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Pine, A.

Publications and source records attributed to Pine, A..

2 recordsLinked to original sources

Poloxamer dilution as an on-demand alternative to agar dilution-based antimicrobial susceptibility testing

Agar dilution is a reference susceptibility testing method uniquely or preferentially recommended for certain antimicrobials. However, the effort required to pour individual agar plates spanning a doubling dilution range precludes its practical implementation in hospital clinical laboratories. Here, we describe an on-demand replacement for agar dilution (AD), specifically substituting poloxamer 407 (also known as Pluronic F-127) for Bacto Agar as the solidifying agent. Notably, 20% poloxamer 407 solutions (e.g., with Mueller-Hinton broth) remain liquid at refrigerated temperatures, but solidify upon warming, enabling facile set-up of poloxamer dilution testing (PD) in Petri dish or microwell format. For fosfomycin susceptibility testing, PD and reference agar dilution (AD) showed excellent categorical (CA) and essential (EA) agreement for E. coli (100% and 87%, respectively, n=31). For other Enterobacterales, excluding Klebsiella spp; CA and EA were both 82% (n=17, respectively). For P. aeruginosa, CA and EA were 60% and 100% (n=10), respectively, with the lower CA reflecting the large number of strains tested with MICs near categorical breakpoints. There were no very major errors, while major errors were only observed for Klebsiella spp. Additionally, PD substantially reduced the number of skipped dilutions 6-fold for E. coli (P < 0.0001) and inhibited swarming of Proteus species. We conclude that PD and AD, an imperfect gold standard, have essentially equivalent practical performance and that PD can therefore serve as an on-demand alternative testing methodology in clinical laboratories for fosfomycin testing of gram-negative pathogens. A broader exploration of PDs utility is thus warranted. ImportanceAccurate antibiotic susceptibility testing is essential for guiding treatment of bacterial infections. For the antibiotic fosfomycin, used to treat Escherichia coli urinary tract infections, the most reliable testing method requires solid media prepared by hand for each antibiotic concentration, which is too time consuming for most clinical laboratories to perform. Our study shows that replacing agar with an alternative temperature-sensitive gelling agent called poloxamer enables laboratories to prepare solid test plates rapidly without special equipment. This approach, which is essentially identical to traditional agar dilution, provides a practical alternative that can be implemented by hospital clinical microbiology laboratories for accurate fosfomycin testing near the point of patient care. This strategy may also be applicable to other drugs for which agar dilution is the preferred testing method, supporting expedited testing to inform treatment decisions for bacterial infections.

microbiology↗

A unified atlas of CD8 T cell dysfunctional states in cancer and infection

CD8 T cells play an essential role in defense against viral and bacterial infections and in tumor immunity. Deciphering T cell loss of functionality is complicated by the conspicuous heterogeneity of CD8 T cell states described across different experimental and clinical settings. By carrying out a unified analysis of over 300 ATAC-seq and RNA-seq experiments from twelve independent studies of CD8 T cell dysfunction in cancer and infection we defined a shared differentiation trajectory towards terminal dysfunction and its underlying transcriptional drivers and revealed a universal early bifurcation of functional and dysfunctional T cell activation states across models. Experimental dissection of acute and chronic viral infection using scATAC-seq and allele-specific scRNA-seq identified state-specific transcription factors and captured the early emergence of highly similar TCF1+ progenitor-like populations at an early branch point, at which epigenetic features of functional and dysfunctional T cells diverge. Our atlas of CD8 T cell states will facilitate mechanistic studies of T cell immunity and translational efforts.

genomics↗