Re-examining the association of AmpC variants with Enterobacter species in the context of updated taxonomy

2021 ◽  
Author(s):  
Yu Feng ◽  
Ya Hu ◽  
Zhiyong Zong
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Enterobacter Cloacae ◽  
Whole Genome ◽  
Large Reservoir ◽  
Clinical Strains ◽  
Enterobacter Species ◽  
Enterobacter Ludwigii ◽  
Enterobacter Asburiae ◽  
Exact Origin

We performed whole genome sequencing for 17 Enterobacter clinical strains and analyzed all available Enterobacter genomes and its closely-related genera (n=3,389) from NCBI. The exact origin of plasmid-borne bla CMH and bla MIR genes is Enterobacter cloacae and Enterobacter roggenkampii , respectively, while plasmid-borne bla ACT genes originated from multiple other Enterobacter species including Enterobacter xiangfangensis , Enterobacter hoffmannii , and Enterobacter asburiae , Enterobacter ludwigii , and Enterobacter kobei . The genus of Enterobacter represents a large reservoir of plasmid-borne AmpC β-lactamase.

scholarly journals Putative Integrative Mobile Elements That Exploit the Xer Recombination Machinery Carrying blaIMI-Type Carbapenemase Genes in Enterobacter cloacae Complex Isolates in Singapore

2017 ◽  
Vol 62 (1) ◽  
Author(s):  
Tse H. Koh ◽  
Nurdyana Binte Abdul Rahman ◽  
Jeanette W. P. Teo ◽  
My-Van La ◽  
Balamurugan Periaswamy ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Multilocus Sequence Typing ◽  
Enterobacter Cloacae ◽  
Mobile Elements ◽  
Whole Genome ◽  
Content Type ◽  
Flanking Regions ◽  
Enterobacter Cloacae Complex

ABSTRACT Whole-genome sequencing was performed on 16 isolates of the carbapenemase-producing Enterobacter cloacae complex to determine the flanking regions of bla IMI-type genes. Phylogenetic analysis of multilocus sequence typing (MLST) targets separated the isolates into 4 clusters. The bla IMI-type genes were all found on Xer-dependent integrative mobile elements (IMEX). The IMEX elements of 5 isolates were similar to those described in Canada, while the remainder were novel. Five isolates had IMEX elements lacking a resolvase and recombinase.

scholarly journals Enterobacter cloacae Complex Sequence Type 171 Isolates Expressing KPC-4 Carbapenemase Recovered from Canine Patients in Ohio

2018 ◽  
Vol 62 (12) ◽  
Author(s):  
Joshua B. Daniels ◽  
Liang Chen ◽  
Susan V. Grooters ◽  
Dixie F. Mollenkopf ◽  
Dimitria A. Mathys ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Companion Animals ◽  
Enterobacter Cloacae ◽  
Sequence Type ◽  
Resistant Bacteria ◽  
Whole Genome ◽  
Content Type ◽  
Complex Sequence ◽  
Enterobacter Cloacae Complex

ABSTRACT Companion animals are likely relevant in the transmission of antimicrobial-resistant bacteria. Enterobacter xiangfangensis sequence type 171 (ST171), a clone that has been implicated in clusters of infections in humans, was isolated from two dogs with clinical disease in Ohio. The canine isolates contained IncHI2 plasmids encoding blaKPC-4. Whole-genome sequencing was used to put the canine isolates in phylogenetic context with available human ST171 sequences, as well as to characterize their blaKPC-4 plasmids.

scholarly journals Annotated Genome Sequences of 16 Lineage 4 Mycobacterium tuberculosis Strains from Guatemala

2018 ◽  
Vol 6 (7) ◽  
Author(s):  
Joseph W. Saelens ◽  
Dalia Lau-Bonilla ◽  
Anneliese Moller ◽  
Ana M. Xet-Mull ◽  
Narda Medina ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Whole Genome Sequencing ◽  
Central America ◽  
Genome Sequencing ◽  
Genomic Data ◽  
Whole Genome ◽  
Genome Sequences ◽  
Clinical Strains ◽  
Complete Genomes

ABSTRACT Whole-genome sequencing has resulted in new insights into the phylogeography of Mycobacterium tuberculosis . However, only limited genomic data are available from M. tuberculosis strains in Guatemala. Here we report 16 complete genomes of clinical strains belonging to the Euro-American lineage 4, the most common lineage found in Guatemala and Central America.

scholarly journals Genomically Informed Surveillance for Carbapenem-Resistant Enterobacteriaceae in a Health Care System

mBio ◽  
2015 ◽  
Vol 6 (4) ◽  
Author(s):  
Nicole D. Pecora ◽  
Ning Li ◽  
Marc Allard ◽  
Cong Li ◽  
Esperanza Albano ◽  
...  
Keyword(s):  
Health Care ◽  
Drug Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Resistance Genes ◽  
Enterobacter Cloacae ◽  
Mobile Elements ◽  
Whole Genome ◽  
Content Type ◽  
Carbapenem Resistant

ABSTRACT Carbapenem-resistant Enterobacteriaceae (CRE) are an urgent public health concern. Rapid identification of the resistance genes, their mobilization capacity, and strains carrying them is essential to direct hospital resources to prevent spread and improve patient outcomes. Whole-genome sequencing allows refined tracking of both chromosomal traits and associated mobile genetic elements that harbor resistance genes. To enhance surveillance of CREs, clinical isolates with phenotypic resistance to carbapenem antibiotics underwent whole-genome sequencing. Analysis of 41 isolates of Klebsiella pneumoniae and Enterobacter cloacae, collected over a 3-year period, identified K. pneumoniae carbapenemase (KPC) genes encoding KPC-2, −3, and −4 and OXA-48 carbapenemases. All occurred within transposons, including multiple Tn4401 transposon isoforms, embedded within more than 10 distinct plasmids representing incompatibility (Inc) groups IncR, -N, -A/C, -H, and -X. Using short-read sequencing, draft maps were generated of new KPC-carrying vectors, several of which were derivatives of the IncN plasmid pBK31551. Two strains also had Tn4401 chromosomal insertions. Integrated analyses of plasmid profiles and chromosomal single-nucleotide polymorphism (SNP) profiles refined the strain patterns and provided a baseline hospital mobilome to facilitate analysis of new isolates. When incorporated with patient epidemiological data, the findings identified limited outbreaks against a broader 3-year period of sporadic external entry of many different strains and resistance vectors into the hospital. These findings highlight the utility of genomic analyses in internal and external surveillance efforts to stem the transmission of drug-resistant strains within and across health care institutions. IMPORTANCE We demonstrate how detection of resistance genes within mobile elements and resistance-carrying strains furthers active surveillance efforts for drug resistance. Whole-genome sequencing is increasingly available in hospital laboratories and provides a powerful and nuanced means to define the local landscape of drug resistance. In this study, isolates of Klebsiella pneumoniae and Enterobacter cloacae with resistance to carbapenem antibiotics were sequenced. Multiple carbapenemase genes were identified that resided in distinct transposons and plasmids. This mobilome, or population of mobile elements capable of mobilizing drug resistance, further highlighted the degree of strain heterogeneity while providing a detailed timeline of carbapenemase entry into the hospital over a 3-year period. These surveillance efforts support effective targeting of infection control resources and the development of institution-specific repositories of resistance genes and the mobile elements that carry them.

scholarly journals Genomic Characterization of Multidrug-Resistant Carbapenemase-Producing Enterobacter cloacae ECL189, Co-producing KPC-2, NDM-1, TEM-1, TEM-95, and SHV-66

2021 ◽  
Vol 13 (11) ◽  
Author(s):  
Na Du ◽  
Shumin Liu ◽  
Jing Yao ◽  
Kai Yang ◽  
Yun Lin ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Resistance Genes ◽  
Virulence Genes ◽  
Enterobacter Cloacae ◽  
Biological Information ◽  
Whole Genome ◽  
Carbapenem Resistant ◽  
Transmission Mechanisms ◽  
Antimicrobial Resistance Genes

Background: Carbapenem-resistant Enterobacteriaceae (CRE) has become a public health threat due to resistance to multiple antibiotics. The production of β-lactamase is the most important resistance mechanism of Enterobacteriaceae. Although isolates producing KPC-2 or NDM-1 enzymes have been reported widely, isolates co-producing KPC-2, NDM-1, TEM-1, TEM-95, SHV-66, and other β-lactamases have rarely been detected in the same strain, especially in Enterobacter cloacae. Objectives: In this study, we identified and sequenced the genome of carbapenem-resistant E. cloacae ECL189 to in-depth analyze the resistance and transmission mechanisms of E. cloacae. Methods: We investigated the antimicrobial susceptibility of ECL189 by a VITEK 2 system, E-test gradient strips, and K-B method. Whole-genome sequencing was used by the PacBio RS II platform and Illumina HiSeq 4000 platform. Antimicrobial resistance genes, virulence genes, non-coding RNA, and repeat sequences were predicted by biological information databases. A PCR was used to further confirm that the blaKPC-2, blaNDM-1, blaTEM-1, blaTEM-95, and blaSHV-66 genes existed in ECL189. A conjugation experiment was performed to determine the transferability of resistance. Molecular typing of ECL189 was done by multilocus sequence typing (MLST). Results: Enterobacter cloacae ECL189 was resistant to 21 out of 23 tested antibiotics, but its transconjugant was resistant to 10 out of 18 tested antibiotics. The genome of ECL189 consisted of a 5,026,406 bp chromosome and four circular plasmids. In total, 26 resistance genes and 58 resistance proteins were identified. In addition, 77 determinants associated with bacterial virulence were identified. A large number of resistance and virulence genes were located in the plasmids. The results of whole-genome sequencing were consistent with the β-lactamase genes. The MLST analysis revealed that this strain belonged to ST74. Conclusions: This study further revealed the resistance, virulence, and transmission mechanisms of carbapenem-resistant E. cloacae. Resistance and virulence genes spread in bacteria by the horizontal transfer of plasmids, which should attract more attention in relevant departments.

scholarly journals Institutional outbreak involving multiple clades of IMP-producing Enterobacter cloacae complex sequence type 78 at a cancer center in Tokyo, Japan

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Sohei Harada ◽  
Kotaro Aoki ◽  
Daisuke Ohkushi ◽  
Koh Okamoto ◽  
Kazumi Takehana ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Enterobacter Cloacae ◽  
Sequence Type ◽  
Cancer Center ◽  
Snp Analysis ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Class 1 Integron ◽  
Clonal Relatedness

Abstract Background Information 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. Methods Antimicrobial 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. Results Fourteen 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. Conclusions Whole-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.

scholarly journals Whole-Genome Sequencing Overrules a Suspected Case of Carbapenem-Resistant Enterobacter cloacae Transmission

2017 ◽  
Vol 55 (9) ◽  
pp. 2868-2870 ◽  
Author(s):  
Mark Chen ◽  
Sean Conlan ◽  
Anna F. Lau ◽  
John P. Dekker ◽  
Clay Deming ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Enterobacter Cloacae ◽  
Suspected Case ◽  
Whole Genome ◽  
Carbapenem Resistant

scholarly journals Characterization of an Enterobacter cloacae Strain Producing both KPC and NDM Carbapenemases by Whole-Genome Sequencing

2015 ◽  
Vol 59 (10) ◽  
pp. 6625-6628 ◽  
Author(s):  
Wenjing Wu ◽  
Yu Feng ◽  
Alessandra Carattoli ◽  
Zhiyong Zong
Keyword(s):  
Whole Genome Sequencing ◽  
Bloodstream Infection ◽  
Genome Sequencing ◽  
Carbapenem Resistance ◽  
Enterobacter Cloacae ◽  
Whole Genome ◽  
Content Type ◽  
Carbapenem Resistant

ABSTRACTA carbapenem-resistantEnterobacter cloacaestrain, WCHECl-14653, causing a fatal bloodstream infection, was characterized by genome sequencing and conjugation experiments. The strain carried two carbapenemase genes,blaNDM-1andblaKPC-2, on separate IncF plasmids. The coexistence ofblaNDM-1andblaKPC-2conferred slightly higher-level carbapenem resistance compared with that ofblaNDM-1orblaKPC-2alone, and the coexistence of two IncF plasmids may generate new platforms for spreading carbapenemase genes.

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