Antibiotic Resistance, Virulence Factors, Phenotyping, and Genotyping of Non-Escherichia coli Enterobacterales from the Gut Microbiota of Healthy Subjects.

Alberto Amaretti,Maddalena Rossi,Lucia Righini,Giovanna Angela Gentilomi,Francesco Candeliere,Eliana Musmeci,Francesca Bonvicini,Stefano Raimondi

doi:10.3390/ijms21051847

Abstract

Non-Escherichia coli Enterobacterales (NECE) can colonize the human gut and may present virulence determinants and phenotypes that represent severe heath concerns. Most information is available for virulent NECE strains, isolated from patients with an ongoing infection, while the commensal NECE population of healthy subjects is understudied. In this study, 32 NECE strains were isolated from the feces of 20 healthy adults. 16S rRNA gene sequencing and mass spectrometry attributed the isolates to Klebsiella pneumoniae, Klebsiella oxytoca, Enterobacter cloacae, Enterobacter aerogenes, Enterobacter kobei, Citrobacter freundii, Citrobacter amalonaticus, Cronobacter sp., and Hafnia alvei, Morganella morganii, and Serratia liquefaciens. Multiplex PCR revealed that K. pneumoniae harbored virulence genes for adhesins (mrkD, ycfM, and kpn) and enterobactin (entB) and, in one case, also for yersiniabactin (ybtS, irp1, irp2, and fyuA). Virulence genes were less numerous in the other NECE species. Biofilm formation was spread across all the species, while curli and cellulose were mainly produced by Citrobacter and Enterobacter. Among the most common antibiotics, amoxicillin-clavulanic acid was the sole against which resistance was observed, only Klebsiella strains being susceptible. The NECE inhabiting the intestine of healthy subjects have traits that may pose a health threat, taking into account the possibility of horizontal gene transfer.

Highlights

Important enteric pathogens belong to Enterobacterales, a bacterial order within the phylum Proteobacteria
32 Non-Escherichia coli Enterobacterales (NECE) strains were isolated from the feces of 20 healthy adults. 16S rRNA gene sequencing and mass spectrometry attributed the isolates to Klebsiella pneumoniae, Klebsiella oxytoca, Enterobacter cloacae, Enterobacter aerogenes, Enterobacter kobei, Citrobacter freundii, Citrobacter amalonaticus, Cronobacter sp., and Hafnia alvei, Morganella morganii, and Serratia liquefaciens
Thirty-two NECE strains were isolated from the feces of 20 healthy adults that did not present any dysbiosis, and as members of a relatively balanced gut microbiota

Summary

Introduction

Important enteric pathogens belong to Enterobacterales, a bacterial order within the phylum Proteobacteria. This order encompasses permanent colonizers of the human gut that, in healthy conditions, constitute minor bacterial components of the microbiota. Opportunistic Enterobacterales can persist as gut commensals without inducing any infections, as long as the microbiota is balanced and the complex and dense bacterial community prevents their overgrowth. Escherichia coli is the most studied among the Enterobacterales with regards to the traits that differentiate commensalism and pathogenicity. It normally colonizes the intestine but comprises both harmless commensals and different pathogenic variants that may instigate infections in the gut or in other tissues [1,2]. Virulent strains of E. coli isolated from infected patients attracted most research interest [3,4], and fecal isolates from healthy subjects and environmental strains are the target of increasing attention, aiming to determine the pathogenic potential of a wider biodiversity reservoir [5,6]

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Conclusion