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Escherichia coli of sequence type 3835 carrying bla NDM-1, bla CTX-M-15, bla CMY-42 and bla SHV-12.

Feng Y, Yang P, Xie Y, Wang X, McNally A, Zong Z - Sci Rep (2015)

Bottom Line: It was resistant to imipenem (MIC, >256 μg/ml) and meropenem (MIC, 128 μg/ml) and belonged to ST3835. bla NDM-1 was the only carbapenemase gene detected.In conclusion, a multidrug-resistant ST3835 E. coli clinical strain carrying bla NDM-1, bla CTX-M-15, bla CMY-42 and bla SHV-12 was identified.IncX3 plasmids may be making a significant contribution to the dissemination of bla NDM among Enterobacteriaceae in China.

View Article: PubMed Central - PubMed

Affiliation: 1] Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China [2] Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China.

ABSTRACT
New Delhi metallo-β-lactamase (NDM) represents a serious challenge for treatment and public health. A carbapenem-resistant Escherichia coli clinical strain WCHEC13-8 was subjected to antimicrobial susceptibility tests, whole genome sequencing and conjugation experiments. It was resistant to imipenem (MIC, >256 μg/ml) and meropenem (MIC, 128 μg/ml) and belonged to ST3835. bla NDM-1 was the only carbapenemase gene detected. Strain WCHEC13-8 also had a plasmid-borne AmpC gene (bla CMY-42) and two extended-spectrum β-lactamase genes (bla CTX-M-15 and bla SHV-12). bla NDM-1 and bla SHV-12 were carried by a 54-kb IncX3 self-transmissible plasmid, which is identical to plasmid pNDM-HF727 from Enterobacter cloacae. bla CMY-42 was carried by a 64-kb IncI1 plasmid and bla CTX-M-15 was located on a 141-kb plasmid with multiple F replicons (replicon type: F36:A4:B1). bla CMY-42 was in a complicated context and the mobilisation of bla CMY-42 was due to the transposition of ISEcp1 by misidentifying its right-end boundary. Genetic context of bla NDM-1 in strain WCHEC13-8 was closely related to those on IncX3 plasmids in various Enterobacteriaceae species in China. In conclusion, a multidrug-resistant ST3835 E. coli clinical strain carrying bla NDM-1, bla CTX-M-15, bla CMY-42 and bla SHV-12 was identified. IncX3 plasmids may be making a significant contribution to the dissemination of bla NDM among Enterobacteriaceae in China.

No MeSH data available.


Related in: MedlinePlus

Genetic context of blaCMY-42 and its formation on pCMY42_EC8.Panel A, The context of blaCMY-42. Δ and shapes with a forked tail represent truncated genes or insertion sequences. The broken line represents a 27.4 kb region between traC and finQ, which is not scaled. The putative alternative IRR (IRR2) of ISEcp1 is depicted as a red pole and the alignment of the IRL of ISEcp1 and the IRR2 is shown. ISEcp1 and traB are both interrupted into two parts. The 9-bp nucleotide repeats belonging to ISEcp1 are depicted in blue and those of traB are in red, while the 5-bp nucleotide repeats belonging to finQ is shown in bold. Panel B, The proposed scheme for the formation of the context of blaCMY-42. The ISEcp1-blaCMY-42-IRR2 region (structure 1) is inserted into the finQ gene of the traA-trbA region (structure 2) on an IncI1 plasmid and then generates the structure 3 with the 5-bp characteristic DR (GATAA). Two copies of IS1 (structure 4) are then inserted into traB and ISEcp1, respectively, generating the structure 5 with the 9-bp DR (CCGTCAATA for traB and CGTTTGAAG for ISEcp1), which is the characteristic of IS1 insertion. The subsequent homologous recombination between the two copies of IS1 mediates the inversion (shown by two broken arrows) of the intervening region (grey part) and then forms the context of blaCMY-42 on pCMY42_EC8 (structure 6).
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f1: Genetic context of blaCMY-42 and its formation on pCMY42_EC8.Panel A, The context of blaCMY-42. Δ and shapes with a forked tail represent truncated genes or insertion sequences. The broken line represents a 27.4 kb region between traC and finQ, which is not scaled. The putative alternative IRR (IRR2) of ISEcp1 is depicted as a red pole and the alignment of the IRL of ISEcp1 and the IRR2 is shown. ISEcp1 and traB are both interrupted into two parts. The 9-bp nucleotide repeats belonging to ISEcp1 are depicted in blue and those of traB are in red, while the 5-bp nucleotide repeats belonging to finQ is shown in bold. Panel B, The proposed scheme for the formation of the context of blaCMY-42. The ISEcp1-blaCMY-42-IRR2 region (structure 1) is inserted into the finQ gene of the traA-trbA region (structure 2) on an IncI1 plasmid and then generates the structure 3 with the 5-bp characteristic DR (GATAA). Two copies of IS1 (structure 4) are then inserted into traB and ISEcp1, respectively, generating the structure 5 with the 9-bp DR (CCGTCAATA for traB and CGTTTGAAG for ISEcp1), which is the characteristic of IS1 insertion. The subsequent homologous recombination between the two copies of IS1 mediates the inversion (shown by two broken arrows) of the intervening region (grey part) and then forms the context of blaCMY-42 on pCMY42_EC8 (structure 6).

Mentions: The genetic context of blaCMY-42 has not been described before. On pCMY42_EC8, blaCMY-42 is adjacent to the insertion sequence ISEcp1, which was truncated by the insertion of IS1, at upstream and a gene encoding outer membrane lipoprotein at downstream (Panel A, Fig. 1). The remaining part of ISEcp1 was found 24.7-kb further upstream of blaCMY-42 and was also truncated by IS1. After carefully examining the flanking sequences of ISEcp1 and IS1, it became evident that the complex genetic context of blaCMY-42 has been formed by the transposition of ISEcp1 and the insertion of two copies of IS1 followed by homologous recombination between the two IS1 (Panel B, Fig. 1) as explained as below. First, both of the two IS1 were flanked by a remnant of ISEcp1 and a part of the traB gene, which is involved in plasmid conjugation. The two remnants of ISEcp1 form a complete ISEcp1 plus a 9-bp repeat, which abuts the two IS1 and is characteristic of the insertion of IS1. Similarly, the two parts of traB make the complete traB plus the characteristic 9-bp repeat. It is therefore clear that both ISEcp1 and traB had been interrupted by the insertion of IS1 and the subsequent homologous recombination between the two copies of IS1 could result in the inversion of the intervening region (Panel B, Fig. 1). Second, it has been proven that a single copy of ISEcp1 is able to mobilise its downstream genetic components by using alternative sequences as the right-hand inverted repeat (IRR)15. By comparing genetic contexts of blaCMY-2 and its variants available in GenBank using BLAST, the same 4 kb element comprising ISEcp1, blaCMY, blc (encoding an outermembrane lipoprotein) and sugE (encoding a quaternary ammonium compound-resistance protein) has been found on different plasmids but with varied abutting sequences. This element is bounded by a 14 bp sequence (AACCAGAAAGTCGA) at one end, which shows some similarity with the left-hand inverted repeat (IRL) of ISEcp1 (Panel B, Fig. 1) and might have served as the alternative IRR (IRR2) for ISEcp1 to mobilise blaCMY to different locations. Indeed, when we put the two remnants of ISEcp1 back together, we found that the finQ gene (the transcriptional inhibitor of plasmid transfer) has been interrupted by the ISEcp1-blaCMY-42-IRR2 region with the presence of 5-bp direct target repeats (DR), which characterises the insertion of ISEcp1 (Panel B, Fig. 1). This confirms that the mobilisation of blaCMY-42 has been mediated by ISEcp1 by misidentifying its IRR.


Escherichia coli of sequence type 3835 carrying bla NDM-1, bla CTX-M-15, bla CMY-42 and bla SHV-12.

Feng Y, Yang P, Xie Y, Wang X, McNally A, Zong Z - Sci Rep (2015)

Genetic context of blaCMY-42 and its formation on pCMY42_EC8.Panel A, The context of blaCMY-42. Δ and shapes with a forked tail represent truncated genes or insertion sequences. The broken line represents a 27.4 kb region between traC and finQ, which is not scaled. The putative alternative IRR (IRR2) of ISEcp1 is depicted as a red pole and the alignment of the IRL of ISEcp1 and the IRR2 is shown. ISEcp1 and traB are both interrupted into two parts. The 9-bp nucleotide repeats belonging to ISEcp1 are depicted in blue and those of traB are in red, while the 5-bp nucleotide repeats belonging to finQ is shown in bold. Panel B, The proposed scheme for the formation of the context of blaCMY-42. The ISEcp1-blaCMY-42-IRR2 region (structure 1) is inserted into the finQ gene of the traA-trbA region (structure 2) on an IncI1 plasmid and then generates the structure 3 with the 5-bp characteristic DR (GATAA). Two copies of IS1 (structure 4) are then inserted into traB and ISEcp1, respectively, generating the structure 5 with the 9-bp DR (CCGTCAATA for traB and CGTTTGAAG for ISEcp1), which is the characteristic of IS1 insertion. The subsequent homologous recombination between the two copies of IS1 mediates the inversion (shown by two broken arrows) of the intervening region (grey part) and then forms the context of blaCMY-42 on pCMY42_EC8 (structure 6).
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Related In: Results  -  Collection

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f1: Genetic context of blaCMY-42 and its formation on pCMY42_EC8.Panel A, The context of blaCMY-42. Δ and shapes with a forked tail represent truncated genes or insertion sequences. The broken line represents a 27.4 kb region between traC and finQ, which is not scaled. The putative alternative IRR (IRR2) of ISEcp1 is depicted as a red pole and the alignment of the IRL of ISEcp1 and the IRR2 is shown. ISEcp1 and traB are both interrupted into two parts. The 9-bp nucleotide repeats belonging to ISEcp1 are depicted in blue and those of traB are in red, while the 5-bp nucleotide repeats belonging to finQ is shown in bold. Panel B, The proposed scheme for the formation of the context of blaCMY-42. The ISEcp1-blaCMY-42-IRR2 region (structure 1) is inserted into the finQ gene of the traA-trbA region (structure 2) on an IncI1 plasmid and then generates the structure 3 with the 5-bp characteristic DR (GATAA). Two copies of IS1 (structure 4) are then inserted into traB and ISEcp1, respectively, generating the structure 5 with the 9-bp DR (CCGTCAATA for traB and CGTTTGAAG for ISEcp1), which is the characteristic of IS1 insertion. The subsequent homologous recombination between the two copies of IS1 mediates the inversion (shown by two broken arrows) of the intervening region (grey part) and then forms the context of blaCMY-42 on pCMY42_EC8 (structure 6).
Mentions: The genetic context of blaCMY-42 has not been described before. On pCMY42_EC8, blaCMY-42 is adjacent to the insertion sequence ISEcp1, which was truncated by the insertion of IS1, at upstream and a gene encoding outer membrane lipoprotein at downstream (Panel A, Fig. 1). The remaining part of ISEcp1 was found 24.7-kb further upstream of blaCMY-42 and was also truncated by IS1. After carefully examining the flanking sequences of ISEcp1 and IS1, it became evident that the complex genetic context of blaCMY-42 has been formed by the transposition of ISEcp1 and the insertion of two copies of IS1 followed by homologous recombination between the two IS1 (Panel B, Fig. 1) as explained as below. First, both of the two IS1 were flanked by a remnant of ISEcp1 and a part of the traB gene, which is involved in plasmid conjugation. The two remnants of ISEcp1 form a complete ISEcp1 plus a 9-bp repeat, which abuts the two IS1 and is characteristic of the insertion of IS1. Similarly, the two parts of traB make the complete traB plus the characteristic 9-bp repeat. It is therefore clear that both ISEcp1 and traB had been interrupted by the insertion of IS1 and the subsequent homologous recombination between the two copies of IS1 could result in the inversion of the intervening region (Panel B, Fig. 1). Second, it has been proven that a single copy of ISEcp1 is able to mobilise its downstream genetic components by using alternative sequences as the right-hand inverted repeat (IRR)15. By comparing genetic contexts of blaCMY-2 and its variants available in GenBank using BLAST, the same 4 kb element comprising ISEcp1, blaCMY, blc (encoding an outermembrane lipoprotein) and sugE (encoding a quaternary ammonium compound-resistance protein) has been found on different plasmids but with varied abutting sequences. This element is bounded by a 14 bp sequence (AACCAGAAAGTCGA) at one end, which shows some similarity with the left-hand inverted repeat (IRL) of ISEcp1 (Panel B, Fig. 1) and might have served as the alternative IRR (IRR2) for ISEcp1 to mobilise blaCMY to different locations. Indeed, when we put the two remnants of ISEcp1 back together, we found that the finQ gene (the transcriptional inhibitor of plasmid transfer) has been interrupted by the ISEcp1-blaCMY-42-IRR2 region with the presence of 5-bp direct target repeats (DR), which characterises the insertion of ISEcp1 (Panel B, Fig. 1). This confirms that the mobilisation of blaCMY-42 has been mediated by ISEcp1 by misidentifying its IRR.

Bottom Line: It was resistant to imipenem (MIC, >256 μg/ml) and meropenem (MIC, 128 μg/ml) and belonged to ST3835. bla NDM-1 was the only carbapenemase gene detected.In conclusion, a multidrug-resistant ST3835 E. coli clinical strain carrying bla NDM-1, bla CTX-M-15, bla CMY-42 and bla SHV-12 was identified.IncX3 plasmids may be making a significant contribution to the dissemination of bla NDM among Enterobacteriaceae in China.

View Article: PubMed Central - PubMed

Affiliation: 1] Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China [2] Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China.

ABSTRACT
New Delhi metallo-β-lactamase (NDM) represents a serious challenge for treatment and public health. A carbapenem-resistant Escherichia coli clinical strain WCHEC13-8 was subjected to antimicrobial susceptibility tests, whole genome sequencing and conjugation experiments. It was resistant to imipenem (MIC, >256 μg/ml) and meropenem (MIC, 128 μg/ml) and belonged to ST3835. bla NDM-1 was the only carbapenemase gene detected. Strain WCHEC13-8 also had a plasmid-borne AmpC gene (bla CMY-42) and two extended-spectrum β-lactamase genes (bla CTX-M-15 and bla SHV-12). bla NDM-1 and bla SHV-12 were carried by a 54-kb IncX3 self-transmissible plasmid, which is identical to plasmid pNDM-HF727 from Enterobacter cloacae. bla CMY-42 was carried by a 64-kb IncI1 plasmid and bla CTX-M-15 was located on a 141-kb plasmid with multiple F replicons (replicon type: F36:A4:B1). bla CMY-42 was in a complicated context and the mobilisation of bla CMY-42 was due to the transposition of ISEcp1 by misidentifying its right-end boundary. Genetic context of bla NDM-1 in strain WCHEC13-8 was closely related to those on IncX3 plasmids in various Enterobacteriaceae species in China. In conclusion, a multidrug-resistant ST3835 E. coli clinical strain carrying bla NDM-1, bla CTX-M-15, bla CMY-42 and bla SHV-12 was identified. IncX3 plasmids may be making a significant contribution to the dissemination of bla NDM among Enterobacteriaceae in China.

No MeSH data available.


Related in: MedlinePlus