Accurate Identification of Klebsiella variicola by MALDI-TOF Mass Spectrometry in Clinical Microbiology Laboratories

Ohama, Yuki; Nomura, Yusuke; Mizoguchi, Miyuki; Higurashi, Yoshimi; Okamoto, Koh; Harada, Sohei

doi:10.1128/spectrum.02844-22

Cited by 10 publications

(3 citation statements)

References 20 publications

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“…similipneumoniae ) and K. aerogenes . K. variicola and K. quasipneumoniae are relatively common pathogens causing hospital-acquired infections, but traditional clinical laboratory methods (MALDI-TOF MS, multilocus sequence typing, or capsule genotyping) may misclassify them as K. pneumoniae , which would underestimate the clinical infection they cause and the actual prevalence ( Wyres et al, 2020 ; Ohama et al, 2022 ).…”

Section: Discussionmentioning

confidence: 99%

Class 1 integrons and multiple mobile genetic elements in clinical isolates of the Klebsiella pneumoniae complex from a tertiary hospital in eastern China

Wang

Zhu²,

Yan³

et al. 2023

Front. Microbiol.

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BackgroundThe emergence of highly drug-resistant K. pneumoniae, has become a major public health challenge. In this work, we aim to investigate the diversity of species and sequence types (STs) of clinical Klebsiella isolates and to characterize the prevalence and structure of class 1 integrons.MethodsBased on the whole genome sequencing, species identification was performed by 16S rRNA gene homology and average nucleotide identity (ANI) analysis. STs were determined in accordance with the international MLST schemes for K. pneumoniae and K. variicola. Integron characterization and comparative genomic analysis were performed using various bioinformatic tools.ResultsSpecies identification showed that the 167 isolates belonged to four species: K. pneumoniae, K. variicola subsp. variicola, K. quasipneumoniae and K. aerogenes. Thirty-six known and 5 novel STs were identified in K. pneumoniae, and 10 novel STs were identified in K. variicola subsp. variicola. Class 1 integrons were found in 57.49% (96/167) of the isolates, and a total of 169 resistance gene cassettes encoding 19 types of resistance genes, including carbapenem resistance gene (blaIPM-4) and class D β-lactamases gene (blaOXA-1 and blaOXA-10), were identified. Among the 17 complete genomes, 29 class 1 integrons from 12 groups were found, only 1 group was encoded on chromosomes. Interestingly, one plasmid (pKP167-261) carrying two copies of approximately 19-kb IS26-Int1 complex resistance region that contains an integron and a multidrug resistance gene fragment.ConclusionThe results of this work demonstrated that the species and STs of the clinical Klebsiella isolates were more complex by the whole genome sequence analysis than by the traditional laboratory methods. Finding of the new structure of MGEs related to the resistance genes indicates the great importance of deeply exploring the molecular mechanisms of bacterial multidrug resistance.

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Section: Discussionmentioning

confidence: 99%

Class 1 integrons and multiple mobile genetic elements in clinical isolates of the Klebsiella pneumoniae complex from a tertiary hospital in eastern China

Wang

Zhu²,

Yan³

et al. 2023

Front. Microbiol.

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“…Even after enrichment of the Klebsiella spp. database in Bruker Daltonics library version 6, the MS data for K. ozaenae remained unchanged with only three strains (22). Further research is needed to determine whether the enrichment of MS data will enable the differentiation of these species and strains.…”

Section: Discussionmentioning

confidence: 99%

First Report of <i>Klebsiella pneumoniae</i> subsp. <i>ozaenae</i> Meningitis in Japan

Hosono Honda,

Harada,

Suzuki

et al. 2024

Intern. Med.

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Although the frequency of community-acquired infections caused by Klebsiella pneumoniae subsp. ozaenae (K. ozaenae) is low, they are often detected in sputum specimens. In addition, lung abscesses, necrotizing pneumonia, and urinary tract infections caused by K. ozaenae have also been reported. We herein report the first detection of K. ozaenae as an etiological agent of bacterial meningitis in Japan. Cases of K. ozaenae meningitis complicated by diabetes mellitus and sinusitis have been reported elsewhere. When Klebsiella pneumoniae is detected in such cases, it is important to use other detection methods in addition to mass spectrometry for correct identification.

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“…This challenge persisted until the adoption of advanced techniques such as matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and whole-genome sequencing for accurate species identification. 6 , 7 The past misidentification, particularly within the K. pneumoniae complex, has hindered comprehensive research on K. variicola within the healthcare system.…”

Section: Introductionmentioning

confidence: 99%

Global Emergence and Genomic Epidemiology of blaNDM-Carrying Klebsiella variicola

Li,

Zhang,

Wang

et al. 2024

IDR

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Purpose Klebsiella variicola has emerged as a human pathogen in the past decade. Here, we present findings related to a K. variicola strain carrying the bla NDM-1 gene, which was isolated from a urinary tract infection in China. Global transmission dynamics and genomic epidemiology of bla NDM -carrying K. variicola were further investigated. Material and Methods The complete genome sequence of the strain was determined using the Illumina NovaSeq 6000 and Nanopore MinION sequencer. Genomic features and resistance mechanisms were analyzed through diverse bioinformatics approaches. Additionally, genome sequences of K. variicola strains carrying bla NDM were retrieved from the NCBI database, and a comprehensive analysis of the global dissemination trends of these strains was conducted. Results K. variicola strain 353 demonstrated resistance to multiple antimicrobials, including carbapenems. Within its genome, we identified fourteen antimicrobial resistance genes associated with β-lactam, aminoglycoside, fosfomycin, quinolone, trimethoprim, rifamycin, and sulfonamide resistance. The carbapenem-resistant gene bla NDM-1 was located on an IncU-type plasmid spanning 294,608 bp and flanked by IS CR1 and IS 26 . Downstream of bla NDM-1 , we identified an Intl1 element housing numerous antibiotic resistance genes. A comprehensive search of the NCBI database revealed 72 K. variicola strains carrying bla NDM from twelve different countries, predominantly from clinical sources, with the highest prevalence observed in the USA and China. A total of 28 distinct sequence types (STs) were identified, with ST115 being the most prevalent, followed by ST60. Conclusion In summary, this study presents the genomic characterization of a K. variicola strain carrying bla NDM-1 on an IncU-type plasmid. The research highlights the global dissemination of bla NDM -carrying K. variicola , observed in both healthcare settings and natural environments. Our data have revealed a diverse array of antimicrobial resistance determinants in K. variicola , providing valuable insights that could aid in the development of strategies for the prevention, diagnosis, and treatment of K. variicola infections.

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Accurate Identification of Klebsiella variicola by MALDI-TOF Mass Spectrometry in Clinical Microbiology Laboratories

Cited by 10 publications

References 20 publications

Class 1 integrons and multiple mobile genetic elements in clinical isolates of the Klebsiella pneumoniae complex from a tertiary hospital in eastern China

Class 1 integrons and multiple mobile genetic elements in clinical isolates of the Klebsiella pneumoniae complex from a tertiary hospital in eastern China

First Report of <i>Klebsiella pneumoniae</i> subsp. <i>ozaenae</i> Meningitis in Japan

Global Emergence and Genomic Epidemiology of blaNDM-Carrying Klebsiella variicola

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