Exploring clonality and virulence gene associations in bloodstream infections using whole-genome sequencing and clinical data.

Background: Bloodstream infections (BSIs) remain a significant cause of mortality worldwide. Causative pathogens are routinely identified and susceptibility tested but only very rarely investigated for their resistance genes, virulence factors, and clonality. Our aim was to gain insight into the clonality patterns of different species causing BSI and the clinical relevance of distinct virulence genes. Methods: For this study, we whole-genome-sequenced over 400 randomly selected important pathogens isolated from blood cultures in our diagnostic department between 2016 and 2021. Genomic data on virulence factors, resistance genes, and clonality were cross-linked with in-vitro data and demographic and clinical information. Results: The investigation yielded extensive and informative data on the distribution of genes implicated in BSI as well as on the clonality of isolates across various species. Conclusion: Associations between survival outcomes and the presence of specific genes must be interpreted with caution, and conducting replication studies with larger sample sizes for each species appears mandatory. Likewise, a deeper knowledge of virulence and host factors will aid in the interpretation of results and might lead to more targeted therapeutic and preventive measures. Monitoring transmission dynamics more efficiently holds promise to serve as a valuable tool in preventing in particular BSI caused by nosocomial pathogens.

Hospital sanitary facilities on wards with high antibiotic exposure play an important role in maintaining a reservoir of resistant pathogens, even over many years.

BACKGROUND: Hospitals with their high antimicrobial selection pressure represent the presumably most important reservoir of multidrug-resistant human pathogens. Antibiotics administered in the course of treatment are excreted and discharged into the wastewater system. Not only in patients, but also in the sewers, antimicrobial substances exert selection pressure on existing bacteria and promote the emergence and dissemination of multidrug-resistant clones. In previous studies, two main clusters were identified in all sections of the hospital wastewater network that was investigated, one K. pneumoniae ST147 cluster encoding NDM- and OXA-48 carbapenemases and one VIM-encoding P. aeruginosa ST823 cluster. In the current study, we investigated if NDM- and OXA-48-encoding K. pneumoniae and VIM-encoding P. aeruginosa isolates recovered between 2014 and 2021 from oncological patients belonged to those same clusters. METHODS: The 32 isolates were re-cultured, whole-genome sequenced, phenotypically tested for their antimicrobial susceptibility, and analyzed for clonality and resistance genes in silico. RESULTS: Among these strains, 25 belonged to the two clusters that had been predominant in the wastewater, while two others belonged to a sequence-type less prominently detected in the drains of the patient rooms. CONCLUSION: Patients constantly exposed to antibiotics can, in interaction with their persistently antibiotic-exposed sanitary facilities, form a niche that might be supportive for the emergence, the development, the dissemination, and the maintenance of certain nosocomial pathogen populations in the hospital, due to antibiotic-induced selection pressure. Technical and infection control solutions might help preventing transmission of microorganisms from the wastewater system to the patient and vice versa, particularly concerning the shower and toilet drainage. However, a major driving force might also be antibiotic induced selection pressure and parallel antimicrobial stewardship efforts could be essential.

Comparison of Antimicrobial Susceptibility Test Results of Disk Diffusion, Gradient Strip, and Automated Dilution with Broth Microdilution for Piperacillin-Tazobactam.

In the treatment of septic patients, the prediction of a pathogen's susceptibility to piperacillin-tazobactam can be crucial. Commercial tests are available to measure the pathogen's susceptibility to piperacillin-tazobactam, but there is conflicting evidence regarding their accuracy. Therefore, this study compared the accuracy of disk diffusion, gradient strip, and automated dilution with the accepted standard broth microdilution. Testing was performed on 150 blood culture isolates from hospitalized patients at the University Hospital Bonn. The most recent Escherichia coli (n = 50), Klebsiella pneumoniae (n = 50), and Pseudomonas aeruginosa (n = 50) isolates were chosen. All measurements were performed strictly according to the manufacturer's instructions. Minimal inhibitory concentrations were primarily interpreted based on EUCAST (European Committee on Antimicrobial Susceptibility Testing) 8.1 and supplementarily based on CLSI (Clinical and Laboratory Standards Institute) 28th. The results of automated dilution showed a categorical agreement of 93.3% and presented five minor errors, four major errors, and one very major error. The results for gradient strip and disk diffusion were similar, except for the three additional major errors in the gradient strip and two additional very major errors in disk diffusion. Most of the major errors and very major errors were associated with P. aeruginosa. In conclusion, there was no relevant difference in accuracy between the three compared tests. Their overall categorical agreement ranged from 90.7% to 93.3% and was therefore at the lower end of the threshold. The possibly increased error rate for P. aeruginosa could be relevant in the preparation of empirical antibiotic guidelines and the treatment of septic patients. Universal Trial Number: U1111-1224-0035.

Detection and Characterization of Clinical Bordetella trematum Isolates from Chronic Wounds.

Bordetella trematum is a relatively newly discovered and potentially frequently overlooked Bordetella species, mostly isolated from chronic wounds and predominantly in those of the lower extremities. Its susceptibility profile and clinical significance is still debated, given the limited amount of available data. We contribute providing a molecular and phenotypical analysis of three unique clinical B. trematum isolates detected between August 2019 and January 2020 to aid the matter. Cryo-conserved isolates were subcultured and re-identified using various routine means of identification. Bacterial genomes were fully Illumina-sequenced and phenotypical susceptibility was determined by broth microdilution and gradient-strip tests. All isolates displayed increased susceptibility to piperacillin-tazobactam (<2/4 mg/L), imipenem (<1 mg/L), and meropenem (<0.047 mg/L), whereas they displayed decreased susceptibility to all tested cephalosporins and fluoroquinolones (according to PK-PD, EUCAST 10.0 2020). One isolate carried a beta-lactamase (EC 3.5.2.6) and a sulfonamide resistance gene (sul2) and cells displayed resistance to ampicillin, ampicillin/sulbactam, and trimethoprim/sulfamethoxazole. All isolates carried genes conferring decreased susceptibility to aminoglycosides (aadA), fosfomycin (fosA) and fluoroquinolones (gyrB EC 5.99.1.3). Awareness that B. trematum can be resistant to trimethoprim/sulfamethoxazole is warranted.