Whole-Genome Sequence Analysis of Multidrug-Resistant Enterobacter hormaechei Isolated from Imported Retail Shrimp

Indugu, Nagaraju; Sharma, Laxmi; Jackson, Charlene R.; Singh, Prashant

doi:10.1128/mra.01103-20

Cited by 5 publications

(5 citation statements)

References 10 publications

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“…E. hormaechei deriving aadA2 and sul1 , a sulfonamide resistant dihydropteroate synthase gene that is described to appear in Gram-negative bacteria 21 have been reported to appear in the genom of Enterobacter spp. and E. hormaechei , respectively in former publications as well 24 , 25 . Within the Enterococcus genus, two perfect ARG matches were identified, namely aph(3’)-IIIa in E. faecalis and poxtA in E. faecium .…”

Section: Discussionmentioning

confidence: 87%

Antimicrobial resistance determinants in silage

Nagy

Tóth

Papp

et al. 2022

Sci Rep

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Animal products may play a role in developing and spreading antimicrobial resistance in several ways. On the one hand, residues of antibiotics not adequately used in animal farming can enter the human body via food. However, resistant bacteria may also be present in animal products, which can transfer the antimicrobial resistance genes (ARG) to the bacteria in the consumer’s body by horizontal gene transfer. As previous studies have shown that fermented foods have a meaningful ARG content, it is indicated that such genes may also be present in silage used as mass feed in the cattle sector. In our study, we aspired to answer what ARGs occur in silage and what mobility characteristics they have? For this purpose, we have analyzed bioinformatically 52 freely available deep sequenced silage samples from shotgun metagenome next-generation sequencing. A total of 16 perfect matched ARGs occurred 54 times in the samples. More than half of these ARGs are mobile because they can be linked to integrative mobile genetic elements, prophages or plasmids. Our results point to a neglected but substantial ARG source in the food chain.

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Section: Discussionmentioning

confidence: 87%

Antimicrobial resistance determinants in silage

Nagy

Tóth

Papp

et al. 2022

Sci Rep

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“…To test the accuracy of our system, we analyzed the probabilistic relationship of antibiotic resistance genes that have been previously observed to occur together in Enterobacteriaceae. These genes include the streptomycin resistance genes aph ( 6 ) -Id and aph(3’’)-Ib , and the sulfonamide resistance gene, sul2 (9,45,46). In E. coli , strong positive probabilistic relationships were observed between aph(3’’)-Ib to aph(6)-Id (cond.…”

Section: Resultsmentioning

confidence: 99%

“…Alternatively, we observed similar relationships in a genomic population of E. coli isolated from hospitalized patients in Salt Lake City, Utah (unpublished data). This suggests that the co- occurrence of chloramphenicol and other resistance genes could be evidence of the mobilization of MDR strains through the food chain, as bacteria harboring phenicol resistance genes have been identified in food animals (46,54).…”

Section: Discussionmentioning

confidence: 99%

Resistance Gene Association and Inference Network (ReGAIN): A Bioinformatics Pipeline for Assessing Probabilistic Co-Occurrence Between Resistance Genes in Bacterial Pathogens

Bring Horvath,

Stein,

Mulvey

et al. 2024

Preprint

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The rampant rise of multidrug resistant (MDR) bacterial pathogens poses a severe health threat, necessitating innovative tools to unravel the complex genetic underpinnings of antimicrobial resistance. Despite significant strides in developing genomic tools for detecting resistance genes, a gap remains in analyzing organism-specific patterns of resistance gene co-occurrence. Addressing this deficiency, we developed the Resistance Gene Association and Inference Network (ReGAIN), a novel web-based and command line genomic platform that uses Bayesian network structure learning to identify and map resistance gene networks in bacterial pathogens. ReGAIN not only detects resistance genes using well- established methods, but also elucidates their complex interplay, critical for understanding MDR phenotypes. Focusing on ESKAPE pathogens, ReGAIN yielded a queryable database for investigating resistance gene co-occurrence, enriching resistome analyses, and providing new insights into the dynamics of antimicrobial resistance. Furthermore, the versatility of ReGAIN extends beyond antibiotic resistance genes to include assessment of co-occurrence patterns among heavy metal resistance and virulence determinants, providing a comprehensive overview of key gene relationships impacting both disease progression and treatment outcomes.Graphical Abstract

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“…Body of Knowledge E. hormaechei has been isolated as a contaminant from food (Indugu et al, 2020;Sadek et al, 2020), as an endophyte from plants (Khalaf and Raizada, 2020;Tshishonga and Serepa-Dlamini, 2019) and from the gastrointestinal tracts of insects (Asimakis et al, 2019). Isolates of E. hormaechei are able to degrade lutein, a plant carotenoid (Zhong et al, 2017).…”

Section: Enterobacter Hormaecheimentioning

confidence: 99%

“…Multiresistant E. hormaechei has been isolated from several food products. Examples are a shrimp sample from a farmers' market in the US harbouring sul1, sul2, qnrA1, oqxAB, dfrA23, blaACT, floR, fosA, tet(A), aph(6)-Id and aph(30)-Ib antibiotic resistance genes and several plasmids (Indugu et al, 2020); an isolate from a raw beef patty with bla VIM-1 , mcr-9 aac(6 0 )-Il, ΔaadA22, aac(6 0 )-Ib-cr, sul1, dfrA1 on a plasmid (Sadek et al, 2020).…”

Section: Enterobacter Hormaecheimentioning

confidence: 99%

Update of the list of QPS‐recommended biological agents intentionally added to food or feed as notified to EFSA 14: suitability of taxonomic units notified to EFSA until March 2021

Koutsoumanis¹,

Allende²,

Álvarez‐Ordóñez³

et al. 2021

EFS2

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The qualified presumption of safety (QPS) approach was developed to provide a regularly updated generic pre-evaluation of the safety of biological agents, intended for addition to food or feed, to support the work of EFSA's Scientific Panels. The QPS approach is based on an assessment of published data for each agent, with respect to its taxonomic identity, the body of relevant knowledge, safety concerns and occurrence of antimicrobial resistance. Safety concerns identified for a taxonomic unit (TU) are, where possible, confirmed at the species/strain or product level and reflected by 'qualifications'. In the period covered by this statement, no new information was found that would change the status of previously recommended QPS TUs. Schizochytrium limacinum, which is a synonym for Aurantiochytrium limacinum, was added to the QPS list. Of the 78 microorganisms notified to EFSA between October 2020 and March 2021, 71 were excluded; 16 filamentous fungi, 1 Dyella spp., 1 Enterococcus faecium, 7 Escherichia coli, 1 Streptomyces spp., 1 Schizochytrium spp. and 44 TUs that had been previously evaluated. Seven TUs were evaluated: Corynebacterium stationis and Kodamaea ohmeri were re-assessed because an update was requested for the current mandate. Anoxybacillus caldiproteolyticus, Bacillus paralicheniformis, Enterobacter hormaechei, Eremothecium ashbyi and Lactococcus garvieae were assessed for the first time. The following TUs were not recommended for QPS status: A. caldiproteolyticus due to the lack of a body of knowledge in relation to its use in the food or feed chain, E. hormaechei, L. garvieae and K. ohmeri due to their pathogenic potential, E. ashbyi and C. stationis due to a lack of body of knowledge on their occurrence in the food and feed chain and to their pathogenic potential. B. paralicheniformis was recommended for the QPS status with the qualification 'absence of toxigenic activity' and 'absence of genetic information to synthesize bacitracin'.

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Whole-Genome Sequence Analysis of Multidrug-Resistant Enterobacter hormaechei Isolated from Imported Retail Shrimp

Cited by 5 publications

References 10 publications

Antimicrobial resistance determinants in silage

Antimicrobial resistance determinants in silage

Resistance Gene Association and Inference Network (ReGAIN): A Bioinformatics Pipeline for Assessing Probabilistic Co-Occurrence Between Resistance Genes in Bacterial Pathogens

Update of the list of QPS‐recommended biological agents intentionally added to food or feed as notified to EFSA 14: suitability of taxonomic units notified to EFSA until March 2021

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