218: Metagenomics in Clinical Microbiology
Let's Talk Micro
In this episode of Let’s Talk Micro, we break down metagenomic next-generation sequencing (mNGS) and how it’s changing the way we diagnose complex infectious diseases. I’m joined by Steve Miller, MD, PhD—Chief Medical Officer at Delve Bio—to discuss how unbiased metagenomics moved from research labs into real-world clinical practice. We cover what metagenomics is, how it differs from targeted PCR and sequencing, and where it adds the most value—especially in meningitis and encephalitis, immunocompromised patients, and cases where routine testing comes back negative. Dr. Miller...
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217: Micro Minutes: Don’t Let PEA Fool You
Let's Talk Micro
PEA agar is often treated as “the gram-positive plate,” but that shortcut can lead to real bench-level mistakes. In this MicroMinutes episode, we break down what phenylethyl alcohol agar actually does, why growth on PEA does not automatically mean an organism is gram-positive, and how selective media can change colony appearance and behavior. You’ll hear about: What PEA inhibits — and what it doesn’t Why Pseudomonas aeruginosa can grow quite well on PEA How colony morphology and hemolysis may differ from blood agar Why Lancefield grouping should never be performed directly...
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216: AMR Summit 2025: One Health, One Fight
Let's Talk Micro
In this special episode, I’m joined by three leaders who helped shape the conversation at the 2025 Antimicrobial Resistance (AMR) Summit in Detroit: Dr. Lauren Hunt, Dr. Linoj Samuel, and Dr. Robert Tibbetts. Together, we explore how this intimate, multidisciplinary summit brought together clinical microbiology, infectious diseases, stewardship, public health, policy, and veterinary medicine to tackle the growing challenges of antimicrobial resistance. We break down the key themes that emerged throughout the meeting—shared accountability, One Health collaboration, diagnostic innovation,...
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215: One Health, Many Species: AMR Through a Veterinary Lens
Let's Talk Micro
What does antimicrobial resistance look like when your patients range from dogs and cats to cattle, wildlife, and everything in between? And how do we make sense of AST, breakpoints, contamination, and genotypic tools across such a diverse microbiological world? In this episode, Luis is joined by Dr. Kelli Maddock, DrPH (North Dakota State University Veterinary Diagnostic Laboratory) and Dr. Stephen Cole (University of Pennsylvania), two leaders shaping the future of veterinary microbiology, antimicrobial stewardship, and CLSI veterinary standards. Together, they explore AMR and AST through a...
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214: Beyond the Bench: Optimization & Stewardship in Action
Let's Talk Micro
In this final episode of our special four-part series in partnership with bioMérieux, we bring all the pieces together. Throughout the series, we explored the diagnostic pathway from multiple angles: Episode 1: The evolution of antimicrobial susceptibility testing (AST) Episode 2: Molecular diagnostics for bloodstream infections Episode 3: FAST AST and the impact of getting susceptibility data hours sooner Today, in Episode 4, we shift to diagnostic stewardship and lab optimization — the strategies that ensure the right tests are used at the right time, and that workflows support...
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213: Micro Minutes: When Bacteria Break the Rules
Let's Talk Micro
In this Micro Minutes episode, Luis breaks down classic microbiology traits that usually hold true, but not always. From indole-negative E. coli to non-swarming Proteus and oxidase-negative Pseudomonas, this quick episode highlights real-world exceptions that can catch techs and students off guard. Learn how to spot: Indole-negative E. coli (98% rule + inactive biotypes) Lactose-fermenting look-alikes like Citrobacter freundii Proteus species that don’t swarm Pseudomonas species that test oxidase negative A fast, practical reminder that no single biochemical test should...
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212: Micro Minutes: Sometimes MacConkey Lies
Let's Talk Micro
Welcome to the very first Micro Minutes, a new quick-hit series from Let’s Talk Micro designed for students, techs, and anyone who wants fast, practical microbiology insights in under 10 minutes. In this episode, we tackle a common misconception that microbiologists can make at the bench when interpreting a single plate: MacConkey agar. Many assume: “If it doesn’t grow on MacConkey, it’s not a gram-negative rod.” “If it does grow on MacConkey, it must be a gram-negative rod.” Both are wrong — and today we break down why. Stay connected with Let’s Talk Micro: Website:...
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211: At the Speed of AST: Diagnosing Resistance Faster
Let's Talk Micro
In the third installment of our special series in partnership with bioMérieux, Luis welcomes back Dr. Sonali Kalathiya, infectious diseases pharmacist and medical advisor at bioMérieux, to explore how innovation is accelerating antimicrobial susceptibility testing (AST). Together they dive into FAST AST—a phenotypic susceptibility test that delivers actionable results directly from positive blood cultures in hours instead of days. They discuss how this technology works, how it complements molecular testing, and how it’s transforming patient care, antimicrobial stewardship, and...
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210: IDWeek 2025 Highlights: From Bench to Bedside
Let's Talk Micro
Just back from IDWeek 2025 in Atlanta, Luis shares the sessions and posters that defined this year’s meeting — from next-generation sequencing and diagnostic stewardship to AI in the microbiology lab and new antimicrobials on the horizon. Tune in for insights on: NGS test utilization and stewardship New β-lactamase inhibitors like nacubactam AI’s growing role in clinical microbiology Tedizolid and the importance of optimizing existing agents 🎧 Whether you were in Atlanta or following from afar, this episode captures the energy and innovation of IDWeek — and what it...
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209: CLSI y resistencia antimicrobiana (In Spanish)
Let's Talk Micro
En este episodio en español de Let 's Talk Micro, el Dr. Germán Esparza Sánchez , microbiólogo clínico, miembro del CLSI y consultor de la OPS/OMS, comparte las actualizaciones más recientes del documento M100 y cómo impactan la práctica microbiológica. Desde la eliminación de puntos de corte para Burkholderia cepacia hasta los nuevos antibióticos como aztreonam-avibactam, durlobactam-sulbactam y cefiderocol, analizamos los retos de aplicar las guías del CLSI en los laboratorios latinoamericanos, las diferencias epidemiológicas regionales y la importancia de la educación continua...
info_outlineIn this episode of Let’s Talk Micro, we break down metagenomic next-generation sequencing (mNGS) and how it’s changing the way we diagnose complex infectious diseases.
I’m joined by Steve Miller, MD, PhD—Chief Medical Officer at Delve Bio—to discuss how unbiased metagenomics moved from research labs into real-world clinical practice.
We cover what metagenomics is, how it differs from targeted PCR and sequencing, and where it adds the most value—especially in meningitis and encephalitis, immunocompromised patients, and cases where routine testing comes back negative.
Dr. Miller shares insights from years of clinical experience, including how mNGS can improve diagnostic yield, shorten time to diagnosis, guide targeted therapy, and reduce unnecessary testing and hospital stays. We also touch on challenges like cost, result interpretation, diagnostic stewardship, and where metagenomics is headed next—including its role in public health and emerging infections.
Links & Resources
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Clinical metagenomics for meningitis and encephalitis (Nature Medicine)
https://www.nature.com/articles/s41591-024-03275-1
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