Genetic background of neomycin resistance in clinical Escherichia coli isolated from Danish pig farms
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Genetic background of neomycin resistance in clinical Escherichia coli isolated from Danish pig farms. / Subramani, Prabha; Menichincheri, Gaia; Pirolo, Mattia; Arcari, Gabriele; Kudirkiene, Egle; Polani, Riccardo; Carattoli, Alessandra; Damborg, Peter; Guardabassi, Luca.
In: Applied and Environmental Microbiology, Vol. 89, No. 10, e00559-23, 2023.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Genetic background of neomycin resistance in clinical Escherichia coli isolated from Danish pig farms
AU - Subramani, Prabha
AU - Menichincheri, Gaia
AU - Pirolo, Mattia
AU - Arcari, Gabriele
AU - Kudirkiene, Egle
AU - Polani, Riccardo
AU - Carattoli, Alessandra
AU - Damborg, Peter
AU - Guardabassi, Luca
N1 - Publisher Copyright: Copyright © 2023 American Society for Microbiology. All Rights Reserved.
PY - 2023
Y1 - 2023
N2 - Neomycin is the first-choice antibiotic for the treatment of porcine enteritis caused by enterotoxigenic Escherichia coli. Resistance to this aminoglycoside is on the rise after the increased use of neomycin due to the ban on zinc oxide. We identified the neomycin resistance determinants and plasmid contents in a historical collection of 128 neomycin-resistant clinical E. coli isolates from Danish pig farms. All isolates were characterized by whole-genome sequencing and antimicrobial susceptibility testing, followed by conjugation experiments and long-read sequencing of eight selected representative strains. We detected 35 sequence types (STs) with ST100 being the most prevalent lineage (38.3%). Neomycin resistance was associated with two resistance genes, namely aph(3′)-Ia and aph(3′)-Ib, which were identified in 93% and 7% of the isolates, respectively. The aph(3′)-Ia was found on different large conjugative plasmids belonging to IncI1α, which was present in 67.2% of the strains, on IncHI1, IncHI2, and IncN, as well as on a multicopy ColRNAI plasmid. All these plasmids except ColRNAI carried genes encoding resistance to other antimicrobials or heavy metals, highlighting the risk of co-selection. The aph(3′)-Ib gene occurred on a 19 kb chimeric, mobilizable plasmid that contained elements tracing back its origin to distantly related genera. While aph(3′)-Ia was flanked by either Tn903 or Tn4352 derivatives, no clear association was observed between aph(3′)-Ib and mobile genetic elements. In conclusion, the spread of neomycin resistance in porcine clinical E. coli is driven by two resistance determinants located on distinct plasmid scaffolds circulating within a highly diverse population dominated by ST100. IMPORTANCE Neomycin is the first-choice antibiotic for the management of Escherichia coli enteritis in pigs. This work shows that aph(3′)-Ia and to a lesser extent aph(3′)-Ib are responsible for the spread of neomycin resistance that has been recently observed among pig clinical isolates and elucidates the mechanisms of dissemination of these two resistance determinants. The aph(3′)-Ia gene is located on different conjugative plasmid scaffolds and is associated with two distinct transposable elements (Tn903 and Tn4352) that contributed to its spread. The diffusion of aph(3′)-Ib is mediated by a small non-conjugative, mobilizable chimeric plasmid that likely derived from distantly related members of the Pseudomonadota phylum and was not associated with any detectable mobile genetic element. Although the spread of neomycin resistance is largely attributable to horizontal transfer, both resistance determinants have been acquired by a predominant lineage (ST100) associated with enterotoxigenic E. coli, which accounted for approximately one-third of the strains.
AB - Neomycin is the first-choice antibiotic for the treatment of porcine enteritis caused by enterotoxigenic Escherichia coli. Resistance to this aminoglycoside is on the rise after the increased use of neomycin due to the ban on zinc oxide. We identified the neomycin resistance determinants and plasmid contents in a historical collection of 128 neomycin-resistant clinical E. coli isolates from Danish pig farms. All isolates were characterized by whole-genome sequencing and antimicrobial susceptibility testing, followed by conjugation experiments and long-read sequencing of eight selected representative strains. We detected 35 sequence types (STs) with ST100 being the most prevalent lineage (38.3%). Neomycin resistance was associated with two resistance genes, namely aph(3′)-Ia and aph(3′)-Ib, which were identified in 93% and 7% of the isolates, respectively. The aph(3′)-Ia was found on different large conjugative plasmids belonging to IncI1α, which was present in 67.2% of the strains, on IncHI1, IncHI2, and IncN, as well as on a multicopy ColRNAI plasmid. All these plasmids except ColRNAI carried genes encoding resistance to other antimicrobials or heavy metals, highlighting the risk of co-selection. The aph(3′)-Ib gene occurred on a 19 kb chimeric, mobilizable plasmid that contained elements tracing back its origin to distantly related genera. While aph(3′)-Ia was flanked by either Tn903 or Tn4352 derivatives, no clear association was observed between aph(3′)-Ib and mobile genetic elements. In conclusion, the spread of neomycin resistance in porcine clinical E. coli is driven by two resistance determinants located on distinct plasmid scaffolds circulating within a highly diverse population dominated by ST100. IMPORTANCE Neomycin is the first-choice antibiotic for the management of Escherichia coli enteritis in pigs. This work shows that aph(3′)-Ia and to a lesser extent aph(3′)-Ib are responsible for the spread of neomycin resistance that has been recently observed among pig clinical isolates and elucidates the mechanisms of dissemination of these two resistance determinants. The aph(3′)-Ia gene is located on different conjugative plasmid scaffolds and is associated with two distinct transposable elements (Tn903 and Tn4352) that contributed to its spread. The diffusion of aph(3′)-Ib is mediated by a small non-conjugative, mobilizable chimeric plasmid that likely derived from distantly related members of the Pseudomonadota phylum and was not associated with any detectable mobile genetic element. Although the spread of neomycin resistance is largely attributable to horizontal transfer, both resistance determinants have been acquired by a predominant lineage (ST100) associated with enterotoxigenic E. coli, which accounted for approximately one-third of the strains.
KW - AMR
KW - clonal diversity
KW - conjugation
KW - enterotoxigenic Escherichia coli
KW - neomycin
KW - plasmids
U2 - 10.1128/aem.00559-23
DO - 10.1128/aem.00559-23
M3 - Journal article
C2 - 37787538
AN - SCOPUS:85175741367
VL - 89
JO - Applied and Environmental Microbiology
JF - Applied and Environmental Microbiology
SN - 0099-2240
IS - 10
M1 - e00559-23
ER -
ID: 375056705