Whole-genome sequence-informed MALDI-TOF MS diagnostics reveal importance of Klebsiella oxytoca group in invasive infections: a retrospective clinical study

Autor: Ali Kassim, Adrian Egli, Carlo Casanova, Christina Homberger, Helke A. van Dessel, Stefanie von Felten, Belén Rodríguez-Sánchez, Sarah Tschudin-Sutter, Orli Sagi, Daniel Wüthrich, Gunturu Revathi, Stefano Bassetti, Frédéric Foucault, Claudia Daubenberger, Franco Müller, Timm Hettich, Valentin Pflüger, Christian Gehringer, Deborah R. Vogt, Helena M. B. Seth-Smith, Aline Cuénod, Claudia Müller, Götz Schlotterbeck, Roxanne Mouchet, Chantal Ott, Valeria Gaia, Jacob Moran-Gilad, Greetje A. Kampinga, Martina Aerni
Přispěvatelé: University of Zurich, Cuénod, Aline, Egli, Adrian, Med Microbiol, Infect Dis & Infect Prev, MUMC+: DA MMI Staf (9), RS: FHML non-thematic output, Faculteit Medische Wetenschappen/UMCG
Jazyk: angličtina
Rok vydání: 2021
Předmět:
Male
Klebsiella
Cephalosporin
DIVERSITY
QH426-470
Antimicrobial resistance
Drug Resistance
Multiple
Bacterial
610 Medicine & health
Genetics (clinical)
Species identification
Klebsiella oxytoca
Anti-Bacterial Agents
Klebsiella pneumoniae
Klebsiella spp
BACTERIA
Medicine
Molecular Medicine
Female
2716 Genetics (clinical)
GENES
Virulence Factors
medicine.drug_class
Virulence
Invasive infections
Biology
Microbiology
Antibiotic resistance
Species Specificity
1311 Genetics
1312 Molecular Biology
Genetics
medicine
Humans
MALDI-TOF MS
POPULATION-STRUCTURE
Molecular Biology
Retrospective Studies
Whole Genome Sequencing
IDENTIFICATION
Research
10060 Epidemiology
Biostatistics and Prevention Institute (EBPI)
Odds ratio
Ribosomal RNA
biology.organism_classification
EVOLUTION
Klebsiella Infections
Spectrometry
Mass
Matrix-Assisted Laser Desorption-Ionization
1313 Molecular Medicine
PNEUMONIAE
VIRULENCE
Genome
Bacterial
Bacteria
RESISTANCE
Zdroj: Genome Medicine, 13(1):150. BioMed Central Ltd
Genome medicine, 13(1):150. BMC
Genome Medicine, Vol 13, Iss 1, Pp 1-16 (2021)
Cuénod, Aline; Wüthrich, Daniel; Seth-Smith, Helena M B; Ott, Chantal; Gehringer, Christian; Foucault, Frédéric; Mouchet, Roxanne; Kassim, Ali; Revathi, Gunturu; Vogt, Deborah R; von Felten, Stefanie; Bassetti, Stefano; Tschudin-Sutter, Sarah; Hettich, Timm; Schlotterbeck, Götz; Homberger, Christina; Casanova, Carlo; Moran-Gilad, Jacob; Sagi, Orli; Rodríguez-Sánchez, Belén; ... (2021). Whole-genome sequence-informed MALDI-TOF MS diagnostics reveal importance of Klebsiella oxytoca group in invasive infections: a retrospective clinical study. Genome medicine, 13(1), p. 150. BioMed Central 10.1186/s13073-021-00960-5
Genome Medicine
ISSN: 1756-994X
Popis: Background Klebsiella spp. are opportunistic pathogens which can cause severe infections, are often multi-drug resistant and are a common cause of hospital-acquired infections. Multiple new Klebsiella species have recently been described, yet their clinical impact and antibiotic resistance profiles are largely unknown. We aimed to explore Klebsiella group- and species-specific clinical impact, antimicrobial resistance (AMR) and virulence. Methods We analysed whole-genome sequence data of a diverse selection of Klebsiella spp. isolates and identified resistance and virulence factors. Using the genomes of 3594 Klebsiella isolates, we predicted the masses of 56 ribosomal subunit proteins and identified species-specific marker masses. We then re-analysed over 22,000 Matrix-Assisted Laser Desorption Ionization - Time Of Flight (MALDI-TOF) mass spectra routinely acquired at eight healthcare institutions in four countries looking for these species-specific markers. Analyses of clinical and microbiological endpoints from a subset of 957 patients with infections from Klebsiella species were performed using generalized linear mixed-effects models. Results Our comparative genomic analysis shows group- and species-specific trends in accessory genome composition. With the identified species-specific marker masses, eight Klebsiella species can be distinguished using MALDI-TOF MS. We identified K. pneumoniae (71.2%; n = 12,523), K. quasipneumoniae (3.3%; n = 575), K. variicola (9.8%; n = 1717), “K. quasivariicola” (0.3%; n = 52), K. oxytoca (8.2%; n = 1445), K. michiganensis (4.8%; n = 836), K. grimontii (2.4%; n = 425) and K. huaxensis (0.1%; n = 12). Isolates belonging to the K. oxytoca group, which includes the species K. oxytoca, K. michiganensis and K. grimontii, were less often resistant to 4th-generation cephalosporins than isolates of the K. pneumoniae group, which includes the species K. pneumoniae, K. quasipneumoniae, K. variicola and “K. quasivariicola” (odds ratio = 0.17, p < 0.001, 95% confidence interval [0.09,0.28]). Within the K. pneumoniae group, isolates identified as K. pneumoniae were more often resistant to 4th-generation cephalosporins than K. variicola isolates (odds ratio = 2.61, p = 0.003, 95% confidence interval [1.38,5.06]). K. oxytoca group isolates were found to be more likely associated with invasive infection to primary sterile sites than K. pneumoniae group isolates (odds ratio = 2.39, p = 0.0044, 95% confidence interval [1.05,5.53]). Conclusions Currently misdiagnosed Klebsiella spp. can be distinguished using a ribosomal marker-based approach for MALDI-TOF MS. Klebsiella groups and species differed in AMR profiles, and in their association with invasive infection, highlighting the importance for species identification to enable effective treatment options.
Databáze: OpenAIRE
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