Diphtheria Toxin-Producing Corynebacterium ramonii in Inner-City Population, Vancouver, British Columbia, Canada, 2019-2023.

We conducted patient chart reviews and whole-genome sequencing of wound specimens containing presumptive Corynebacterium ulcerans from Vancouver, British Columbia, Canada, during July 2019-July 2023. Sequencing confirmed 8/14 isolates were C. ramonii and identified 2 distinct clusters.

Learning the fitness dynamics of pathogens from phylogenies.

The dynamics of the genetic diversity of pathogens, including the emergence of lineages with increased fitness, is a foundational concept of disease ecology with key public-health implications. However, the identification of such lineages and estimation of associated fitness remain challenging, and is rarely done outside densely sampled systems. Here we present phylowave, a scalable approach that summarizes changes in population composition in phylogenetic trees, enabling the automatic detection of lineages based on shared fitness and evolutionary relationships.

Multiple regional outbreaks caused by global and local VIM-producing Klebsiella pneumoniae clones in Poland, 2006-2019.

Purpose: This study was aimed at comprehensive genomic analysis of VIM-type carbapenemase-producing Klebsiella pneumoniae species complex (KpSC) in Poland.

Methods: All non-duplicate 214 VIM-producing KpSC isolates reported in Poland in 2006-2019 were short-read sequenced and re-identified by the average nucleotide identity scoring. Their clonality/phylogeny was assessed by cgMLST and SNP in comparison with genomes from international databases.

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

Unlabelled: species complex (KpSC) members, including the most important species (phylogroup Kp1 of the KpSC), are important opportunistic pathogens that display increasing rates of antimicrobial resistance worldwide. As they are widespread in food and the environment, there is a need for fast, sensitive, and reliable methods to detect KpSC members in complex matrices. Previously, the ZKIR real-time PCR assay was developed to detect all KpSC members without distinction.

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

Interpreting the phenotypes of alleles in genomes is complex. Whilst all strains are expected to carry a chromosomal copy conferring resistance to ampicillin, they may also carry mutations in chromosomal alleles or additional plasmid-borne alleles that have extended-spectrum β-lactamase (ESBL) activity and/or β-lactamase inhibitor (BLI) resistance activity. In addition, the role of individual mutations/a changes is not completely documented or understood.

Cutaneous diphtheria from 2018 to 2022: an observational, retrospective study of epidemiological, microbiological, clinical, and therapeutic characteristics in metropolitan France.

The incidence of diphtheria has been rising over the past decade, particularly in its cutaneous form. A clinical review of the case series was therefore required. We reviewed the epidemiological, clinical, microbiological and therapeutic data of cutaneous diphtheria cases, in adult patients living in metropolitan France with a skin sample positive for corynebacteria of the complex between 2018 and 2022.

Towards unified reporting of genome sequencing results in clinical microbiology.

Whole genome sequencing (WGS) has become a vital tool in clinical microbiology, playing an important role in outbreak investigations, molecular surveillance, and identification of bacterial species, resistance mechanisms and virulence factors. However, the complexity of WGS data presents challenges in interpretation and reporting, requiring tailored strategies to enhance efficiency and impact. This study explores the diverse needs of key stakeholders in healthcare, including clinical management, laboratory work, public surveillance and epidemiology, infection prevention and control, and academic research, regarding WGS-based reporting of clinically relevant bacterial species.

Resurgence of , including one macrolide-resistant isolate, France, 2024.

As other European countries, France is experiencing a resurgence of pertussis in 2024. Between 1 January and 31 May 2024, 5,616 (24.9%) positive qPCR tests were identified, following a 3-year period of almost null incidence.

Transient reemergence of in France in 2022.

Between March and October 2022, a peak of detection of by qPCR, real-time PCR was observed in France. Whether this peak was due to resurgence from previous circulating lineages or reintroduction into the country was unknown. The objective of this study is to understand transient increase observed in France in 2022 whereas it had virtually stopped being reported since the start of the COVID-19 pandemic in 2020.

Bacteraemia associated with multiple septic localizations caused by Klebsiella pneumoniae sequence type ST660.

We report a case of Klebsiella pneumoniae bacteraemia in an 80-year-old man in France with no history of travel to Asia, complicated by endogenous endophthalmitis, multiple cerebral microbleeds and hepatic microabscesses, associated with a Bentall endocarditis. Hypervirulence pathotype was suggested based on clinical picture, bacterial isolate genomic sequence and hypermucoidy. Interestingly, the isolate had the non-K1/K2-capsular serotype locus KL113-like, carried a KpVP-1-like virulence plasmid, and belonged to the emerging sublineage SL660 (comprising the sequence type ST660).

Stability and Qualification of a Legacy Fungal Collection.

Microbial culture collections are valuable repositories for qualified and diverse microorganisms, playing a pivotal role in research, education, innovation, as well as in our response to current and emerging public health and societal challenges. However, such precious holdings, when not integrated in professional biobank infrastructures, may be vulnerable to major risks such as staff retirement, changes in the institutional strategy, or natural disasters. The process of preserving and rescuing "historical" collections can be long and treacherous with a loss of a part of the collection.

Corynebacterium diphtheriae and Corynebacterium ulcerans: development of EUCAST methods and generation of data on which to determine breakpoints.

Background: Evidence-based clinical susceptibility breakpoints have been lacking for antimicrobial agents used for diphtheria.

Objectives: We aimed to evaluate broth microdilution and disc diffusion methods and create a dataset of MIC values and inhibition zone diameters (ZDs) from which breakpoints could be determined.

Methods: We included 400 recent clinical isolates equally distributed by species (Corynebacterium diphtheriae and Corynebacterium ulcerans) and by national surveillance programmes (France and Germany).

Molecular characteristics, fitness, and virulence of high-risk and non-high-risk clones of carbapenemase-producing .

Extensively drug-resistant (XDR) inflict a notable burden on healthcare worldwide. Of specific concern are strains producing carbapenem-hydrolyzing enzymes, as the therapeutic options for these strains are still very limited. Specific sequence types of have been noted for their epidemic occurrence globally, but the mechanisms behind the success of specific clones remain unclear.

Multidrug-resistant in people with travel history from West Africa to France, March to September 2023.

We describe 10 unlinked cases of infection (nine cutaneous, one respiratory) in France in 2023 in persons travelling from Guinea, Mali, Senegal, Niger or Nigeria and Central African Republic. Four isolates were toxigenic. Seven genomically unrelated isolates were multidrug-resistant, including a toxigenic respiratory isolate with high-level resistance to macrolides and beta-lactams.

Phylogenomics of species and analysis of antimicrobial resistance genes.

Introduction: Non- species are increasingly isolated in the clinical setting and the environment. The aim of the present study was to analyze a genome database of 837 spp. isolates, which included 798 non- genomes, in order to define the concordance of classification and discriminatory power of 7-gene MLST, 53-gene MLST, and single-nucleotide polymorphism (SNPs) phylogenies.

Corynebacterium ramonii sp. nov., a novel toxigenic member of the Corynebacterium diphtheriae species complex.

The Corynebacterium diphtheriae species complex comprises seven bacterial species, including Corynebacterium ulcerans, a zoonotic pathogen from multiple animal species. In this work, we characterise phenotypically and genotypically isolates belonging to two C. ulcerans lineages.