SARS-CoV-2 intra-host evolution during prolonged infection in an immunocompromised patient.

OBJECTIVES: Intra-host SARS-CoV-2 evolution during chronic infection in immunocompromised hosts has been suggested as being the possible trigger of the emergence of new variants. METHODS: Using a deep sequencing approach, we investigated the SARS-CoV-2 intra-host genetic evolution in a patient with HIV over a period of 109 days. RESULTS: Sequencing of nasopharyngeal swabs at three time points demonstrated dynamic changes in the viral population, with the emergence of 26 amino acid mutations and two deletions, 57% of them in the Spike protein. Such a combination of mutations has never been observed in other SARS-CoV-2 lineages detected so far. CONCLUSION: Our data confirm that persistent infection in certain immunocompromised individuals for a long time may favor the dangerous emergence of new SARS-CoV-2 variants with immune evasion properties.

A case of necrotizing fasciitis caused by Finegoldia magna in a patient with type 2 diabetes mellitus.

Diabetes mellitus is one of the serious conditions associated with necrotizing fasciitis, a severe bacterial skin infection that spreads quickly and is characterized by extensive necrosis of the deep and superficial fascia resulting in devascularization and necrosis of the associated tissues. In addition to debridement and aggressive surgery procedures, the effectiveness of therapy depends on choosing the appropriate antibacterial agents. Hence the key to successful management is an early and accurate diagnosis. We report a case of necrotizing fasciitis caused by Finegoldia magna in a patient with type 2 diabetes mellitus.

Integration of Diagnostic Microbiology in a Model of Total Laboratory Automation.

BACKGROUND: Although automation has become widely utilized in certain areas of diagnostic testing, its adoption in diagnostic microbiology has proceeded much more slowly. OBJECTIVE: To describe our real-world experience of integrating an automated instrument for diagnostic microbiology (Walk-Away Specimen Processor, WASPLab) within a model of total laboratory automation (TLA). METHODS: The implementation process was divided into 2 phases. The former period, lasting approximately 6 weeks, entailed the installation of the WASPLab processor to operate as a stand-alone instrumentation, whereas the latter, lasting approximately 2 weeks, involved physical connection of the WASPLab with the automation. RESULTS: Using the WASPLab instrument in conjunction with the TLA model, we obtained a time savings equivalent to the work of 1.2 full-time laboratory technicians for diagnostic microbiology. The connection of WASPLab to TLA allowed its management by a generalist or clinical chemistry technician, with no need for microbiology skills on the part of either worker. Hence, diagnostic microbiology could be performed by the staff that is already using the TLA, extending their activities to include processing urgent clinical chemistry and hematology specimens. The time to result was also substantially improved. CONCLUSIONS: According to our experience, using the WASPLab instrument as part of a TLA in diagnostic microbiology holds great promise for optimizing laboratory workflow and improving the quality of testing.