Characterization of mobile genetic elements in multidrug-resistant Bacteroides fragilis isolates from different hospitals in the Netherlands

K. E. Boiten; E. J. Kuijper; L. Schuele; J. van Prehn; L. G.M. Bode; I. Maat; S. A.V. van Asten; D. W. Notermans; J. W.A. Rossen; A. C.M. Veloo

doi:10.1016/j.anaerobe.2023.102722

Characterization of mobile genetic elements in multidrug-resistant Bacteroides fragilis isolates from different hospitals in the Netherlands

K. E. Boiten^*, E. J. Kuijper, L. Schuele, J. van Prehn, L. G.M. Bode, I. Maat, S. A.V. van Asten, D. W. Notermans, J. W.A. Rossen, A. C.M. Veloo

^*Corresponding author for this work

Microbes in Health and Disease (MHD)

Research output: Contribution to journal › Article › Academic › peer-review

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Abstract

Objectives: Five human clinical multidrug-resistant (MDR) Bacteroides fragilis isolates, including resistance to meropenem and metronidazole, were recovered at different hospitals in the Netherlands between 2014 and 2020 and sent to the anaerobic reference laboratory for full characterization. Methods: Isolates were recovered from a variety of clinical specimens from patients with unrelated backgrounds. Long- and short-read sequencing was performed, followed by a hybrid assembly to study the presence of mobile genetic elements (MGEs) and antimicrobial resistance genes (ARGs). Results: A cfxA gene was present on a transposon (Tn) similar to Tn4555 in two isolates. In two isolates a novel Tn was present with the cfxA gene. Four isolates harbored a nimE gene, located on a pBFS01_2 plasmid. One isolate contained a novel plasmid carrying a nimA gene with IS1168. The tetQ gene was present on novel conjugative transposons (CTns) belonging to the CTnDOT family. Two isolates harbored a novel plasmid with tetQ. Other ARGs in these isolates, but not on an MGE, were: cfiA, ermF, mef(EN2), and sul2. ARGs harboured differed between isolates and corresponded with the observed phenotypic resistance. Conclusions: Novel CTns, Tns, and plasmids were encountered in the five MDR B. fragilis isolates, complementing our knowledge on MDR and horizontal gene transfer in anaerobic bacteria.

Original language	English
Article number	102722
Number of pages	8
Journal	Anaerobe
Volume	81
DOIs	https://doi.org/10.1016/j.anaerobe.2023.102722
Publication status	Published - Jun-2023

Keywords

Antimicrobial resistance genes
Bacteroides fragilis
Horizontal gene transfer
Mobile genetic elements
Multidrug-resistant
Whole genome sequencing

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Boiten, K. E., Kuijper, E. J., Schuele, L., van Prehn, J., Bode, L. G. M., Maat, I., van Asten, S. A. V., Notermans, D. W., Rossen, J. W. A., & Veloo, A. C. M. (2023). Characterization of mobile genetic elements in multidrug-resistant Bacteroides fragilis isolates from different hospitals in the Netherlands. Anaerobe, 81, Article 102722. https://doi.org/10.1016/j.anaerobe.2023.102722

@article{3c0c00ab23d54a9ab574acd8e1089311,

title = "Characterization of mobile genetic elements in multidrug-resistant Bacteroides fragilis isolates from different hospitals in the Netherlands",

abstract = "Objectives: Five human clinical multidrug-resistant (MDR) Bacteroides fragilis isolates, including resistance to meropenem and metronidazole, were recovered at different hospitals in the Netherlands between 2014 and 2020 and sent to the anaerobic reference laboratory for full characterization. Methods: Isolates were recovered from a variety of clinical specimens from patients with unrelated backgrounds. Long- and short-read sequencing was performed, followed by a hybrid assembly to study the presence of mobile genetic elements (MGEs) and antimicrobial resistance genes (ARGs). Results: A cfxA gene was present on a transposon (Tn) similar to Tn4555 in two isolates. In two isolates a novel Tn was present with the cfxA gene. Four isolates harbored a nimE gene, located on a pBFS01_2 plasmid. One isolate contained a novel plasmid carrying a nimA gene with IS1168. The tetQ gene was present on novel conjugative transposons (CTns) belonging to the CTnDOT family. Two isolates harbored a novel plasmid with tetQ. Other ARGs in these isolates, but not on an MGE, were: cfiA, ermF, mef(EN2), and sul2. ARGs harboured differed between isolates and corresponded with the observed phenotypic resistance. Conclusions: Novel CTns, Tns, and plasmids were encountered in the five MDR B. fragilis isolates, complementing our knowledge on MDR and horizontal gene transfer in anaerobic bacteria.",

keywords = "Antimicrobial resistance genes, Bacteroides fragilis, Horizontal gene transfer, Mobile genetic elements, Multidrug-resistant, Whole genome sequencing",

author = "Boiten, {K. E.} and Kuijper, {E. J.} and L. Schuele and {van Prehn}, J. and Bode, {L. G.M.} and I. Maat and {van Asten}, {S. A.V.} and Notermans, {D. W.} and Rossen, {J. W.A.} and Veloo, {A. C.M.}",

note = "Funding Information: The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: JWAR has received consulting fees from IDbyDNA, ARES genetics, and Illumina. ACMV has received a grant from the National Institute for Public Health and the Environment. All other authors have none to declare. Publisher Copyright: {\textcopyright} 2023 The Authors",

year = "2023",

month = jun,

doi = "10.1016/j.anaerobe.2023.102722",

language = "English",

volume = "81",

journal = "Anaerobe",

issn = "1075-9964",

publisher = "ELSEVIER SCI LTD",

}

TY - JOUR

T1 - Characterization of mobile genetic elements in multidrug-resistant Bacteroides fragilis isolates from different hospitals in the Netherlands

AU - Boiten, K. E.

AU - Kuijper, E. J.

AU - Schuele, L.

AU - van Prehn, J.

AU - Bode, L. G.M.

AU - Maat, I.

AU - van Asten, S. A.V.

AU - Notermans, D. W.

AU - Rossen, J. W.A.

AU - Veloo, A. C.M.

N1 - Funding Information: The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: JWAR has received consulting fees from IDbyDNA, ARES genetics, and Illumina. ACMV has received a grant from the National Institute for Public Health and the Environment. All other authors have none to declare. Publisher Copyright: © 2023 The Authors

PY - 2023/6

Y1 - 2023/6

N2 - Objectives: Five human clinical multidrug-resistant (MDR) Bacteroides fragilis isolates, including resistance to meropenem and metronidazole, were recovered at different hospitals in the Netherlands between 2014 and 2020 and sent to the anaerobic reference laboratory for full characterization. Methods: Isolates were recovered from a variety of clinical specimens from patients with unrelated backgrounds. Long- and short-read sequencing was performed, followed by a hybrid assembly to study the presence of mobile genetic elements (MGEs) and antimicrobial resistance genes (ARGs). Results: A cfxA gene was present on a transposon (Tn) similar to Tn4555 in two isolates. In two isolates a novel Tn was present with the cfxA gene. Four isolates harbored a nimE gene, located on a pBFS01_2 plasmid. One isolate contained a novel plasmid carrying a nimA gene with IS1168. The tetQ gene was present on novel conjugative transposons (CTns) belonging to the CTnDOT family. Two isolates harbored a novel plasmid with tetQ. Other ARGs in these isolates, but not on an MGE, were: cfiA, ermF, mef(EN2), and sul2. ARGs harboured differed between isolates and corresponded with the observed phenotypic resistance. Conclusions: Novel CTns, Tns, and plasmids were encountered in the five MDR B. fragilis isolates, complementing our knowledge on MDR and horizontal gene transfer in anaerobic bacteria.

AB - Objectives: Five human clinical multidrug-resistant (MDR) Bacteroides fragilis isolates, including resistance to meropenem and metronidazole, were recovered at different hospitals in the Netherlands between 2014 and 2020 and sent to the anaerobic reference laboratory for full characterization. Methods: Isolates were recovered from a variety of clinical specimens from patients with unrelated backgrounds. Long- and short-read sequencing was performed, followed by a hybrid assembly to study the presence of mobile genetic elements (MGEs) and antimicrobial resistance genes (ARGs). Results: A cfxA gene was present on a transposon (Tn) similar to Tn4555 in two isolates. In two isolates a novel Tn was present with the cfxA gene. Four isolates harbored a nimE gene, located on a pBFS01_2 plasmid. One isolate contained a novel plasmid carrying a nimA gene with IS1168. The tetQ gene was present on novel conjugative transposons (CTns) belonging to the CTnDOT family. Two isolates harbored a novel plasmid with tetQ. Other ARGs in these isolates, but not on an MGE, were: cfiA, ermF, mef(EN2), and sul2. ARGs harboured differed between isolates and corresponded with the observed phenotypic resistance. Conclusions: Novel CTns, Tns, and plasmids were encountered in the five MDR B. fragilis isolates, complementing our knowledge on MDR and horizontal gene transfer in anaerobic bacteria.

KW - Antimicrobial resistance genes

KW - Bacteroides fragilis

KW - Horizontal gene transfer

KW - Mobile genetic elements

KW - Multidrug-resistant

KW - Whole genome sequencing

U2 - 10.1016/j.anaerobe.2023.102722

DO - 10.1016/j.anaerobe.2023.102722

M3 - Article

C2 - 37001724

AN - SCOPUS:85152680315

SN - 1075-9964

VL - 81

JO - Anaerobe

JF - Anaerobe

M1 - 102722

ER -

Characterization of mobile genetic elements in multidrug-resistant Bacteroides fragilis isolates from different hospitals in the Netherlands

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Keywords

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