Carla Rodrigues

Ciprofloxacin resistance in Klebsiella pneumoniae: phenotype prediction from genotype and global distribution of resistance determinants

The paper develops a rules-based classifier to predict ciprofloxacin resistance in Klebsiella pneumoniae from genotype data and demonstrates its global distribution association with quinolone consumption.

Life Identification Numbers: A bacterial strain nomenclature approach

The paper proposes the Life Identification Number (LIN) system as a stable, multilevel strain taxonomy for bacterial pathogens based on core genome MLST to improve epidemiological tracking and nomenclature consistency.

Pangenome structure and ecological adaptation in the Klebsiella pneumoniae species complex: insights from a geographically and time limited multi-habitat study

This study analyzes the pangenome structure and ecological adaptation of Klebsiella pneumoniae species complex across different habitats, revealing phylogroup- and niche-specific genomic features.

No innocent bystanders: pertussis vaccination epitomizes evolutionary parallelisms between Bordetella parapertussis and B. pertussis

This paper shows that Bordetella parapertussis evolved similarly to Bordetella pertussis after pertussis vaccination, including loss of pertactin and changes in regulatory regions.

Accurate genotyping of three major respiratory bacterial pathogens with ONT R10.4.1 long-read sequencing

This study evaluates ONT R10.4.1 long-read sequencing for accurate genotyping of three respiratory pathogens, showing error rates below 1% for cgMLST.

Diversity, functional classification and genotyping of SHV β-lactamases in Klebsiella pneumoniae

This paper reclassifies SHV β-lactamase alleles in K. pneumoniae genomes based on mutations, improving genotype-phenotype understanding and updating the Kleborate tool.

Triplex real-time PCR ZKIR-T assay for simultaneous detection of the Klebsiella pneumoniae species complex and identification of K. pneumoniae sensu stricto

The paper develops a triplex real-time PCR assay (ZKIR-T) to detect all Klebsiella pneumoniae species complex members and specifically identify K. pneumoniae sensu stricto.

Phylogenomics of globally spread Clonal Groups 14 and 15 of Klebsiella pneumoniae

This study analyzes the phylogenetic structure and evolution of Klebsiella pneumoniae clonal groups 14 and 15 using genomic data, revealing independent evolutionary trajectories and the role of plasmids and accessory genomes in their diversification.

Genomic evolution of the globally disseminated multidrug-resistant Klebsiella pneumoniae clonal group 147

This paper analyzes the genomic evolution of Klebsiella pneumoniae clonal group 147, identifying its global spread and resistance mechanisms through comparative genomics and phylogenetic analysis.

Klebsiella MALDI TypeR: a web-based tool for Klebsiella identification based on MALDI-TOF mass spectrometry

The paper introduces a web-based tool for identifying Klebsiella isolates at species complex and phylogroup levels using MALDI-TOF mass spectrometry data.

On the front line of Klebsiella pneumoniae surface structures understanding: establishment of Fourier Transform Infrared (FT-IR) spectroscopy as a capsule typing method

This paper validates Fourier Transform Infrared (FT-IR) spectroscopy as a cost-effective method for K-type characterization of Klebsiella pneumoniae, achieving resolution comparable to whole-genome sequencing.