Dataset Information

A Retrospective Whole-Genome Sequencing Analysis of Carbapenem and Colistin-Resistant Klebsiella Pneumoniae Nosocomial Strains Isolated during an MDR Surveillance Program.

ABSTRACT: Multidrug-resistant Klebsiella pneumoniae (MDR Kp), in particular carbapenem-resistant Kp (CR-Kp), has become endemic in Italy, where alarming data have been reported on the spread of colistin-resistant CR-Kp (CRCR-Kp). During the period 2013-2014, 27 CRCR-Kp nosocomial strains were isolated within the Modena University Hospital Policlinico (MUHP) multidrug resistance surveillance program. We retrospectively investigated these isolates by whole-genome sequencing (WGS) analysis of the resistome, virulome, plasmid content, and core single nucleotide polymorphisms (cSNPs) in order to gain insights into their molecular epidemiology. The in silico WGS analysis of the resistome revealed the presence of genes, such as blaKPC, related to the phenotypically detected resistances to carbapenems. Concerning colistin resistance, the plasmidic genes mcr 1-9 were not detected, while known and new genetic variations in mgrB, phoQ, and pmrB were found. The virulome profile revealed the presence of type-3 fimbriae, capsular polysaccharide, and iron acquisition system genes. The detected plasmid replicons were classified as IncFIB(pQil), IncFIB(K), ColRNAI, IncX3, and IncFII(K) types. The cSNPs genotyping was consistent with the multi locus sequence typing (MLST) and with the distribution of mutations related to colistin resistance genes. In a nosocomial drug resistance surveillance program, WGS proved to be a useful tool for elucidating the spread dynamics of CRCR-Kp nosocomial strains and could help to limit their diffusion.

SUBMITTER: Gentile B

PROVIDER: S-EPMC7277725 | biostudies-literature | 2020 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

A Retrospective Whole-Genome Sequencing Analysis of Carbapenem and Colistin-Resistant Klebsiella Pneumoniae Nosocomial Strains Isolated during an MDR Surveillance Program.

Gentile Bernardina B Grottola Antonella A Orlando Gabriella G Fregni Serpini Giulia G Venturelli Claudia C Meschiari Marianna M Anselmo Anna A Fillo Silvia S Fortunato Antonella A Lista Florigio F Pecorari Monica M Mussini Cristina C

Antibiotics (Basel, Switzerland) 20200512 5

Multidrug-resistant Klebsiella pneumoniae (MDR Kp), in particular carbapenem-resistant Kp (CR-Kp), has become endemic in Italy, where alarming data have been reported on the spread of colistin-resistant CR-Kp (CRCR-Kp). During the period 2013-2014, 27 CRCR-Kp nosocomial strains were isolated within the Modena University Hospital Policlinico (MUHP) multidrug resistance surveillance program. We retrospectively investigated these isolates by whole-ge ...[more]

PMID: 32408565

Similar Datasets

Project description:Colistin has been considered a last-line option for the treatment of infections caused by carbapenem-resistant Klebsiella pneumoniae (CRKP). Heterogeneous resistance to colistin leads to unexplained clinical colistin treatment failure for CRKP. Our study aimed to investigate the extent of colistin heteroresistance among CRKP strains in China. A total of 455 colistin-susceptible strains, collected from six tertiary care hospitals in China, were characterized. The overall rate of colistin heteroresistance was 6.2%, as determined by the population analysis profiles (PAPs). Genomic analysis revealed that 60.7% of the colistin-heteroresistant isolates belonged to the epidemic sequence type 11 (ST11) clone. Single-nucleotide polymorphisms (SNPs) suggested that 6 ST5216 strains shared the same origin. Each of the subpopulations had a ≥8-fold decrease in colistin MIC in the presence of carbonyl cyanide m-chlorophenylhydrazone (CCCP), which indicated that heteroresistance could be suppressed by an efflux pump inhibitor. In addition, our results suggested that the PhoPQ pathway plays an important role in the mechanisms of heteroresistance. IMPORTANCE The problem of CRKP has raised alarms concerning global health. Our study enriches the epidemiological study of colistin heteroresistance among CRKP strains in China, where the prevalence of this phenomenon was previously unknown. Importantly, colistin-heteroresistant strains may cause the failure of clinical treatment with colistin, even if the clinical laboratory reports that the strains are sensitive. The commonly used broth microdilution method is unable to detect this special phenomenon. Additionally, our results indicate that efflux pumps play a major role in colistin heteroresistance, and inhibitors can effectively reverse it. Our study is the first to provide a detailed analysis of the prevalence of colistin heteroresistance in China, as well as an analysis of the genetic mechanisms of this phenomenon.

Project description:The emergence and dissemination of carbapenemases, bacterial enzymes able to inactivate most β-lactam antibiotics, in Enterobacteriaceae is of increasing concern. The concurrent spread of resistance against colistin, an antibiotic of last resort, further compounds this challenge further. Whole-genome sequencing (WGS) can play a significant role in the rapid and accurate detection/characterization of existing and emergent resistance determinants, an essential aspect of public health surveillance and response activities to combat the spread of antimicrobial resistant bacteria. In the current study, WGS data was used to characterize the genomic content of antimicrobial resistance genes, including those encoding carbapenemases, in 10 multidrug-resistant Klebsiella pneumoniae isolates from Pakistan. These clinical isolates represented five sequence types: ST11 (n = 3 isolates), ST14 (n = 3), ST15 (n = 1), ST101 (n = 2), and ST307 (n = 1). Resistance profiles against 25 clinically-relevant antimicrobials were determined by broth microdilution; resistant phenotypes were observed for at least 15 of the 25 antibiotics tested in all isolates except one. Specifically, 8/10 isolates were carbapenem-resistant and 7/10 isolates were colistin-resistant. The blaNDM-1 and blaOXA-48 carbapenemase genes were present in 7/10 and 5/10 isolates, respectively; including 2 isolates carrying both genes. No plasmid-mediated determinants for colistin resistance (e.g. mcr) were detected, but disruptions and mutations in chromosomal loci (i.e. mgrB and pmrB) previously reported to confer colistin resistance were observed. A blaOXA-48-carrying IncL/M-type plasmid was found in all blaOXA-48-positive isolates. The application of WGS to molecular epidemiology and surveillance studies, as exemplified here, will provide both a more complete understanding of the global distribution of MDR isolates and a robust surveillance tool useful for detecting emerging threats to public health.

Project description:Klebsiella pneumoniae is emerging as an important nosocomial pathogen due to its rapidly increasing multidrug resistance, which has led to a renewed interest in polymyxin antibiotics, such as colistin, as antibiotics of last resort. However, heteroresistance (i.e., the presence of a subpopulation of resistant bacteria in an otherwise susceptible culture) may hamper the effectiveness of colistin treatment in patients. In a previous study, we showed that colistin resistance among extended-spectrum-beta-lactamase (ESBL)-producing K. pneumoniae isolates emerged after the introduction of selective digestive tract decontamination (SDD) in an intensive care unit (ICU). In this study, we investigated heteroresistance to colistin among ESBL-producing K. pneumoniae isolates by using population analysis profiles (PAPs). We used whole-genome sequencing (WGS) to identify the mutations that were associated with the emergence of colistin resistance in these K. pneumoniae isolates. We found five heteroresistant subpopulations, with colistin MICs ranging from 8 to 64 mg/liter, which were derived from five clonally related, colistin-susceptible clinical isolates. WGS revealed the presence of mutations in the lpxM, mgrB, phoQ, and yciM genes in colistin-resistant K. pneumoniae isolates. In two strains, mgrB was inactivated by an IS3-like or ISKpn14 insertion sequence element. Complementation in trans with the wild-type mgrB gene resulted in these strains reverting to colistin susceptibility. The MICs for colistin-susceptible strains increased 2- to 4-fold in the presence of the mutated phoQ, lpxM, and yciM alleles. In conclusion, the present study indicates that heteroresistant K. pneumoniae subpopulations may be selected for upon exposure to colistin. Mutations in mgrB and phoQ have previously been associated with colistin resistance, but we provide experimental evidence for roles of mutations in the yciM and lpxM genes in the emergence of colistin resistance in K. pneumoniae.

Project description:Here, a program was designed to surveil the colonization and associated infection of OXA-232-producing carbapenem-resistant Klebsiella pneumoniae (CRKP) (OXA-232-CRKP) in an intensive care unit (ICU) and to describe the epidemiological characteristics during surveillance. Samples were sourced from patient and environment colonization sites in the ICU from August to December 2019. During the surveillance, 106 OXA-232-CRKP strains were isolated from 8,656 samples of colonization sites, with an average positive rate of 1.22%. The rate from patient colonization sites was 3.59% (60/1,672 samples), over 5 times higher than that of the environment (0.66% [46/6,984 samples]). Rectal swabs and ventilator-related sites had the highest positive rates among patient and environment colonization sites, respectively. Six of the 15 patients who had OXA-232-CRKP at colonization sites suffered from OXA-232-CRKP-related infections. Patients could obtain OXA-232-CRKP from the environment, while long-term patient colonization was mostly accompanied by environmental colonization with subsequent infection. Antimicrobial susceptibility testing presented similar resistance profiles, in which all isolates were resistant to ertapenem but showed different levels of resistance to meropenem and imipenem. Whole-genome sequencing and single-nucleotide polymorphism (SNP) analysis suggested that all OXA-232-CRKP isolates belonged to the sequence type 15 (ST15) clone and were divided into two clades with 0 to 45 SNPs, sharing similar resistance genes, virulence genes, and plasmid types, indicating that the wide dissemination of OXA-232-CRKP between the environment and patients was due to clonal spread. The strains all contained β-lactam resistance genes, including blaOXA-232, blaCTX-M-15, and blaSHV-106, and 75.21% additionally carried blaTEM-1. In brief, wide ST15 clonal spread and long-term colonization of OXA-232-CRKP between patients and the environment were observed, with microevolution and subsequent infection. IMPORTANCE OXA-232 is a variant of OXA-48 carbapenemase, which has been increasingly reported in nosocomial outbreaks in ICUs. However, the OXA-232-CRKP transmission relationship between the environment and patients in ICUs was still not clear. Our study demonstrated the long-term colonization of OXA-232-CRKP in the ICU environment, declared that the colonization was a potential risk to ICU patients, and revealed the possible threat that this OXA-232-CRKP clone would bring to public health. The wide dissemination of OXA-232-CRKP between the environment and patients was due to ST15 clonal spread, which presented a multidrug-resistant profile and carried disinfectant resistance genes and virulence clusters, posing a challenge to infection control. The study provided a basis for environmental disinfection, including revealing common environmental colonization sites of OXA-232-CRKP and suggesting appropriate usage of disinfectants to prevent the development of disinfectant resistance.

Dataset Information

A Retrospective Whole-Genome Sequencing Analysis of Carbapenem and Colistin-Resistant Klebsiella Pneumoniae Nosocomial Strains Isolated during an MDR Surveillance Program.

Publications

A Retrospective Whole-Genome Sequencing Analysis of Carbapenem and Colistin-Resistant <i>Klebsiella Pneumoniae</i> Nosocomial Strains Isolated during an MDR Surveillance Program.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets