Model Answers Microbiology Written examinations 2007 - RCPA

Model Answers Microbiology Written examinations 

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Part 2, 2007 

Queensland Trainee paper, 2007 

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Part 1, 2007 

Answer all 5 Questions. All Questions have equal marks 

Introduction: 

1. Each of these following questions was marked by two examiners each of 

whom is an experienced examiner and a Fellow of the RCPA in the discipline 

of microbiology. Each examiner was asked to provide a “model‟ answer to 

the Chief examiner and the “model answers” provided below are based on a 

combination of these answers from experts in the field who are also 

examiners. The answers were also reviewed by the Chief Examiner 

Microbiology 

2. It is important to define your subject and to answer the question carefully and 

accurately 

3. If your writing is not easy to read try spacing out your words and leaving a 

line between the lines. You will not lose marks for underlining and ruling off. 

Etc. If your writing is truly indecipherable you should contact the CEX and 

the exam invigilator there is a college Policy on this issue and it is possible to 

arrange for an alternative method for submitting the answers provided this is 

arranged in plenty of time prior to the examination and you are prepared to 

bear the cost of using an alternative method. 

4. You must also answer each question ONLY for the time allotted. You will 

not get more marks for spending twice the time on one section. 5 questions, 

20 marks each, 4 sections/ question = 5 marks per section. If you miss one 

section out you are immediately down 5 points. 

5. You should also read the instructions to candidates provided in the 

examination room so that you are aware of the marking system for that 

examination. You must carefully note the number of questions to answer and 

the time (duration) of the examination. NOTE: not all examinations are the 

same, so be ready to read and understand the instructions for each (written) 

examination.

Question 1. Write short notes on the laboratory detection of: 

H5N1 Influenza A virus 

AmpC resistance 

Sensitivity testing of yeasts 

Detection of T. vaginalis 

Model Answers for Question 1 (Areas to cover): 

H5NI Influenza A virus 

Discuss: the best specimens for detection, and why, the safety aspects of testing for 

this organism, the role of point of care tests, definitive laboratory tests eg antigen 

detection, viral culture (appropriate cell lines) and identification of isolates, RNA 

detection 

What tests are available, how they are performed, sensitivity and specificity of each, 

turnaround times and usefulness 

Role of serology 

See PHLN document “Detection of Influenza”. influenza.pdf 

AmpC resistance 

When to suspect it 

Which organisms are involved? 

Where does it come from? 

Results with conventional sensitivity testing-disc, automated devices, other 

Definitive testing: phenotypic and genotypic 

Different screening methods especially disc diffusion and other methods for 

inducing the enzyme 

Technical details and interpretation of same (in considerable detail) 

Genotyping 

See attached document on Amp C

Sensitivity testing of yeasts 

Brief but comprehensive description of all methods used in diagnostic laboratories 

Macro broth 

Micro broth (sensititre) 

Disc diffusion (CLSI) 

Etests 

Others 

How to perform, how to interpret, standardisation, controls, limitations, and practical 

difficulties 

Differences between different organisms, different antifungals 

CLSI document on yeast sensitivity testing (reference and example pages attached) 

Article: Antifungal Susceptibility testing: New trends 

Detection of T vaginalis 

Specimens, transport and storage conditions, on the spot microscopy vv transported 

specimens 

Direct microscopy , wet films, permanent preparations, how performed, sensitivity, 

advantages and disadvantages 

Culture-methods, indications 

Non microscopic methods (molecular) 

Comments: 

This is a microbiology examination so a detailed discussion of the clinical 

presentation, treatment, importance of the organism and public health aspects is NOT 

required. Time spent on those issues will mean less time to specifically answer the 

question and therefore lower marks will be obtained. 

The introduction to the question above specifically states “write short notes on the 

laboratory detection of:”. 

Everything relevant to the laboratory detection should be considered including 

sample collection, specimen transport, methods of processing in the laboratory and 

the reasons why some methods are “better,” (used more frequently, automated, cost 

less, commercially available) and the advantages and disadvantages of each and the 

reporting and report comments, can, and should be considered in your answers

Question 2 Compare the advantages and disadvantages of: 

 

 

 

 

RTPCR and viral culture 

Chromogenic media and selective media 

Swabs versus fluid samples for examination for bacteria 

Serum versus plasma for antibody detection 

RTPCR and viral culture 

Confusion over whether RT means Real time or reverse transcriptase therefore you 

must define your topic and indicate what you are addressing if there is confusion. 

General discussion about PCR is acceptable 

PCR- Rapid TAT especially important when infection control public health 

intervention required. Detects non cultivable viruses. Can be used to detect dangerous 

viruses without the need for P3/4 facility, Sensitive, Transport and storage of 

specimens less important than fro culture, Initial set up is expensive, Easier to train 

staff in PCR techniques than those for viral culture, Problems with false positives and 

inhibitors resulting in false negative results, Can only detect specific viruses tested for 

. there is no isolate available for further characterisation or sensitivity testing 

although sequencing can reveal some known genes associated with resistance in some 

viruses eg CMV, HIV 

Viral culture: Slow, need to maintain cell cultures, CPE can be subtle or non specific, 

experienced staff needed to undertake viral cultures, increasingly hard to find. Cell 

lines prone to contamination, can detect many different viruses including novel 

strains, less sensitive but more specific although new PCR techniques to trawl 

samples for DNA/RNA have detected several new viruses recently that have not been 

identified in culture previously, Virus available for further characterisation eg typing, 

resistance testing and to enable fulfilment of Koch‟s postulates 

Chromogenic media and selective media 

Candidates need to show that they understand the difference between differential and 

selective media. Chromogenic media: commercial , less flexible, expensive. Useful 

in mixed culture where provisional ID only of pathogen may be sufficient. Advantage 

relates to ease opf plate reading and rapid provisional ID. Colour differences may be 

sublte, Some important organisms can not be differentiated eg klebsiella/enterobacter. 

Expensive if further ID still required. Selective media: often in house so flexible and 

cheaper, isolates always require additional ID tests. Some straines of bacteria may be 

inhibited.

Swabs versus fluid samples for examination for bacteria 

Swabs: Cheap and readily available. 

Usually easy to collect specimen. Easiy storage and transport. Only collects small 

superficial sample. Less suitable for anaerobic or fastidious organisms, Not suitable 

for AFB detection. Some swab types are inhibitory to some bacteria and other 

organisms. Easy to plate, Microscopy , quantitation can be problematic, culture 

results often reflect superficial colonising bacteria only. 

Fluids: Usually large sample from a normally sterile site. Requires invasive 

procedure to collect, Immediate processing required, Provides additional information 

eg cell count, crystals etc. All bacteria are potentially detectable. A concentration step 

may be required, may be abole to perform other tests eg PCR, viral culture. Isolates 

usually more significant than isolates from swabs. 

Serum versus plasma for antibody detection 

Need to know the difference between plasma (cell free blood with proteins and 

clotting factors) and anticoagulant. Serum, extracellular portion of blood after 

coagulation (cell free and protein free blood (clotted)). Plasma is preferred sample in 

biochemistry laboratories because of faster TAT, larger volume to test and easier to 

automate. One tube fits all. Serum is preferred for antibody tests. Plasma can not be 

used for agglutination or Complement Fixation tests. Plasma may be used in some 

EIA tests if they have been calibrated. NAA tests can be undertaken on plasma and 

serum

Question 3: Discuss the differences between: 

 

 

 

 

Virulence and pathogenicity 

Colonisation and infection 

S. aureus and MRSA 

Planktonic and sessile bacteria 

Virulence and pathogenicity 

Pathogenicity is the ability of an organism to cause disease due to structural and 

biochemical mechanisms. Pathogenic organisms have the ability to invade tissues and 

initiate infection. Involves both host and microbial factors. Pathogen requires ability 

to colonise, bypass host defences, invade deeper tissues. Due to the [presence of 

adhesions, resistance to phagocytosis, intracellular invasion and survival within cells, 

impairment of complement functions, lytic effect on PMN 

Virulence is the degree of pathogenicity within a group of organisms. Multifactorial 

microbial and host factors. Infectivity is the ability to initiate infection. Severity 

depends on the presence of virulence factors. These are substances produced by 

bacteria to harm the host. Eg exotoxins, haemolysins, lipases, elastases, proteases, 

alginate polysaccharides, antimicrobial resistance factors, leucocidin, hyaluronidase, 

streptokinase, staphylokinase, cytolysins, siderophores, protein M, TSST, PVL 

Virulence could be manifest in one host (eg immune suppressed vv another). 

Microbial virulence factors can be the target of effective immune responses eg 

antibody response demonstrating that host immunity influences virulence. Virulence 

factors may be used as vaccine antigens to reduce or negate virulence in certain 

microbes 

Colonisation and infection 

Colonisation requires attachment of bacteria via adhesions to receptors in host tissues, 

may be part of the normal flora, may be symbiotic with the host, may precede 

infection, examples of adhesions include: pili, fimbriae, lipoteichoic acid, protein F, 

examples of normal colonisation are skin, GI tract, upper respiratory tract 

Normal flora organisms colonise surfaces 

Infection is acquisition of a microbe by a host then invasion of the host by organisms 

with virulence factors to produce local or systematic disease. Ie there is presence of 

the organism, invasion and a host response. Infecting organisms penetrate the skin or 

mucous membranes by the production of invasions (spreading factors, hyaluronidase, 

collagenase, etc) and more extensive effects if exotoxins are produced. 

Clinical examples of infection compared with colonisation, normal flora compared 

with pathogens.

S. aureus and MRSA 

S. aureus: traditional pathogen sensitive to antibiotics, community and hospital, 

spectrum of disease virulence, treatment. Catalase pos, coag pos, gram positive 

coccus. Reservoir is anterior nares. Grows on non selective agar as golden colonies. 

Causes boils, food poisoning,(preformed toxin) endocarditis. Selective media 

including mannitol salt agar, salt broth, treat with flucloxacillin 

MRSA sub set of S. aureus. Resistance to beta lactams (and other classes). Mec A 

SCC, laboratory detection, hospital pathogen, virulence, nature of host, community 

strains caMRSA, PVL, treatment, infection control issues. 

Treat with vancomycin, linezolid, teicoplanin. 

Planktonic and sessile bacteria 

Planktonic bacteria are those that are suspended or growing in a fluid environment as 

opposed to those attached to a surface. Mobile, active metabolism, more sensitive to 

antibiotics, different DNA to sessile forms 

Sessile bacteria live on a surface in a community or biofilm. Reduced growth rate 

compared with planktonic bacteria, enmeshed in a matrix of extracellular polymeric 

substances, growth regulated by quorum sensing system. MIC much higher in old 

biofilms compared with planktonic bacteria. Antibiotics have difficulty penetrating 

biofilm and therefore difficult to eradicate. 

Examples IV lines, prosthetic valves, joints.

Question 4. Write short notes on: 

 

 

 

 

Norovirus detection 

Role of anaerobic blood cultures 

Flocked swabs 

Non cultivable bacteria 

Norovirus detection 

+ss RNA virus; Calciviridae, human calici virus distantly related to the other human 

calicivirus....sapovirus. 2 strains of Norovirus, genotype 1 and 2. Responsible for 

acute gastroenteritis. Nausea 9%, vomiting 69% and diarrhoea 66%, abdominal 

cramps 33% also headache, fever, chills reported. first recorded epidemic in 1968. 

Norwark virus. Epidemics occur in winter and spring and low background disease 

throughout the year. Often associated with hospitals, nursing homes, cruise ships, 

restaurant s and schools. Virus shed in vomitus and faeces. Faecal oral and vomitus 

oral eg alleged vomitus aerosol landing on food or fomites and then being consumed. 

In developed countries 50% population infected by 5 th decade. Acquired earlier in 

developing companies with poor sanitation. Gut virus receptor related to certain 

blood group antigens. Blood group B individuals are resistant to infection. RNA 

codes 3 ORF: ORF 1 encodes a non structural polyprotein that self cleaves to form 6 

structural proteins. ORF2 the capsid protein; ORF3 a minor structural protein. 

Diagnosis : RT-PCR of faeces or vomit. EM and IEM used in the past. Antigen 

based tests available but have low sensitivity and do not cover all human strains of 

norovirus probably due to antigenic variability/instability. (genotype 2 common 

strain in Australia 

Role of anaerobic blood cultures 

Past blood culture studies have shown rates of anaerobic bacteraemia of 10-15%. 

More recently this rate has fallen. ~5%. Finding anaerobes must be taken seriously 

as they can indicate important underlying primary infection or underlying disease. B 

frag = intraabdominal infection, F necrophorum + Lemmiere‟s disease or 

necrobacillosis with venoocclusive complications, clostridial sp and association with 

colonic cancer, gas gangrene. Often polymicrobial bacteria in gut disease. 

Automated systems detect anaerobes at similar rates 

Flocked swabs 

Used for 2 reasons; > nasopharyngeal cells cp cotton tipped swabs or NPAs, better 

detection of N gono and Chlamydia. Nylon, > absorbtive surface, non inhibitory 

Non cultivable bacteria 

Recent molecular tools suggest that non cultivable bacteria exist in many situations 

such as the gut. These organisms do not yet grow on defined media. An example is

Tropheryma whippelii the cause of whipples disease. This organisms was visualised 

in tissues but has not yet been cultured., identified using 16sRNA PCR. Interest in 

these organisms in chrons disease, inflammatory joint disease. T pallidum, C 

trachomatis are also non cultivable. Other reasons for inability to culture include 

prior use of antibiotics, dormant bacteria 

Question 5: Write short notes on 

Kohler illumination 

Gram‟s stain 

Use of a biological safety cabinet 

Disinfectants for use in the microbiology laboratory 

See attached paper for answers to all of these questions

Microbiology PART 2, 2007 Model answers 

Question 1, Marker 1 

What is the role of antenatal serology in modern medical practice and why? 

Roles of serology 

Routine screening 

At risk screening 

Diagnosis where risk of consequences 

When the infection is likely to have consequence for the foetus – eg contact with 

rash or rash-like illness in pregnancy. This is incorporated into the discussion of 

each of the specific infections. 

Diagnosis of acute disease 

Where interventions are available or where reassurance can be given that no foetal 

harm is likely e.g. EBV BFV RRV etc

General principles 

Routine vs selective 

The following factors should be taken into account when selecting a screening 

strategy: 

1. Detect infection 

Does the test detect potential foetal infection and damage? 

2. Assay 

Is there a sensitive and specific reliable assay available? 

3. Intervention 

Is there a safe and effective intervention strategy available if detected? 

4. Frequency 

Problems 

Does the infection occur at a frequency that has a cost benefit for the 

screening? 

Asymptomatic infections 

Poor positive predictive value 

Requiring further investigative actions 

Repeat serology/avidity etc 

Amniotic fluid examination 

Foetal blood examination 

Cord blood examination 

Often the true state of affairs remains unresolved 

Can generate angst for mother and family 

Termination as a result of not tolerating even minimal risk 

Psychological, Medicolegal, Ethical, Medical dilemmas 

Practical points 

Never base management decisions on a single test result 

Repeat tests preferably using a different method and on a second collection 

False positive IgM‟s are not that uncommon 

Serial sample testing important 

Avidity testing also may help – proportional to the maturation response of 

antibodies 

High avidity excludes infection in the previous 3- 4 months 

Low avidity usually BUT, not always, implies recent infection 

Stored serum samples at least for one year are important 

Examples 

Syphilis 

1. Detect potential foetal infection and damage

Primary, Secondary, Latent, Tertiary – Risk of foetal infection inversely 

proportional to stage 

2. Sensitive and specific reliable assay available 

EIA and other specific serology TPPA, FTA Abs WB 

RPR to monitor disease activity 

Note EIA false positives 

Note biological false positives in pregnancy 

Follow RPR to monitor treatment response 

3. Availability of a safe effective intervention strategy if detected 

Penicillin especially before 12 weeks as the damage to the foetus is 

immunological 

4. Occurs at a frequency that has a cost benefit for the screening 

Cost of caring for an infected infant high – recent cost benefit analysis in 

Australia means that women at risk from bisexual men, 

 

 

Rubella 

Capturing the appropriate population an issue – aboriginal population 

Need to attend antenatal care and have repeat testing if at risk exposures 

1. Detect potential foetal infection and damage - Primary infection CRS 

< 8 weeks – 90-100% 

8-12 weeks – 50% 

12-20 weeks – 20% 

>20 weeks < 1% 

Rubella reinfection 19 IU/ML = immune 

o If


Not generally recommended 

IgM may persist for weeks to months to years following infection 

IgA or avidity testing may be more helpful 

Recently recommending testing infants at birth (Massuchuses) 


Antibiotic therapy – spiramycin T1 and pyrimethamine and sulphadiazine 

T2 and T3 

Diagnosis of foetal infection – US and amniocentesis and PCR at least 4 

weeks after documented infection 

Treatment of newborn for 12 months following delivery to halt progressive 

disease (Chicago studies) 


Pros and cons complex; Seroprevalence 14% 

Educative protocols in place 

Some recommend repeat testing after 1-6 months or at delivery to identify 

seroconversion 

HIV 

1. Detect potential foetal infection and damage 

Perinatal transmission 

No HIV embryopathy described 

1/3 of perinatal transmission occurs in utero 

2/3 of perinatal transmission occurs in post partum 


Screen with EIA 

Confirm with Western Blot 

May require repeat test if recent exposure or indeterminate WB 


AZT from 14-34 weeks gestation 

Mode of delivery – CS (IV AZT 3 hours before section +/- nevaripine) 

HIV viral load – proportional risk of transmission at delivery 

o V1 10000 9-29% 

ROM > 4 hours (x4 fold increase in risk) 

Avoidance of invasive procedures (foetal scalp electrodes, episiotomy etc) 

Recommend bottle feeding (x2 risk of breast feeding) 

Follow up with 6 weeks of AZT to infant and cotrimoxazole for 3 months 

Follow infant – t cell subsets, PCR, virus isolation, HIV ab 

4. Occur at a frequency that has a cost benefit for the screening 

Although low prevalence in population – 

o 50% of HIV + pregnant women are unaware of their HIV status 

o 66% of HIV + pregnant women have no risk factors 

Risk factors: 

o Recipients of blood product or human tissue prior to 1985 

o Past history of IVDU 

o Partner of IVDU or resident/partner for high prevalence area 

o Bisexual relationship 

o Seroconversion illness

Hepatitis B 


High risk groups 

Areas of high prevalence 

Household contacts of carriers 

Multiple sexual partners 

Tattoos, body piercing 

If HBsAg negative offer vaccination post partum 

Ensure screening and vaccination of family members 

Sag pos+ eag - - vertical transmission 5-20% 

Sag+ eag+ - vertical transmission 70-90% 

90% of infected infants become chronic carriers 


Yes: HBsAg; if positive HBeAb HBeAg 

LFT‟s and DNA if abnormal LFT‟s 


No need for C/S 

HBIg (0.5ml) and HBV vaccine (0.5ml imi) 

Breast feeding: - although detectable HBV DNA in breast milk – no added 

transmission risk demonstrated 


Note that universal screening recommended as earlier attempt at 

identifying a risk group was not successful 

Hepatitis C 


If mother HCV Ab pos and HCV RNA PCR negative – prenatal 

transmission 0% 

If mother HCV Ab pos and HCV RNA PCR positive – prenatal 

transmission 0% 

Coinfection with HIV – prenatal transmission 9-45% 

Transmission proportional to RNA load 


Yes 

HCV Ab – but need to confirm with a second assay with different 

antigenic matrix: 

RIBA may be useful to sort out in determinates or discordant serology 

Also HCV RNA/PCR viral load 


No clear evidence re mode of delivery and reduction of perinatal 

transmission 

Breastfeeding: no increased risk of transmission demonstrated 

Most uninfected infants HCV Ab negative at 12 months 

Follow up infant HCV Ab at 12-18 months 

Or if concerned earlier HCV Ab and HCV RNA PCR 

If infected LFT‟s and HCV RNA PCR 

Refer for possible therapy (IFN and Ribaviron) 


Detection allows evaluation of treatment in the mother post partum

CMV 

VZV 

HSV 

1. Detect foetal damage or well being of the mother 

Leading cause of congenital infection; (0.3- 2%) of live births 

Approx 6/1000 pregnancies 

Diagnosis: 40-50% risk of transmission 

Symptomatic disease 10% (normal 10%; sequelae 90%) 

Asymptomatic disease 90% (normal 90%: sequelae eg deafness 10%) 

2. Sensitive and specific reliable assay available – limitations 

Asymptomatic v infectious mononucleosis syndrome 

IgM EIA 75% sensitivity and specificity 

May persist for months or years after primary infection 

Reappear with reactivation or reinfection 

False positives – other herpes viruses, pregnancy, autoimmune disease 

Serial rise in antibody levels v seroconversion v avidity 

May require ultrasound (30-50% sensitivity; Amniocentesis PCR +/- foetal 

serology 


None effective for either prevention of transmission or for effective 

treatment of congenital CMV 


Risk groups 

Day care workers – seroconversion 11% per annum 

Parents with child in day care – 20- 30% per annum 

General population – 2-3% seroconversion per annum 


CVS 

20 weeks – isolated case reports – zoster in infancy 


Yes for wild disease 

No for past vaccination status 

VZVIgM; also VZV PCR for acute diagnosis 


Passive immunisation VZV IgG < 96 hours 

Acyclovir to protect mother from severe varicella zoster not necessarily 

the foetus 

T2 

Underlying lung disease 

Immunocompromised 

Smoker 


Common – however 90 +% immune; increasingly likelihood of varicella 

vaccine immunity 

1. Detect potential foetal infection and damage

NA 


Limited probably to detection of discordant partners in pregnancy 

HSV positive male and HSV negative female at risk of primary HSV 

infection in pregnancy 

Risk when primary infection occurring at delivery – 50% 


Practice safe sex at time from 36 weeks 

4. Occurs at a frequency that has a cost benefit for the screening ? 

Parvovirus 

Detect potential foetal infection and damage 

Not teratogenic 

Foetal hydrops – intrauterine transfusion 


IgM – 

IgG – Immune status 

Recent infection ? recent infection, susceptible, immune 

Repeat in 2-4 weeks after exposure or if symptoms occur 


Foetal hydrops – intrauterine transfusion 

Ultrasound 


Diagnosis of infection following contact or illness with rash during 

pregnancy 

Common non notifiable infection


What is the role of antenatal serology in modern medical practice and why? 

Role to allow intervention 

 

 

 

 

 

Opportunity to terminate pregnancy/counsel re possible outcomes of 

pregnancy 

Prevent transmission 

Prevent infection/sequelae of infection if transmission occurs 

Allow early therapeutic intervention/monitoring of infant 

Opportunistic screening of women who are presenting to health care workers 

Discussion points: 

 

 

 

Screening vs symptomatic 

Universal vs targeted 

Cost effective 

Timing of screening eg preconception/early „booking‟ bloods ~ 12 weeks +/- 

later in pregnancy 

 

Australia 

 

 

If no useful intervention or cost/benefit not favourable then screening not 

recommended. Confirmatory testing – may involve further cost, anxiety, 

procedures eg amniocentesis, foetal blood sampling – risks to pregnancy 

Hepatitis B surface antigen – passive and active immunisation at birth 

prevents > 95% transmission 

Rubella IgG – if non immune vaccinate post partum

Syphilis – treatment of mother and monitoring/treatment of infant 

HIV – treatment of mother and infant 

Hepatitis C (medicare rebate will now cover this) counsel/monitor 

infant/caesarean may reduce transmission 

Other countries 

Toxoplasma – France – monitor seronegative women in pregnancy, offer treatment if 

seroconvert 

Issues 

Screening for eg MCV, VZV, parvovirus, HSV 1 and 2 

 

Testing if symptomatic or exposure 

o 

o 

o 

Timing of exposure relevant 

Rash – parvovirus, VZV, Rubella 

Exposure eg VZV – VZIG


What do you consider the essential features of a microbiology laboratory 

information system? Describe the main features you would consider when 

choosing a new LIS and how would you ensure its smooth implementation? 

Candidates should be able to discuss 5-7 points well 

Essential features 

 

 

 

 

 

 

 

 

 

 

 

 

 

Data entry efficient: Screens, click through, ease of use, and enable paperless 

workflow 

Interface with machines 

Audit trails 

Expert rules: CAR, insert comments, suppress reporting 

On-line worksheets, validation and record of communications 

Tag pathogens: nosocomial, notification 

Antibiogram and other data extracts 

Management reports, epidemiology 

Autovalidation with blood cultures 

Data fields and c compliant with 15189 requirements 

Response time, IT architecture 

Vendor support 

Storage – in-house v commercial 

Implementation 

 

 

 

 

Evaluation process: operational IT architecture, IT and professional (practice) 

considerations 

Set up databases, dictionaries, codes and rules, plan and time line 

Test environment before going live 

Staff training

Test and verify interfaces, data transfer epidemiology reports and extracts 

System to make and track changes 

Verify data transfer 

Change management, benefit patient, physicians, lab staff 

LIS team or rep 

Objectives 

 

 

 

Operational efficiency 

Reduce errors 

Enhance patient care


What do you consider the essential features of a microbiology laboratory 

information system? Describe the main features you would consider when 

choosing a new LIS and how would you ensure its smooth implementation? 

Candidates should be able to discuss 5-7 points well 

Basic essential features 

 

 

 

 

 

 

 

 

 

Robust technical specification 

Referential integrity 

Security 

Resilience 

Traceability 

Auditable by ad hoc enquiry 

Capacity 

Speed 

Paperless 

Other essential features 

 

 

 

 

User friendly graphic interface 

User privileges commensurate with needs 

Flexible user configuration without the need to involve the vendor, e.g. users, 

facilities, work lists, reporting lists, report formats, comments, laboratories, 

referral laboratories, test codes, comment codes, organism codes, 

susceptibility panels, susceptibility suppression rules etc. 

Adequate patient identification and demographic fields

Automated barcode label generation 

Flexible interfacing to instruments and other peripherals 

Data accession from external databases, e.g. from clinical PMI 

Auditable free text lab user notes linked to specific lab numbers/tests 

Ability to scan and store requests to meet Medicare Australia requirements 

Multi-site capability with flexible pre- analytical systems for specimen 

accession and tracking 

Streamlined validation of data transfer from interfaced instrumentation 

Ability to trace user for each step in pre- analytical, analytical and postanalytical 

process 

Multi-step validation process including final pathologist validation 

Automatic fax capability for results 

Secure and verifiable transfer of results to external information systems with 

no corruption of date type or content 

Functional billing module to meet accountancy standards and Medicare 

Australia requirements 

System compliant with NPAAC standards 

System compliant with ISO quality system requirements 

User friendly and flexible search functions including the ability to search for 

bulk data satisfying user defined criteria. 

Automated notification of notifiable diseases 

Ability to notify infection control practitioners of relevant results 

Real time secure access to up to date validated laboratory information for 

clinical users preferably through a continuously updated application separate 

from the LIS and not effected by LIS scheduled or unscheduled downtime 

Desirable 

 

Electronic order entry with lab configurable essential fields, test rules and 

prompts 

Implementation 

 

 

Chose the right system 

Planning and training with adequate resources including dedicated staff


Laboratory notification of MRSA has been proposed. Present your reasons for and 

against this proposal. 

Background 

MRSA endemic in hospitals in eastern Australia since 1980‟s 

 

 

o 

o 

o 

o 

o 

o 

Healthcare associated (HCA) MRSA is predominately EA- MRSA 

(ST93-MRSA-III) – multi- resistant 

EMRSA-15 (UK) (ST22-MRSA- IV) recently introduced – resistant to 

cip or cip/ery and urease negative 

Prevalence still increasing in NSW and Vic but decreasing in QLD 

SA level intermediate 

WA low level but EMRSA-15 perdominates 

Other overseas strains also seen some of which have marked epidemic 

potential 

Increasing consensus that HCA MRSA can be controlled best with screening 

and isolation and the standard measures including standard hand hygiene are 

inadequate 

Therefore, evidence exists for widely varying rates of HCA MRSA throughout 

Australia and for opportunities to optimise MRSA IC measures. Notification 

would provide for benchmarking and monitoring of progress in efforts to 

combat the nosocomial MRSA problem. 

New strains of MRSA have appeared in the community since the late 1980‟s 

in WA and mid 1990‟s elsewhere. The major strains are: 

 

o 

o 

o 

ST1-MRSA-IV (WA-1) _ PVL neg 

ST30-MRSA-IV (WWSP1/2, southwest Pacific, Oceania) – PVL pos 

ST93-MRSA-IV (QLD) – PVL pos 

Many other strains are also seen indicating active acquisition of SCCmec by 

multiple lineages

For 

 

 

 

 

 

 

 

This epidemic in gaining pace throughout Australia and ST93 in increasing 

rapidly and will probably overtake ST1 as the predominant strain 

PVL – give explanation 

PVL positive strains associated with furunculosis, and occasionally 

necrotising pneumonia, osteomyelitis (+septic thrombophebitis and PE in 

children), septicaemia. Fatal cases occur in young otherwise healthy children 

and adults. 

MRSA bacteraemia is a major issue as is S. aureus bacteraemia in general and 

is now being studied nationally (ANZCOSS). Thousands of cases are thought 

to occur annually with a mortality of approx. 30% (probably higher for 

MRSA) 

All of the above provides rationale for notification and intervention 

Intervention in CA-MRSA has occurred successfully in Denmark and is now 

being tried in WA. Contact tracing (household contacts) – increased hygiene, 

mupirocin, phisohex or chlorhexidine washes and follow up screening 

Establish baseline and benchmark 

Identify problem areas for intervention 

Evidence for successful HCA intervention strategies based on targeted 

screening and isolation is available and increased hand hygiene has also 

apparently been successful as an intervention in some settings 

Reduction of HCA MRSA has shown to reduce morbidity and mortality and to 

be cost effective in terms of overall health budget (through reducing 

morbidity, mortality and LOS) 

Establish population rates of CA MRSA 

Provide guidance to practitioners at a local level (empiric therapy etc.) 

Allow for community intervention 

Against 

 

 

 

 

Potential for stigmatisation of institutions based on MRSA rates 

Perception that intervention may be associated with increased costs 

Insufficient resources may be provided to labs or service providers to make the 

program work successfully 

Increased litigation may follow at the instigation of unscrupulous legal firms


List the samples that you would examine for fungi. Include how and why you 

would do this and when you would undertake sensitivity testing and referral to a 

reference laboratory. 

Samples 

Skin 

Scraping 

Hair 

Nails 

Biopsy tissue 

Respiratory 

Sputum 

Induced sputum 

Bronchoscopy specimens 

Aspirates 

Rarely pleural effusions 

Ear Swabs 

Sinus swabs include – tissue 

Urinary tract 

Urine catheters 

Renal disease 

Gastrointestinal 

Rare need 

Genital tract 

High vaginal swabs

Eyes 

Corneal scrapings – fungal keratitis 

Aqueous vitreous humour 

Tissue biopsies of any kind 

E.g. disseminated disease 

Brain 

Adrenals 

Thyroid 

Blood cultures 

Candidemias or fungemias 

How and why 

Media 

SAB (+ chlor, gent) 25-30C 

SD (SAB + cycoheximide) = MYCOSEL or (actidione) + (chlo + gent) 25- 

30C 

DTM = (chlo + gent + cycl) 25-30C 

SAB without antibiotics (may use for tissues from sterile sites) 

Chromogenic agar 

Dixons or overlay with olive oil for M.furfur from blood and occas skin but 

generally not indicated as microscopy sufficient from skin – 37C 

Set up in tubes to prevent drying as media held 3-4 weeks 

Avoid opening lids unless growth to prevent contamination 

Sporing for microscopy 

OA 

SACHs 

PDA – slide cultures/species etc 

CMA 

Basic techniques 

Macroscopic description of colonies 

Colour – surface reverse etc 

Appearance 

Microscopy from sample 

Hyphae – hyaline 

Hyphae – pigmented – T.nigra and other demateaciuos fungi 

Spores 

Yeast cells 

Pseudohyphae 

Copper pennies (Chromo) – SAB 28 

Spaghetti meat ball – M.f 

Microscopy of colonies 

Microconidia 

Macrocondidia 

Chlamydospores 

Other techniques 

Dimorphism demonstration: Mycelial conversion at 28 to Yeast at 37 

Exoantigen test – Histoplasmosis 

Differential temps of incubation 

Canavanine to speciate Cryptococcus – gattii v neoformans: association with 

HIV and prognosis

Bird seed – to confirm Crypto 

Ectoag test e.e. confirmation of culture Histoplasmosis esp when dimorphism 

difficult 

Vitek or API if not conclusive for yeast identification 

Details 

Skin and subcutaneous infections 

Specimens 

Scraping 

Hair 

Nails 

Biopsy tissue 

Diseases: 

Superficial: Pityriasis Versicolor (Malazzesia, Tinea Nigra) – Dixons 

Cutaneous: Dermatophytes – onychomycosis, tinea capitus and tinea 

 

corporis/cruris/pedis 

Subcutaneous: Sporo, Chrom, opportunists (Coelomycetes etc) traumatic 

implantation 

Collection: 

Scrapings, clippings, hair – adequate specimen an issue 

Microscopy 

calcofluor white/Evans blue in glycerol KOH, Calcofluor, - hyphae 

(allows terbinafine on PBS), spaghetti and meatballs = Malazessia furfur 

Culture media: SAB, SD, DTM 

Incubation 28C 

Duration 3 weeks 

Identification 

Edothrix, Ectothrix 

Anthropophilic, Zoophilic, Geophilic – management/source of infection 

Infection control issues 

New innovations: PCR 

Subcutaneous infections: 

 

 

 

 

Sporo – S.schenkii (dimorphism) 

Chromoblastomycoses 

o Cladiophilaophora grows on clclo 37 

o Fonseca 

Systemic infections with skin manifestations 

Often grow on the MCS blood agar at 37C e.g Fusarium 

Respiratory 

Respiratory 

Grow on routine bacto plates – normal flora: SAB (ABS) 25-30C, SD 25- 

30C + BHI (ABS0 (35) 

 

 

 

 

 

Nocardias on BHI 

Aspergillus spp, Scedospoium prolificans apiosperman 

Cryptococcus sensitive to cycloheximide 

Note lab safety issues: white fluffy fungi esp from resp tract but other 

tissues as well- arthroconidia of Coccidioides etc lab hazard 

DFA/silver staining/toluidine blue/PCR with quantification on respiratory 

specimens in immunosuppressed patients who have ground glass 

appearance suggestive of PCP (NB also stain with calcoflur)

Urinary tract 

Urine catheters/Renal disease 

Mainly candida – standard urine set up 

Germ tube 

Gastrointestinal 

Rare need 

Genital tract 

Mainly Candida – standard genital set up 

Correlate with microscopy 

Intractable vaginitis – may require speciation and sensitivity testing e.g. 

glabrata 

Tissue biopsies of any kind 

SABS (no Abs) SAB (Abs_ 25-30C, SD 25- 30C, BHI 25- 30C 

e.g. disseminated disease, brain, adrenals 

NB Zygomycetes – don‟t grind – non viable 

Blood cultures 

Liquid blood culture media (BacT Alert – good for mould and Candida) 

Lysis centrifugation 

Non-culture methods 

18S RNA PCR 

Galactoma Nan and other assay for Aspergillosis – monitoring function x 

2 weekly 

Susceptibility testing 

Often susceptibilities – predictable 

Relatively new – only just standardised 

Difficulties 

Inoculum preparation 

End point reading 

Fresh 24 H culture on SAB 

Methods 

CLSI – standardised guidelines – methods for yeast and moulds 

Difficult to do if only occasional 

Yeasts 

o Broth dilution M27-A2 standard for yeasts 

o RPMI 

o 24 hour reads 

o Trailing endpoints 

o Breakpoints for 24 and 48 hours 

o Numerical score 1 -4 

Commercial products: 

o Sensititer 

• AMB 

• FLU 

• ITRA 

• KETA 

• 5FC 

• VORI 

• POSI 

• CAS

o Disc diffusion 

• M$$-P standard for yeasts 

• For Candida species 

• Fluconazole (25ug) and Voriconazole (1ug) 

• MH glucose and MB 

Moulds 

o Yeasts easier than moulds 

o Broth dilution M38-A 

o RPMI 1640 glutamine 

E Strip 

o End points often difficult to read 

o Trailing …….. 

Neosensitabs 

Indications 

Unusual fungi where susceptibility less difficult to predict – difficulties with 

breakpoints 

Epidemiological purposes to accumulate invitro knowledge and correlation 

within vivo response 

Candida spp where prior imidazole therapy and possibility of resistance 

developing or selection of innately resistant Candida e.g. C.krusei 

Genital tract – glabrate and non response to imidazole 

Synergy voriconazole and terbinafine 

Non response to treatment 

Candidemias – especially non albicans (possible SDD or R to fluconazole) 

options: echinocandidin; caspofungin, ?voriconazole, posiconazole (esp 

Mucor) 

When to refer 

 

 

 

 

 

 

Sterile site isolate – difficult to identify 

e.g. non sporing 

Where fungus may be a laboratory hazard and appropriate facilities 

unavailable 

Confirm sensitivities and perform synergy testing 

Use of newer modalities – presence in histology or microscopy but culture 

negative e.g pan fungal PCR 

Specialised serological tests e.g galactoma Nan in immunosuppressed patients


Multi resistant M tuberculosis (XDR) is being increasingly isolated world wide. 

Define XDR and discuss the detection and laboratory implications of the emergence 

of XDR mycobacteria. 

Definitions 

 

 

Drug resistant TB – One first line drug 

Multidrug resistant TB (XDR) – Resistant to INH+Rif AND fluroquinolones 

+ kanamycin, amikacin or capreomycin (ie resistant to both first and second 

line drugs) 

Brief overview 

XDR epidemiology (up to 10% of MTB in Russia, India, China) emergence in 

 

 

 

 

Detection 

 

 

 

 

 

 

Africa, Iran and United States 

Rates in Australia 

Risk factors for acquisitions 

Previous treated TB, inappropriate treatment (see WHO guidelines), HIV 

coinfection, poor compliance, poor nutritional state, low socioeconomic status 

Mortality increase 

Clinical suspicion – previous treated TB, travel to or from an endemic region, 

clinical failure of standard regimes, HIV infection 

Standard laboratory detection and identification of MRB – ZN of sputum 

smears, Aura mine/Rhodamine, decontamination, culture in a liquid media, 

confirmation by standard phenotypic methods or molecular detection 

Phenotypic methods are more likely to be used in regions where the organism 

is prevalent. 

Growth characteristics and ZN appearance in broth, Nitrate, Niacin, Semi 

quant catalase, NAP, Pyruvate/glycerol growth, Tween 80 hydroslysis, 

Pyrazinamidase 

Molecular identification or detection, either from an isolate or from a clinical 

specimen 

o DNA-DNA hybridisation 

o IS6110 PCR detection 

Susceptibility testing

o 

o 

o 

Agar dilution – Middlebrook 7H11. Traditional method. Results 

expressed as resistance rations MIC test divided by MIC control 

Broth method – growth inhibition – Bactec, MGIT 

Molectlar detection of mutations in resistance associated genes. E.g. 

INH- katG, inhA, kasA, Rifampicin – rpoB, Streptomycin – s12, 

pyrazinamide – either phenotypic detection of pyrazinamidase or 

pncA, ethambutol embB 

Laboratory implications 

 

 

 

 

 

 

 

 

 

 

Safety and compliance with Australian standards 

XDR is a risk group 3 organism 

To be handled in a PC 3 laboratory – define 

Staff need appropriate training and experience 

Staff need BCG if Mantoux negative, regular CXR 

Dedicated space and equipment 

Increased testing, typing of isolates 

Liaison with Public Health 

Standardised methods and awareness of current WHO definitions and 

requirements 

Participation in an appropriate QAP


Multi resistant M tuberculosis (XDR) is being increasingly isolated world wide. 

Define XDR and discuss the detection and laboratory implications of the emergence 

of XDR mycobacteria. 

Answer 

XDR TB: detection and laboratory implications 

 

 

 

 

 

 

 

Drug resistant TB = isolate of MTB resistant to one of the 1 st line anti TB drugs; 

isoniazid, rifampicin, pytazinamide, ethambutol and streptomycin 

Multi drug resistant TB (MDR-TB) = isolate resistant to at least isoniazid and 

rifampicin 

Treatment for MDR TB patients use of 2 nd line drugs for greater than or equal to 

12 months 

MDR TB patients whose isolates are resistant to any fluoroquinolone and 

resistant to at least on 2 nd line injectable drug (amikacin, capreomycin or 

kanamycin) have been classified as extensively drug resistant (XDR-TB) 

(revised definition from WHO task force Oct 2006). An earlier definition of 

XDR TB was MDR TB + resistant to greater than or equal to 3 of the 2 nd line 

drugs. 2 nd line drugs (SLD‟s) include aminoglycosides, capreomycin, 

fluorquinolones, thiomides, cycloserine, para-aminosalicyclic acid 

The rationale for the revised definition: (i) protocols for drug 

susceptibility testing of fluoroquinolones and injectable anti 

TB agents are established and there is good inter laboratory 

agreement; there is less agreement for the other SLD‟s and 

none whatsoever for cycloserine, (ii) the fluoroquinolones 

and injectable agents are the most potent SLD‟s and form the 

corner stones of most MDR TB treatment regimes and (iii) 

are often the only SLD‟s available in developing countries. 

Losing the FQs and the injectable agents means losing the most potent and least 

toxic options for the 2 nd line therapy 

XDR TB is now documented in many countries – highest known rates in Eastern 

Europe and Asia 

XDR TB is a microbiological diagnosis – documenting the emergence of XDR 

TB requires the collection and processing of adequate specimens for culture and 

susceptibility testing, prior to institution of therapy. 

If a patient cannot produce expectorate sputum, sputum 

induction should be performed with necessary protection of 

supervising HCW e.g sputum collection and cough-inducing 

procedures should be performed in negative pressure ventilation 

rooms. HCWs should wear respiratory protection when present 

in room or enclosure in which cough-inducing procedures are 

being performed on patients who my have infectious TB. These 

high-risk patients should also be managed appropriately before 

and after specimen collection to limit cross-infection to other 

patients and to HCWs.

Collection of tissue for those with extrapulmonary disease e.g. 

lymph node, bone omentum 

Smear results reported within 24 hours 

All specimens should be inoculated in broth-based culture 

system +/- onto solid media 

 

 

 

Susceptibility testing should be performed by a reference laboratory 

The DSTs must be performed using a broth-based culture system so that results 

are available promptly. Using these methods, laboratories should aim to report 

MTBC DST results within an average of 15-30 days from the time of the 

original specimen reception. The DSTs themselves can generally be completed 

within 7-14 days of obtaining the initial M. tuberculosis isolate from the primary 

cultures 

Drug susceptibility tests must be performed in the following circumstances: 

All initial isolates of M. tuberculosis 

Isolates from patients who remain culture-positive after 3 

months of treatment 

Isolates from patients who are clinically failing treatment: or 

An initial isolated from a patient relapsing after previously 

successful TB treatment. 14,15 

Second line drug susceptibility tests should be performed on: 

 

 

 

 

 

 

All MDR TB isolates (i.e. isolated demonstrating isoniazid and rifampicin 

resistance) 

All isolates demonstrating resistance to greater than or equal to 2 first line drugs 

and 

Isolates from patients experiencing severe adverse reactions to first line agents 

Laboratories performing susceptibility testing must be involved with an external 

quality assurance program 

Laboratories performing susceptibility tests should ideally have PC3 facilities 

At this time – WHO does not recommend testing of thioamides, cycloserine or 

PAS as reproducibility of testing is poor. Testing of a fluoriqyubikibe (cuori ir 

ifkixacub) then moxifloxacin if cipro/oflox is resistant, an aminoglycoside 

(amidacin and/or kanamycin) and capromycin


Describe, with examples, the full laboratory investigation of CSF obtained by 

lumbar puncture. 

Specimen arrives in laboratory 

 

 

 

Next 

 

 

 

 

Check name and details on sample match the request slip 

Macroscopic appearance 

o 

o 

o 

Is it clear? 

Is it bloodstained? 

• all tubes evenly bloodstained – subarachnoid haemorrhage 

more likely 

• blood staining decreases from tube 1 to later tubes – traumatic 

tap more likely 

Turbid – meningitis more likely xanthochromias 

Record volume of CSF (prefer at least 1 ml) 

If possible leave a tube for any PCR work which may be required (usually 

tube 4) 

Take sample of fluid with sterile pipette from each of tubes 1-3 and examine 

under the microscope in a counting chamber with cell grain e.g. (cell count) 

?????????? 

In a traumatic tap, no of RBC‟s usually decreases in each successive tube 

taken. 

In meningitis, little difference between each tube

Normal cell count

Common CSF findings 

Viral 

Meningitis 

Bacterial 

Menignitis 

Cryptococcal 

meningitis 

TB 

meningitis 

Viral 

encephalitis 

Protein Glucose Cells Gm 

stain 

Bacterial 

culture 

Comments 

No or No Predominately Neg Neg Can do 

Slightly 

Lymphs 

enterovirus 

raised 

(some pdys 

PCR 

Raised 

Raised 

Raised 

No or 

raised 

day 1-3) 

Decreased May be pos, 

predominately 

pdys 

No or 

decreased 

Predominately 

lymphs 

Decreased Predominately 

lymphs 

No 

Predominately 

lymphs 

May be 

positive 

May be 

pos (Abs 

suggested) 

Neg Neg Can do 

India ink 

stain & 

CSF 

crypto AG 

Neg 

TB 

culture 

slow often 

6-8 weeks 

Can do 

AFB often 

neg TB 

PCR or 

LCX 

Neg Neg Can do 

HSV PCR 

 

Bacterial antigens no longer done – poor sensitivity and specificity. 

Extra tests 

Rarely useful unless abnormal protein/glucose/cell count 

 

 

 

 

 

 

 

 

 

 

crytpococcal antigen 

India ink stain (Cryptococcus) 

TB PCR/LCX 

AFB stain – rarely positive, need a lot of cells 

TB culture (6-8 weeks) 

HSV 1 & 2 PCR 

Enterovirus PCR 

JC virus PCR 

Meningococcal PCR 

Syphilis serology e.g. RPR, PTHA


Describe, with examples, the full laboratory investigation of CSF obtained by 

lumbar puncture. 

General points 

 

 

 

 

 

 

Emphasise how the nature and extent of testing is dictated by information 

about the patient: 

Importance of reading the history given 

Necessity of obtaining more history or speaking directly to the clinician, if 

indicated, both on receipt of specimen and when early results are available 

(microscopy, protein, glucose) as this may direct further investigations. 

Discuss the tests which are routinely performed 

Discuss testing which might be performed at the discretion of the 

microbiologist. (Perhaps discuss what testing in not indicated or is of limited 

benefit in some situations) 

Indicate how to prioritise testing when sample volume is limited. 

Microscopy 

 

 

 

Routine cell counts and interpretation of these 

Investigation of abnormal cells – eosinophils, cells with abnormal morphology 

Visual detection of organisms (include dark field microscopy for spirochaetes)

Organism identification 

Bacteria 

 

 

 

 

Fungi 

 

 

 

Viruses 

 

 

 

 

Choice of media, conditions of culture 

Non-cultural detection of bacterial infection 

o Ag detection 

o PCR 

Tests for tuberculosis 

o AFB staining 

o Culture 

o PCR (discuss methods) 

o (Chemical tests eg. adenine deaminase) 

Tests for syphilis 

o Especially critical evaluation for evidence of neurosyphilis 

Tests for Cryptococcus 

o Testing and significance of Ag detection 

o Serial CSF testing in evaluation of success of therapy 

Testing for other fungi e.g. dimorphic fungi 

CNS aspergillosis and other invasive mycoses 

Culture 

Noncultural methods especially PCRs 

Test selection for meningitis, encephalitis 

Special testing: 

o HIV – viral load 

o Testing in travellers e.g. arboviruses 

o Tests in immune-compromised patients e.g. EBV infection, JC virus 

o Testing for SSPE 

Parasites 

Diagnosis of CNS toxoplasmosis, cysticercosis, amoebic meningoencephalitis, 

African trypanosomiasis, angiostrongyliasis etc 

Prions 

Safety considerations

Mock exam Queensland trainees 2007 

General points: 

1. It is important to define your subject and to answer the question carefully and 

accurately 

2. If your writing is not easy to read try spacing out your words and leaving a 

line between the lines. You will not lose marks for underlining and ruling off. 

etc 

3. You must also answer each question ONLY for the time allotted. You will 

Not get more marks for spending twice the time on one section. 5 questions, 

20 marks each, 4 sections/ question = 5 marks per section. If you miss one 

section out you are immediately down 5 points. 

Question 2: Write short notes on: 

LGV Lymphogranuloma venereum 

Streptococcus gallolyticus 

Serological methods for the detection of deep seated mycoses 

The hazards of rain water tanks 

Answers 

Lymphomgranuloma venereum: 

LGV is a sexually transmitted disease. It was originally described in 1833 by 

Wallace . Synonyms include Lymphopathia venerea, tropical bubo, climatic bubo and 

lymphgranuloma inguinale. It is caused by serovars L1, L2 and L3 of C trachomatis. 

It enters via skin breaks or abrasions or it crosses the epithelial cells of mucous 

membranes. It enters the lymphatics and multiplies within the mononuclear 

phagocytes in the regional lymph nodes. 

While transmission is mainly sexual fomites and laboratory accidents have been 

reported to cause disease. 

LGV occurs in 3 stages . 

Stage 1 is the formation of a painless herpetiform ulcer at the site of entry . 

Stage 2 is characterised by lymphadenopathy and constitutional symptoms. Including 

fever, headache, nausea, vomiting and arthralgias Suppuration occurs later and the 

nodes may coalesce. Clinically they can be confused with cat scratch disease and TB. 

Histological appearances are said to be diagnostic. 

Stage 3 occurs years after the initial infection and may present as rectal stricture or 

genital elephantiasis. Organisms are rarely present at this stage.

Extragenital inoculation sites also produce regional lymphadenopathy. 

LGV is endemic in Northern Australia. And internationally is found in East and West 

Africa, India, Southeast Asia, South Caribbean. There have been recent outbreaks in 

Europe associated with MSM 

Symptoms resolve completely with appropriate treatment but death can occur in 

unresolved tertiary illness from associated symptoms. 

Incubation period is 3-21 days, secondary stage occurs after 10-30 days 

Risk factors include unprotected sexual intercourse from an infected individual, anal 

intercourse, prostitution, residing in an endemic area 

Lab studies are usually unhelpful. The Frei was an intradermal skin hypersensitivity 

test that is no longer available. CF testing sensitivity is 80% for LGV, a titre of 1/16 

is suggestive and a changing titre may be diagnostic. MIF for the L serovar is 

diagnostic if the titre is 1:512, PCR is superior if it is available. Serology for syphilis 

should be undertaken as the patient may have other STD‟s. 

Doxycycline is the drug of choice for treatment in a dose of 100 mg bd for 21 days. 

Infection confers no immunity against future infection 

Contacts should be examined and patients counselled to use safe sex practices. 

References: 

CDC fact sheet: http://www.cdc.gov/std/lgv/STDFact-LGV.htm 

Streptococcus gallolyticus 

Strep bovis/Strep equinus is a large bacterial complex including different species 

frequently isolated from humans and animals. 

Strep bovis has been separated in to 3 different biotypes correlated with genetic 

differentiation. S bovis biotype 2, S gallolyticus S macedonicus and S waius form a 

single DNA cluster separated in to 3 different sub species. They are delineated by 

different biochemical traits, limited DNA-DNA relatedness and divergent 16SrDNA 

sequences. 

In 1977 Klein reported a strong association between S bovis bacteraemia and colonic 

cancer. 

S gallolyticus is gram positive non motile, non sporulating, in pairs or short chains. 

Catalase is negative. Alpha or non haemolytic on blood agar, tellurite neg, and 

hydrolyses aesculin but does not grow on 6.5% NaCl and is PYR neg. They are 

group D streptococci. 

S gallolyticus is a mannitol hydrolysing strain and has tannase and gallate activity ( 

decarboxylate gallic acid to pyrogallol and hydrolyse methyl gallate (tannase 

activity)). It was previously identified as S bovis biotype 1 and has been associated 

with endocarditis and colonic cancer. It is also found in marsupial stool including 

koala, kangaroo, brushtails and possums. There are 3 subspecies which can be 

separated by various biochemical tests.

Serological methods for detection of deep seated mycoses. 

1. List of deep seated mycoses. Candida sp, paracoccidiomycosis, 

histoplasmosis, zygomycosis including mucormycoses eg mucor, rhizopus, 

phycomycoses , aspergillosis. The type of mycosis will depend on the 

geographical region as some strains are very location dependent. 

2. Occurrence: Many of these infections occur in immunocompromised patients 

so the detection of IgM and Ig G antibodies is unreliable even if there were 

good antigens available to detect antibodies produced against these organisms. 

3. Serology is defined as the detection of antibodies or antigens in serum 

4. Commercial serological tests available: Candida antibodies latex 

agglutination) , galactomannin (detecting aspergillus antigen EIA), 

Histoplasma antibodies (CF), western blot, 

Microbial hazards associated with use of rain water tanks 

Airborne microbes and chemicals can enter rainwater tanks via water collection 

processes either directly from the atmosphere or indirectly by leaching of materials 

from water collection surfaces animal excreta, debris and organic waste can also 

accumulate. Biofilm will form when the concentration of dissolved organics falls 

below 25mg/L. these develop complexity in time and they may assist in removing 

contaminants but there has been little work undertaken to examine this. There is 

current research starting to examine this issue. 

Microbes found in water tanks are likely to survive because of the lack of inhibiting 

substances, eg chlorine, the absence of filters and the leaching of bird and animal 

excreta which may contain enteric bacteria such as salmonella, campylobacter and 

parasites such as Giardia, cryptosporidium 

Also risk of breeding of mosquitoes spreading dengue, malaria, RRV, BF, other 

arbovirus infections. 

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