Basic microbiology

7 Basic microbiology

Andrew T. Raftery

SURGICALLY IMPORTANTMICRO-ORGANISMS

This section will concentrate only on those micro-organisms which cause surgical problems. Microbes may be divided into:

• conventional pathogens, i.e. those which may cause infection in the previously healthy person;

• conditional pathogens, i.e. those which cause infection in those who have a predisposition to infection; and

• opportunistic pathogens, i.e. those that are usually of low virulence but which will cause infection in the immunocompromised patient.

Examples of the above are shown in Box 7.1.

Micro-organisms which are of the greatest significance in surgery are usually bacteria. Bacteria may be classified as follows:

— bacilli – rod shaped;

— cocci – spherical;

• Gram staining:

— Gram positive – blue;

— Gram negative – pink;

• growth requirements:

— anaerobic; and

— facultatively anaerobic.

GRAM POSITIVE COCCI

The important ones are staphylococci and streptococci.

Staphylococci

These tend to be arranged in grape-like clusters. They may be divided into coagulase positive and coagulase negative. Coagulase positive staphylococci are called Staph. aureus. They are responsible for the following:

1. superficial infections; e.g. boils, abscesses, styes, conjunctivitis, wound infections.

2. deep infection; e.g. septicaemia, endocarditis, osteomyelitis, pneumonia

3. food poisoning; and

4. toxic shock syndrome.

Coagulase negative staphylococci, e.g. Staph. epidermidis are of lower pathogenicity and rarely cause infection in healthy people. They form part of the normal skin flora. However, they may be responsible for infection in association with foreign bodies, e.g. prosthetic cardiac valves, intravenous lines, continuous ambulatory peritoneal dialysis, and vascular grafts. These infections may lead to septicaemia and endocarditis and become life threatening. Their treatment with antibiotic alone is often inadequate, and the prosthesis may require removal.

Staph. saprophyticus, a commensal, may cause urin-ary tract infections in sexually active women.

Streptococci

These are spherical or oval cocci occurring in chains. They are classified by their ability to lyse red blood cells present in blood containing culture medium. They are further subdivided by serology, on the basis of polysaccharide antigens present on their surface, into Lancefield groups. The species responsible for sepsis are the beta-haemolytic strains where colonies completely lyse the blood cells on a culture plate, causing a colourless, clear, sharply defined zone. They include Lancefield groups A, B, C and G.

Lancefield Group D

‘Viridans’ streptococci

These show alpha haemolysis on blood-containing culture plates with a green (hence the term viridans) discoloration around the colonies. Most human strains are commensals of the upper respiratory tract and are of low pathogenicity. They are responsible for endocarditis. ‘Strep. milleri’ may be classified with this group but it is now more often classified with pyogenic streptococci. It may cause liver, lung or brain abscesses.

Antibiotic sensitivity

All strains are sensitive to penicillin and erythromycin.

Enterococci

Enterococcus faecalis is the most surgically important in this group. It may cause urinary tract infections and abdominal wound infections and may be isolated from bile in acute cholecystitis. Enterococci are usually sensitive to ampicillin, moderately resistant to penicillin, and resistant to cephalosporins.

GRAM POSITIVE RODS

Anaerobic Gram positive rods are mainly soil saprophytes but a few are pathogens. The surgically import-ant ones include species which produce powerful toxins, e.g. Clostridium perfringens (gas gangrene), C. tetani (tetanus), C. botulinum (botulism) and C. difficile (diarrhoea in association with antibiotic-induced colitis). Gas gangrene, tetanus and antibiotic-induced colitis will be dealt with later in the chapter.

GRAM NEGATIVE COCCI

They include Neisseria gonorrhoea, Neisseria meningitidis and Moraxella catarrhalis. N. gonorrhoea and N. meningitidis are intracellular Gram negative diplococci. N. gonorrhoea may cause fever and severe lower abdominal pain in females or be the cause of a ureth-ral discharge in males. A Gram stain of a smear from a high vaginal swab in the female or from a urethral discharge in the male may confirm the diagnosis by demonstrating the presence of Gram negative intra-cellular diplococci.

GRAM NEGATIVE BACILLI

This is a large group of micro-organisms of surgical importance. They may be divided into facultative anaerobes, e.g. E. coli and Klebsiella, and aerobes, of which Pseudomonas is the most commonly encountered in surgical practice.

Facultative anaerobes (Coliforms)

Proteus

Proteus spp. are responsible for:

• wound infections, e.g. burns, pressure sores; and

• septicaemia.

Shigella

They are intestinal parasites in man. They cause dysentery. Sh. dysenteriae which produces exotoxins causes the most severe illness. Other shigellae may cause a milder form of dysentery, Sh. sonnei being the most common cause in the UK.

Yersinia

These are animal parasites which occasionally cause disease in humans. Yersinia pseudotuberculosis and Yersinia enterocolitica are the most common, causing food poisoning and mesenteric adenitis.

Antibiotic sensitivity

Since many strains are now resistant to commonly-used antibiotics, sensitivity should be determined. In systemic infection, cephalosporins, gentamicin, ciprofloxacin or carbapenems may be used. In UTIs trimethoprim, amoxicillin and nitrofurantoin may be used for sensitive organisms.

Aerobic Gram negative bacilli

Pseudomonas aeruginosa

This inhabits human and animal gastrointestinal tracts, water and soil. The organism survives in moist environments in hospitals and may also survive in aqueous antiseptics and other fluids. It is an important cause of hospital-acquired infections. It particularly affects patients with serious underlying conditions, e.g. burns and malignancy, or as a result of therapeutic interventions, e.g. urinary catheters, endotracheal tubes. It is a frequent cause of infection in the immuno-compromised patient. It is a pathogen in the following conditions:

• UTIs, especially within indwelling catheters;

• wound infections;

• septicaemia;

• pressure sores;

• venous stasis ulcers;

• chest infections, especially patients on mechanical ventilation and those with cystic fibrosis; and

• eye infections (it may contaminate certain types of eye drops).

Antibiotic sensitivity

The presence of Ps. aeruginosa is not necessarilyan indication for antibiotic therapy especially if it is isolated from a superficial site. Clinical and bacteriological assessment in the individual patient is appropriate before prescribing antibiotics. Ps. aeruginosais resistant to most common antibiotics. The most suitable antibiotics are aminoglycosides, ciprofloxacin, ceftazidime, and piperacillin/tazobactam.

Other Gram negative bacilli

Campylobacter

These are curved or spiral rods which are micro-aerophilic. They are found in various animal species, including chickens, domestic animals and seagulls. Campylobacter is the most common cause of bac-terial food poisoning in the UK.

Haemophilus influenzae

This is mainly found in the respiratory tract, often as part of the normal flora but may also cause respiratory disease, especially community-acquired respiratory disease. It exists in non-capsulated and capsulated strains.

Non-capsulated strains are responsible for exacer-bation of chronic bronchitis and bronchiectasis. Cap-sulated strains often cause severe infections in young children, e.g. meningitis, acute epiglottitis, osteomyelitis, arthritis and orbital cellulitis. Septicaemia may occur especially as part of postsplenectomy sepsis. A vaccine is available against H. influenzae type B (HiB).

Antibiotic sensitivity

These are usually sensitive to amoxicillin, tetracycline, cephalosporins (second and third generations) and trimethoprim. Chloramphenicol should be reserved for severe infections, e.g. meningitis and acute epiglottitis.

Pasteurella multocida

This is a small ovoid gram negative bacillus. It inhabits the respiratory tract of many animals, notably dogs and cats. In man it may cause septic wounds after animal bites. It is usually sensitive to penicillin, tetra-cycline, erythromycin and aminoglycosides.

SPECIFIC ANTIBIOTICS AND ANTIMICROBIALS

This section deals with antibiotics particularly as they are used for the surgical patient. The list is not meant to be comprehensive.

PENICILLINS

Benzyl penicillin

This is active against streptococci, pneumococci, clostridia, N. gonorrhoea and N. meningitidis. Fewstaphylococci are now sensitive. The main surgical indications are for the prophylaxis of gas gangrene and tetanus and for streptococcal wound infections. It may be given parenterally, either i.v. or i.m.

Phenoxymethyl penicillin (penicillin V)

This is administered orally. It is used prophylactically following splenectomy to prevent pneumococcal septi-caemia, especially in children where it is used long term. It may also be used for prophylaxis in patients with rheumatic heart disease.

Flucloxacillin

This is administered either orally, i.m. or i.v. forpenicillinase-resistant Staphylococcus aureus. It is often used as an adjunct to drainage of abscesses, especially in diabetics or immunosuppressed patients.

Amoxicillin and ampicillin

These may be administered either orally, i.m. or i.v. Their use in the surgical context is largely for chest infections or urinary tract infections. Many staphylococci and coliforms produce β-lactamase and are, therefore, resistant. Amoxicillin and ampicillin are usually active against Enterococcus faecalis and Haemophilus influenzae.

Co-amoxiclav (Augmentin®)

This contains amoxicillin and potassium clavulanate. It may be administered either orally or i.v. The clavulanate is inhibitory to β-lactamase and extends the spectrum of amoxicillin. It is active against some coliforms, staphylococci and bacteroides. It is also useful in surgery as prophylaxis in bowel, hepatobiliary and GU surgery.

Piperacillin/tazobactam (Tazocin®)

This may be administered i.m. or i.v. It is active against bacteroides, coliforms, klebsiella and Pseudomonas aeruginosa. It is often used in combination with an aminoglycoside for life-threatening infections.

When administering penicillins, care should be taken to check for previous sensitivity. Caution should be particularly exercised in asthmatics and others with a history of allergic conditions. Hypersensitivity reactions are usually manifested by an urticarial rash, although anaphylaxis may occur. Cross-sensitivity occurs between different penicillins. Most penicillins are relatively non-toxic, and, therefore, large doses may be given. Caution must be exercised in patients with renal and/or cardiac failure, as injectable forms contain potassium and sodium salts. Rarely, convulsions may occur after giving high doses i.v. or following intrathecal injection.

CARBAPENEMS

These are β-lactam drugs which resist most common β-lactamases and have a very broad spectrum. They should be reserved for ‘difficult to treat’ infections.

Meropenem and imipenem

These are administered by the i.v. route and are indicated for respiratory, abdominal and other infections due to resistant gram negative organisms. Imipenem may cause convulsions.

CEPHALOSPORINS

These drugs are assigned to three generations. Specific examples of each generation in surgical usage are described below. Unfortunately, resistance levels are increasing rapidly.

Cefradine, cefalexin and cefaclor

These are first generation cephalosporins which are usually given orally. They are active against a wide range of Gram positive and Gram negative organisms, including E. coli, klebsiella, proteus, and Staph. aureus (unless methicillin-resistant). They are not active against Enterococcus faecalis, Ps. aeruginosa or bacteroides. They are useful as second line drugs for the treatment of urinary tract infections, respiratory tract infections, skin and soft tissue infections.

Cefuroxime

This is a second generation cephalosporin which may be given orally, i.m. or i.v. In practice it is used most commonly i.v. It is a broad spectrum antibiotic against Gram positive and Gram negative organisms. It is not active against bacteroides or against Pseudomonas. It is widely used in prophylaxis, especially in combin-ation with metronidazole in colorectal and biliary tract surgery.

Cefotaxime and ceftazidime

These are third generation cephalosporins which are administered i.m. or i.v. They have a broad spectrum similar to second generation drugs and ceftazidime is also active against Pseudomonas. They are normally reserved for use in serious sepsis due to susceptible aerobic Gram negative bacilli.

About 10% of patients who are allergic to penicillin are also allergic to cephalosporins. Rashes and fever may occur. In patients with renal failure, dose reduction is required. Mild transient rises in liver enzymes may occur.

SULPHONAMIDES AND TRIMETHOPRIM

Co-trimoxazole (sulphamethoxazole + trimethoprim)

This may be given either orally or i.v. It is used for treatment of urinary tract infections and respiratory infections. It is active against Gram positive and Gram negative organisms. Ps. aeruginosa is resistant. It may be used for Salmonella septicaemia and Pneumocystis pneumonia. Nausea, vomiting, rashes and mouth ulcers may occur. Leucopenia and thrombocytopenia may also occur occasionally. Life threatening reactions are not uncommon in the elderly.

Trimethoprim

This may be administered orally or i.v. by slow infusion. It is used for urinary tract infections and respira-tory infections. It should be avoided in pregnancy. Nausea, vomiting, rashes, stomatitis and marrow suppression may occur. It potentiates the action of war-farin and phenytoin.

MACROLIDES

Erythromycin

This is usually administered orally or i.v. by slowinfusion. Its use in surgical patients is limited. It is usually used as a second-line drug in patients allergic to penicillin. It is active against streptococci, staphylo-cocci, clostridia and Campylobacter. It is used for skin and soft tissue infections and respiratory tract infections. It is valuable in atypical pneumonia, Legionnaire’s disease and Campylobacter enteritis. The chief side effect when given orally is diarrhoea. When given i.v. phlebitis at the site of infusion is a common side effect. It may potentiate warfarin and cyclosporin.

AMINOGLYCOSIDES

They are valuable drugs for severe Gram negative infections, usually given in combination with a β-lactamase antibiotic. The most commonly used are gentamicin, amikacin and tobramycin.

QUINOLONES

Ciprofloxacin

This is usually given orally or i.v. It is a broad spectrum antibiotic against Gram negative bacteria, including Ps. aeruginosa, and staphylococci. Anaerobes are resistant. Its uses in surgery include urinary tract infections, especially those that are catheter-related, prostatitis and skin and soft tissue infections with Ps. aeruginosa. It is also useful for chest infections, especially those due to Gram negative organisms. Most strains of MRSA and an increasing proportion of Gram negative organisms are now resistant. The side effects include nausea, diarrhoea and vomiting. CNS side effects include anxiety, nervousness, insomnia and rarely convulsions. Ciprofloxacin potentiates warfarin.

OTHER ANTIBIOTICS AND ANTIMICROBIALS

Metronidazole

This is widely used in surgery both prophylactically and therapeutically. It may be given orally, i.v. or rectally. It is active against anaerobic bacteria, e.g. bacteroides and clostridia. It is also active against the protozoal organisms Entamoeba histolytica and Giardia lamblia. It is used for intraperitoneal sepsis and gynaecological sepsis.

It is used prophylactically in appendicitis against wound infection (usually given rectally) and in colorectal surgery, where it is given i.v. with induction of anaesthesia. It is also administered for giardiasis, intestinal amoebiasis and amoebic liver abscess. The side effects include anorexia, a sore tongue and an unpleasant metallic taste. It potentiates warfarin.

Tetracycline

This is of limited use in surgery. It may be used in chronic bronchitis, non-specific urethritis and atypical pneumonia.

Fusidic acid

This is usually used for penicillin-resistant staphylo-coccal infections and staphylococcal osteomyelitis. Tissue concentrations are good. It may be administered orally or i.v. Resistance arises easily and preferably it should be used in combination with another anti-staphylococcal agent.

Vancomycin

This may be given orally or i.v. It is active against staphylococci (including methicillin-resistant strains), streptococci, enterococci and clostridia. Its chief use is for severe infections. Recently its use has increased due to intraperitoneal administration in CAPD peritonitis. Side effects include phlebitis when given i.v. ototoxicity and nephrotoxicity. Serum levels must be monitored to control dosage.

Teicoplanin

Teicoplanin is a bacteriocidal glycopeptide active against both aerobic and anaerobic Gram positive bacteria. It is usually administered i.v. but may be given i.m. It is active against Staph. aureus and coagulase positive staphylococci (sensitive or resistant to methicillin), streptococci, enterococci, Listeria monocytogenes, micrococci and Gram positive anaerobes, including Clostridium difficile. Teicoplanin is chemically related to vancomycin, with similar activity and toxicity.

ANTIBIOTICS IN SURGERY

Antibiotics are never a substitute for sound surgical technique. Pus, dead tissue and slough need removing. Antibiotics should be used carefully and only with positive indications. Prolonged or inappropriate use of antibiotics may encourage resistant strains of organisms to emerge. Except in straightforward cases, advice should be sought from a microbiologist.

PRINCIPLES OF ANTIBIOTIC THERAPY

Selection of antibiotic

The decision to prescribe antibiotics is usually clinicaland is based initially on a ‘best guess’ policy, i.e. based on experience of the particular condition, what the organism is likely to be, and to which antibiotic it is most likely to be sensitive.

The following sequence of events usually occurs in selection of an antibiotic:

1. A decision is made on clinical grounds that an infection exists.

2. Based on signs symptoms and clinical experience, a guess is made at the likely infecting organism.

3. The appropriate specimens are taken for microbiological examination, i.e. culture and sensitivity.

4. The cheapest, safest and most effective drug or combination of drugs effective against the suspected organism is given.

5. The clinical response to treatment is monitored.

6. The antibiotic treatment is altered if necessary in response to laboratory reports of culture and sensitivity.

Occasionally the response of the infection to an apparently appropriate antibiotic is poor. Possible causes for this include:

• failure to drain pus, excise necrotic tissue, or remove foreign bodies;

• failure of the drug to reach the tissues in therapeutic concentration, e.g. ischaemic limb;

• the organism isolated is not the one responsiblefor the infection;

• after prolonged antibiotic therapy, infection with new organisms develops;

• inadequate dosage; and

• inappropriate route of administration.

Route of administration

Antibiotics should be given intravenously in severe infections in seriously ill patients. Some antibiotics, e.g. gentamicin, can only be given by the parenteral route. When the patient has had gastrointestinal surgery, antibiotics are best given parenterally until GI function is resumed, and then the drugs may be given orally. It is best to avoid the intramuscular route if possible, as it is uncomfortable for the patient and, in shocked patients, absorption would be inadequate.

Duration of therapy

This depends upon the individual’s response andlaboratory investigations. For most infections which show an appropriate response to treatment after 48 h, a suitable ‘course’ should be for 3–5 days but prolonged treatment may be needed for some staphylo-coccal and pseudomonal infections. A clinical response is the most appropriate guide, and this should be taken in conjunction with microbiological data.

Dosage

The dosage of a drug may need to be modified in renal and liver disease. In renal failure the dosage of drugs eliminated by the kidney may require major adjustment, e.g. aminoglycosides or vancomycin, whereas those eliminated by the liver, e.g. erythromycin, can usually be given in normal dosage.

Penetration of tissue

The drug must penetrate to the site of the infection: e.g. in meningitis the antibiotic must pass into the CSF. Deep abscesses are a particular problem and an important cause of antibiotic failure. An antibiotic cannot penetrate through the wall of the abscess to a collection of pus but may allow healing around the pus and may create an antibioma. The importance of draining pus cannot be overemphasised.

Hypersensitivity or allergy

This is most often due to penicillin and may manifest itself merely in the development of a rash but may also manifest in the form of life-threatening anaphylaxis. A clear history of allergy to antibiotics must be sought.

Drug toxicity

Some antibiotics are toxic, e.g. ototoxicity and nephrotoxicity with aminoglycosides, bone marrow depression with chloramphenicol.

Superinfection

Superinfection may occur with antibiotic-resistantmicro-organisms, e.g. yeasts. This is probably most common in immunosuppressed patients. Antibiotic-associated pseudo-membranous colitis due to Clostridium difficile may occur in any patient takingantibiotics. Initially this was thought to be due speci-fically to clindamycin, but it is now realised that broadspectrum β-lactam antibiotics are most often involved.

PROPHYLACTIC ANTIBIOTICS

Despite aseptic techniques, some operations carry a high risk of postoperative wound infection, bacteraemia, or septicaemia. Administration of antibiotics in the perioperative period will reduce the risks.

Indications for prophylactic antibiotics

• implantation of foreign bodies, e.g. cardiac prosthetic valves, artificial joints, prosthetic vascular grafts;

• patients with pre-existing cardiac disease who are undergoing surgical procedures, including dental procedures, e.g. patients with mitral valve disease, as prophylaxis against subacute bacterial endocarditis;

• amputation, especially for ischaemia or crush injuries where there is dead muscle. The risk of gas gangrene is high, especially in contaminated wounds. Penicillin is the antibiotic of choice;

• immunosuppressed patients;

• organ transplantation;

• compound fractures and penetrating wounds; and

• surgical incisions where there is a high risk of bacterial contamination, i.e. clean contaminated wounds or frankly contaminated wounds(e.g. bowel preparation for colonic surgery).

Most prophylactic antibiotics are given to prevent wound infection. In some cases they are given prior to instrumental procedures in potentially infected sites, e.g. when performing cystoscopy, when they are given to prevent bacteraemia. Any patients with congenital heart disease, rheumatic heart disease, or prosthetic valves should be given antibiotics before an elective procedure which may result in bacteraemia. Procedures include dental procedures (including scaling and polishing), GU instrumentation, some types of GI endoscopy, respiratory tract instrumentation and open surgery. In most cases one dose is given preoperatively, either orally if the procedure is under local anaesthetic (1 h preoperatively) or intravenously if the procedure is under general anaesthetic. An additional dose is sometimes given postoperatively. The aim is to achieve therapeutic levels at the time of surgery. Table 7.1 shows some indications for prophylactic antibiotics, the likely organism involved, and a recommended prophylactic regime.

Table 7.1 Prophylactic antibiotics

Clinical situation	Likely organism(s)	Prophylactic regime
Appendicectomy	Anaerobes	Metronidazole (single dose pr 1 h preop)
Biliary tract surgery	Coliforms	Cephalosporin (i.v. immediately preop and for 24 h postop)
Colorectal surgery	Coliforms Anaerobes	Metronidazole + cephalosporin or gentamicin (i.v. immediately preop and for up to 48 h postop)
GU surgery (open surgery)	Coliforms	Gentamicin (single i.v. dose preprocedure). Cephalosporin (i.v. immediately preop and for 24–48 h post-op) or gentamicin (single i.v. dose immediately preop)
Insertion of prosthetic joints	Staph. aureus	Flucloxacillin (i.v. immediately preop and for 24–48 h postop)
Insertion of prosthetic joints	Staph. epidermidis
Amputation of limb	C. perfringens	Penicillin (i.v. immediately preop and for 24 h postop)
Vascular surgery with prosthetic graft	Staph. aureus	Cephalosporin (i.v. immediately preop and for 24 h postop)
Vascular surgery with prosthetic graft	Staph. epidermidis Coliforms	Cephalosporin (i.v. immediately preop and for 24 h postop)
Prevention of tetanus in contaminated wound (+ immunoprophylaxis)	C. tetanus	Penicillin (i.v. or i.m. on presentation)
Prophylaxis of endocarditis
Minor dental procedure under LA	Oral streptococci	Amoxicillin (single oral dose 1 h preop; clindamycin if allergic)
Major dental procedure under GA		Low risk: amoxicillin (oral dose 4 h preop and one dose postop)
		High risk: amoxicillin & gentamicin (i.m. or i.v. immediately preop; vancomycin if allergic)
FGU instrumentation	Enterococci	Amoxicillin + gentamicin (i.v. immediately preop)

SURGICAL SEPSIS

The term sepsis covers several purulent infections which the surgeon may encounter in surgical practice.

SKIN INFECTIONS

Boils, styes and carbuncles

A boil (furuncle) is an infection of a hair follicle. A stye (hordeolum) is an infection of a hair follicle on the eye lid. A carbuncle is a group of boils interconnecting in the subcutaneous tissue by tracts. These infections are painful but not serious. Antibiotics are rarely indicated for boils and styes but may be appropriate for carbuncles. Infection is usually due to Staph. aureus, which is usually an endogenous strain carried in the nose or on the skin. Boils may be recurrent, appearing in crops over several weeks or several months. They may be a presenting sign of diabetes. Antibiotic therapy is indicated only in certain cases: e.g. boils on the ‘dangerous area’ of the face where venous drainage is to the cavernous sinus and where cavernous sinus thrombosis may result; and also in the immunocompromised patient and diabetics.

Only gold members can continue reading. Log In or Register to continue

Related

Stay updated, free articles. Join our Telegram channel

Tags: Applied Basic Science for Basic Surgical Training

Dec 12, 2016 | Posted by admin in GENERAL & FAMILY MEDICINE | Comments Off

Full access? Get Clinical Tree

Get Clinical Tree app for offline access

Get Clinical Tree app for offline access