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Genetic diversity and mobile genetic element associated multidrug resistance in Salmonella enterica from broiler chickens in Egypt.

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Title: Genetic diversity and mobile genetic element associated multidrug resistance in Salmonella enterica from broiler chickens in Egypt.
Authors: Salem M; Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Mansoura University, Mansoura, 35516, Egypt., Abukhadra BA; Department of Virology, Faculty of Veterinary Medicine, Mansoura University, 35516 El Gomhoria Street, Mansoura, Egypt., Ghabbour R; Gastro-Enterology Surgery Center (GEC), Mansoura University, Mansoura, Egypt., El-Metwaly ME; Department of Preclinical Veterinary Sciences, Faculty of Veterinary Medicine, Delta University for Science and Technology, Gamasa, Egypt., Younis G; Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Mansoura University, Mansoura, 35516, Egypt., Awad A; Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Mansoura University, Mansoura, 35516, Egypt. amalabdo@mans.edu.eg.
Source: Scientific reports [Sci Rep] 2026 Jul 03; Vol. 16 (1). Date of Electronic Publication: 2026 Jul 03.
Publication Type: Journal Article; Research Support, Non-U.S. Gov't
Language: English
Journal Info: Publisher: Nature Publishing Group Country of Publication: England NLM ID: 101563288 Publication Model: Electronic Cited Medium: Internet ISSN: 2045-2322 (Electronic) Linking ISSN: 20452322 NLM ISO Abbreviation: Sci Rep Subsets: MEDLINE
Imprint Name(s): Original Publication: London : Nature Publishing Group, copyright 2011-
MeSH Terms: Salmonella enterica*/genetics , Salmonella enterica*/drug effects , Salmonella enterica*/isolation & purification , Chickens*/microbiology , Drug Resistance, Multiple, Bacterial*/genetics , Salmonella Infections, Animal*/microbiology , Salmonella Infections, Animal*/epidemiology , Poultry Diseases*/microbiology , Interspersed Repetitive Sequences*/genetics , Genetic Variation*, Anti-Bacterial Agents/pharmacology ; Animals ; Egypt ; Integrons ; Microbial Sensitivity Tests ; Genotype
Abstract: Salmonella enterica remains a leading foodborne zoonotic pathogen worldwide, with poultry serving as a major reservoir and vehicle for antimicrobial resistance dissemination to humans. This study investigated the genotypic basis and distribution of multidrug resistance (MDR) among 29 S. enterica isolates from broiler farms in Egypt, emphasizing the role of mobile genetic elements as integrons and the assessment of genetic relatedness using ERIC-PCR. Molecular screening revealed high prevalence of resistance determinants, including floR (93.1%), tetA (86.2%), aphA1 (82.8%), cmlA (75.9%), ereA (75.9%), sulI (62.1%), aadA1 (51.7%), dfrA1 (48.3%), aac(3)-IV (44.8%), tetB (41.4%), sulII (31.0%), aac(6')-Ib-cr (24.1%), catA1 (20.7%), fosA3 (20.7%), and qnrA (10.3%). High-risk serovars, including S. Jerusalem, S. Colorado, and S. Kentucky, harbored multiple resistance genes and exhibited pronounced XDR profiles. Notably, this study reports the detection of aphA1 and fosA3 in Salmonella isolates derived from broiler chickens, which may represent an early or uncommon finding in Egypt. Many resistance genes were associated with horizontally transferable class 1 integron, underscoring its key role in the dissemination of multidrug resistance (MDR) within poultry systems and along the food chain. ERIC-PCR genotyping segregated isolates into two major genetic groups with seven sub-clusters, reflecting clustering patterns and genetic diversity among the isolates, alongside notable heterogeneity in resistance, virulence, and biofilm-associated genes.Overall, poultry in Egypt represents a significant reservoir of genetically diverse and potentially transmissible MDR S. enterica, highlighting the need for enhanced antimicrobial stewardship and genomic surveillance to mitigate public health risks.
(© 2026. The Author(s).)
Competing Interests: Declarations. Competing interests: The authors declare no competing interests. Ethical approval: The study protocol was reviewed and approved by the Research Ethics Committee of the Faculty of Veterinary Medicine, Mansoura University, Egypt [Approval Code: MU-ACUC (VM.PhD.23.10.24)]. All experimental procedures were conducted in full compliance with the institutional guidelines and relevant national regulations for the care and use of animals.
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Contributed Indexing: Keywords: Salmonella enterica; Antimicrobial resistance; Broiler chicken; ERIC-PCR; Egypt; Integron; Public health concern
Substance Nomenclature: 0 (Anti-Bacterial Agents)
Entry Date(s): Date Created: 20260703 Date Completed: 20260703 Latest Revision: 20260813
Update Code: 20260814
PubMed Central ID: PMC13332045
DOI: 10.1038/s41598-026-59913-w
PMID: 42399277
Database: MEDLINE
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  – Url: https://dx.doi.org/doi:10.1038/s41598-026-59913-w
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  Data: Genetic diversity and mobile genetic element associated multidrug resistance in Salmonella enterica from broiler chickens in Egypt.
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  Data: <searchLink fieldCode="AU" term="%22Salem+M%22">Salem M</searchLink>; Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Mansoura University, Mansoura, 35516, Egypt.<br /><searchLink fieldCode="AU" term="%22Abukhadra+BA%22">Abukhadra BA</searchLink>; Department of Virology, Faculty of Veterinary Medicine, Mansoura University, 35516 El Gomhoria Street, Mansoura, Egypt.<br /><searchLink fieldCode="AU" term="%22Ghabbour+R%22">Ghabbour R</searchLink>; Gastro-Enterology Surgery Center (GEC), Mansoura University, Mansoura, Egypt.<br /><searchLink fieldCode="AU" term="%22El-Metwaly+ME%22">El-Metwaly ME</searchLink>; Department of Preclinical Veterinary Sciences, Faculty of Veterinary Medicine, Delta University for Science and Technology, Gamasa, Egypt.<br /><searchLink fieldCode="AU" term="%22Younis+G%22">Younis G</searchLink>; Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Mansoura University, Mansoura, 35516, Egypt.<br /><searchLink fieldCode="AU" term="%22Awad+A%22">Awad A</searchLink>; Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Mansoura University, Mansoura, 35516, Egypt. amalabdo@mans.edu.eg.
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  Data: <searchLink fieldCode="JN" term="%22101563288%22">Scientific reports</searchLink> [Sci Rep] 2026 Jul 03; Vol. 16 (1). <i>Date of Electronic Publication: </i>2026 Jul 03.
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  Data: Journal Article; Research Support, Non-U.S. Gov't
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  Data: <i>Publisher: </i><searchLink fieldCode="PB" term="%22Nature+Publishing+Group%22">Nature Publishing Group </searchLink><i>Country of Publication: </i>England <i>NLM ID: </i>101563288 <i>Publication Model: </i>Electronic <i>Cited Medium: </i>Internet <i>ISSN: </i>2045-2322 (Electronic) <i>Linking ISSN: </i><searchLink fieldCode="IS" term="%2220452322%22">20452322 </searchLink><i>NLM ISO Abbreviation: </i>Sci Rep <i>Subsets: </i>MEDLINE
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  Data: <i>Original Publication</i>: London : Nature Publishing Group, copyright 2011-
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  Data: <searchLink fieldCode="MM" term="%22Salmonella+enterica%22">Salmonella enterica*</searchLink>/<searchLink fieldCode="MM" term="%22Salmonella+enterica+genetics%22">genetics</searchLink> <br /><searchLink fieldCode="MM" term="%22Salmonella+enterica%22">Salmonella enterica*</searchLink>/<searchLink fieldCode="MM" term="%22Salmonella+enterica+drug+effects%22">drug effects</searchLink> <br /><searchLink fieldCode="MM" term="%22Salmonella+enterica%22">Salmonella enterica*</searchLink>/<searchLink fieldCode="MM" term="%22Salmonella+enterica+isolation+%26+purification%22">isolation & purification</searchLink> <br /><searchLink fieldCode="MM" term="%22Chickens%22">Chickens*</searchLink>/<searchLink fieldCode="MM" term="%22Chickens+microbiology%22">microbiology</searchLink> <br /><searchLink fieldCode="MM" term="%22Drug+Resistance%2C+Multiple%2C+Bacterial%22">Drug Resistance, Multiple, Bacterial*</searchLink>/<searchLink fieldCode="MM" term="%22Drug+Resistance%2C+Multiple%2C+Bacterial+genetics%22">genetics</searchLink> <br /><searchLink fieldCode="MM" term="%22Salmonella+Infections%2C+Animal%22">Salmonella Infections, Animal*</searchLink>/<searchLink fieldCode="MM" term="%22Salmonella+Infections%2C+Animal+microbiology%22">microbiology</searchLink> <br /><searchLink fieldCode="MM" term="%22Salmonella+Infections%2C+Animal%22">Salmonella Infections, Animal*</searchLink>/<searchLink fieldCode="MM" term="%22Salmonella+Infections%2C+Animal+epidemiology%22">epidemiology</searchLink> <br /><searchLink fieldCode="MM" term="%22Poultry+Diseases%22">Poultry Diseases*</searchLink>/<searchLink fieldCode="MM" term="%22Poultry+Diseases+microbiology%22">microbiology</searchLink> <br /><searchLink fieldCode="MM" term="%22Interspersed+Repetitive+Sequences%22">Interspersed Repetitive Sequences*</searchLink>/<searchLink fieldCode="MM" term="%22Interspersed+Repetitive+Sequences+genetics%22">genetics</searchLink> <br /><searchLink fieldCode="MM" term="%22Genetic+Variation%22">Genetic Variation*</searchLink><br /><searchLink fieldCode="MH" term="%22Anti-Bacterial+Agents%22">Anti-Bacterial Agents</searchLink>/<searchLink fieldCode="MH" term="%22Anti-Bacterial+Agents+pharmacology%22">pharmacology</searchLink> ; <searchLink fieldCode="MH" term="%22Animals%22">Animals</searchLink> ; <searchLink fieldCode="MH" term="%22Egypt%22">Egypt</searchLink> ; <searchLink fieldCode="MH" term="%22Integrons%22">Integrons</searchLink> ; <searchLink fieldCode="MH" term="%22Microbial+Sensitivity+Tests%22">Microbial Sensitivity Tests</searchLink> ; <searchLink fieldCode="MH" term="%22Genotype%22">Genotype</searchLink>
– Name: Abstract
  Label: Abstract
  Group: Ab
  Data: Salmonella enterica remains a leading foodborne zoonotic pathogen worldwide, with poultry serving as a major reservoir and vehicle for antimicrobial resistance dissemination to humans. This study investigated the genotypic basis and distribution of multidrug resistance (MDR) among 29 S. enterica isolates from broiler farms in Egypt, emphasizing the role of mobile genetic elements as integrons and the assessment of genetic relatedness using ERIC-PCR. Molecular screening revealed high prevalence of resistance determinants, including floR (93.1%), tetA (86.2%), aphA1 (82.8%), cmlA (75.9%), ereA (75.9%), sulI (62.1%), aadA1 (51.7%), dfrA1 (48.3%), aac(3)-IV (44.8%), tetB (41.4%), sulII (31.0%), aac(6')-Ib-cr (24.1%), catA1 (20.7%), fosA3 (20.7%), and qnrA (10.3%). High-risk serovars, including S. Jerusalem, S. Colorado, and S. Kentucky, harbored multiple resistance genes and exhibited pronounced XDR profiles. Notably, this study reports the detection of aphA1 and fosA3 in Salmonella isolates derived from broiler chickens, which may represent an early or uncommon finding in Egypt. Many resistance genes were associated with horizontally transferable class 1 integron, underscoring its key role in the dissemination of multidrug resistance (MDR) within poultry systems and along the food chain. ERIC-PCR genotyping segregated isolates into two major genetic groups with seven sub-clusters, reflecting clustering patterns and genetic diversity among the isolates, alongside notable heterogeneity in resistance, virulence, and biofilm-associated genes.Overall, poultry in Egypt represents a significant reservoir of genetically diverse and potentially transmissible MDR S. enterica, highlighting the need for enhanced antimicrobial stewardship and genomic surveillance to mitigate public health risks.<br /> (© 2026. The Author(s).)
– Name: Abstract
  Label: Competing Interests
  Group: Ab
  Data: Declarations. Competing interests: The authors declare no competing interests. Ethical approval: The study protocol was reviewed and approved by the Research Ethics Committee of the Faculty of Veterinary Medicine, Mansoura University, Egypt [Approval Code: MU-ACUC (VM.PhD.23.10.24)]. All experimental procedures were conducted in full compliance with the institutional guidelines and relevant national regulations for the care and use of animals.
– Name: Ref
  Label: References
  Group: RefInfo
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– Name: SubjectMinor
  Label: Contributed Indexing
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  Data: <i>Keywords: </i>Salmonella enterica; Antimicrobial resistance; Broiler chicken; ERIC-PCR; Egypt; Integron; Public health concern
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  Data: <i>Date Created: </i>20260703 <i>Date Completed: </i>20260703 <i>Latest Revision: </i>20260813
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  Data: 10.1038/s41598-026-59913-w
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        Value: 10.1038/s41598-026-59913-w
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      – Code: eng
        Text: English
    Subjects:
      – SubjectFull: Anti-Bacterial Agents pharmacology
        Type: general
      – SubjectFull: Animals
        Type: general
      – SubjectFull: Egypt
        Type: general
      – SubjectFull: Integrons
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      – SubjectFull: Salmonella enterica isolation & purification
        Type: general
      – SubjectFull: Chickens microbiology
        Type: general
      – SubjectFull: Drug Resistance, Multiple, Bacterial genetics
        Type: general
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      – SubjectFull: Salmonella Infections, Animal epidemiology
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      – SubjectFull: Interspersed Repetitive Sequences genetics
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      – SubjectFull: Genetic Variation
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    Titles:
      – TitleFull: Genetic diversity and mobile genetic element associated multidrug resistance in Salmonella enterica from broiler chickens in Egypt.
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              Text: 2026 Jul 03
              Type: published
              Y: 2026
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