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

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.

Hypervirulent and hypermucoviscous extended-spectrum β-lactamase-producing Klebsiella pneumoniae and Klebsiella variicola in Chile

“…Both isolates contained the aerobactin gene iutA , mannose-sensitive type 1 fimbriae (fimABCD operon), the mannose-resistant Klebsiella -like (type III) fimbriae cluster (mrkABCDFHIJ ), and the E. coli common pilus operon ( ecpABCDE ) and biofilm related ( treC, sugE ) genes, which are associated with mucoviscosity and CPS production [ 26 ]. Only hmKp UCO-494 carried additionally the enterobactin ( entB, entF, and ycfH ), yersiniabactin siderophore cluster ybtAEPQSTUX and the siderophore genes irp1 and irp2 , which are considered as genetic markers for high-pathogenicity island [ 27 ] ( Table 1 ). It is important to highlight that in both strains the presence of rmpA/A2 was not identified.…”

Relevance of Citrobacter species in urinary tract infections: a 10 year surveillance study

“…A Citrobacter-Enterobacter-Serratia fajok (ún. CESbaktériumok vagy non -E. coli Enterobacteriaceae (NECE) fajok) együtt tárgyalását a hasonló biokémiai tulajdonságaik, prevalenciájuk és genetikailag kódolt (természetes és szerzett) rezisztencia-mechanizmusaik indokolják [10,11]. A Citrobacter fajok kórokozó jellegét UTI-kban, légúti infekciókban, bacteriaemiában és szepszisben, gastroenteritisben, kötőhártya-gyulladásban, szívbelhártya-gyulladásban, meningitisben (mind felnőttek, mind újszülöttek esetén) és agytályogok kialakulásában leírták [12,13].…”

Microbial Virulence Factors

“…The isolates were further characterized concerning the presence in their genomes of genes encoding selected virulence factors, as well as their phenotypes related to biofilm formation and resistance to a selection of antibiotics. Results point out that the isolates do not encompass particularly virulent strains and in most of the cases were susceptible to antibiotics [2].…”

“…The presence of genes related to virulence factors including adhesins, siderophores, protectines or invasins, and involved in allantoin metabolism were investigated among 32 non-E. coli Enterobacterales isolates obtained from the feces of 20 healthy adults [2]. Similar studies analyzed virulent NECE strains from patients with an ongoing infection, and not commensal NECE from healthy subjects as in the present study [2]. Isolates were taxonomically characterized by 16S RNA sequencing and MALDI-TOF MS analysis, and profiled by pulsed-field gel electrophoresis.…”

“…Isolates were taxonomically characterized by 16S RNA sequencing and MALDI-TOF MS analysis, and profiled by pulsed-field gel electrophoresis. The genus Klebsiella was found as the most represented, followed by Enterobacter and Citrobacter [2]. The isolates were further characterized concerning the presence in their genomes of genes encoding selected virulence factors, as well as their phenotypes related to biofilm formation and resistance to a selection of antibiotics.…”