I met a patient on her 8th admission for Clostridium difficile infection in 2 years.
Yes, a real patient.
Let's call her Helen.
We did everything right. Vancomycin worked. Fidaxomicin worked. She eventually needed FMT, which also worked.
But here's the thing that bothers me: Did we have to wait till multiple recurrences to think about her microbiome?
We knew from day one - from her first CDI after broad-spectrum antibiotics for pneumonia- that her microbiome was devastated. We knew each course of anti-CDI therapy could damage it further. We knew the recurrence risk climbed with each episode.
Yet our entire treatment paradigm was reactive.
Kill C. diff. Wait for recurrence. Kill it again. Repeat until FMT.
What if we approached this completely differently?
The Question Nobody's Asking
Here's what every ID consult note addresses when called for CDI:
Which antimicrobial to use?
How long to treat?
When to escalate therapy?
Whether to add Bezlotoxumab?
Here's what almost no ID consult note addresses:
How do we restore this patient's microbiome?
How do we prevent the next infection from occurring?
What's our strategy for maintaining colonization resistance long-term?
We're doctors of infectious disease, but we practice almost entirely as doctors of infections - prescribing treatment after problems occur.
And the microbiome is the most important ecological barrier we have.
What Preventive Microbiome Medicine Looks Like
Let me reframe Helen’s care through a preventive lens:
Day 1 (hospitalized with an infection requiring broad-spectrum antibiotics):
Risk-stratify for microbiome disruption and CDI
Counsel about C. diff risk (we do this)
Consider microbiome-protective strategies during therapy (we sometimes do this)
Plan for microbiome assessment and restoration post-treatment (we almost never do this)
Post-discharge (after pneumonia treatment):
Assess microbiome recovery
Identify persistent disruption that predicts infection risk
Intervene before first CDI occurs, not after multiple recurrences
This is not science fiction. The tools to do this are emerging now.
The question is whether ID physicians will lead their implementation or wait for other specialties to do it without us.
The Bigger Transformation ID Should Lead
Recurrent CDI is just the most obvious example. Consider how preventive microbiome thinking changes our entire approach:
Antimicrobial stewardship becomes microbiome stewardship:
We already say "use narrow-spectrum when possible" - but we frame it as resistance prevention
Reframe it as microbiome preservation and colonization resistance maintenance
That changes the risk-benefit calculation for empiric broad-spectrum therapy
ICU infection prevention becomes microbiome optimization:
We know ICU patients have profoundly disrupted microbiomes from illness, antibiotics, NPO status
We know this disruption predicts ventilator-associated pneumonia, bacteremia, CDI
What if we actively monitored and maintained microbiome health as infection prevention?
Post-transplant care becomes proactive microbiome management:
These patients get intense immunosuppression plus prophylactic antimicrobials
We wait for infections to occur, then treat them
What if we identified microbiome signatures predicting infection risk and intervened early?
This is the future of Infectious Diseases medicine - and nobody's claiming this space.
Why ID Physicians Should Lead This
Other specialties are already moving into microbiome territory:
GI owns therapeutics (FMT, microbiome drugs in development)
Primary care prescribes probiotics
Critical care implements gut decontamination protocols
Preventive medicine talks about microbiome and wellness
But none of them understand what we understand:
How antimicrobial pressure reshapes microbial ecosystems
How colonization resistance prevents infection
How to risk-stratify for infection based on microbiome disruption
How to balance microbiome preservation with necessary antimicrobial therapy
Preventive microbiome medicine is infectious disease prevention. We should be leading it.
The Honest Challenges
Let me be clear about what's standing in the way:
The evidence is still emerging.
We have proof-of-concept studies, not treatment guidelines. You can't bill for "microbiome optimization" in your clinic tomorrow. 😃
The infrastructure is still emerging.
Accessible microbiome diagnostics, validated intervention strategies, reimbursement models - we're building this in real-time.
It requires fundamental behavior change.
We're trained to react to infections, not prevent them through ecological maintenance. This is a different clinical mindset.
But these are reasons to start building now, not reasons to wait.
What You Can Actually Do
Start thinking preventively:
When you start a patient on prolonged broad-spectrum therapy, don't just think "what infections might occur."
Think "how do I preserve colonization resistance and prevent infections from becoming likely?"
Integrate microbiome thinking into stewardship:
When you recommend narrow-spectrum therapy, explicitly frame it as microbiome preservation. Make that part of the value proposition.
Identify high-risk patients proactively:
Post-transplant, post-chemotherapy, prolonged ICU stays - these patients have predictably disrupted microbiomes. Can you intervene before infections occur?
Advocate for institutional investment:
When your hospital considers microbiome diagnostics or therapeutics, make sure ID has a seat at the table. Frame it as infection prevention infrastructure.
Talk about prevention, not just treatment:
With patients, with colleagues, with hospital leadership. Shift the conversation from "how do we treat this infection" to "how do we prevent the next one."
The Real Opportunity
Helen eventually did well. FMT worked. But we spent a long time and multiple hospitalizations getting there.
What if we'd thought about her microbiome on day one?
This is the question that should reshape how we practice infectious disease medicine.
It is about fundamentally transforming ID from just reactive sick care to proactive health maintenance.