Epidemiology and Genetic Characteristics of Carbapenem-Resistant Escherichia coli in Chinese Intensive Care Unit Analyzed by Whole-Genome Sequencing: a Prospective Observational Study

Ding, Ying; Zhuang, Hemu; Zhou, Junxin; Li-jie, XU; Yang, Yi; He, Jintao; Liang, Min; Jia, Shicheng; Guo, Xiuliu; Han, Xinhong; Liu, Haiyang; Zhang, Linghong; Jiang, Yan; Yu, Yunsong

doi:10.1128/spectrum.04010-22

Cited by 4 publications

(3 citation statements)

References 42 publications

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“…ST361 has been previously associated with bla NDM−5 in patients worldwide (Park et al, 2020;Chakraborty et al, 2021;Huang et al, 2023). ST1193 has been the dominant ST of carbapenem-sensitive E. coli isolates in patients at an intensive care unit in China (Ding et al, 2023). Carbapenem-resistant E. coli ST1193, an isolate encoding NDM-5 found in this study, might be a cause for concern due to its ability to acquire carbapenem resistance and the potential to cause a future outbreak in hospitals.…”

Section: Characterization Of Bla Ndm -Positive E Coli Isolatesmentioning

confidence: 63%

Low prevalence of mobilized resistance genes blaNDM, mcr-1, and tet(X4) in Escherichia coli from a hospital in China

Sun

Sun²,

Jiang

et al. 2023

Front. Microbiol.

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The emergence and spread of carbapenemase genes, colistin resistance genes mcr-1, and tigecycline resistance gene tet(X) represent a significant threat to clinical therapy and public health. In this study, we investigated the presence of carbapenemase genes, mcr-1, and tet(X) in 298 Escherichia coli strains obtained from a teaching hospital in China. In total, eight (2.68%), six (2.01%), and one (0.34%) E. coli isolates carried blaNDM, mcr-1, and tet(X4), respectively. The blaNDM gene was located on IncX3 (n = 4), F2:A-:B- (n = 3), and F2:A1:B1 (n = 1) plasmids, with high similarity to multiple plasmids belonging to the same incompatibility type from Enterobacteriaceae. Six MCR-producing strains contained mcr-1-carrying IncI2 plasmids, organized similarly to other mcr-1-bearing IncI2 plasmids from animals in China. The blaCTX−M−55/64/132/199 gene located within a typical transposition unit (ISEcp1-blaCTX−M-orf477Δ) was inserted near dnaJ to generate 5-bp direct repeats in four mcr-1-positive plasmids. The tet(X) and another four resistance genes [aadA2, tet(A), floR, and Δlnu(F)] were co-located on an IncX1 plasmid, highly similar to other tet(X4)-carrying IncX1 plasmids from Escherichia and Klebsiella of animal or food origin, except that the conjugative transfer region of IncX1 plasmids was absent in our plasmid. Although a low prevalence of blaNDM, mcr-1, and tet(X) was observed in E. coli from patients in this study, their dissemination associated with some successful pandemic plasmids is of great concern. The continued surveillance of these crucial resistance genes in patients should be strengthened.

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Section: Characterization Of Bla Ndm -Positive E Coli Isolatesmentioning

confidence: 63%

Low prevalence of mobilized resistance genes blaNDM, mcr-1, and tet(X4) in Escherichia coli from a hospital in China

Sun

Sun²,

Jiang

et al. 2023

Front. Microbiol.

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“…The main ST of CRECs isolated from clinical patients was ST131 carrying the bla KPC gene [ 2 , 43 ]. The ST131 E. coli is a widely distributed exenteral-pathogenic E. coli , which has attracted extensive public attention due to its carriage of a variety of ARGs and VFs [ 44 ].…”

Section: Discussionmentioning

confidence: 99%

National genomic epidemiology investigation revealed the spread of carbapenem-resistant Escherichia coli in healthy populations and the impact on public health

Li,

Zhang,

Sun

et al. 2024

Genome Med

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Background Carbapenem-resistant Escherichia coli (CREC) has been considered as WHO priority pathogens, causing a great public health concern globally. While CREC from patients has been thoroughly investigated, the prevalence and underlying risks of CREC in healthy populations have been overlooked. Systematic research on the prevalence of CREC in healthy individuals was conducted here. We aimed to characterize CREC collected from healthy populations in China between 2020 and 2022 and to compare the genomes of CREC isolates isolated from healthy individuals and clinical patients. Methods We present a nationwide investigation of CREC isolates among healthy populations in China, employing robust molecular and genomic analyses. Antimicrobial susceptibility testing, whole-genome sequencing, and bioinformatics were utilized to analyze a cohort of CREC isolates (n = 113) obtained from fecal samples of 5 064 healthy individuals. Representative plasmids were extracted for third-generation nanopore sequencing. We previously collected 113 non-duplicate CREC isolates (59 in 2018, 54 in 2020) collected from ICU patients in 15 provinces and municipalities in China, and these clinical isolates were used to compare with the isolates in this study. Furthermore, we employ comparative genomics approaches to elucidate molecular variations and potential correlations between clinical and non-clinical CREC isolates. Results A total of 147 CREC isolates were identified from 5 064 samples collected across 11 provinces in China. These isolates were classified into 64 known sequence types (STs), but no dominant STs were observed. In total, seven carbapenemase genes were detected with blaNDM-5 (n = 116) being the most prevalent one. Genetic environments and plasmid backbones of blaNDM were conserved in CREC isolated from healthy individuals. Furthermore, we compared clinical and healthy human-originated CRECs, revealing noteworthy distinctions in 23 resistance genes, including blaNDM-1, blaNDM-5, and blaKPC (χ2 test, p < 0.05). Clinical isolates contained more virulence factors associated with iron uptake, adhesion, and invasion than those obtained from healthy individuals. Notably, CREC isolates generally found healthy people are detected in hospitalized patients. Conclusions Our findings underscore the significance of healthy populations-derived CRECs as a crucial reservoir of antibiotic resistance genes (ARGs). This highlights the need for ongoing monitoring of CREC isolates in healthy populations to accurately assess the potential risks posed by clinical CREC isolates.

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“…previous studies [26][27][28]. Resistance genes present in E. coli isolates against other commonly used inexpensive and readily available drugs such as quinolones, trimethoprim and sulfonamide and increase the risk of rendering these drugs ineffective in the long run.…”

Section: Aac(3)-iid Aac(3)-iie Aac(6')-ib-d181y Aac(6')-ib-cr5 Aph(3'...mentioning

confidence: 99%

Application of nanopore sequencing to identify antimicrobial resistance genes, mobile genetic elements and virulence factors in clinical isolates

Kimani,

Musundi,

Wakaba

et al. 2023

Preprint

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The global health challenge posed by the emergence of antibiotic resistance pathogen is further exacerbated in African countries by the indiscriminate use of antibiotics, poor surveillance and lack of stewardship programs. To address this issue, we employed the Oxford Nanopore Technologies (ONT) to sequence 17 clinical isolates from a referral hospital in Kenya. Our comprehensive bioinformatics approach facilitated the assembly, identification of sequence types and prediction of antimicrobial resistance genes, mobile genetic elements (plasmids and integrons) and virulence genes. Of the 17 isolates, five were A. baumannii, four E. coli, three S. haemolyticus, three were E. cloacae, while S. aureus and E. faecalis were single isolates. For the detection of AMR genes, A. baumannii isolates harbored genes such as blaOXA-23 which mediates resistance to carbapenems, E. coli and E. cloacae carried blaCTX-M-15 which confers resistance to cephalosporins and S. haemolyticus harbored blaZ, responsible for resistance against penicillins. S. aureus co-haboured mecA and blaZ genes. In addition,, various other different AMR genes to chloramphenicol, macrolides, aminoglycosides, tetracycline were also observed. For plasmid replicons, E. coli carried the most number of plasmids and shared ColRNAI_1 and IncFIB(pB171)_1_pB171 with A. baumannii and IncR_1 with E. cloacae. Many genes encoding various virulence factors including fimA-I and ompA,senB were identified in E. coli,hlgA-C and hla/hly, hlb, hld in S. aureus and efaA, ebpA-C in E. faecalis. In conclusion, most isolates contained a combination of different AMR genes harbored in plasmids and integrons and virulence genes. This study provides significant information on genetic determinants of antibiotic resistant pathogens in clinical isolates and could assist in developing strategies that improve patient treatment.

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Epidemiology and Genetic Characteristics of Carbapenem-Resistant Escherichia coli in Chinese Intensive Care Unit Analyzed by Whole-Genome Sequencing: a Prospective Observational Study

Cited by 4 publications

References 42 publications

Low prevalence of mobilized resistance genes blaNDM, mcr-1, and tet(X4) in Escherichia coli from a hospital in China

Low prevalence of mobilized resistance genes blaNDM, mcr-1, and tet(X4) in Escherichia coli from a hospital in China

National genomic epidemiology investigation revealed the spread of carbapenem-resistant Escherichia coli in healthy populations and the impact on public health

Application of nanopore sequencing to identify antimicrobial resistance genes, mobile genetic elements and virulence factors in clinical isolates

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