The Pan-Genomic Analysis of Corynebacterium striatum Revealed its Genetic Characteristics as an Emerging Multidrug-Resistant Pathogen

Contribution of the Mobilome to the Configuration of the Resistome of Corynebacterium striatum

Corynebacterium striatum, present in the microbiota of human skin and nasal mucosa, has recently emerged as a causative agent of hospital-acquired infections, notable for its resistance to multiple antimicrobials. Its mobilome comprises several mobile genetic elements, such as plasmids, transposons, insertion sequences and integrons, which contribute to the acquisition of antimicrobial resistance genes. This study analyzes the contribution of the C. striatum mobilome in the transfer and dissemination of resistance genes. In addition, integrative and conjugative elements (ICEs), essential in the dissemination of resistance genes between bacterial populations, whose role in C. striatum has not yet been studied, are examined. This study examined 365 C. striatum genomes obtained from the NCBI Pathogen Detection database. Phylogenetic and pangenome analyses were performed, the resistance profile of the bacterium was recognized, and mobile elements, including putative ICE, were detected. Bioinformatic analyses identified 20 antimicrobial resistance genes in this species, with the Ermx gene being the most predominant. Resistance genes were mainly associated with plasmid sequence regions and class 1 integrons. Although an ICE was detected, no resistance genes linked to this element were found. This study provided valuable information on the geographic spread and prevalence of outbreaks observed through phylogenetic and pangenome analyses, along with identifying antimicrobial resistance genes and mobile genetic elements that carry many of the resistance genes and may be the subject of future research and therapeutic approaches.

Suboptimal bioinformatic predictions of antimicrobial resistance from whole-genome sequences in multidrug-resistant Corynebacterium isolates

Herein, we combined different bioinformatics tools and databases (BV-BRC, ResFinder, RAST, and KmerResistance) to perform a prediction of antimicrobial resistance (AMR) in the genomic sequences of 107 Corynebacterium striatum isolates for which trustable antimicrobial susceptibility (AST) phenotypes could be retrieved. Then, the reliabilities of the AMR predictions were evaluated by different metrics: area under the ROC curve (AUC); Major Error Rates (MERs) and Very Major Error Rates (VMERs); Matthews Correlation Coefficient (MCC); F1-Score; and Accuracy. Out of 15 genes that were reliably detected in the C. striatum isolates, only tetW yielded predictive values for tetracycline resistance that were acceptable considering Food and Drug Administration (FDA)'s criteria for quality (MER < 3.0% and VMER with a 95% C.I. ≤1.5-≤7.5); this was accompanied by a MCC score higher than 0.9 for this gene. Noteworthy, our results indicate that other commonly used metrics (AUC, F1-score, and Accuracy) may render overoptimistic evaluations of AMR-prediction reliabilities on imbalanced datasets. Accordingly, out of 10 genes tested by PCR on additional multidrug-resistant Corynebacterium spp. isolates (n = 18), the tetW gene rendered the best agreement values with AST profiles (94.11%). Overall, our results indicate that genome-based AMR prediction can still be challenging for MDR clinical isolates of emerging Corynebacterium spp.

Phylogenomic analyses of multidrug resistant Corynebacterium striatum strains isolated from patients in a tertiary care hospital in the UK

Corynebacterium striatum is an emerging nosocomial pathogen. This is the first report showing the presence of three distinct multidrug resistant lineages of C. striatum among patients in a UK hospital. The presence of ErmX, Tet(W), Bla and AmpC proteins, and mutations in gyrA gene are associated with the resistance to clindamycin, doxycycline, penicillin and moxifloxacin, respectively. These strains are equipped with several corynebacterial virulence genes including two SpaDEF-type and a novel pilus gene cluster, which needs further molecular characterisation. This study highlights a need of developing an active surveillance strategy for routine monitoring and preventing potential cross-transmission among susceptible patients.

Ovine and Caprine Strains of Corynebacterium pseudotuberculosis on Czech Farms-A Comparative Study

Caseous lymphadenitis (CLA) is a worldwide disease of small ruminants caused by Corynebacterium pseudotuberculosis, a facultative intracellular pathogen that is able to survive and multiply in certain white blood cells of the host. In this study, 33 strains of C. pseudotuberculosis were isolated from sheep and goats suffering from CLA on nine farms in the Czech Republic. All these strains were tested for their antibiotic susceptibility, ability to form a biofilm and resistance to the effects of commonly used disinfectant agents. To better understand the virulence of C. pseudotuberculosis, the genomes of strains were sequenced and comparative genomic analysis was performed with another 123 genomes of the same species, including ovis and equi biovars, downloaded from the NCBI. The genetic determinants for the virulence factors responsible for adherence and virulence factors specialized for iron uptake and exotoxin phospholipase D were revealed in every analyzed genome. Carbohydrate-Active Enzymes were compared, revealing the presence of genetic determinants encoding exo-α-sialidase (GH33) and the CP40 protein in most of the analyzed genomes. Thirty-three Czech strains of C. pseudotuberculosis were identified as the biovar ovis on the basis of comparative genome analysis. All the compared genomes of the biovar ovis strains were highly similar regardless of their country of origin or host, reflecting their clonal behavior.

Infective Endocarditis Caused by Corynebacterium striatum: Navigating Challenges and Treatment Strategies in an Emerging Threat

Corynebacterium striatum is a type of bacteria normally found in the environment and is considered a benign microbe on the human body surface. However, it can induce severe medical conditions, including bacteremia, infective endocarditis, osteomyelitis, and infections, in other organs. This case study focuses on a 56-year-old male patient with multiple comorbidities who presented with an ischemic stroke. Several days after the insertion of a right internal jugular line, the patient developed fever and tachycardia. Blood cultures revealed the presence of Corynebacterium striatum, a Gram-positive bacilli. Transesophageal echocardiography confirmed the diagnosis of complicated infective endocarditis (IE) with mitral valve vegetation and moderate mitral regurgitation. Prompt treatment with appropriate antibiotics, including linezolid and later vancomycin, led to the patient's improvement and eventual discharge in good condition. This case highlights the importance of early recognition, aggressive management, and accurate diagnosis in cases of IE caused by Corynebacterium striatum. Proper antibiotic selection is crucial, considering the emerging antibiotic resistance patterns associated with this pathogen. By addressing these aspects, patient outcomes can be improved, and potential complications such as IE can be prevented.