Precise Species Identification by Whole-Genome Sequencing of <i>Enterobacter</i> Bloodstream Infection, China

Wu, Wenjing; Li, Wei; Feng, Yu; Xie, Yi; Zong, Zhiyong

doi:10.3201/eid2701.190154

Cited by 20 publications

(15 citation statements)

References 23 publications

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“…Additionally, the inter-hospital clonal transmission of ST171 strains was also detected. For example, WCHEH090011, WCHEH090023, WCHEH090059, and WCHEX016162 were collected from another hospital in Chengdu [ 5 ] and shared 2–4 SNPs difference with HD8671 and HD7437 from our study, supporting the inter-hospital transmission of NDM producing ST171 strains in China.…”

Section: Resultssupporting

confidence: 63%

“…Clinical laboratories usually only classify Enterobacter species as E. cloacae complex, resulting in the inability to correlate antimicrobial resistance to Enterobacter at the species level. The combination of average nucleotide identity (ANI) and in silico DNA–DNA hybridization (isDDH) based on whole-genome sequencing analysis was recently recommended for more precise identification of Enterobacter species [ 5 ]. These methods provide high resolution to further divide Enterobacter into different species.…”

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confidence: 99%

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Epidemiological characteristics and molecular features of carbapenem-resistant Enterobacter strains in China: a multicenter genomic study

Zhu

Xie

Yu³

et al. 2022

Emerging Microbes & Infections

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Epidemiological characteristics and molecular features of carbapenem-resistant Enterobacter (CR- Ent ) species remain unclear in China. In this study, we performed a genomic study on 92 isolates from Enterobacter -caused infections from a multicenter study in China. Whole genome sequencing (WGS) was used to determine the genome sequence of 92 non-duplicated CR- Ent strains collected from multiple tertiary health centres. The precise species of Enterobacter strains were identified by average nucleotide identity (ANI) and in silico DNA–DNA hybridization (isDDH). Molecular features of high-risk CR- Ent sequence type (ST) lineages and carbapenemase-encoding plasmids were determined. The result revealed that the most common human-source CR- Ent species in China was E. xiangfangensis (66/92, 71.93%), and the proportion of carbapenemase-producing Enterobacter (CP- Ent ) in CR- Ent was high (72/92, 78.26%) in comparison to other global regions. Furthermore, ST171 and ST116 E. xiangfangensis were the major lineages of CP- Ent strains, and ST171 E. xiangfangensis was more likely to cause infections in older patients. Genomic analysis also highlighted the likelihood of intra-hospital/inter-hospital clonal transmission of ST171 and ST116 E. xiangfangensis . In addition, the bla NDM -harbouring IncX3-type plasmid was identified as the prevalent carbapenemase-encoding plasmid carried by CR- Ent strains, and was experimentally confirmed to be able to self-transfer with high frequency. This study detailed the genomic and clinical characteristics of CR- Ent in China in the form of multicenter for the first time. The high risk of carbapenemase-producing ST171 and ST116 E. xiangfangensis , and the bla NDM -harbouring IncX3-type plasmid were detected and emphasized.

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Section: Resultssupporting

confidence: 63%

mentioning

confidence: 99%

Epidemiological characteristics and molecular features of carbapenem-resistant Enterobacter strains in China: a multicenter genomic study

Zhu

Xie

Yu³

et al. 2022

Emerging Microbes & Infections

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“…Furthermore, clusters VI and VIII belong to a species named E. xiangfangensis as recommended by Wu et al [ 4 ]. Most (63.5%) Enterobacter strains from human bloodstream infection in China are E. xiangfangensis [ 27 ]. According to the new nomenclature system, this species was also the most common Enterobacter species in our clinical isolates.…”

Section: Discussionmentioning

confidence: 99%

The Resistance Mechanisms and Clinical Impact of Resistance to the Third Generation Cephalosporins in Species of Enterobacter cloacae Complex in Taiwan

Chang

Huang

2022

Antibiotics

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Enterobacter cloacae complex (ECC) is ubiquitous in the environment and is an important pathogen causing nosocomial infections. Because routine methods used in clinical laboratories cannot identify species within ECC, the clinical significance of each species within ECC is less known. We applied hsp60 gene sequencing to identify the species/clusters of ECC and detected β-lactamase genes and class 1 integrons with PCR for 184 clinical ECC isolates in Taiwan from 2013 to 2014 to investigate the clinical impact of species within ECC. The four most common clusters were E. hormaechei subsp. steigerwaltii (cluster VIII) (29.9%), E. hormaechei subsp. oharae (cluster VI) (20.1%), E. cloacae subsp. cloacae (cluster XI) (12%), and E. kobei (cluster II) (10.3%). E. hormaechei, which consisted of four clusters (clusters III, VI, VII, and VIII), is the predominant species and accounted for 57.1% of the isolates. The ceftazidime resistance rate was 27.2%, and the ceftriaxone resistance rate was 29.3%. Resistance to third generation cephalosporin was associated with a higher 30-day mortality rate. In total, 5 (2.7%), 24 (13.0%), and 1 (0.5%) isolates carried ESBL, AmpC, and carbapenemase genes, respectively. Class 1 integrons were present in 24.5% of the isolates, and most of the cassettes pertain to antibiotic resistance. Resistance to third generation cephalosporins, multidrug resistance, and class 1 integrons were significantly more in E. hormaechei (clusters III, VI, VII, and VIII) than in the other species. The 30-day mortality rate and 100-day mortality did not differ significantly between patients with E. hormaechei and those with infections with the other species. In conclusion, the distribution of third generation cephalosporin resistance, multidrug resistance, and class 1 integrons were uneven among Enterobacter species. The resistance to third generation cephalosporins possessed significant impact on patient outcome.

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“…Enterobacter (E. cloacae) belongs to facultative anaerobic Gram-negative bacilli, grouping into the E. cloacae complex group, the family Enterobacterale [1]. Generally, such bacteria colonize soil and water as well as the animal and human gut, representing one of the most leading species described in clinical infections, particularly in vulnerable patients [2].…”

Section: Introductionmentioning

confidence: 99%

Molecular characteristics of global β-lactamase-producing Enterobacter cloacae by genomic analysis

Liu

et al. 2022

BMC Microbiol

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Objective To analyze the characteristics of global β-lactamase-producing Enterobacter cloacae including the distribution of β-lactamase, sequence types (STs) as well as plasmid replicons. Methods All the genomes of the E. cloacae were downloaded from GenBank. The distribution of β-lactamase encoding genes were investigated by genome annotation after the genome quality was checked. The STs of these strains were analyzed by multi-locus sequence typing (MLST). The distribution of plasmid replicons was further explored by submitting these genomes to the genome epidemiology center. The isolation information of these strains was extracted by Per program from GenBank. Results A total of 272 out of 276 strains were found to carry β-lactamase encoding genes. Among them, 23 varieties of β-lactamase were identified, blaCMH (n = 130, 47.8%) and blaACT (n = 126, 46.3%) were the most predominant ones, 9 genotypes of carbapenem-hydrolyzing β-lactamase (CHβLs) were identified with blaVIM (n = 29, 10.7%) and blaKPC (n = 24, 8.9%) being the most dominant ones. In addition, 115 distinct STs for the 272 ß-lactamase-carrying E. cloacae and 48 different STs for 106 CHβLs-producing E. cloacae were detected. ST873 (n = 27, 9.9%) was the most common ST. Furthermore, 25 different plasmid replicons were identified, IncHI2 (n = 65, 23.9%), IncHI2A (n = 64, 23.5%) and IncFII (n = 62, 22.8%) were the most common ones. Notably, the distribution of plasmid replicons IncHI2 and IncHI2A among CHβLs-producing strains were significantly higher than theat among non-CHβLs-producing strains (p < 0.05). Conclusion Almost all the E. cloacae contained β-lactamase encoding gene. Among the global E. cloacae, blaCMH and blaACT were main blaAmpC genes. BlaTEM and blaCTX-M were the predominant ESBLs. BlaKPC, blaVIM and blaNDM were the major CHβLs. Additionally, diversely distinct STs and different replicons were identified.

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Precise Species Identification by Whole-Genome Sequencing of Enterobacter Bloodstream Infection, China

Cited by 20 publications

References 23 publications

Epidemiological characteristics and molecular features of carbapenem-resistant Enterobacter strains in China: a multicenter genomic study

Epidemiological characteristics and molecular features of carbapenem-resistant Enterobacter strains in China: a multicenter genomic study

The Resistance Mechanisms and Clinical Impact of Resistance to the Third Generation Cephalosporins in Species of Enterobacter cloacae Complex in Taiwan

Molecular characteristics of global β-lactamase-producing Enterobacter cloacae by genomic analysis

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