Development and validation of a quick, automated, and reproducible ATR FT-IR spectroscopy machine-learning model for <i>Klebsiella pneumoniae</i> typing

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Abstract

We created and validated an automated and simple workflow for the identification of clinically relevant Klebsiella pneumoniae lineages by FT-IR spectroscopy and machine-learning, a method that can be extremely useful to provide quick and reliable typing information to support real-time decisions of outbreak management and infection control. This method and workflow is of interest to support clinical microbiology diagnostics and to aid public health surveillance.

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Hypervirulent Klebsiella pneumoniae

Thomas Russo, Candace Marr (2019)

Hypervirulent K. pneumoniae (hvKp) is an evolving pathotype that is more virulent than classical K. pneumoniae (cKp). hvKp usually infects individuals from the community, who are often healthy. Infections are more common in the Asian Pacific Rim but are occurring globally. hvKp infection frequently presents at multiple sites or subsequently metastatically spreads, often requiring source control. hvKp has an increased ability to cause central nervous system infection and endophthalmitis, which require rapid recognition and site-specific treatment. The genetic factors that confer hvKp’s hypervirulent phenotype are present on a large virulence plasmid and perhaps integrative conjugal elements. Increased capsule production and aerobactin production are established hvKp-specific virulence factors. Similar to cKp, hvKp strains are becoming increasingly resistant to antimicrobials via acquisition of mobile elements carrying resistance determinants, and new hvKp strains emerge when extensively drug-resistant cKp strains acquire hvKp-specific virulence determinants, resulting in nosocomial infection. Presently, clinical laboratories are unable to differentiate cKp from hvKp, but recently, several biomarkers and quantitative siderophore production have been shown to accurately predict hvKp strains, which could lead to the development of a diagnostic test for use by clinical laboratories for optimal patient care and for use in epidemiologic surveillance and research studies.

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Epidemic of carbapenem-resistant Klebsiella pneumoniae in Europe is driven by nosocomial spread

Sophia David, Sandra Reuter, Simon R. Harris … (2019)

Public health interventions to control the current epidemic of carbapenem-resistant Klebsiella pneumoniae are reliant upon a comprehensive understanding of their emergence and spread over a wide range of geographical scales. We analysed the genome sequences and epidemiological data of >1700 K. pneumoniae, isolated from patients in 244 hospitals in 32 countries, during the European survey of carbapenemase-producing Enterobacteriaceae (EuSCAPE). We demonstrate that carbapenemase acquisition is the main cause of carbapenem resistance and has occurred across diverse phylogenetic backgrounds. However, 477/682 (69.9%) of carbapenemase-positive isolates are concentrated in four clonal lineages, sequence types (ST) 11, 15, 101, 258/512, and their derivatives. Combined analysis of the genetic and geographic distances between isolates with different beta-lactam resistance determinants suggests that the propensity of K. pneumoniae to spread in hospital environments correlates with the degree of resistance and that carbapenemase-positive isolates have the highest transmissibility. Indeed, we found that over half of hospitals contributing carbapenemase-positive isolates likely experienced within-hospital transmission, and inter-hospital spread is far more frequent within, rather than between, countries. Finally, we propose a value of 21 for the number of single nucleotide polymorphisms (SNPs) that optimises discrimination of hospital clusters, and detail the international spread of the successful epidemic lineage, ST258/512.

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A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex

Margaret Lam, Ryan Wick, Stephen C Watts … (2021)

Klebsiella pneumoniae is a leading cause of antimicrobial-resistant (AMR) healthcare-associated infections, neonatal sepsis and community-acquired liver abscess, and is associated with chronic intestinal diseases. Its diversity and complex population structure pose challenges for analysis and interpretation of K. pneumoniae genome data. Here we introduce Kleborate, a tool for analysing genomes of K. pneumoniae and its associated species complex, which consolidates interrogation of key features of proven clinical importance. Kleborate provides a framework to support genomic surveillance and epidemiology in research, clinical and public health settings. To demonstrate its utility we apply Kleborate to analyse publicly available Klebsiella genomes, including clinical isolates from a pan-European study of carbapenemase-producing Klebsiella , highlighting global trends in AMR and virulence as examples of what could be achieved by applying this genomic framework within more systematic genomic surveillance efforts. We also demonstrate the application of Kleborate to detect and type K. pneumoniae from gut metagenomes. Klebsiella pneumoniae is a pathogen of increasing public health concern and antimicrobial resistance is becoming more prevalent. Here, the authors describe a K. pneumoniae genotyping tool, Kleborate, that can be used to identify lineages and detect antimicrobial resistance and virulence loci.

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Author and article information

Contributors

Ângela Novais: (View ORCID Profile)

Ana Beatriz Gonçalves: (View ORCID Profile)

Teresa G. Ribeiro: (View ORCID Profile)

Lorena López-Cerero: (View ORCID Profile)

Jesús Rodríguez-Baño: (View ORCID Profile)

Luísa Peixe: (View ORCID Profile)

Journal

Title: Journal of Clinical Microbiology

Abbreviated Title: J Clin Microbiol

Publisher: American Society for Microbiology

ISSN (Print): 0095-1137

ISSN (Electronic): 1098-660X

Publication date Created: February 14 2024

Publication date (Print): February 14 2024

Volume: 62

Issue: 2

Affiliations

[1 ]UCIBIO, Applied Molecular Biosciences Unit, Department of Biological Sciences, Faculty of Pharmacy, University of Porto , Porto, Portugal

[2 ]Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto , Porto, Portugal

[3 ]CCP, Culture Collection of Porto, Faculty of Pharmacy, University of Porto , Porto, Portugal

[4 ]1H-TOXRUN, One Health Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL , Gandra, Portugal

[5 ]CLOVER Bioanalytical Software , Granada, Spain

[6 ]Clinical Microbiology Laboratory, Local Healthcare Unit , Matosinhos, Portugal

[7 ]Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Vírgen Macarena, Instituto de Biomedicina de Sevilla (IBIS; CSIC/Hospital Virgen Macarena/Universidad de Sevilla) , Sevilla, Spain

[8 ]Departamentos de Microbiología y Medicina, Universidad de Sevilla , Sevilla, Spain