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Molecular Characterization of Carbapenem-Resistant Serratia marcescens Clinical Isolates in a Tertiary Hospital in Hangzhou, China.

ABSTRACT: Introduction:Although carbapenem-resistant Enterobacteriaceae (CRE) have been thoroughly investigated as the pathogens most commonly associated with clinical infections, data on Serratia marcescens are inadequate and superficial. Methods:In this study, we characterized 36 carbapenem-resistant Serratia marcescens (CRSM) isolates in our hospital from April 2018 to March 2019 by analysing whole-genome sequencing (WGS) data. The molecular typing of the isolates was performed using both pulsed-field gel electrophoresis (PFGE) and core genome multilocus sequence typing (cgMLST). Results:Thirty-three of the 36 isolates showed carbapenem resistance conferred by a bla KPC-2-harbouring plasmid, while the remaining three isolates were characterized by overexpression of beta-lactamase combined with porin loss. The bla KPC-2 genes in all the isolates were located on a plasmid of ~103 kb, except one, which was on a plasmid of ~94 kb. The gene structure surrounding bla KPC-2 in the plasmids was confirmed by integration of a partial Tn4401 structure and an intact IS26 as previously reported. Most of the plasmids also contained a mobile genetic element (MGE) comprising qnr and ISKpn19, which provided evidence of horizontal transfer of antibiotic resistance genes. Conclusion:The thirty-six CRSM isolates were mainly clonally disseminated with a bla KPC-2-harbouring plasmid in our hospital. The gene structure surrounding bla KPC-2 as an MGE, as well as the qnr segment, might be acquired by horizontal gene transfer, and it could aggravate the infection and increase the difficulty of clinical treatment.

SUBMITTER: Xu Q

PROVIDER: S-EPMC7152788 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Molecular Characterization of Carbapenem-Resistant <i>Serratia marcescens</i> Clinical Isolates in a Tertiary Hospital in Hangzhou, China.

Xu Qian Q Fu Ying Y Zhao Feng F Jiang Yan Y Yu Yunsong Y

Infection and drug resistance 20200407

<h4>Introduction</h4>Although carbapenem-resistant Enterobacteriaceae (CRE) have been thoroughly investigated as the pathogens most commonly associated with clinical infections, data on <i>Serratia marcescens</i> are inadequate and superficial.<h4>Methods</h4>In this study, we characterized 36 carbapenem-resistant <i>Serratia marcescens</i> (CRSM) isolates in our hospital from April 2018 to March 2019 by analysing whole-genome sequencing (WGS) data. The molecular typing of the isolates was perfo ...[more]

PMID: 32308441

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Project description:The prevalence of carbapenem-resistant Enterobacteriaceae (CRE) is increasing globally, with different molecular mechanisms described. Here we studied the molecular mechanisms of carbapenem resistance, including clonal and plasmid dissemination, of 67 CRE isolates collected between 2012 and 2016 from a tertiary hospital in Eastern China, an CRE endemic region. Species identification and susceptibility testing were performed using the BD Phoenix Automated Microbiology System. Isolates were characterized by PCR (for carbapenemases, ESBLs, AmpC and porin genes), multilocus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE), and conjugation transfer experiments. Selected bla KPC-2 -harboring plasmids were subjected to next-generation sequencing using the Illumina Miseq platform. Among the 67 CRE isolates, 42 Klebsiella pneumoniae, 10 Serratia marcescens, 6 Enterobacter cloacae, 2 Raoultella ornithinolytica, 2 K. oxytoca, 1 K. aerogenes, and 4 Escherichia coli isolates were identified. Six different carbapenemases were detected, including bla KPC-2 (n = 45), bla KPC-3 (n = 1), bla NDM-1 (n = 6), bla NDM-5 (n = 1), bla IMP-4 (n = 2), and bla VIM-1 (n = 2); bla OXA-48-like genes were not detected. One E. cloacae strain possessed both bla NDM-1 and bla KPC-3, while two E. cloacae isolates harbored bla NDM-1 and bla VIM-1. ESBLs (CTX-M, SHV, and TEM) and/or AmpC (CMY, DHA, and ACT/MIR) genes were also identified in 59 isolates, including 13 strains that lacked carbapenemases. Several insertions or stop codon mutations were found within porin genes of K. pneumoniae, E. coli and S. marcescens isolates, both with and without carbapenemases. The 42 K. pneumoniae isolates belonged to 12 different sequence types (ST), with ST11 being the most common, while the 6 E. cloacae isolates comprised 4 different STs. The 10 S. marcescens all shared the same PFGE pulsotype, suggestive of clonal spread. Complete plasmid sequencing and PCR screening revealed both intra-strain and inter-species spread of a common bla KPC-2-harboring plasmid in our hospital. Taken together, our study revealed extensive genetic diversity among CRE isolates form a single Chinese hospital. CRE isolates circulating in the hospital differ significantly in their species, STs, porin genes, carbapenemase genes, and their plasmid content, highlighting the complex dissemination of CRE in this endemic region.

Project description:Serratia marcescens has emerged as an important opportunistic pathogen responsible for nosocomial and severe infections. Here, we determined phenotypic and molecular characteristics of 54 S. marcescens isolates obtained from patient samples from intensive-care-unit (ICU) and neonatal intensive-care-unit (NIUC) of a Brazilian tertiary hospital. All isolates were resistant to beta-lactam group antibiotics, and 92.6% (50/54) were not susceptible to tigecycline. Furthermore, 96.3% showed intrinsic resistance to polymyxin E (colistin), a last-resort antibiotic for the treatment of infections caused by MDR (multidrug-resistant) Gram-negative bacteria. In contrast, high susceptibility to other antibiotics such as fluoroquinolones (81.5%), and to aminoglycosides (as gentamicin 81.5%, and amikacin 85.2%) was found. Of all isolates, 24.1% were classified as MDR. The presence of resistance and virulence genes were examined by PCR and sequencing. All isolates carried KPC-carbapenemase (bla KPC ) and extended spectrum beta-lactamase bla TEM genes, 14.8% carried bla OXA- 1, and 16.7% carried bla CTX-M- 1 group genes, suggesting that bacterial resistance to β-lactam antibiotics found may be associated with these genes. The genes SdeB/HasF and SdeY/HasF that are associated with efflux pump mediated drug extrusion to fluoroquinolones and tigecycline, respectively, were found in 88.9%. The aac(6')-Ib-cr variant gene that can simultaneously induce resistance to aminoglycoside and fluoroquinolone was present in 24.1% of the isolates. Notably, the virulence genes to (i) pore-forming toxin (ShlA); (ii) phospholipase with hemolytic and cytolytic activities (PhlA); (iii) flagellar transcriptional regulator (FlhD); and (iv) positive regulator of prodigiosin and serratamolide production (PigP) were present in 98.2%. The genetic relationship among the isolates determined by ERIC-PCR demonstrated that the vast majority of isolates were grouped in a single cluster with 86.4% genetic similarity. In addition, many isolates showed 100% genetic similarity to each other, suggesting that the S. marcescens that circulate in this ICU are closely related. Our results suggest that the antimicrobial resistance to many drugs currently used to treat ICU and NIUC patients, associated with the high frequency of resistance and virulence genes is a worrisome phenomenon. Our findings emphasize the importance of active surveillance plans for infection control and to prevent dissemination of these strains.

Project description:Hypervirulent and multidrug-resistant Klebsiella pneumoniae poses a significant threat to public health. We aimed to determine the common carbapenemase genotypes and the carriage patterns, main antibiotic resistance mechanisms, and in vitro susceptibility of clinical isolates of carbapenem-resistant K. pneumoniae (CRKP) to ceftazidime/avibactam (CZA) for the reasonable selection of antimicrobial agents and determine whether hypermucoviscous (HMV) phenotype and virulence-associated genes are key factors for CRKP colonization and persistence. Antibiotics susceptibility of clinical CRKP isolates and carbapenemase types were detected. CRKP isolates were identified as hypermucoviscous K. pneumoniae (HMKP) using the string test, and detection of virulence gene was performed using capsular serotyping. The bla KPC-2, bla NDM, bla IMP, and/or bla OXA-48-like were detected in 96.4% (402/417) of the isolates, and the bla KPC-2 (64.7%, 260/402) was significantly higher (P<0.05) than those of bla NDM (25.1%), bla OXA-48-like (10.4%), and bla IMP (4.2%). Carriage of a single carbapenemase gene was observed in 96.3% of the isolates, making it the dominant antibiotic resistance genotype carriage pattern (P < 0.05). Approximately 3.7% of the isolates carried two or more carbapenemase genotypes, with bla KPC-2 + bla NDM and bla NDM + bla IMP being the dominant multiple antibiotic resistance genotype. In addition, 43 CRKP isolates were identified as HMKP, with a prevalence of 10.3% and 2.7% among CRKP and all K. pneumoniae isolates, respectively. Most clinical CRKP isolates were isolated from elderly patients, and carbapenemase production was the main mechanism of drug resistance. Tigecycline and polymyxin B exhibited exceptional antimicrobial activity against CRKP isolates in vitro. Furthermore, bla KPC-2, bla NDM, and bla OXA-48-like were the main carbapenemase genes carried by the CRKP isolates. CZA demonstrated excellent antimicrobial activity against isolates carrying the single bla KPC-2 or bla OXA-48-like genotype. Capsular serotype K2 was the main capsular serotype of the carbapenem-resistant HMKP isolates. Survival rates of Galleria mellonella injected with K. pneumoniae 1-7 were 20.0, 16.7, 6.7, 23.3, 16.7, 3.3, and 13.3, respectively. Therefore, worldwide surveillance of these novel CRKP isolates and carbapenem-resistant HMKP isolates as well as the implementation of stricter control measures are needed to prevent further dissemination in hospital settings.

Dataset Information

Molecular Characterization of Carbapenem-Resistant Serratia marcescens Clinical Isolates in a Tertiary Hospital in Hangzhou, China.

Publications

Molecular Characterization of Carbapenem-Resistant <i>Serratia marcescens</i> Clinical Isolates in a Tertiary Hospital in Hangzhou, China.

Similar Datasets

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