Neisseria gonnorhoeae – brief review and data on AMR in PNG

A brief Neisseria gonorrhoeae update from our registrar Ian Marr at our regular bug of the week teaching round. We still culture it regularly from our samples – susceptibility testing is done at a reference laboratory. PCR diagnosis from early pass urine is the mainstay for most patients (main test method for C. trachomatis as well.

Please seek out this reference – here is the full text link.  Abstract below.   Good for a journal club.  I’ve not found anything more recent. Perhaps someone can check with PNGIMR and with Dr Valleley.  

P N G Med J. 2010 Mar-Jun;53(1-2):15-20.  Neisseria gonorrhoeae isolates from four centres in Papua New Guinea remain susceptible to amoxycillin-clavulanate therapy.  Toliman PJ1, Lupiwa T, Law GJ, Reeder JC, Siba PM.

Antibiotic-resistant strains of Neisseria gonorrhoeae have the potential to undermine treatment and control of gonorrhoea, which remains a highly prevalent sexually transmitted infection (STI) in Papua New Guinea (PNG). The standard treatment regimen for gonorrhoea in PNG based on amoxycillin and clavulanic acid (amoxycillin-clavulanate) was introduced about 15 years ago and there is some concern that over time circulating strains may have developed resistance to this therapy. To investigate this, N. gonorrhoeae isolates (n = 52) were collected from STI clinics in geographically representative centres in PNG and tested for their in vitro susceptibility to a range of antibiotics. All 52 isolates tested were found susceptible to amoxycillin-clavulanate, despite 40% (n = 21) being penicillinase producers and thus resistant to penicillin. These findings indicate that amoxycillin-clavulanate therapy remains an effective treatment for gonococcal infections in PNG, and support the maintenance of the present standard treatment for gonorrhoea in PNG.


  • WHO STD Laboratory Reference Manual – this is a good reference to go to for advice on key techniques – it is essential that we get a reliable culture system working again in PMGH for instance and this is a good starting point.
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WHO Core Components for Infection Control

Essential guidelines published last year by the WHO.  There is an excellent brief (2 minute) video review of the components. This is the single page info graphic:

Remember also to complete the 10 free Australian Commission on Safety and Quality in Healthcare short online learning modules for Infection Prevention and Control. Enroll here!

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Q fever and other rickettsia

This Q fever presentation from Professor Stephen Graves is worthwhile of review.  The presence of Q fever in PNG is likely but not proven as yet.   Dr Ak’s paper to be appended soon!

Also review this summary of laboratory diagnosis of rickettsial infection from Prof Graves.


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Module 6: Central nervous system infections- case studies and references

  1. Acute meningitides – CNS infection cases Ferguson 2017 acute

2. Chronic meningitis and encephalitis  –  Encephalitis and chronic meningitis Ferguson 2017

See also this posting concerning cryptococcal antigen detection for HIV patients.

Potential viva questions (practice with each other!):

  • What are the causes of acute meningitis in adults … in children  … in neonates
  • What are the typical CSF findings in viral m … bacterial m.
  • What is a parameningeal focus and explain what CSF findings might be expected
  • Interpret this CSF picture – e.g one of the cases above
  • Discuss the laboratory diagnosis of cryptococcal meningitis
  • Discuss the lab dx of TB meningitis
  • What are viral envelopes made of ? Contrast the properties of enveloped and non-enveloped viruses.
  • Describe the causes of chronic meningitis
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UPNG May revision M Med sessions – presentations and further references

2nd May 2017

  1. UPNG Infection prevention and control including TB IC Ferguson– presentation

2.  UPNG 2 AMR including Bacterial genetics Ferguson  –  presentation

These two posting from our sister blog may help with understanding antibiotic classes:

3rd and 4th May

3. UPNG 3 Antibiotic usage and practical AMS Ferguson –  presentation

Example management approach to Staphylococcus aureus BSI – n.b. 60 events at PMGH in 2016 (40% MRSA)

Potential M Med projects list relating to the national AMR plan (discuss with your supervisors) : Potential projects!

Local antimicrobial resistance studies:


  • Management of bone and joint infections due to Staphylococcus aureus. Davis-JS. Intern Med J. 2005 Dec;35 Suppl 2:S79-96.  An authoritative review.  Contact me if a copy required. 
  • Antibiotics for treating chronic bone infection in adults – Cochrane systematic review 2013:  poor quantity and quality of evidence; no evidence for IV superiority over oral. Old studies.

Posted in A/m resistance, Infection prev & control, Part 2 M Med Micro topics, PNG | 1 Comment

HTLV-1 in Papua New Guinea

Guest posting: Dr Ian Marr, Senior Microbiology Registrar, Pathology North, NSW. 

Human T cell lymphotropic virus 1 (HTLV-1), the first human retrovirus discovered, is found in some PNG populations and is an important topic for M. Med. post-grads and established clinicians!

What is a retrovirus? What is the process whereby HTLV-1 infects human cells? And can you name other significant retroviruses that infect humans?

A retrovirus is a virus that has a single stranded positive sense segment of RNA. The virus carries a reverse transcriptase enzyme that  makes complementary DNA from the viral RNA once inside the host cell. This DNA is then incorporated into the host T lymphocyte genome for life.

Human T cell Lymphotrophic virus (HTLV) is in the genus Deltaretrovirus. There are currently 4 different types of HTLV. These are named sequentially, HTLV-1, HTLV-2, HTLV-3, and HTLV-4. Only HTLV1 and 2 have been seen in any large number in people, with HTLV-3 and 4 being found rarely. There is 65% correspondence between the DNA structure of HTLV-1 and HTLV-2.  Other significant retroviruses include HIV1 and HIV2!

HTLV-1/2 is 100nm in diameter and has a thin protein envelope. As detailed proviral DNA is integrated into host T lymphocyte DNA. Once these lymphocytes increase in number (e.g. in association with an inflammatory response) the HTLV viral load increases. HTLV-1/2 is unique in that it is difficult to find free viral RNA/DNA outside of the cell (unlike HIV), hence transmission of infection is thought to occur by transfer of the cells that carry virus internally. This may occur with blood product transfusion. 95% of the provirus (dsDNA) is located in CD4+ T lymphocytes, and the rest in CD8+ T cells and dendritic cells. See this article for a good explanation whereby HTLV-1/2 infects T cells.

In 1999 HTLV-1 was found in PNG in the Madang, Chimbu and Enga regions.

What were the prevalence rates in Madang from this study? Where else in the world is HTLV1 and 2 found? 

Madang had the highest prevalence from this study conducted in 1999. It showed 39 out of 267 tested were positive for HTLV-1 antibodies on Western Blott analysis.

HTLV1 and 2 are found in clusters around the world. HTLV-1 is found in PNG, Melanesia, Solomons, central Australia, central Africa, the Caribbean, Brazil, and southern Japan. PNG, Melanesia and central Australia have a unique subtype named ‘c’ [HTLV-1c]. The significance of this subtype on clinical outcomes is not clear.

HTLV-2 is found in the Americas. Certain subtypes of the virus predominate in different countries.

What diseases have been associated with HTLV1/2?

The diseases associated with HTLV include:

  • Malignancy – Adult T cell leukemia/lymphoma (ATLL). This T cell associated malignancy occurs after 20-30 years of infection with HTLV-1 and has four different clinical presentations which display varying speed of onset: 1) acute, 2) lymphomatous, 3) chronic, and 4) smouldering. It is estimated that 2-4% of chronically infected HTLV-1 persons will develop ATLL. Survival is poor although treatment is still available in the form of chemotherapy.
  • HAM (HTLV-1 associated myelopathy – also known as Tropical spastic paraparesis – [TSP]). This is a degeneration of the spinal cord that causes a spastic transverse myelitis involving predominantly the lower limbs and impaired bladder function. It is estimated that 0.25-3.7% of chronically infected HTLV-1 persons will develop this syndrome. Symptoms do not present until at least 30-40 years of HTLV-1 infection. The current hypothesis behind the mechanism of damage is that the neuronal and glial cells are destroyed as a ‘bystander effect’, whereby the infected close by CD4+ T cells are targeted by cytotoxic T cells for destruction and the toxic cellular contents and effect of cytotoxic T cells damages the surrounding neurons. This is yet to be conclusively proven. There are some treatments (all with little evidence that are used to help). These include corticosteroids, and Interferon alpha and beta. See attached article on HAM.
  • Strongyloides – HTLV-1 has been associated with disseminated strongyloidiasis that reoccurs.
  • Dermatitis – HTLV-1 associated infective dermatitis (HAID) is the most common presentation in children. It is characterised by chronic eczema like eruption with persistent Gram positive skin infections.
  • Blood stream infection -. There are increased rates of blood stream infection in those infected with HTLV-1.
  • Bronchiectasis – HTLV-1 has been shown to be associated with bronchiectasis

What are the most common methods of HTLV-1 spread in communities?

3 major routes for infection:

  • mother-to-child transmission (mostly with breast-feeding)
  • sexual transmission
  • transfusion of cellular blood products infected with HTLV-1

What are the techniques for testing for HTLV1 and 2?

Methods of testing include screening for antibodies produced in defense of infection. This typically involves an enzyme immunoassay (EIA) which is then confirmed by a western blot (see references).

Pro-viral DNA can be detected in these cases but is often left only for research purposes.


  1. Takao et al. Journal of Clinical Virology, Seroprevalence of human T-lymphotropic virus type 1 in Papua New Guinea and Irian Jaya measured using different Western blot criteria.  
  2. Lab tests online HTLV 
  3. Buxton et al. NRL, Presentation: HIV-1 western blot interpretation/analysis
  4. McGill et al 2012.  HTLV-1-associated infective dermatitis: updates on the pathogenesis 

Image reference –

HTLV1 prevalence 2005

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Module 4- urinary tract infections – annotated SAQ

Urine bench Ferguson 2013: summary to go with your reading of the relevant text chapter.


 1.       Discuss sterile pyuria

Presence of white cells (>10/10^9/L) without growth of conventional uropathogens.     Causes include:

  • UTI- patient may have been on antibiotics and the urine has been rendered sterile
  • Interstitial nephritis – phase contrast microscopy does not distinguish neutrophils from tubular epitelial cells.
  • Fastidious organism present that requires special growth requirements or duration – classically, this is genito-urinary tuberculosis but also things like Chlamydia trachomatis, Neisseria gonnorrhoeae, Haemophilus influenzae are other possibilities.
  • Inflammation adjacent to the renal tract – e.g. appendicitis
  • Renal calculi or even just the presence of an indwelling catheter may be associated with pyuria by itself
  • Bladder carcinoma

Also something to think about – situations where uropathogens are grown but the microscopy shows no evidence of inflammation.  Our comment on such urines looks like this:

A neutropenic patient won’t make pyuria either during an infection.

2.       Discuss Pyelonephritis

Clinical Epidemiology,  Pathogens,  Laboratory diagnosis and treatment-  examine your standard treatment guideline sections (adults and children). See above and your textbook.

3.       What are the defining characteristics of Enterobacteriaceae?

Seven common characteristics- a nice Microbeonline summary.  Essential knowledge– Gram negative rods, facultative anaerobes (what does that mean btw?), oxidase negative, convert nitrate to nitrite (hence the urinalysis test for nitrite)

4.       Discuss gentamicin resistance mechanisms in Gram negative bacteria.

Review the RCPA video tutorial on Gram negative resistance.

  • Reduced uptake or decreased cell permeability – e.g. in Pseudomonas – causes pan resistance to all a-g drugs.
  • Modification of the antibiotic -aminoglycoside modification enzymes- may affect just one agent – e.g. gentamicin monoresistance due to the AAC(3)-I mechanism.  Basic types include AAC, ANT, or APH.
  • Modification of the target- altered ribosomal binding sites – e.g. mutational change responsible for streptomycin resistance and also  now, very topical, due to discovery of ribosomal methylases that are carried in multi-resistant GNB that have NDM metallobetalactamases- causes pan-resistance to all agents.

5.       Discuss indications for urine culture and how the specimen should be collected and handled.

In basic terms, collect urine cultures only from patients who have compatible symptoms for UTI (which may include autonomic dysreflexia in paralysed patients).

Asymptomatic bacteriuria becomes highly prevalent in older people and may also be associated with pyuria. Collecting a culture will lead to a false positive result and unnecessary treatment.  Specimens need to be kept refrigerated (4degC)  and set up within 24 hours. Alternatively a container with boric acid can be used for collection- this will prevent overgrowth for up to 24 hours – it is bacteriostatic.

N.B. Avoid collecting samples from indwelling catheters unless the catheter has been in for less than 24 hours.

Specimen collection for urine – also a potential topic to consider – we do not recommend perineal or penile cleansing – foreskin should be retracted and vulva parted for MSU. Bailey and Scott text on urine collection for MSU is not correct- certainly don’t use antiseptic on the perineum prior to collection!

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Invasive pneumococcal disease – the impetus for immunisation

Invasive Pneumococcal Disease Surveillance (Australia) recent report gives you a good idea of which serotypes of pneumococcus are within the different vaccines and the recent changes to serotype-specific IPD indidence – we are seeing quite an impact that is focused on serotypes within the vaccine. Some evidence of non-vaccine serotype escape in recent years.  Figure–  Australian IPD notifications 2002-2016.

Australian Indigenous rates (age > 50 yrs) (Figure 3 in above report) remain much higher than comparable data for non-indigenous adults (> 65 yrs) (Figure 4).

Australian childhood rates dropped in 2011 coincident with implementation of the 7vPCV – currently around 250-300 childhood events per annum.   Contrast this to an estimate from PNG that approximately 826,000 children, mostly young infants, die annually from invasive pneumococcal disease provided in this important recent 7vPCV RCT in PNG which examined safety and immunogenicity of neonatal pneumococcal conjugate vaccination in children.  Implementation of neonatal and childhood pneumococcal vaccination is one of the  highest priority issues for PNG.

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Pertussis – diagnosis, outbreaks and incidence

  • Culture appearances – see the Atlas – bisected pearl appearance of the colonies on charcoal agar.

  • Nepal:


Posted in Bacteria (GNEG), Module-Respiratory infections, Nepal, PNG | Tagged | 1 Comment

Module 3 – Respiratory infections SAQ annotated

Remember to be systematic about the key syndromes, pathogens and antimicrobials- read/revise the relevant chapters of Bailey and Scott and make notes for later! 

Respiratory infections PNG overview Ferguson Jan 2015

  1. Describe the Gram stain appearance and how a lab identifies pneumoniae.  TEXT BOOK STUDY!   What antibiotics are useful for treating pneumococcal pneumonia?  Benzylpenicillin/amoxycillin are the mainstays – very little resistance that is relevant to treatment of pneumonia;  erythromycin, tetracycline, cotrimoxazole (low levels of resistance in PNG). What about pneumococcal meningitis?     Important PNG CSF isolate data recently published (do read it!) :       Meningitis isolates.PNG                            Ceftriaxone susceptibility maintained and that is the mainstay for treatment of acute bacterial meningitis. Remember that although chloramphenicol susceptibility appears high (95%), the penicillin non-susceptible isolates will be tolerant to chloramphenicol and treatment failure then expected in a larger number of cases (reference available).        
  2. Describe what vaccines are available world-wide for pneumococcus in children and adults.  Distinguish conjugate (e.g. 13-PCV) from polysaccharide vaccines and how they differ in immune response.  Some famous PNG trials of the polysaccharide vaccine in Adults . Pneumonia in PNG review.     Australian childhood rates dropped in 2011 coindident with implementation of the 7vPCV – currently around 250-300 childhood events per annum. Contrast this to an estimate from PNG that approximately 826,000 children, mostly young infants, die annually from invasive pneumococcal disease  provided in this important recent 7vPCV RCT in PNG which examined safety and immunogenicity of neonatal pneumococcal conjugate vaccination in children.                                                             
  3. How does influenza evade the immune response?  Antigenic shift and drift – need to know what these mean!  What drugs are available to treat influenza? PRIMARILY the NEURAMIDIDASE inhibitors.  How well do they work?  NOT VERY WELL- if oseltamivir given within 48 hrs of symptom onset, then reduction in symptoms by average of 17 hours only. No change to need for hospital admission.         
  4. What is the natural history of whooping cough (pertussis) in children and adults? IN PNG AND MOST DEVELOPING WORLD COUNTRIES, recognise by clinical diagnosis – see text book- three stages- the cough of a 100 days!   Adult – persistent nocturnal cough without whoop; largely well during day. Children – paroxysmal cough, +/- whoop, pneumonia, secondary phenomena; monocytosis sometimes on blood film.   How is whooping cough diagnosed by the lab?  Used to be DFA and culture – now PCR from nasopharyngeal swab (optimal) or throat swab (less sensitive); positive results expected up to 3 weeks following onset of cough. Serology not a great deal of help.   N.B. pertussis vaccine and its effectiveness. See subsequent pertussis posting.                                                                                                                                               
  5. What are potential side effects or toxicity of doxycycline? What is its mechanism of action and spectrum?           TEXT BOOK!                                                  
  6. What are some of the unusual causes of bacterial or fungal pneumonia in PNG?  Pneumocystis (childhood respiratory infection and adults with advanced HIV),  Cryptococcus neoformans (mostly presents with meningitis but can cause pneumonia or mass lesion),  Melliodosis  (Important for part 2- see references by Dr B Currie from NT),  Disemminated strongyloidiasis, eosinophilic pneumonia from helminthic infection. ADD to the list! 

Remember this is a good place to look at Gram stains and culture pics.

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