ClinicalDesk

Clinical Decision Support — Microbiology & Therapeutics

⚠ All decisions must be made in conjunction with current BNF, local microbiology guidance, and clinical judgement. Not a substitute for professional advice.

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Microbiology

Organisms, sensitivities & treatment

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Calculators

eGFR, CrCl, dosing, BMI & more

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Clinical Scores

NEWS2, CURB-65, Wells, SOFA

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Side-Effect Checker

Antibiotic & drug ADR lookup

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Resistance Lookup

AMR patterns & mechanisms

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Stewardship

AMR education & best practice

⚡ Quick Access

📢 NHS Alerts

🔴 Increased carbapenem-resistant Enterobacterales (CRE) in ICUs — review isolation policy

🟡 National shortage of IV co-amoxiclav — see local formulary alternatives

🔵 Updated NICE NG15 UTI guidelines now in effect — see Guidelines panel

📈 Resistance Trends

Organism	Antibiotic	Resistance %
E. coli	Ciprofloxacin	48%
E. coli	Co-amoxiclav	35%
S. aureus	Flucloxacillin	3%
Klebsiella	3rd Gen Ceph	28%

Organism Library

Microbiology reference with typical sensitivities & treatment guidance

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Gram Positive

Gram Negative

Anaerobes

Fungi / Atypical

Staphylococcus aureus (MSSA)

Gram-positive coccus · Aerobe · Coagulase-positive

Skin & Soft TissueBacteraemiaEndocarditisOsteomyelitis

Staphylococcus aureus (MRSA)

Gram-positive coccus · Aerobe · Multi-drug resistant

HIGH RISKBacteraemiaSSTI

Streptococcus pneumoniae

Gram-positive coccus · Alpha-haemolytic

PneumoniaMeningitisOtitis Media

Enterococcus faecalis / faecium

Gram-positive coccus · Facultative anaerobe · UTI/Endocarditis

UTIEndocarditisVRE Risk

Escherichia coli

Gram-negative rod · Facultative anaerobe · Enterobacterales

UTIBacteraemiaBiliaryESBL Risk

Pseudomonas aeruginosa

Gram-negative rod · Aerobe · Non-fermenter · HCAI

DIFFICULT TO TREATHAP/VAPWound

Klebsiella pneumoniae

Gram-negative rod · Enterobacterales · ESBL/Carbapenem risk

PneumoniaUTICRE Risk

Haemophilus influenzae

Gram-negative coccobacillus · Aerobe · COPD/Respiratory

LRTISinusitisMeningitis (unvac)

Neisseria meningitidis

Gram-negative diplococcus · Aerobe · Meningococcal disease

EMERGENCYNOTIFIABLEMeningitisSepticaemia

Stenotrophomonas maltophilia

Gram-negative rod · Aerobe · Multi-drug resistant · HCAI

INTRINSIC CARBAPENEM RHAPImmunocompromised

Clostridioides difficile

Gram-positive rod · Obligate anaerobe · Spore-forming

NOTIFIABLEColitis

Bacteroides fragilis

Gram-negative rod · Obligate anaerobe · Bowel flora

Abdo AbscessPeritonitis

Clostridium perfringens

Gram-positive rod · Obligate anaerobe · Spore-forming · Gas gangrene

SURGICAL EMERGENCYGas GangreneFood Poisoning

Peptostreptococcus / Prevotella

Mixed anaerobes · Polymicrobial · Oral/Dental/Abdominal flora

Dental abscessAspiration pneumoniaIntra-abdominal

Candida albicans

Yeast · Dimorphic fungus · Common HCAI pathogen

CandidaemiaCandidiasis

Atypical — Mycoplasma / Legionella / Chlamydophila

Intracellular organisms · No cell wall · Community pneumonia

CAPNo Beta-lactam

Aspergillus fumigatus

Mould · Hyalohyphomycosis · Immunocompromised host

HIGH MORTALITYInvasive AspergillosisIPA

Pneumocystis jirovecii (PCP)

Fungus (atypical) · Immunocompromised · HIV/Transplant

ImmunocompromisedPneumoniaHIV

Legionella pneumophila

Gram-negative rod · Intracellular · Atypical pneumonia · Notifiable

NOTIFIABLESevere CAPLegionnaires Disease

Clinical Calculators

eGFR · Creatinine Clearance · BMI · IBW · Anion Gap

eGFR

CrCl / Dosing

BMI

IBW / AdjBW

Anion Gap

🫘 eGFR — CKD-EPI Formula (NICE Recommended)

Age (years)

Serum Creatinine (µmol/L)

Sex at Birth

Ethnicity

💊 Cockcroft-Gault — Creatinine Clearance for Drug Dosing

Age (years)

Weight (kg)

Serum Creatinine (µmol/L)

Sex

⚖️ BMI Calculator

Weight (kg)

Height (cm)

📏 Ideal Body Weight & Adjusted Body Weight

Height (cm)

Actual Weight (kg)

Sex

🧪 Anion Gap & Corrected Values

Na⁺ (mmol/L)

K⁺ (mmol/L)

Cl⁻ (mmol/L)

HCO₃⁻ (mmol/L)

Albumin (g/L)

Lab Result Interpretation

CRP · WCC · Blood cultures · ABG interpretation

🧪 Inflammatory Markers

CRP (mg/L)

WBC (×10⁹/L)

Neutrophils (×10⁹/L)

Procalcitonin (ng/mL)

🩸 ABG Quick Interpretation

pCO₂ (kPa)

pO₂ (kPa)

HCO₃⁻ (mmol/L)

Lactate (mmol/L)

Side-Effect Checker

Antibiotic & antimicrobial adverse drug reactions

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👆 Start typing an antibiotic name above to see adverse effects, monitoring requirements, and contraindications.

Resistance Lookup

AMR mechanisms, intrinsic resistance patterns & EUCAST breakpoints

🛡 Intrinsic Resistance Patterns

Organism	Intrinsically Resistant To
Pseudomonas aeruginosa	Amoxicillin, Co-amoxiclav, Cephalosporins (most), Ertapenem
Enterococcus spp.	Cephalosporins, TMP, Clindamycin
Klebsiella pneumoniae	Amoxicillin, Ampicillin
Stenotrophomonas	Carbapenems, Aminoglycosides — use Co-trimoxazole
MRSA	All beta-lactams, Flucloxacillin

⚙️ Resistance Mechanisms

Mechanism	Example	Impact
ESBL	TEM, SHV, CTX-M	3rd Gen Ceph resistance
Carbapenemase	KPC, NDM, OXA-48	Carbapenems resistant
MRSA (mecA)	PBP2a altered	All beta-lactams
VRE (vanA/B)	Ligase modification	Glycopeptides
Efflux pumps	MexAB-OprM	Multi-drug (Pseudo)

🔬 Special Organisms — Treatment Guidance

🚨 MRSA / CRE / VRE / ESBL — ALWAYS discuss with Microbiology or Infectious Diseases before prescribing

Organism	Preferred Agent(s)	Alternative	Comment
MRSA bacteraemia	Vancomycin IV	Daptomycin	Target AUC/MIC 400–600. Daily BCx until clear.
ESBL E. coli / Klebsiella	Meropenem	Temocillin (UTI/biliary)	Avoid carbapenems where temocillin suitable.
CRE (KPC)	Ceftazidime-avibactam	Aztreonam-avibactam	ID consultation mandatory. Colistin last resort.
VRE (E. faecium)	Linezolid	Daptomycin	Linezolid — max 28 days, weekly FBC. ID input.
C. difficile (severe)	Fidaxomicin PO	Vancomycin PO	Surgery input if toxic megacolon.

Culture Interpretation

Blood cultures · MSU · Sputum · Wound swabs

🩸 Blood Culture Interpretation

Result	Likely Significance	Action
Both bottles: S. aureus	True bacteraemia	Echo, ID review, 14 days minimum
1 of 4 bottles: CoNS	Likely contaminant	Repeat cultures, assess clinical context
All bottles: E. coli	True bacteraemia	Source control, 14-day course, de-escalate
1 bottle: Propionibacterium	Skin contaminant	Likely no treatment; review if immunocompromised

🧪 MSU Interpretation

Result	Interpretation	Treatment
>10⁵ CFU/mL + symptoms	UTI	Treat per sensitivities
>10⁵ CFU/mL, asymptomatic	Asymptomatic bacteriuria	Usually no treatment (except pregnancy)
Mixed growth >2 organisms	Contamination	Repeat MSU with good technique
10³–10⁵ CFU/mL	Equivocal	Correlate with symptoms, repeat

Drug Interactions

Key antimicrobial drug-drug interactions

⚠ Always verify with BNF, Stockley's, or a clinical pharmacist before prescribing.

Antibiotic	Interacting Drug	Effect	Severity	Action
Metronidazole	Warfarin	↑ INR (inhibits CYP2C9)	Major	Halve warfarin dose, monitor INR
Clarithromycin	Statins (simva/lova)	↑ Statin levels — rhabdomyolysis	Major	Withhold statin during course
Rifampicin	COCP / OCP	↓ Contraceptive efficacy	Major	Additional contraception 4 weeks after
Linezolid	SSRIs / SNRIs	Serotonin syndrome risk	Major	Avoid if possible; monitor closely
Ciprofloxacin	Theophylline	↑ Theophylline levels	Moderate	Monitor levels, reduce dose
Fluconazole	Warfarin	↑ INR significantly	Major	Monitor INR daily during course
Co-trimoxazole	Methotrexate	↑ MTX toxicity	Major	Avoid combination; use alternative
Gentamicin	Loop diuretics	↑ Nephrotoxicity & ototoxicity	Moderate	Monitor levels & renal function daily

Antimicrobial Stewardship

AMR education · IV to oral switch · Prescribing principles

Core Principles

IV to Oral

Duration Guide

AMR Education

🎯 Right Drug

Choose the most targeted antibiotic based on likely or confirmed pathogen. Check local formulary and sensitivity data. Consult microbiology for complex cases.

📏 Right Dose

Calculate dose based on weight, renal function (CrCl), and site of infection. Under-dosing drives resistance; over-dosing causes toxicity.

⏱ Right Duration

Use the shortest effective duration. Review at 48–72 hours — "antibiotic review" should be a daily ward task.

🔄 IV to Oral Switch

Switch when patient can tolerate oral medication, is apyrexial for 24h, improving clinically, and oral bioavailability is sufficient.

📝 Review & De-escalate

Review at 48–72h with culture results. De-escalate from broad to narrow spectrum. Document indication, duration, and review date on every prescription.

✅ IV to Oral switch saves money, reduces CLABSI risk, and shortens admission. Use when patient meets all CAPS criteria.

✅ CAPS Criteria for IV→Oral Switch

C — Can swallow and absorb oral medication

A — Apyrexial for ≥24 hours

P — Patient is improving (WBC trending down, CRP falling)

S — Suitable oral agent available with good bioavailability

🔄 Common IV→Oral Switches

Infection	IV Agent	Oral Switch	Bioavailability
CAP	Amoxicillin IV	Amoxicillin PO 500mg TDS	~90%
CAP (atypical)	Clarithromycin IV	Clarithromycin PO 500mg BD	~52%
SSTI (MSSA)	Flucloxacillin IV	Flucloxacillin PO 1g QDS (empty stomach)	~50%
UTI	Co-amoxiclav IV	Co-amoxiclav PO 625mg TDS	~90%
Metronidazole	Metronidazole IV 500mg TDS	Metronidazole PO 400mg TDS	>90%
Fluconazole	Fluconazole IV	Fluconazole PO	>90%

⏱ Evidence-Based Antibiotic Durations

Infection	Recommended Duration	Evidence
cLUTI (women)	3 days (nitrofurantoin 5–7d)	NICE NG112
Complicated UTI	7 days	NICE NG112
CAP (low severity)	5 days	NICE NG191
CAP (moderate–severe)	7–10 days	BTS Guidelines
Cellulitis (mild-mod)	5 days (extend if not improving)	CREST/NICE
MSSA bacteraemia	14 days minimum (IV)	BSAC
Endocarditis (native valve)	4–6 weeks (IV)	ESC Guidelines
Osteomyelitis	6 weeks total (IV + oral)	BSAC
C. difficile (1st episode)	10 days (fidaxomicin)	ESCMID 2021
Meningitis	7–14 days (organism dependent)	NICE/ESCMID

🌍 The AMR Crisis

Antimicrobial resistance (AMR) is one of the greatest global health threats. By 2050, AMR could cause 10 million deaths annually. Every antibiotic prescription either helps or harms the antibiotic commons.

🔬 Why Resistance Develops

Bacteria mutate rapidly. Antibiotic exposure kills susceptible organisms but allows resistant mutants to survive. Sub-therapeutic dosing, inadequate duration, and inappropriate use all accelerate this.

💉 Role of Every Prescriber

Unnecessary prescriptions select for resistant organisms that affect future patients. Stewardship is a clinical, ethical, and public health duty.

🚫 When NOT to Prescribe

Viral URTIs, self-limiting diarrhoea, asymptomatic bacteriuria (non-pregnant), and colonisation (not infection) do not require antibiotics.

📋 NICE Resources

Use NICE antimicrobial prescribing guidelines, local trust antibiogram data, and PHE toolkit. Microbiology and ID teams are available for advice — use them.

NHS Guidelines

Key NICE, BNF & NHS England guidelines for infection management

⚠ Always verify with current BNF, local formulary and your microbiology/ID team. Guidelines change — check for the latest version.

📋 Core Prescribing Guidelines

Guideline	Topic	Key Points	Status
NICE NG112	UTI in Adults	3-day nitrofurantoin or trimethoprim for uncomplicated UTI. Send MSU first. 7 days for complicated UTI.	Active 2023
NICE NG191	CAP (Pneumonia)	5-day course low severity. CURB-65 for risk stratification. IV→oral switch when CAPS met.	Active 2022
NICE NG15	Antimicrobial Stewardship	Document indication, dose, route, duration and review date on ALL antibiotic prescriptions.	Active
NICE NG51	Sepsis	Sepsis Six within 1 hour. Antibiotics within 1 hour of recognition — every hour delay increases mortality.	Time Critical
NICE NG109	Cellulitis	Flucloxacillin 1g QDS 5 days. Clarithromycin if penicillin allergic. Mark margins, review 24–48h.	Active 2020
ESCMID 2021	C. difficile (CDI)	Fidaxomicin first-line. Vancomycin PO alternative. Metronidazole no longer recommended.	Active 2021
PHE ESPAUR	Resistance Surveillance	Annual English AMR report. Use local antibiogram from your microbiology lab.	Annual
BNF	Prescribing Reference	Doses, interactions, contraindications. Updated continuously. NHS BNF app available free.	Live
NEWS2 Policy	Early Warning Score	NEWS2 ≥5 urgent review. ≥7 critical care. Mandatory across NHS England.	Mandatory NHS
BSAC	Endocarditis / Bone	4–6 weeks IV endocarditis. 6 weeks total osteomyelitis. Always seek ID input.	Active

⏱ Antibiotic Duration Quick Reference

Infection	Duration	Guideline	Notes
cLUTI (women)	3 days	NICE NG112	Nitrofurantoin 5–7 days
Upper UTI / Pyelonephritis	7–10 days	NICE NG112	Review on sensitivities
CAP — low severity	5 days	NICE NG191	Extend if not improving at 3 days
CAP — moderate/severe	7–10 days	BTS	IV→oral when CAPS met
Cellulitis	5 days min	NICE NG109	Extend if not improving at 48h
MSSA bacteraemia	14 days IV min	BSAC	Daily blood cultures until clear
MRSA bacteraemia	14 days IV min	BSAC	Echo + ID review mandatory
Endocarditis (native valve)	4–6 weeks IV	ESC 2023	Organism/valve dependent
Osteomyelitis (acute)	6 weeks total	BSAC	IV then oral step-down
Meningitis (pneumococcal)	10–14 days	ESCMID	Add dexamethasone
C. difficile 1st episode	10 days	ESCMID 2021	Fidaxomicin preferred

🔗 Key External Resources

escmid.org/guidelines

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NEWS2 / RCP

rcplondon.ac.uk

🔗 Always verify with bnf.nice.org.uk, nice.org.uk, and your local trust antimicrobial formulary. For complex prescribing decisions, always involve Microbiology or Infectious Diseases.