The microbiologist's role in sepsis management is critical: identifying the causative organism and its antibiotic susceptibility provides the foundation for appropriate antibiotic therapy. The transition from empiric broad-spectrum antibiotics (started to cover all likely pathogens pending results) to targeted narrow-spectrum therapy guided by microbiological results (de-escalation) is a core antibiotic stewardship principle that saves lives, reduces antibiotic resistance, and reduces adverse drug effects.
Sepsis Definition: Sepsis-3
The Third International Consensus Definitions for Sepsis and Septic Shock (Sepsis-3, 2016) define:
Sepsis: life-threatening organ dysfunction caused by a dysregulated host response to infection. Organ dysfunction is operationalised as an acute change in SOFA (Sequential Organ Failure Assessment) score of 2 or more points from baseline, associated with a suspected infection. In non-ICU settings, qSOFA (quick SOFA) with 2 or more criteria (altered mental status, respiratory rate above 22/min, systolic BP below 100 mmHg) identifies patients at increased risk.
Septic shock: a subset of sepsis in which circulatory, cellular, and metabolic dysfunction is associated with greater risk of mortality. Defined as: vasopressor requirement to maintain MAP above 65 mmHg despite adequate fluid resuscitation AND serum lactate above 2 mmol/L. Septic shock hospital mortality is approximately 40 per cent.
The Surviving Sepsis Campaign (SSC) Hour-1 Bundle and the UK Sepsis-6: these evidence-based care bundles require: blood cultures before antibiotics, lactate measurement, IV antibiotic administration within 1 hour of sepsis recognition, IV fluids, oxygen for hypoxaemia, and urine output monitoring (Sepsis-6 elements) or vasopressor administration if MAP remains below 65 mmHg.
Blood Cultures: The Cornerstone of Sepsis Microbiology
Blood cultures are the fundamental microbiological investigation in suspected sepsis. They should be collected before antibiotics are started whenever possible, but should not delay antibiotic administration by more than 30 to 45 minutes in septic shock.
Collection standard: two sets of blood cultures collected from two separate venepuncture sites (not from an existing catheter unless catheter infection is specifically suspected). Each set consists of one aerobic and one anaerobic bottle, each inoculated with 8 to 10 mL of blood. The volume of blood per bottle is the most critical factor for blood culture sensitivity: each mL of blood in a bacteraemic patient with low-grade bacteraemia may contain only 1 to 10 organisms. Underfilling blood culture bottles dramatically reduces sensitivity.
Skin decontamination before venepuncture: chlorhexidine-based (ChloraPrep 2 per cent CHG in 70 per cent isopropyl alcohol) skin decontamination applied for 30 seconds and allowed to dry before needle insertion substantially reduces skin contaminant false-positive rates. The most common contaminant is CoNS from skin.
Sensitivity of a single two-bottle set: approximately 80 to 85 per cent for bacteraemia from a single venepuncture site. Two sets (four bottles) from two sites increase sensitivity to approximately 90 to 95 per cent and allow better discrimination between true bacteraemia (positive in both sets) and skin contamination (positive in one set only).
Common Sepsis Causative Organisms
Gram-positive organisms:
S. aureus (MSSA and MRSA): S. aureus bacteraemia (SAB) is associated with 30-day mortality of 15 to 30 per cent even with appropriate treatment. All S. aureus bacteraemias are significant: they require a minimum 14 days IV therapy for uncomplicated bacteraemia (no endocarditis, no metastatic infection, catheter removed) and urgent echocardiography to exclude endocarditis. MRSA bacteraemia is a mandatory reportable outcome in UK NHS trusts.
Streptococcus pneumoniae: the most common cause of community-acquired bacteraemia in adults. Associated with pneumococcal pneumonia, meningitis, and spontaneous peritonitis. Penicillin-susceptible strains: amoxicillin or penicillin G first-line.
Enterococcus faecalis and faecium: common causes of hospital-acquired bacteraemia, frequently catheter-associated or from the GI tract. E. faecium is intrinsically resistant to ampicillin (unlike E. faecalis) and increasingly VRE (vancomycin-resistant enterococci). Treatment of E. faecalis: ampicillin or amoxicillin. E. faecium: vancomycin (if susceptible), or linezolid/daptomycin for VRE.
Gram-negative organisms:
E. coli: the most common cause of gram-negative bacteraemia, typically from a urinary or intra-abdominal source. ESBL-producing E. coli requires carbapenem or alternative treatment.
Klebsiella pneumoniae: common cause of bacteraemia particularly in hospitalised patients with biliary, urinary, or intra-abdominal sources. CPE-Kp (carbapenemase-producing Klebsiella) has very high mortality and very limited treatment options.
Pseudomonas aeruginosa: important cause of bacteraemia in immunocompromised and ICU patients. Intrinsic and acquired resistance to many antibiotics. Empiric antipseudomonal coverage is required in neutropenic patients.
Rapid Diagnostics in Sepsis: Closing the Time Gap
Several rapid molecular diagnostic platforms have transformed the time to organism identification in sepsis:
MALDI-TOF direct from blood culture broth (after lysis and centrifugation): reduces time from blood culture positivity to organism identification by 12 to 24 hours compared to waiting for colony growth on solid media.
Multiplex blood culture PCR (Unyvero, BioFire FilmArray Blood Culture Identification Panel, BCID2): directly identifies 30 to 40 organisms and resistance genes (mecA for MRSA, vanA/B for VRE, KPC/NDM/OXA-48/VIM for carbapenemases, CTX-M for ESBLs) from a flagged blood culture bottle in approximately 1 hour. This allows antibiotic de-escalation (in susceptible organisms) or escalation (in resistant organisms) hours before conventional culture and susceptibility results.
T2 Biosystems Candida Panel: detects five Candida species directly from blood without culture in 3 to 5 hours. Useful in high-risk patients (ICU, post-abdominal surgery, TPN) where Candida is suspected and blood cultures have low sensitivity for candidaemia.
Frequently Asked Questions
What is the Sepsis-3 definition?
Sepsis-3 defines sepsis as life-threatening organ dysfunction caused by a dysregulated host response to infection. Organ dysfunction is identified by an acute increase in SOFA score of 2 or more points. Septic shock is sepsis with vasopressor requirement to maintain MAP above 65 mmHg and lactate above 2 mmol/L.
When should blood cultures be drawn in sepsis?
Blood cultures should be drawn immediately when sepsis is suspected, ideally from two separate venepuncture sites (two sets). They should be collected before antibiotic administration whenever possible, but antibiotic administration should not be delayed more than 30 to 45 minutes in septic shock to obtain blood cultures. Volume of blood inoculated per bottle (8 to 10 mL per bottle) is the most critical factor for sensitivity.
What is the significance of S. aureus in blood culture?
All S. aureus blood culture positives are clinically significant true bacteraemia until proven otherwise. S. aureus bacteraemia requires: investigation of source (find where the bacteraemia is coming from), echocardiography (to exclude endocarditis), minimum 14 days of IV antibiotics for uncomplicated bacteraemia, and follow-up blood cultures to confirm clearance. CoNS in blood culture is usually contamination in most clinical contexts.
What is de-escalation and why is it important?
De-escalation is the practice of narrowing antibiotic therapy from a broad-spectrum empiric regimen to a narrower-spectrum regimen targeted to the identified organism and its susceptibility pattern. It reduces antibiotic selective pressure (slowing resistance emergence), reduces adverse drug effects, and reduces costs. De-escalation should be performed within 48 to 72 hours of empiric therapy initiation when culture results are available.
What is the Surviving Sepsis Campaign Hour-1 Bundle?
The Hour-1 Bundle requires completion within 1 hour of sepsis recognition: measure lactate, blood cultures before antibiotics, administer broad-spectrum antibiotics, 30 mL/kg IV crystalloid bolus for hypotension or lactate above 4 mmol/L, and apply vasopressors for MAP below 65 mmHg refractory to fluids.
What does blood culture contamination mean?
Blood culture contamination means a skin organism (usually CoNS: coagulase-negative staphylococci) entered the blood culture bottle during collection. It is not from the patient's bloodstream. Clues: CoNS in one bottle only, no clinical signs of infection, no source for true bacteraemia. True bacteraemia with CoNS occurs in patients with prosthetic valves, permanent pacemakers, other implanted devices, or in neonates. True CoNS bacteraemia requires clinical correlation.
What is the significance of gram-negative bacteraemia?
Gram-negative bacteraemia (E. coli, Klebsiella, Pseudomonas) carries substantial mortality (10 to 25 per cent in most series), substantially higher with MDR organisms. It requires urgent appropriate antibiotic therapy: delays in covering an ESBL-producing organism with a cephalosporin (when a carbapenem is needed) are associated with increased mortality. ESBL screening of blood isolates is essential.
What are the most common sources of sepsis?
The most common infection sources in sepsis: urinary tract (30 to 40 per cent of community sepsis), respiratory tract (25 to 35 per cent, particularly in ICU and ventilated patients), intra-abdominal (15 to 25 per cent), skin and soft tissue (5 to 15 per cent), intravascular catheter (5 to 15 per cent in hospital-acquired sepsis), unknown source (15 to 20 per cent of all sepsis).
What is Candida sepsis?
Invasive candidiasis with candidaemia (Candida in blood culture) is a life-threatening infection predominantly in ICU patients, post-abdominal surgery patients, and those on prolonged broad-spectrum antibiotics or TPN. Mortality is 35 to 50 per cent. Blood culture sensitivity for candidaemia is only 50 to 60 per cent: T2 Candida panel or beta-D-glucan provides complementary sensitivity. Treatment: echinocandins (caspofungin, micafungin, anidulafungin) are first-line for invasive candidiasis.
How does procalcitonin help in sepsis management?
PCT-guided therapy uses rising PCT to support antibiotic initiation and falling PCT (by 80 per cent from peak, or below 0.5 microg/L) to guide antibiotic cessation. Multiple randomised trials show PCT-guided antibiotic discontinuation reduces antibiotic duration by approximately 2 days in ICU patients without increasing mortality. PCT is also useful for distinguishing bacterial sepsis from non-infectious systemic inflammatory response (SIRS) from surgery or trauma.