SMI (note): Investigation of swabs from the skin and superficial soft tissue infection

Specimen

Advice for the users:

• A sample of pus/ exudate is preferred over a swab.
• If a small amount of fluid is available, put it in an appropriate transport medium to prevent drying.
• Put the bacterial and fungal swabs in an appropriate transport medium.
• Send samples from where the infection is – sending dry crust or dead tissue or a superficial swab from an ulcer is not useful.
• For an ulcer – remove all the debris, clean the wound with normal saline, and take a biopsy/needle aspirate from the edge of the ulcer. Alternatively, irrigate the area under the ulcer margin with 1ml sterile 0.85% normal saline (no preservative), massage the ulcer margin, irrigate again with 1ml, massage again and aspirate 0.25ml fluid. Send for culture and sensitivity.

Safety

• Containment level 2.
• If performing an aerosol-generating procedure – perform it in a safety cabinet.
• If suspecting a category 3 organism (either notified or from clinical details) – E.g. Bacillus anthracis (exposure to animal hide, bioterrorism event etc), perform the processing of specimen in containment level 3, in a microbiological safety cabinet.
  All work on suspected isolates of C. diphtheriae which is likely to generate aerosols must be performed in a safety cabinet.
  A medical microbiologist must be informed of all suspected isolates of C. diphtheria as soon as possible. Isolate should be referred to the reference lab.
• PHE and infection control should be notified as per local/national policy.

Processing

Gram stain – usually not done unless deep-seated pus from a normally sterile site

Plate selection

CONDITION	PLATES
All clinical conditions	Blood agar CLED/MacConkey agar
Wound swab	Selective anaerobic agar with metronidazole disc
Pus	Fastidious anaerobic, cooked meat broth; then Subculture to blood agar.
Cellulitis in children Human bite	Chocolate agar with bacitracin (for Haemophilus and fastidious organisms)
Burn patients, Immunocompromised patients, Paronychia (Will need a layer of oil to culture for mould), Intertrigo, Diabetic patient	Sabouraud agar (Yeast, Moulds)
Suspecting cutaneous diphtheria (foreign travel <10 days, non-healing ulcer)	Hoyle’s tellurite agar

Anaerobic agar/broths – incubate for five days, may need longer if suspecting Actinomyces.

Which antibiotics to test

Release antibiotics based on

• the information provided in the clinical details (previously used antibiotic, intended antibiotic, any allergy or intolerance, any failure to treatment etc),
• likelihood of the organism being a pathogen (may suppress antibiotics if the organism is likely to represent colonising flora)
• patient's age or status (e.g tetracycline is contraindicated in children and in pregnancy, use of cephalosporins, clindamycin, and ciprofloxacin should be done with caution in older patients due to the risk of C difficile associated diarrhoea)
• Preexisting microbiology (may not use ciprofloxacin in a patient with previous MRSA or C difficile diarrhoea)
• local and national policy.
• Consider releasing antibiotics that are resistant (good practice)

ORGANISM	PRIMARY TEST PANEL	SUPPLEMENTARY TEST PANEL	NOTE
Staph aureus	-Cefoxitin or oxacillin (screen for flucloxacillin) -Erythromycin/Clarithromycin -Tetracycline (do not release in children/pregnant patients)	-Clindamycin (consider dissociative resistance, if erythromycin R), -Co-trimoxazole, -Daptomycin, -Fusidic acid, -Gentamicin, -Linezolid, -Mupirocin, -Penicillin, -Rifampicin, -Teicoplanin, -Vancomycin
Pyogenic Streptococci	– Erythromycin/ Clarithromycin – Penicillin, – Tetracycline (do not release in children/pregnant patients)	-Clindamycin -Co-trimoxazole -Linezolid -Vancomycin
Enterobacteriaceae (from clean surgical sites – only release antibiotic if evidence of infection)	Ampicillin (or Amoxicillin) Cefpodoxime (Screen for ESBL) Co-amoxiclav Gentamicin	-Amikacin -Aztreonam -Cefotaxime (or Ceftriaxone) -Ceftazidime -Cefuroxime -Ciprofloxacin -Co-trimoxazole -Ertapenem -Meropenem (or Imipenem) -Piperacillin/Tazobactam -Temocillin	Test cefpodoxime resistant strains for ESBL and reduced susceptibility to carbapenems. Use an interpretative comment suggesting that it may represent colonising flora. Pure growth may have a higher chance of being significant.
Enterobacteriaceae from sites prone to colonisation (eg ulcers)		-Amikacin -Ampicillin (or Amoxicillin) -Aztreonam -Cefpodoxime -Cefuroxime -Ciprofloxacin -Ceftazidime -Cefotaxime (or Ceftriaxone) -Co-amoxiclav -Cotrimoxazole -Ertapenem -Gentamicin -Meropenem (or Imipenem) -Piperacillin/Tazobactam -Temocillin	These are often considered colonising flora, and a sensitivity test is not undertaken. If a sensitivity test is being done, include co-amoxiclav and cefpodoxime. If cefpodoxime resistant test for ESBL. If either of them is positive, check for reduced susceptibility to carbapenems. Use an interpretative comment suggesting that it may represent colonising flora.
Pseudomonas		-Amikacin -Ceftazidime -Ciprofloxacin -Gentamicin -Meropenem (or Imipenem) -Piperacillin/Tazobactam	Use an interpretative comment suggesting that it may represent colonising flora.

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Target organisms

CONDITION	COMMON ORGANISMS	NOTE
Cellulitis and erysipelas	– β-haemolytic streptococci (including Streptococcus pyogenes), – S. aureus.	Cellulitis involves the deeper layers of the skin and subcutaneous tissues. Erysipelas involves the upper dermis and superficial lymphatic system
Wound infection	– β-haemolytic streptococci (including Streptococcus pyogenes), – S. aureus, – Bacteroides species – anaerobic cocci – Bacillus cereus (especially after trauma or orthopaedic surgery) – Enterobacterales
Ecthyma gangrenosum	– Pseudomonas aeruginosa – haematogenous dissemination of fungal infection (e.g. Candida species, Aspergillus, Fusarium and Mucorales – especially in immunocompromised/neutropenic patients) – Stenotrophomonas maltophilia	a focal skin lesion characterised by haemorrhage, necrosis and surrounding erythema
Impetigo	Bullous impetigo: – S. aureus. Nonbullous impetigo: -Lancefield Group A streptococci, – S. aureus, – Lancefield Groups C and G Streptococci	a superficial, intra-epidermal infection producing erythematous lesions that may be bullous or nonbullous.
Erythrasma	– Corynebacterium minutissimum	chronic, superficial skin infection of the stratum corneum- fine, scaly, reddish-brown plaques usually in the axillae and are often misdiagnosed as a mycotic infection
Superficial mycoses	– Dermatophytes – Candida species – Lipophilic yeasts
Paronychia	– S. aureus – Lancefield Group A streptococci – yeasts – anaerobic bacteria	Infection of the nail fold.
Folliculitis	– S. aureus. – Pseudomonas aeruginosa (hot tub folliculitis, after exposure to swimming pool/whirlpools), – Candida spp. (after prolonged antibiotic or steroid treatment), – Malassezia furfur (diabetes, steroid, granulocytopenia)	infection and inflammation of a hair follicle

Necrotising infections

In these cases, a superficial swab may not be the best specimen. A deeper specimen could be better.

CONDITION	ORGANISMS	NOTES
Meleney’s progressive synergistic gangrene	– S. aureus, – streptococci, – Enterobacterales, – Pseudomonads, – Anaerobic Gram-negative bacilli.	a burrowing lesion or chronic gangrene of the skin usually following abdominal operations and results from mixed infections
Gas gangrene	– Clostridium perfringens – other Clostridium species	a necrotising process associated with systemic signs of toxaemia, clinical shock, leakage of serosanguinous fluid, tissue necrosis and gas is present in the tissues. It often follows traumatic injuries such as penetrating wounds or crush injuries.
Fournier’s gangrene	– Non-sporing anaerobes – Enterobacterales – Streptococci – Clostridium species	infection in the pelvic and scrotal areas are common causes of gangrene in ischaemic and diabetic limbs.
Spontaneous gangrene	– C. perfringens – Clostridium septicum	most commonly seen in patients with colonic carcinoma, leukaemia or neutropenia
Actinomycosis	-Actinomyces species	chronic suppurative infection with abscess formation, fistula, sulphur granules (micro-colonies of Actinomyces species); usually seen in jaw, chest or abdomen,
Necrotising fasciitis	-Group A streptococcus, -Polymicrobial with anaerobes.	Infection primarily affects the subcutaneous fat and superficial fascia of muscles and often the overlying soft tissues.
Myositis	– S aureus – Polymicrobial – Fungi, viruses etc	inflammation of the muscle which may be caused by bacterial, fungal or parasitic infection or non-infectious causes.
Mycetoma	Eumycetoma (commonest form; caused by moulds): – Acremonium species, – Leptosphaeria senegalensis, – Madurella grisea, – M. mycetomatis, – Scedosporium (Pseudallescheria) apiospermum, – Pyrenochaeta romeroi, – Curvularia species, – Exophiala jeanselmei, – Phialophora verrucosa. Actinomycetoma: – Actinomadura species – Nocardia species – Streptomyces species – Madurella species	chronic suppurative infection with abscess formation, fistula, sulphur granules (micro-colonies of Actinomyces species); usually seen in the jaw, chest or abdomen,

Abscess

CONDITION	ORGANISMS	NOTE
Carbuncles, furuncles, cutaneous abscess	Staph aureus (commonest)
Abscess in IVDU	– oral streptococci – Streptococcus anginosus group – Fusobacterium nucleatum – Prevotella species – Porphyromonas species – S. aureus – Clostridium species – Bacillus anthracis (contaminated heroin)
Scalp abscess	– Anaerobes – Polymicrobial with anaerobes: β-haemolytic streptococci,  S. aureus,  Enterobacteriaceae,  enterococci,  coagulase-negative staphylococci,	a complication of electronic monitoring with fetal scalp electrodes during labour
Kerion	dermatophytes	a pustular folliculitis of adjacent hair follicles, creating densely inflamed areas of the scalp

Other

CONDITION	ORGANISM	NOTES
Burn	– S. aureus, – β-haemolytic streptococci, – pseudomonads, especially Pseudomonas aeruginosa, – Acinetobacter species – Bacillus species, – Enterobacteriaceae, – filamentous fungi, e.g., Fusarium species and Aspergillus species, – Candida albicans, non- albicans Candida species and other yeasts, – coagulase-negative staphylococci.
Bite wounds	– Pasteurella multocida – S. aureus – α-haemolytic streptococci – streptococcus anginosus group Other organisms- – Anaerobes (including Bacteriodes species and Fusobacteria) – Capnocytophaga species – Eikenella corrodens – Haemophilus species – coagulase-negative staphylococci – Streptobacillus moniliformis – Staphylococcus intermedius – Weeksella zoohelcum, – Actinobacillus species and – Neisseria canis	Capnocytophaga canimorsus is associated with dog bites and causes septicaemia, particularly in patients with asplenia or underlying hepatic disease. Streptobacillus moniliformis is associated with rat bites, and diagnosis is confirmed by culturing the organism from blood or joint fluid. Insect bite – secondary Group A streptococcus and S. aureus infection
Erysipeloid	Erysipelothrix rhusiopathiae	Uncommon nonsuppurative cellulitis painful purplish areas of inflammation with erythematous advancing edges in hand/fingers. An occupational disease of fishermen, fish handlers, butchers and abattoir workers.
water-related wounds	Aeromonas and non-cholera Vibrio species Edwardsiella tarda and pseudomonads	swimming in fresh or saltwater/ environmentally contaminated wounds, or from fishing or shellfish inflicted injuries/ therapeutic use of leeches
Staph aureus – PVL producers	S aureus	Recurrent or persistent skin infection in healthy individuals due to PVL producing Staph aureus.
Scalded skin syndrome (Lyell’s syndrome in older children; Ritter’s syndrome in infants)	S. aureus phage types group II and 71
Mycobacterium	– M. chelonae (tattoo-related infection), – M. fortuitum, – Mycobacterium marinum (fish tank or swimming pool granuloma), – Mycobacterium ulcerans (ulcers like Bairnsdale ulcer or Buruli ulcer),
Sporotrichosis	Sporothrix schenkii	Cutaneous sporotrichosis is acquired by contamination with soil, sphagnum moss or other vegetable matter and develops at the site of inoculation to form a primary lesion with lymphatic spread
Other	-cutaneous salmonellosis (vets, exposure to farm animals), -Cutaneous listeriosis (HIV patients), -Yersinia enterocolitica

Reference

Public Health England. (2018). Investigation of swabs from skin and superficial soft tissue infections. UK Standards for Microbiology Investigations. B 11 Issue 6.5.