Bench to Bedside — Clinical Microbiology by Dr. Deepika Chakraborty

CLSI Ed36: Cefepime reclassified to SDD for Enterobacterales Aztreonam-avibactam: first β-lactam active against NDM producers HCV seronegative viraemia: when RNA testing overrides serology Graus 2016: mandatory criteria before ordering AE antibody panels Occult HBV: screen anti-HBc before immunosuppression Scopulariopsis keratitis: voriconazole, not natamycin CLSI Ed36: Cefepime reclassified to SDD for Enterobacterales Aztreonam-avibactam: first β-lactam active against NDM producers HCV seronegative viraemia: when RNA testing overrides serology Graus 2016: mandatory criteria before ordering AE antibody panels Occult HBV: screen anti-HBc before immunosuppression Scopulariopsis keratitis: voriconazole, not natamycin

Articles

Clinical insights,
written clearly

Every article will answer a real question from the lab or the ward — hepatitis diagnostics, diagnostic stewardship, AMR and CLSI updates, rare organisms, and mycology — with the depth a clinician needs and none of the textbook padding.

Featured · Bacteriology

Contaminant or true positive? How to read a blood culture result

A positive blood culture is a probability wearing the costume of a fact. Four signals — who grew, how many bottles agreed, how fast it flagged, and whose blood it is — let the bench classify it before the susceptibilities are even done, and decide whether to report, repeat, or suppress.

Dr. Deepika Chakraborty · June 2026 · 9 minRead article →

Case of the Month · Mycology

The Mould That Almost Got Away: Scopulariopsis brevicaulis Keratitis

Negative KOH. Sterile bacteria. Growth on day 10 — only because someone didn't throw the plate away. A masterclass in slow diagnosis, contaminant traps, and why voriconazole beats natamycin here.

Dr. Deepika Chakraborty · June 2026 · 8 min Read article →

Quick Clinical Facts

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HCV window periodAnti-HCV antibody may be undetectable for 8–12 weeks post-exposure. RNA becomes positive within 1–2 weeks — test RNA if acute infection is suspected.

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SDD means dose harderCefepime SDD requires either 2g q8h extended infusion (4h) or high-dose regimens. Standard 2g q12h will fail PK/PD targets.

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LGI1 encephalitis clueFaciobrachial dystonic seizures (FBDS) are the pathognomonic prodrome — often misdiagnosed as epilepsy before AE workup is considered.

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Occult HBV reactivationScreen all immunosuppression candidates with HBsAg + anti-HBc total. A positive anti-HBc warrants HBV DNA before starting biologics or chemotherapy.

Glossary

PPV — Positive Predictive Value

Probability a positive test means true infection. Falls as prevalence drops — why HCV ELISA positives in low-risk groups need RNA confirmation.

LLOQ

Lower Limit of Quantification. "Detected, below LLOQ" = virus present but unquantifiable. Not the same as undetectable.

SDD

Susceptible-Dose-Dependent. Standard dosing fails. High dose or extended infusion required to achieve pharmacodynamic target.

Seronegative Viraemia

Detectable viral RNA despite non-reactive serology. Occurs in immunosuppression, early acute infection, or assay failure.

Q&A

Questions the ward
asks the lab

Tap any question for a clear, evidence-based answer — no jargon, no padding.

Most likely yes — about 25–30% of HCV-exposed individuals clear infection spontaneously, retaining lifelong anti-HCV antibody without detectable RNA. But a false-negative PCR can occur if the viral load is below the LLOQ, if the sample was poorly handled, or during very early acute infection.

Clinical actionRepeat RNA at 12 weeks. Two negative RNA results ≥12 weeks apart, in the right clinical context, confirms spontaneous clearance.

SDD means the organism can be treated with cefepime — but only with the right dose and infusion strategy. Standard dosing (2g q12h over 30 min) will fail to reach PK/PD targets. You need either 2g q8h as an extended infusion over 4 hours, or high-dose 2g q8h.

Key pointSDD ≠ Susceptible with standard dosing. In serious infections the difference is clinically significant.

Apply the Graus 2016 criteria: subacute onset (<3 months) of working memory deficits, altered consciousness, or new psychiatric symptoms, plus at least one of: CSF pleocytosis, suggestive MRI, new-onset unexplained seizures, or abnormal EEG. Common infectious and structural causes must be excluded first — AE testing is a second-step investigation, not a first-line screen.

Stewardship ruleOrder CSF culture, India ink, CBNAAT, and basic neuroimaging before reaching for the AE panel.

Not without checking anti-HBc total first. HBsAg negativity does not rule out hepatitis B. An anti-HBc-positive, HBsAg-negative patient may have occult HBV — and can reactivate when given rituximab, high-dose steroids, or other immunosuppressants, sometimes fatally.

ProtocolScreen with HBsAg + anti-HBc total. If anti-HBc is positive, check HBV DNA. Consider prophylactic tenofovir or entecavir in high-risk scenarios.

This is correct practice. CLSI M100 recommends against routine AST for Burkholderia cepacia complex because in-vitro susceptibility correlates poorly with clinical outcome. Treatment is guided by clinical evidence and expert consensus rather than the antibiogram.

Treatment optionsTMP-SMX (drug of choice), ceftazidime, meropenem, minocycline. Call your clinical microbiologist — Bcc decisions need direct consultation.

LLOQ (Lower Limit of Quantification) is the minimum viral load a PCR assay can measure accurately and reproducibly. Below this threshold, the virus may still be detected but cannot be reliably counted. "Detected, below LLOQ" means the virus is present — the patient is still viraemic.

Clinical implication"Below LLOQ" ≠ undetectable. Do not reassure the patient that virus is absent. Each assay has its own LLOQ — do not compare numbers across different platforms.

Learning Series

Go deep on what
matters most

Each series is a structured sequence from first principles to bedside application — pick a topic and follow it through.

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Hepatitis Diagnostics

From how HCV ELISA works to interpreting discordant results, viral loads, co-infection patterns, and occult HBV. The full picture.

SERIES · COMING SOON

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Diagnostic Stewardship

When to order, when to hold back. Pre-test criteria for AE panels, FilmArray, and other high-cost investigations. Less testing, better outcomes.

SERIES · COMING SOON

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AMR & CLSI Updates

Every CLSI M100 revision explained — what changed, why, and how it affects your antibiogram interpretation and empiric prescribing choices.

SERIES · COMING SOON

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Rare Organisms

Myroides, Burkholderia cepacia complex, Scopulariopsis, and others that stump clinicians. Recognition, reporting, and treatment where evidence exists.

SERIES · COMING SOON

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Case Vignettes

Clinical scenarios with structured teaching points — a self-test format for PGMEE preparation and clinical skill-building.

MONTHLY · COMING SOON

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HBV Deep Dive

IgM anti-HBc, HBsAg seroclearance, occult HBV, reactivation risk — everything you need for hepatology-adjacent clinical decisions.

SERIES · IN DEVELOPMENT

Case of the Month

A clinical puzzle,
worked through

Each month, one teaching case — the report, the reasoning, and the decision points — built around a real clinical microbiology question and presented for education only.

🔬 Mycology Case of the Month · June 2026

The Mould That Almost Got Away

Scopulariopsis brevicaulis keratitis — a 48-year-old welder from the Northern Himalayas. Ocular trauma. Negative KOH. Sterile bacterial cultures. Growth detected on day 10 of incubation, only because the plate was held.

This case covers laboratory diagnosis of a slow-growing rare mould, the three traps that lead to missed diagnoses, why amphotericin B and natamycin fail, and the evidence for voriconazole as the agent of choice.

Based on: Kamboj P et al. Cureus 2026;18(4):e106303 · CC BY 4.0

Read the case →

🧫 Lab at a glance

Organism	Scopulariopsis brevicaulis
KOH mount	Negative
Growth detected	Day 10
Conidiogenous cell	Annellide
Natamycin alone	Insufficient
Drug of choice	Voriconazole 1% topical

About

Dr. Deepika Chakraborty

Senior Resident · Dept. of Microbiology · GIPMER & Lok Nayak Hospital, New Delhi

I am a clinical microbiologist at GIPMER (Govind Ballabh Pant Institute of Postgraduate Medical Education and Research), New Delhi, where I work in clinical microbiology practice, academic research, and education. My interests span hepatitis B and C diagnostics, autoimmune encephalitis antibody stewardship, antimicrobial resistance, and translating CLSI guideline changes into clinical practice.

BenchToBedside exists because I kept seeing the same questions come up at ward rounds — about discordant hepatitis reports, about what SDD actually means for prescribing, about when not to order an AE panel. If the answers are useful to one clinician, they're useful to many. Beyond the lab, I run @deepsays on YouTube — a BookTube channel covering books, travel, and art.

Clinical insights,written clearly

Questions the wardasks the lab

Go deep on whatmatters most

A clinical puzzle,worked through

Stay sharp.Straight to your inbox.

Clinical insights,
written clearly

Questions the ward
asks the lab

Go deep on what
matters most

A clinical puzzle,
worked through

Stay sharp.
Straight to your inbox.