Genotypic Characterization of Clinical Klebsiella spp. Isolates Collected From Patients With Suspected Community-Onset Sepsis, Sweden

Klebsiella is a genus of Gram-negative bacteria known to be opportunistic pathogens that may cause a variety of infections in humans. Highly drug-resistant Klebsiella species, especially K. pneumoniae, have emerged rapidly and are becoming a major concern in clinical management. Although K. pneumoniae is considered the most important pathogen within the genus, the true clinical significance of the other species is likely underrecognized due to the inability of conventional microbiological methods to distinguish between the species leading to high rates of misidentification. Bacterial whole-genome sequencing (WGS) enables precise species identification and characterization that other technologies do not allow. Herein, we have characterized the diversity and traits of Klebsiella spp. in community-onset infections by WGS of clinical isolates (n = 105) collected during a prospective sepsis study in Sweden. The sequencing revealed that 32 of the 82 isolates (39.0%) initially identified as K. pneumoniae with routine microbiological methods based on cultures followed by matrix-assisted laser desorption-time of flight mass spectrometry (MALDI-TOF MS) had been misidentified. Of these, 23 were identified as Klebsiella variicola and nine as other members of the K. pneumoniae complex. Comparisons of the number of resistance genes showed that significantly fewer resistance genes were detected in Klebsiella oxytoca compared to K. pneumoniae and K. variicola (both values of p < 0.001). Moreover, a high proportion of the isolates within the K. pneumoniae complex were predicted to be genotypically multidrug-resistant (MDR; 79/84, 94.0%) in contrast to K. oxytoca (3/16, 18.8%) and Klebsiella michiganensis (0/4, 0.0%). All isolates predicted as genotypically MDR were found to harbor the combination of β-lactam, fosfomycin, and quinolone resistance markers. Multi-locus sequence typing (MLST) revealed a high diversity of sequence types among the Klebsiella spp. with ST14 (10.0%) and ST5429 (10.0%) as the most prevalent ones for K. pneumoniae, ST146 for K. variicola (12.0%), and ST176 for K. oxytoca (25.0%). In conclusion, the results from this study highlight the importance of using high-resolution genotypic methods for identification and characterization of clinical Klebsiella spp. isolates. Our findings indicate that infections caused by other members of the K. pneumoniae complex than K. pneumoniae are a more common clinical problem than previously described, mainly due to high rates of misidentifications.

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Genomic Characterization of A Multidrug-resistant Citrobacter freundii Strain ZT01-0079 Co-Producing blaNDM-1 and blaSHV-12 using MiSeq and MinION

10.21203/rs.3.rs-92305/v1 ◽

2020 ◽

Author(s):

Tingyan Zhang ◽

Yanfeng Lin ◽

Zhonghong Li ◽

Xiong Liu ◽

Jinhui Li ◽

...

Keyword(s):

Resistance Genes ◽

Southern Blotting ◽

Multiple Drug Resistance ◽

Carbapenem Resistance ◽

Multidrug Resistant ◽

Multiple Drug ◽

Citrobacter Freundii ◽

Rapid Spread ◽

Genomic Characterization

Abstract Background: The emergence of multi-drug resistant Citrobacter freundii poses daunting challenges to the treatment of clinical infections. The purpose of this study was to characterize the genome of a C. freundii strain with an IncX3 plasmid encoding both the blaNDM-1 and blaSHV-12 genes.Methods: Strain ZT01-0079 was isolated from a clinical urine sample. The Vitek2 system was used for identification and antimicrobial susceptibility testing. The presence of blaNDM-1 was detected by PCR and sequencing. Conjugation experiments and Southern blotting were performed to determine the transferability of the blaNDM-1- carrying plasmid. Nanopore and Illumina sequencing were performed to better understand the genomic characteristics of the strain.Results: Strain ZT01-0079 was identified as C. freundii, and the coexistence of blaNDM-1 and multiple drug resistance genes was confirmed. Electrophoresis and Southern blotting showed that blaNDM-1 was located on a ~53kb IncX3 plasmid. The NDM-1-encoding plasmid was successfully transferred at a frequency of 1.68×10−3. Both blaNDM-1 and blaSHV-12 were located on the self-transferable IncX3 plasmid.Conclusion: The rapid spread of the IncX3 plasmid highlights the importance of continuous monitoring of the prevalence of NDM-1-encoding Enterobacteriaceae. Mutations of existing carbapenem resistance genes will bring formidable challenges to clinical treatment.

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Identification and characterization of candidateRlm4blackleg resistance genes inBrassica napususing next-generation sequencing

Plant Biotechnology Journal ◽

10.1111/j.1467-7652.2012.00716.x ◽

2012 ◽

Vol 10 (6) ◽

pp. 709-715 ◽

Cited By ~ 28

Author(s):

Reece Tollenaere ◽

Alice Hayward ◽

Jessica Dalton-Morgan ◽

Emma Campbell ◽

Joanne R.M. Lee ◽

...

Keyword(s):

Next Generation Sequencing ◽

Resistance Genes ◽

Next Generation ◽

Identification And Characterization ◽

Generation Sequencing

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Identification and characterization of chemical constituents in Qi-Lin pills and their metabolites in rat bio-samples after oral administration using ultra-high performance liquid chromatography with quadrupole time-of-flight mass spectrometry

Journal of Pharmaceutical and Biomedical Analysis ◽

10.1016/j.jpba.2020.113402 ◽

2020 ◽

Vol 188 ◽

pp. 113402

Author(s):

Xi-yang Tang ◽

Jia-xing Zeng ◽

Zi-qin Dai ◽

Ming-hao Chen ◽

Meng-nan Ye ◽

...

Keyword(s):

Mass Spectrometry ◽

High Performance Liquid Chromatography ◽

Liquid Chromatography ◽

Oral Administration ◽

High Performance ◽

Chemical Constituents ◽

Time Of Flight ◽

Flight Mass Spectrometry ◽

Identification And Characterization

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Whole-genome sequences of multidrug-resistant Escherichia coli in South-Kivu Province, Democratic Republic of Congo: characterization of phylogenomic changes, virulence and resistance genes

BMC Infectious Diseases ◽

10.1186/s12879-019-3763-3 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 14

Author(s):

Leonid M. Irenge ◽

Jerome Ambroise ◽

Bertrand Bearzatto ◽

Jean-François Durant ◽

Raphaël B. Chirimwami ◽

...

Keyword(s):

Escherichia Coli ◽

Resistance Genes ◽

Democratic Republic ◽

Democratic Republic Of Congo ◽

Multidrug Resistant ◽

Whole Genome ◽

Genome Sequences ◽

Republic Of Congo ◽

South Kivu

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Identification and Characterization of Multidrug-Resistant Extended-Spectrum Beta-Lactamase-Producing Bacteria from Healthy and Diseased Dogs and Cats Admitted to a Veterinary Hospital in Brazil

Microbial Drug Resistance ◽

10.1089/mdr.2020.0043 ◽

2020 ◽

Author(s):

Ricardo Antonio Pilegi Sfaciotte ◽

Leandro Parussolo ◽

Fernanda Danielle Melo ◽

Paula Wildemann ◽

Giseli Bordignon ◽

...

Keyword(s):

Multidrug Resistant ◽

Beta Lactamase ◽

Extended Spectrum Beta Lactamase ◽

Extended Spectrum ◽

Veterinary Hospital ◽

Identification And Characterization

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1-(Benzo[b]thiophen-4-yl)piperazine Ring Induced Bioactivation of Brexpiprazole in Liver Microsomes: Identification and Characterization of Reactive Conjugates Using Ultra-High-Performance Liquid Chromatography/Quadrupole Time-of-Flight Mass Spectrometry

European Journal of Drug Metabolism and Pharmacokinetics ◽

10.1007/s13318-020-00606-8 ◽

2020 ◽

Vol 45 (3) ◽

pp. 393-403

Author(s):

Disha Thakkar ◽

Abhijeet S. Kate

Keyword(s):

Mass Spectrometry ◽

High Performance Liquid Chromatography ◽

Liquid Chromatography ◽

High Performance ◽

Liver Microsomes ◽

Time Of Flight ◽

Piperazine Ring ◽

Flight Mass Spectrometry ◽

Identification And Characterization

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Drug Resistance and Biofilm Production among Pseudomonas aeruginosa Clinical Isolates in a Tertiary Care Hospital of Nepal

Nepal Medical College Journal ◽

10.3126/nmcj.v21i2.25109 ◽

2019 ◽

Vol 21 (2) ◽

pp. 110-116

Author(s):

Rajani Shrestha ◽

N. Nayak ◽

D.R. Bhatta ◽

D. Hamal ◽

S.H. Subramanya ◽

...

Keyword(s):

Pseudomonas Aeruginosa ◽

Drug Resistance ◽

Biofilm Formation ◽

Tertiary Care ◽

Clinical Problem ◽

Multidrug Resistant ◽

Clinical Isolates ◽

Diffusion Method ◽

Care Hospital ◽

Microbiological Methods

Clinical isolates of Pseudomonas aeruginosa often exhibit multidrug resistance due to their inherent ability to form biofilms. Drug resistance in Ps. aeruginosa is a major clinical problem, especially in the management of patients with nosocomial infections and those admitted to ICUs with indwelling medical devices. To evaluate the biofilm forming abilities of the clinical isolates of Ps. aeruginosa and to correlate biofilm formation with antibiotic resistance. A total of 90 consecutive isolates of Ps. aeruginosa obtained from various specimens collected from patients visiting the Manipal Teaching Hospital, Pokhara, Nepal between January 2018 - October 2018 were studied. Isolates were identified by standard microbiological methods. Antibiotic susceptibility testing was performed by Kirby-Bauer disc diffusion method. All the isolates were tested for their biofilm forming abilities by employing the tissue culture plate assay. Of the 90 Ps. aeruginosa isolates, maximum i.e 42 (46.6%) were from patients in the age group of > 50 years. Majority (30; 33.3%) of the isolates were obtained from sputum samples. However, percentage isolation from other specimens like urine, endotracheal tube (ETT), pus, eye specimens and blood were 18.9%, 16.7%, 16.7%, 7.8% and 6.7% respectively. All the isolates were sensitive to polymixin B and colistin, 91.1% of the organisms were sensitive to imipenem, and more than 80% to aminoglycosides (80% to gentamicin, 83.3% to amikacin). A total of 29 (32.2%) organisms were biofilm producers. Maximum numbers of biofilm producing strains were obtained from ETT (8 of 15; 53.3%), pus (8 of 15; 53.3%) and blood (2 of 6; 33.3%) i.e from all invasive sites. None of the isolates from noninvasive specimens such as conjunctival swabs were biofilm positive. Significantly higher numbers of biofilm producers (23 of 29; 79.3%) were found to be multidrug resistant as compared to non-biofilm (6 of 61; 9.8%) producers (p=0.000). Ps. aeruginosa colonization leading to biofilm formation in deep seated tissues and on indwelling devices is a therapeutic challenge as majority of the isolates would be recalcitrant to commonly used antipseudomonal drugs. Effective monitoring of drug resistance patterns in all Pseudomonas clinical isolates should be a prerequisite for successful patient management.

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