Metagenomic Approaches Reveal Strain Profiling and Genotyping of Klebsiella pneumoniae from Hospitalized Patients in China

Liu, Jiao; Zhao, Xu; Li, Haibo; Chen, Fuhui; Han, Ke; Hu, Xiaoman; Fang, Yuan; Chen, Dechang

doi:10.1128/spectrum.02190-21

Cited by 3 publications

(2 citation statements)

References 56 publications

(79 reference statements)

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“…Deoxyribonucleic acid extracted from clinical specimens can directly be processed for NGS analysis. Therefore, metagenomics is advantageous for the identification of the strain and virulence of the hvKP in contrast to traditional cultivation ( 15 ). The use of NGS may help in the early and accurate identification of hvKP, ultimately improving patients' outcomes.…”

Section: Discussionmentioning

confidence: 99%

Successful treatment of acute respiratory distress syndrome caused by hypervirulent Klebsiella pneumoniae with extracorporeal membrane oxygenation and continuous renal replacement therapy: A case report and literature review

Peng

et al. 2022

Front. Med.

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Hypervirulent Klebsiella pneumoniae (hvKP) causes invasive infections and leads to high morbidity and mortality rates. Here, we report the case of a Chinese man with diabetes mellitus who developed acute respiratory distress syndrome and septic shock due to hvKP belonging to the K1 strain. The patient was treated with venovenous extracorporeal membrane oxygenation and continuous renal replacement therapy, in combination with antibiotics and recovered well. Clinicians should be aware of fatal infections caused by hvKP and investigate the best treatment options for patients at various stages of infection.

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Section: Discussionmentioning

confidence: 99%

Successful treatment of acute respiratory distress syndrome caused by hypervirulent Klebsiella pneumoniae with extracorporeal membrane oxygenation and continuous renal replacement therapy: A case report and literature review

Peng

et al. 2022

Front. Med.

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“…Conversely, metagenomic next-generation sequencing (mNGS) is a promising tool for rapid, culture-free pathogen surveillance and molecular epidemiology. It also enables coinfection detection without prior knowledge of the etiological agent ( Miller et al, 2013 ; Liu et al, 2022 ). mNGS has proven to be successful in pathogen identification, coinfection detection, and epidemiological studies of the HAdV-55 outbreak in 2019 ( Li P. et al, 2021 ), as well as the HAdV-7 outbreak during 2018–2019 in Hubei Province, China ( Li Y. et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

Genetic characterization of human adenoviruses in patients using metagenomic next-generation sequencing in Hubei, China, from 2018 to 2019

et al. 2023

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ObjectivesThis study aimed to characterize the genomic epidemiology of human adenoviruses (HAdVs) in Hubei, China, using metagenomic next-generation sequencing (mNGS).MethodsIn total, 25 HAdV-positive samples collected from 21 pediatric patients were sequenced and subjected to mNGS using the NextSeq 550 and GenoLab M sequencing platforms. The metagenomic data were assembled de novo for molecular typing, phylogenetic and recombination analyzes.ResultsWe assembled 50 HAdV genomes, 88% (22/25) genomes from GenoLab M, and 84% (21/25) genomes from NextSeq 550 have perfect alignments to reference genomes with greater than 90%. The most fully assembled 25 genomes were categorized into 7 HAdV genotypes, the most abundant of which were HAdV-B3 (9/25) and HAdV-C2 (6/25). Phylogenetic analyzes revealed that the newly isolated HAdV-B3 strains diverged into separate clusters according to their genotypes. Vigilance is needed that HAdV-B3 isolates have begun to form new distinct clusters. High nucleotide identity was observed in the whole genome level within the same HAdV genotypes, while marked differences of three capsid genes across HAdV genotypes were noted. The high nucleotide diversity regions were concordant with the reported hypervariable regions. Further, three recombinant strains were identified: S64 and S71 originated from the parental strains HAdV-B14 and HAdV-B11, and S28 originated from HAdV-C1, HAdV-C5, and HAdV-CBJ113. GenoLab M and NextSeq 550 showed comparable performance with respect to data yield, duplication rate, human ratio, and assembly completeness.ConclusionThe sequencing quality and assembly accuracy showed that mNGS assembled genomes can be used for subsequently HAdV genotyping and genomic characterization. The high nucleotide diversity of capsid genes and high frequency of recombination events has highlighted the necessity for HAdV epidemiological surveillance in China.

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Comprehensive Profiling of Klebsiella in Surface Waters from Northern Portugal: Understanding Patterns in Prevalence, Antibiotic Resistance, and Biofilm Formation

Araújo,

Silva,

de Lurdes Enes Dapkevicius

et al. 2024

Water

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This study investigates the prevalence of resistance and virulence genes in Klebsiella isolates from surface waters in Northern Portugal, within the broader context of freshwater quality challenges in Southern Europe. The aim of this research is to explain how Klebsiella dynamics, antibiotic resistance, and biofilm formation interact in surface waters. Antimicrobial susceptibility was examined using the Kirby–Bauer disk diffusion method against 11 antibiotics and screening for Extended-Spectrum Beta-Lactamase (ESBL) production using the double-disk synergy. PCR was employed to detect resistance and virulence genes, while biofilm production was assessed using the microplate method. Out of 77 water isolates, 33 Klebsiella (14 Klebsiella spp. and 19 K. pneumoniae strains) were isolated. ESBL production was observed in 36.8% of K. pneumoniae and 28.6% of Klebsiella spp. High resistance rates to blaCTX-U were observed in both. The papC gene was prevalent, signifying potential environmental risks. Biofilm production averaged 81.3% for K. pneumoniae and 86.9% for Klebsiella spp. These findings underscore the intricate interplay between Klebsiella’s dynamics and freshwater quality, with ESBL’s prevalence raising concerns about waterborne dissemination and public health implications. This work supports the need for vigilance of Klebsiella in surface waters in Southern Europe.

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Metagenomic Approaches Reveal Strain Profiling and Genotyping of Klebsiella pneumoniae from Hospitalized Patients in China

Cited by 3 publications

References 56 publications

Successful treatment of acute respiratory distress syndrome caused by hypervirulent Klebsiella pneumoniae with extracorporeal membrane oxygenation and continuous renal replacement therapy: A case report and literature review

Successful treatment of acute respiratory distress syndrome caused by hypervirulent Klebsiella pneumoniae with extracorporeal membrane oxygenation and continuous renal replacement therapy: A case report and literature review

Genetic characterization of human adenoviruses in patients using metagenomic next-generation sequencing in Hubei, China, from 2018 to 2019

Comprehensive Profiling of Klebsiella in Surface Waters from Northern Portugal: Understanding Patterns in Prevalence, Antibiotic Resistance, and Biofilm Formation

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