structures in the Shine-Dalgarno region, and the presence of unknown or undescribed mechanisms.…”

Section: Discussionmentioning

confidence: 77%

Mobile genetic elements drive the multidrug resistance and spread of Salmonella serotypes along a poultry meat production line

Krüger

Pardo-Esté²,

Zepeda³

et al. 2023

Front. Microbiol.

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The presence of mobile genetic elements in Salmonella isolated from a chicken farm constitutes a potential risk for the appearance of emerging bacteria present in the food industry. These elements contribute to increased pathogenicity and antimicrobial resistance through genes that are related to the formation of biofilms and resistance genes contained in plasmids, integrons, and transposons. One hundred and thirty-three Salmonella isolates from different stages of the production line, such as feed manufacturing, hatchery, broiler farm, poultry farm, and slaughterhouse, were identified, serotyped and sequenced. The most predominant serotype was Salmonella Infantis. Phylogenetic analyses demonstrated that the diversity and spread of strains in the pipeline are serotype-independent, and that isolates belonging to the same serotype are very closely related genetically. On the other hand, Salmonella Infantis isolates carried the pESI IncFIB plasmid harboring a wide variety of resistance genes, all linked to mobile genetic elements, and among carriers of these plasmids, the antibiograms showed differences in resistance profiles and this linked to a variety in plasmid structure, similarly observed in the diversity of Salmonella Heidelberg isolates carrying the IncI1-Iα plasmid. Mobile genetic elements encoding resistance and virulence genes also contributed to the differences in gene content. Antibiotic resistance genotypes were matched closely by the resistance phenotypes, with high frequency of tetracycline, aminoglycosides, and cephalosporins resistance. In conclusion, the contamination in the poultry industry is described throughout the entire production line, with mobile genetic elements leading to multi-drug resistant bacteria, thus promoting survival when challenged with various antimicrobial compounds.

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Section: Discussionmentioning

confidence: 77%

Mobile genetic elements drive the multidrug resistance and spread of Salmonella serotypes along a poultry meat production line

Krüger

Pardo-Esté²,

Zepeda³

et al. 2023

Front. Microbiol.

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“…3C; Supplementary Table S5). We found that only the HC20_343 cluster harbored most of the pESI-like megaplasmid genes (from 164 to 310 out of 315 genes), including those encoding the three toxinantitoxin systems (pemK/I, vapB/C and ccdA/B), the K88-like and Ipf fimbria, the yersiniabactin synthesis cluster, the mercury resistance cluster, and the conjugative transfer region (tra and type-IV pili-encoding genes), which are part of 20 the pESI-like megaplasmids backbone 29 . Most differences between the megaplasmids harbored by the Chilean strains and the pN55391 megaplasmid were located in the antibiotic resistance region, previously reported as a variable region 5 .…”

Section: Salmonella Infantis Isolates From the Hc20_343 Cluster Inclu...mentioning

confidence: 99%

Widespread dissemination of ESBL-producingSalmonella entericaserovar Infantis exhibiting intermediate fluoroquinolone resistance and harboringbla_CTX-M-65-positive pESI-like megaplasmids in Chile

Piña-Iturbe,

Díaz-Gavidia,

Álvarez

et al. 2023

Preprint

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Background: Multidrug-resistant (MDR)SalmonellaInfantis has disseminated worldwide, mainly linked to the consumption of poultry products. Evidence shows dissemination of this pathogen in Chile; however, studies are primarily limited to phenotypic data or involve few isolates. As human cases ofSalmonellaInfantis infections have substantially increased in recent years, a better understanding of its molecular epidemiology and antimicrobial-resistance profiles are required to inform effective surveillance and control measures. Methods: We sequenced 396SalmonellaInfantis genomes and analyzed them with all publicly available genomes of this pathogen from Chile (440 genomes in total), representing isolates from environmental, food, animal, and human sources obtained from 2009 to 2022. Based on bioinformatic and phenotypic methods, we assessed the population structure, dissemination among different niches, and AMR profiles ofSalmonellaInfantis in the country. Findings: The genomic and phylogenetic analyses showed thatSalmonellaInfantis from Chile comprised several clusters of highly related isolates dominated by sequence type 32. The HC20_343 cluster grouped an important proportion of all isolates. The latter was the only cluster associated with pESI-like megaplasmids, and up to 12 acquired AMR genes/mutations predicted to result in an MDR phenotype. Accordingly, antimicrobial-susceptibility testing revealed a strong concordance between the AMR genetic determinants and their matching phenotypic expression, indicating that a significant proportion of HC20_343 isolates produce extended-spectrum β-lactamases and have intermediate fluoroquinolone resistance. HC20_343SalmonellaInfantis were spread among environmental, animal, food, and human niches, showing a close relationship between isolates from different years and sources, and a low intra-source genomic diversity. Interpretation: Our findings show a widespread dissemination of MDRSalmonellaInfantis from the HC20_343 cluster in Chile. The high proportion of isolates with resistance to first-line antibiotics and the evidence of active transmission between the environment, animals, food, and humans highlight the urgency of improved surveillance and control measures in the country. As HC20_343 isolates predominate in the Americas, our results suggest a high prevalence of ESBL-producingSalmonellaInfantis with intermediate fluoroquinolone resistance in the continent. Funding: Agencia de Investigación y Desarrollo de Chile (ANID) through FONDECYT de Postdoctorado Folio 3230796 and Folio 3210317, FONDECYT Regular Folio 1231082, and ANID - Millennium Science Initiative Program - ICN2021_044.

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“…This conjugative plasmid contributes to virulence-associated phenotypes and pathogenicity, confers resistance to multiple antibiotics such as tetracycline and trimethoprim, heavy metals, and disinfectants [9]. This megaplasmid was also shown to be horizontally transferred to additional salmonella serovars as well as to other bacteria strains in the gut microbiota of infected warm-blooded hosts [10][11][12].…”

Section: Introductionmentioning

confidence: 99%

Curing of a field strain ofSalmonella entericaserovar Infantis isolated from poultry from its highly stable pESI like plasmid

Gruzdev,

Katz,

Yadid

2024

Preprint

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Salmonella enterica serovar Infantis (S. Infantis) is an important emerging pathogen, associated with poultry and poultry products and related to an increasing number of human infections in many countries. A concerning trend among S. Infantis isolates is the presence of plasmid-mediated multi-drug resistance. In many instances, the genes responsible for this resistance are carried on a megaplasmid known as the plasmid of emerging S. Infantis (pESI) or pESI like plasmids. Plasmids can be remarkably stable due to the presence of multiple replicons and post-segregational killing systems (PSKs), which contribute to their maintenance within bacterial populations. To enhance our understanding of S. Infantis and its multidrug resistance determinants toward the development of new vaccination strategies, we have devised a method for targeted plasmid curing. This approach effectively overcomes plasmid addiction by leveraging the temporal overproduction of specific antitoxins coupled with the deletion of the partition region. By employing this strategy, we successfully generated a plasmid-free strain from a field isolate derived from S. Infantis 119944. This method provides valuable tools for studying S. Infantis and its plasmid-borne multidrug resistance mechanisms.

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Large-scale genomic analysis reveals the pESI-like megaplasmid presence in Salmonella Agona, Muenchen, Schwarzengrund, and Senftenberg

Cited by 20 publications

References 54 publications

Mobile genetic elements drive the multidrug resistance and spread of Salmonella serotypes along a poultry meat production line

Mobile genetic elements drive the multidrug resistance and spread of Salmonella serotypes along a poultry meat production line

Widespread dissemination of ESBL-producingSalmonella entericaserovar Infantis exhibiting intermediate fluoroquinolone resistance and harboringbla_CTX-M-65-positive pESI-like megaplasmids in Chile

Curing of a field strain ofSalmonella entericaserovar Infantis isolated from poultry from its highly stable pESI like plasmid

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Large-scale genomic analysis reveals the pESI-like megaplasmid presence in Salmonella Agona, Muenchen, Schwarzengrund, and Senftenberg

Cited by 20 publications

References 54 publications

Mobile genetic elements drive the multidrug resistance and spread of Salmonella serotypes along a poultry meat production line

Mobile genetic elements drive the multidrug resistance and spread of Salmonella serotypes along a poultry meat production line

Widespread dissemination of ESBL-producingSalmonella entericaserovar Infantis exhibiting intermediate fluoroquinolone resistance and harboringblaCTX-M-65-positive pESI-like megaplasmids in Chile

Curing of a field strain ofSalmonella entericaserovar Infantis isolated from poultry from its highly stable pESI like plasmid

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Widespread dissemination of ESBL-producingSalmonella entericaserovar Infantis exhibiting intermediate fluoroquinolone resistance and harboringbla_CTX-M-65-positive pESI-like megaplasmids in Chile