Genomic diversification of IncR plasmids from China

Jing, Ying; Jiang, Xiaoyuan; Yin, Zhe; Hu, Lingfei; Zhang, Ying; Yang, Wenhui; Yang, Huiying; Gao, Bo; Zhao, Yuee; Zhou, Dongsheng; Wang, Chengbin; Luo, Yanping

doi:10.1016/j.jgar.2019.06.007

Cited by 18 publications

(9 citation statements)

References 38 publications

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“…To date, multiple plasmids have been found to be the vesicles for spread of carbapenemase, ESBLs, and PMQRs [34]. The high prevalence of IncFII, IncR and IncFIB plasmid replicons in our study alert us on the urgency of implementing antimicrobial resistance surveillance, since IncFII-type plasmids are highly distributed vesicles for resistant determinants in Enterobacteriaceae [35]; Moreover, IncR plasmid is an important reservoir of multidrug resistance in Enterobacteriaceae strains, because the conserved IncR backbones include the multidrug resistant (MDR) regions [36]; and IncFIB plasmids were reported to be associated with majority of the antimicrobial resistance genes [37]. Similarly, some of the distribution correlations between various plasmid replicons and multiple resistant genes found in our study are consistent with the previous reports [38][39][40].…”

Section: Discussionmentioning

confidence: 67%

Epidemiological characteristics of carbapenem-resistant Enterobacteriaceae collected from 17 hospitals in Nanjing district of China

Zhou

Zhang

Chen

et al. 2020

Antimicrob Resist Infect Control

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Objective In total, 97 carbapenem-resistant Enterobacteriaceae (CRE) were collected from 17 hospitals located in Nanjing, Southeast China, and analyzed for epidemiological characteristics. Methods Antimicrobial susceptibility was determined; followed by determination of the prevalence of resistance determinants, including extended-spectrum β-lactamase (ESBLs), plasmid-mediated AmpC enzyme (pAmpCs), plasmid-mediated quinolone resistance genes (PMQRs), fosfomycin resistance gene and exogenously acquired 16S rRNA methyltransferase (16S-RMTase) using PCR and DNA sequencing. The sequence types (STs) of CRE were determined by multi-locus sequence typing (MLST). The plasmid profiles were detected by PCR-based replicon typing (PBRT). Results All the CRE strains displayed high MIC50 and MIC90 for nearly all clinical available antibiotics, except for aztreonam/avibactam, minocycline, ceftazidime/avibactam, tigecycline, and colistin. KPC-2 (79.4%) and NDM (19.6%) were the main carbapenemases, CTX-M (76.3%) and SHV (60.8%) were the predominant ESBLs. In addition, oqxAB (70.1%) and qnr (63.9%) were the major PMQRs; rmtB (47.4%) was the main 16S-RMTase; fosA (76.3%) and fosA3 (37.1%) were the fosfomycin resistance gene. PBRT analysis showed presence of IncR (66.0%) and IncFII (64.9%) replicon types in the majority of the isolates, followed by IncFIB (46.4%) and IncX3 (16.5%). The IncFII and IncR replicon-types were found mainly in K. pneumoniae (68.8%), whereas the IncX3 replicons dominated in E. coli isolates (100.0%). The three dominating MLST-types ST11, ST15 and ST268 comprised 68.0% of the 77 K. pneumoniae. Seven distinct STs were identified among 8 E. coli. Conclusions The treatment for infections caused by CRE isolates is challenged by the presence of multiple resistance determinants and plasmid replicons. Our results highlighted the expansion of blaKPC-2 carrying K. pneumoniae ST11, the new emergency of single blaNDM-5 carrying K. oxytoca ST36, as well as blaIMP-4 and blaNDM-1 co-carrying E. cloacae ST418, which alert us on the urgency for antimicrobial resistant surveillance, to prevent dissemination of these highly transmissible and dangerous lineages.

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Section: Discussionmentioning

confidence: 67%

Epidemiological characteristics of carbapenem-resistant Enterobacteriaceae collected from 17 hospitals in Nanjing district of China

Zhou

Zhang

Chen

et al. 2020

Antimicrob Resist Infect Control

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“…55,56 Furthermore, the IncR plasmid is a significant reservoir of many antibiotics resistance in Enterobacteriaceae isolates since the preserved IncR backbones contain the multidrug resistant (MDR) sequences. 57 Furthermore, IncFIIk plasmids were described to be related to the mainstream of the antimicrobial resistance genes detected more frequently in our study. 58 The extension of ST11 for the bla KPC-2 carrying K. pneumoniae was in the union as according to the earlier articles representing that, ST11 is the main epidemic clone among K. pneumonia.…”

Section: Discussionmentioning

confidence: 58%

Epidemiological Characterization of Colistin and Carbapenem Resistant Enterobacteriaceae in a Tertiary: A Hospital from Anhui Province

Hameed¹,

Chen²,

Wang³

et al. 2021

IDR

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Purpose Antimicrobial resistance, especially carbapenem resistance Enterobacteriaceae and plasmid mediated mobile colistin resistance, is a serious issue worldwide. This study was designed to determine the epidemiological characteristics of plasmid mediated colistin resistance and carbapenem resistant Enterobacteriaceae from tertiary A hospital located in Hefei, China. Methods Totally, 158 carbapenems resistant Enterobacteriaceae (CRE) were screened for antibiotic susceptibility, mcr-1 , extended spectrum β-lactamases (ESBLs), metallo-β-lactamases (MBLs), and fosfomycin resistance genes using PCR and sequencing. The sequence types were identified by multilocus sequence typing (MLST). Plasmid profiles were determined by PCR based replicon typing (PBRT), and the plasmid sizes were confirmed by southern blotting. Results The isolates showed high MIC 50 and MIC 90 for all antimicrobials, except tigecycline, meropenem, and colistin. The main Carbapenemase genes were bla KPC-2 (90.5%), bla NDM-1 (3.7%), bla OXA-48 (5.6%) and fosA3 (14.5%). The bla CTXM-15 found 36.7%, mcr-1 (3.7%) recorded in six isolates. PBRT revealed bla KPC-2 in K. pneumoniae on IncR, IncFII, and IncA/C. bla NDM-1 in E. coli on IncFII, whereas in E. cloacae noticed on IncHI2 plasmid. mcr-1 was recorded among IncFIIK, IncFII, and IncF in E. coli, K. pneumoniae , and E. cloacae . Resistance genes ( mcr-1, bla NDM-1 , bla KPC-2 ) harboring plasmids are successfully trans-conjugant to EC-600 . A high incidence of ST11 was observed in K. pneumoniae carbapenem resistant isolates. While in E. coli , multiple STs were identified. However, mcr-1 in ST23 was identified for the first time in Anhui Province. Among Enterobacter cloacae , ST270 detected carrying bla NDM-1 . Southern-hybridization confirmed the plasmid sizes 35–150kb. Conclusion This study indicates the co-carrying of mcr-1, bla KPC-2, and bla NDM-1 among clinical isolates, the prevalence of different Enterobacteriaceae STs is alarming, especially in E. coli . Holding such a resistance prof...

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“…qnr genes have been previously associated with IncN plasmids from different Salmonella serovars isolated from human and poultry samples in the Netherlands (García-Fernández et al, 2009). It has been shown previously that IncR plasmids are able to form multireplicons with IncN, IncA/C, IncHI, and IncF type plasmids (Drieux et al, 2013;Jing et al, 2019;Papagiannitsis et al, 2013;Qu et al, 2019). Previous studies indicate that IncR plasmids lack genes involved in conjugation (Bielak et al, 2011;Chen et al, 2006), which indicates that pZPK-H11 is a putatively conjugative plasmid contributing to the transferassociated genes located on the IncN region of the plasmid.…”

Section: Discussionmentioning

confidence: 99%

“…Bacterial multilocus sequence typing (MLST) was determined with MLST 2.0 (Larsen et al, 2012) using E. coli scheme 1 (Wirth et al, 2006). Virulence genes for E. coli isolates were determined with VirulenceFinder 2.0 (Joensen et al, 2014), using an identity threshold of 90% and a minimum length of 60%. PlasmidFinder 2.1 (Carattoli et al, 2014) was used to determine plasmid replicons located in the same contigs as beta-lactamase genes using an identity threshold of 95% and a minimum length of 60%.…”

Section: Bioinformatic Analysesmentioning

confidence: 99%

Plasmids conferring resistance to extended-spectrum beta-lactamases including a rare IncN+IncR multireplicon carrying blaCTX-M-1 in Escherichia coli recovered from migrating barnacle geese (Branta leucopsis)

Kurittu¹,

Khakipoor²,

Brouwer³

et al. 2021

Open Res Europe

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Background: Increasing antimicrobial resistance (AMR) is a global threat and wild migratory birds may act as mediators of resistant bacteria across country borders. Our objective was to study extended-spectrum beta-lactamase (ESBL) and plasmid-encoded AmpC (pAmpC) producing Escherichia coli in barnacle geese using whole genome sequencing (WGS) and to identify plasmids harboring bla genes. Methods: Barnacle geese feces (n=200) were collected during fall 2017 and spring 2018 from an urban area in Helsinki, Finland. ESBL/AmpC-producing E. coli were recovered from nine samples (4.5%) and isolates were subjected to WGS on both short- and long-read sequencers, enabling hybrid assembly and determination of the genomic location of bla genes. Results: A rare multireplicon IncN+IncR was recovered from one isolate carrying blaCTX-M-1 in addition to aadA2b, lnu(F), and qnrS1. Moreover, rarely detected IncY plasmids in two isolates were found to harbor multiple resistance genes in addition to the human-associated blaCTX-M-15. Poultry-associated blaCMY-2 was identified from the widely distributed IncI1 and IncK plasmids from four different isolates. One isolate harbored an IncI1 plasmid with blaCTX-M-1 and flor. A chromosomal point mutation in the AmpC promoter was identified in one of the isolates. WGS analysis showed isolates carried multiple resistance and virulence genes and harbored multiple different plasmid replicons in addition to bla-carrying plasmids. Conclusions: Our findings suggest that wild migratory birds serve as a limited source of ESBL/AmpC-producing E. coli and may act as disseminators of the epidemic plasmid types IncI1 and IncK but also rarely detected plasmid types carrying multidrug resistance. Human and livestock-associated ESBL enzyme types were recovered from samples, suggesting a potential for interspecies transmission. WGS offers a thorough method for studying AMR from different sources and should be implemented more widely in the future for AMR surveillance and detection. Understanding plasmid epidemiology is vital for efforts to mitigate global AMR spread.

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Genomic diversification of IncR plasmids from China

Cited by 18 publications

References 38 publications

Epidemiological characteristics of carbapenem-resistant Enterobacteriaceae collected from 17 hospitals in Nanjing district of China

Epidemiological characteristics of carbapenem-resistant Enterobacteriaceae collected from 17 hospitals in Nanjing district of China

Epidemiological Characterization of Colistin and Carbapenem Resistant Enterobacteriaceae in a Tertiary: A Hospital from Anhui Province

Plasmids conferring resistance to extended-spectrum beta-lactamases including a rare IncN+IncR multireplicon carrying blaCTX-M-1 in Escherichia coli recovered from migrating barnacle geese (Branta leucopsis)

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