Dataset Information

Molecular Characterization of IMP-1-Producing Enterobacter cloacae Complex Isolates in Tokyo.

ABSTRACT: Although KPC enzymes are most common among carbapenemases produced by Enterobacter cloacae complex globally, the epidemiology varies from one country to another. While previous studies have suggested that IMP enzymes are most common in Japan, detailed analysis has been scarce thus far. Here, we carried out a molecular epidemiological study and plasmid analysis of IMP-1-producing E. cloacae complex isolates collected from three hospitals in central Tokyo using whole-genome sequencing. Seventy-one isolates were classified into several sequence types (STs), and 49 isolates were identified as Enterobacter hormaechei ST78. Isolates of ST78 were divided into three clades by core-genome single nucleotide polymorphism (SNP)-based phylogenetic analysis. Whereas isolates of clade 3 were isolated from only one hospital, isolates of clade 1 and 2 were identified from multiple hospitals. Ten of 12 clade 1 isolates and 1 of 4 clade 2 isolates carried blaIMP-1 on IncHI2 plasmids, with high similarity of genetic structures. In addition, these plasmids shared backbone structures with IncHI2 plasmids carrying blaIMP reported from other countries of the Asia-Pacific region. All isolates of clade 3 except one carried blaIMP-1 in In1426 on IncW plasmids. An isolate of clade 3, which lacked IncW plasmids, carried blaIMP-1 in In1426 on an IncFIB plasmid. These observations suggest that IMP-producing E. cloacae complex isolates with a diversity of host genomic backgrounds have spread in central Tokyo, and they indicate the possible contribution of IncHI2 plasmids toward this phenomenon.

SUBMITTER: Aoki K

PROVIDER: S-EPMC5826111 | biostudies-literature | 2018 Mar

REPOSITORIES: biostudies-literature

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Molecular Characterization of IMP-1-Producing Enterobacter cloacae Complex Isolates in Tokyo.

Aoki Kotaro K Harada Sohei S Yahara Koji K Ishii Yoshikazu Y Motooka Daisuke D Nakamura Shota S Akeda Yukihiro Y Iida Tetsuya T Tomono Kazunori K Iwata Satoshi S Moriya Kyoji K Tateda Kazuhiro K

Antimicrobial agents and chemotherapy 20180223 3

Although KPC enzymes are most common among carbapenemases produced by <i>Enterobacter cloacae</i> complex globally, the epidemiology varies from one country to another. While previous studies have suggested that IMP enzymes are most common in Japan, detailed analysis has been scarce thus far. Here, we carried out a molecular epidemiological study and plasmid analysis of IMP-1-producing <i>E. cloacae</i> complex isolates collected from three hospitals in central Tokyo using whole-genome sequencin ...[more]

PMID: 29311089

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Project description:BackgroundInformation about the clinical and microbiological characteristics of IMP-producing Enterobacterales has been limited. Here, we describe an institutional outbreak of IMP-producing Enterobacter cloacae complex (ECC) involving multiple clades of ECC sequence type (ST) 78 strains.MethodsAntimicrobial susceptibility testing, whole-genome sequencing, and conjugation experiments of 18 IMP-producing ECC strains isolated during four-year study period were performed. Species and subspecies were determined by average nucleotide identity analysis and clonal relatedness of the isolates was analyzed with multilocus sequence typing and core-genome single nucleotide polymorphism (SNP) analysis. Relevant clinical information was extracted from medical records.ResultsFourteen of 18 IMP-producing ECC isolates were determined as Enterobacter hormaechei ST78. Sixteen isolates, including 13 isolates belonging to ST78, carried blaIMP-1 in In316-like class 1 integron and also carried IncHI2 plasmids. Conjugation experiments were successful for 12 isolates carrying blaIMP-1 on IncHI2 plasmids and for an isolate carrying blaIMP-11 on an IncL/M plasmid. Although isolation of ST78 strains was clustered in a 14-months period suggesting nosocomial transmission, these strains were subdivided into three clades by SNP analysis: clade A (n = 10), clade B (n = 1), clade C (n = 3). A part of clonal relatedness was unexpected by the epidemiological information at the time of isolation of the strains. Most of the IMP-producing ECC strains were susceptible to non-β-lactam antibiotics and had relatively low minimum inhibitory concentrations to carbapenems (≤4 μg/mL). Five of six infections caused by IMP-producing ECC were treated successfully.ConclusionsWhole-genome sequencing analysis revealed the outbreak was caused by three different clades of ST78 strains, where patients had favorable treatment outcome of the infections compared with that caused by Enterobacterales producing other carbapenemases, possibly due to their non-multidrug-resistant phenotype.

Project description:ObjectivesLittle is known about IMP-producing Enterobacterales (IMP-Ent) in Europe. We analyzed at genomic and phenotypic level IMP-Ent isolates circulating in Spain in a 9-year period.Materials and methodsIMP-Ent isolates submitted to our reference laboratory were included. Antibiotic susceptibility was performed using microdilution method (EUCAST), and IMP-carbapenemase activity was measured with carbapenemase inhibitors, the β-CARBA method, the modified Hodge test (MHT), and the modified carbapenemase inhibition method (mCIM). All isolates collected were sequenced for high-resolution single-nucleotide polymorphism (SNP) typing, core genome multilocus sequence typing (cgMLST), and resistome analysis.ResultsFifty IMP-Ent isolates, collected from 19 hospitals in 13 Spanish provinces, were detected: Klebsiella pneumoniae (IMP-Kpn) (24; 48%), Enterobacter roggenkampii (13; 26%), Enterobacter hormaechei (8, 16%), Klebsiella oxytoca (two; 4%), Enterobacter asburiae (one, 2%), Serratia marcescens (one; 2%) and Escherichia coli (one; 2%). All isolates were positive by the MHT and β-CARBA tests; 48 (96%) were mCIM positive; 12 (24%) and 26 (52%) displayed positive inhibition with dipicolinic (meropenem) and EDTA (ertapenem), respectively. Five IMP-carbapenemase types were identified: IMP-8 (22; 44%), IMP-22 (17; 34%), IMP-13 (7; 14%), IMP-28 (two; 4%), and IMP-15 (two; 4%), predominating IMP-8 in K. pneumoniae and IMP-22 in E. roggenkampii. IMP-28 was exclusively identified in K. oxytoca and IMP-15 in E. hormaechei. Predominant STs were ST405 (29.2%), ST15 (25%) and ST464 (20.8%) in IMP-Kpn; ST96 (100%) in E. roggenkampii and ST182 (62.5%) in E. hormachei. Colistin and amikacin were the most active non-carbapenem antibiotics against IMP-Ent.ConclusionIMP-Ent isolates remain infrequent in Spain, although in recent years have been circulating causing nosocomial outbreaks, being IMP-8-producing K. pneumoniae and IMP-22-producing E. roggenkampii the most frequently detected in this study. Inhibition with EDTA or dipicolinic acid presented false negative results in some IMP-producing strains. Active microbiological and molecular surveillance is essential for a better comprehension and control of IMP-Ent dissemination.

Project description:PurposeTo explore the genetic characteristics of the IMP-4 and SFO-1 co-producing multidrug-resistant (MDR) clinical isolates, Enterobacter hormaechei YQ13422hy and YQ13530hy.MethodsMALDI-TOF MS was used for species identification. Antibiotic resistance genes (ARGs) were tested by PCR and Sanger sequencing analysis. In addition to agar dilution, broth microdilution was used for antimicrobial susceptibility testing (AST). Whole-genome sequencing (WGS) analysis was conducted using the Illumina NovaSeq 6000 and Oxford Nanopore platforms. Annotation was performed by RAST on the genome. The phylogenetic tree was achieved using kSNP3.0. Plasmid characterization was conducted using S1-pulsed-field gel electrophoresis (S1-PFGE), Southern blotting, conjugation experiments, and whole genome sequencing (WGS). An in-depth study of the conjugation module was conducted using the OriTFinder website. The genetic context of bla IMP-4 and bla SFO-1 was analyzed using BLAST Ring Image Generator (BRIG) and Easyfig 2.3.ResultsYQ13422hy and YQ13530hy, two MDR strains of ST51 E. hormaechei harboring bla IMP-4 and bla SFO-1, were identified. They were only sensitive to meropenem, amikacin and polymyxin B, and were resistant to cephalosporins, aztreonam, piperacillin/tazobactam and aminoglycosides, intermediate to imipenem. The genetic context surrounding bla IMP-4 was 5'CS-hin-1-IS26-IntI1-bla IMP-4-IS6100-ecoRII. The integron of bla IMP-4 is In823, which is the array of gene cassettes of 5'CS-bla IMP-4. Phylogenetic analysis demonstrated that E. hormaechei YQ13422hy and YQ13530hy belonged to the same small clusters with a high degree of homology.ConclusionThis observation revealed the dissemination of the bla IMP-4 gene in E. hormaechei in China. We found that bla IMP-4 and bla SFO-1 co-exist in MDR clinical E. hormaechei isolates. This work showed a transferable IncN-type plasmid carrying the bla IMP-4 resistance gene in E. hormaechei. We examined the potential resistance mechanisms of pYQ13422-IMP-4 and pYQ13422-SFO-1, along with their detailed genetic contexts.

Dataset Information

Molecular Characterization of IMP-1-Producing Enterobacter cloacae Complex Isolates in Tokyo.

Publications

Molecular Characterization of IMP-1-Producing Enterobacter cloacae Complex Isolates in Tokyo.

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