“Hug a Microbiologist”

I read the SGH Department of Microbiology’s official blog’s post on Candida auris and marvelled at the extent of quality control that was portrayed and was also implicit in the identification of the yeast – twice, identifications thrown up by biochemical tests (API20) and the machine “black box” VITEK 2 were rejected by conscientious laboratory staff, who went on to perform ITS sequencing before finally concluding that the organism was C. auris. The process was laborious and would have cost far beyond the price of a simple blood culture. In a profit-driven clinical laboratory, this would have been unthinkable. In the hands of less experienced laboratory technicians and less finicky/experienced microbiologists, the process might have been aborted way earlier. Even as we move towards more sophisticated technologies that rely less on the experience and skill of microbiology laboratory staff (think maldi-tof and automated PCR- or sequencing-based testing), it is good to take the opportunity to appreciate high quality meticulous work. Amusing experiments have shown that the majority of us – even so-called experts – cannot distinguish fine wine from plonk, good bedside manners are often mistakenly conflated with good clinical acumen, and therefore I suspect that the even more esoteric area of quality clinical microbiology work is far harder to appreciate.

Infectious disease (ID) physicians have to work far more closely with clinical microbiologists compared to other specialists. In several countries, ID physicians and microbiologists are sometimes the same persons (although I tend to think this has its own downsides), but the extremely stringent requirements in the Singapore setting has meant that no single person here has been accredited to practise both as an ID physician and a microbiologist to date. Now that I have moved around several public and private hospitals, including experiencing some of those overseas, I can safely say that while good microbiologists are not uncommon, good and experienced laboratory technicians are rare, and great microbiologists as well as great laboratory technicians are like hen’s teeth and are potentially near extinction. Treasure them while they are still around.

Clinical Vignette 67

Probably the most beautiful parasite I have seen under the microscope.


View from the microscope via two photographs taken through the eyepiece.

Question: What is the name of the parasite and what disease does it cause in humans?

[Updated 28 September 2016]

This rare (in humans) parasite is Dicroceolium dendriticum – the lancet liver fluke. Humans are only accidental definitive hosts, while ruminants such as sheep, goats and cattle are the main definitive hosts. It is not found in Southeast Asia – I saw this specimen under a microscope whilst participating in the Gorgas course in Peru.

Its life cycle is quite a marvel – eggs which are passed out in feces are consumed by snails, and the larva migrate to the snails’ guts, where a cyst is formed around them by the snails trying to protect themselves. The cysts are then passed out, and consumed by ants (who apparently consume snails’ slime for moisture). One cyst contains hundreds of “baby” flukes, which break out, migrate and encyst themselves again within the ant as metacercaria. 

Now the creepy part – one of ther metacercaria will migrate to the ant’s central nervous system and take control of the ant, such that it will climb to the top of a blade of grass in the evenings and clamp it’s jaws on the grass, staying there until dawn when it returns to the ant hive again (so that it – along with its fluke infestation – doesn’t die due to the sun’s heat). This repeated action maximizes the chance that a definitive grazing host will eat the infected ant, whereupon the flukes will migrate to the liver and finally mature into their adult stage (as seen under the microscope), laying hundreds of thousands of eggs in their lifetime to continue their perilous existence.

So humans can only get infected if they somehow consume an (uncooked) infected ant.

The clinical presentation is otherwise largely similar to other human liver flukes – mostly asymptomatic, occasional biliary colic, very rarely liver cirrhosis and eventually cancer.

Zika Outbreak, Singapore (5)

The Zika epidemic in Singapore appears to be progressing towards endemicity. As of yesterday, there are 387 confirmed cases, with 9 clusters. 

Zika clusters in Singapore, a screenshot from the NEA website last updated on 23 September

Among the confirmed cases are 16 pregnant women, and the Ministry of Health has announced plans to set up a national surveillance programme to monitor the development of babies born to these and other Zika-infected pregnant women in Singapore.

The number of Zika notifications has dropped over the past week, but this may be due to both less intense testing as well as the recent ongoing heavy rainfall – dengue notifications have similarly fallen. Initial aggressive mosquito control measures are likely to have also contributed significantly.

Even as outbreak activities have quietened down, academic activities related to Zika have heated up. The initial publications have already appeared, with a piece on Zika genomics in Eurosurveillance. Investigators from the National Public Health Laboratory and Bioinformatics Institute showed that the primary virus causing the epidemic in Singapore is closely related to viruses circulating in Thailand, and precedes the French Polynesia-Brazil-Latin America clade.

Screenshot from the Eurosurveillance article. The Singapore viruses are 6th and 7th on the tree, counting from the top.

There are two more general articles at this time: a letter in Lancet on migrant workers’ health (the epicenter of our Zika outbreak was in a construction site) by School of Public Health academic staff, and an editorial in the Singapore Medical Journal which I reviewed and decided to let pass despite certai  logic gaps and flawed assumptions – there are still several useful points.

We can probably expect more publications in the near future. I am starting to re-think through the issues of academic publishing and outbreaks. There are inherent issues with the current model of academia that are well known, including the impact factor chase, over-rewarding of “novelty”, and excessive importance attached to authorship positions. All of which appear to be magnified and to create negative incentives for thorough collaborative academic work in the setting of epidemics.

Antimicrobial Resistance at the United Nations General Assembly

Approximately 11 hours from now, the United Nation General Assembly will host a “high level meeting” on antimicrobial resistance at the UN headquarters in New York. There will be statements by the UN secretary-general and the director-generals of the World Health Organization (WHO), Food and Agricultural Organization of the UN (FAO) and World Organization for Animal Health (OIE).


This will be only the 4th time that a specific health issue is raised at the UN General Assembly, highlighting the importance of antimicrobial resistance, which has long been ignored (and will continue to be ignored) or at least sidelined against other competing health issues like Zika pandemics, influenza and cancer.

The draft political declaration for the meeting is already available here. It commits member states to develop multi-sectoral national action plans that establish surveillance and regulatory frameworks on antibiotic use, increase awareness of antimicrobial resistance and change behaviour on antibiotic use, improve access to new antibiotics and vaccines, as well as invest in research on new antimicrobial drugs, diagnostics and other technologies that will help tackle the issue of antimicrobial resistance using a One Health approach. Many prominent scientists and experts have pushed for hard targets and specific timeframes that these plans be implemented by member states of the UN, but realistically, such a document is as good as it gets, given the need for political consensus and the wide disparity of wealth capabilities between the member states.

I was very fortunate in that both the Straits Times and TODAY were willing to consider and publish commentaries on this issue, and both of these op-ed’s were supported by the Saw Swee Hock School of Public Health. But it is a long road to further raise awareness of antimicrobial resistance and antibiotic stewardship in Singapore, as well as foster good antibiotic prescription practices among both doctors and the public. It will be even harder to tackle the issue of antibiotic use as growth promoters in food animals here, or at least change consumption practices significantly.

Clinical Vignette 66

Not so much a clinical but a radiological vignette – a CT image from more than a decade ago.


Question: What is the radiological sign and what is the diagnosis?

[Updated 20th  September 2016]

The CT cut of the lungs shows a “water lily” sign (and thanks for those who suggested that it is an ugly or atypical “water lily”), which is almost diagnostic of a pulmonary hydatid cyst. This patient was seen more than a decade ago when I was in Peru for the famous Gorgas Diploma Course in Clinical Tropical Medicine. I cannot recommend this course highly enough, and there are now quite a number of distinguished alumni from Singapore.

Hydatid disease is caused by an infection by the canine tapeworm Echinococcus granulosus, and humans are an accidental intermediate host (the target intermediate hosts are sheep and cattle). It is still present in a large part of the world, including South America, New Zealand, Australia, Mediterranean countries, the Middle East, and parts of Asia. Hydatid disease most commonly manifests as liver cysts, although the tapeworm larva can also migrate to other organs, including the lungs. Patients are virtually always asymptomatic – the cysts typically grow at a slow rate of 1 cm per year. Treatment of symptomatic hydatid cysts is commonly by surgery (taking care not to rupture the cysts intra-operatively), or by puncture-aspiration-injection-re-aspiration (PAIR), where a scolicidal solution such as hypertonic saline or ethanol is injected. Anti-parasitic drugs such as albendazole work poorly.

Singapore at the 42nd Chess Olympiad – End

The chess olympiads are finally over, with the very strong men’s USA team powering to its first ever Olympiad gold since 1976 (which the Soviets boycotted). They were seeded second behind the Russian team, but had fielded a team comprising three of the top 10 players in the world (Caruana, Nakamura and So) – the Russians in contrast had only 2 of the top 10 players (world championship challenger Karjakin and former world champion Kramnik). The women’s olympiad gold was won by China, finally regaining the title after a hiatus of 12 years.

Singapore had a mixed showing. The men’s team crashed down to earth after reaching 24th position after Round 7, losing 3 matches in a row to Chile (1-3), Poland (1-3), and Bosnia and Herzogovina (1.5-2.5) before redeeming themselves with a final round victory over lower-placed Sri Lanka (3.5-0.5).We finished in a big tie between 58th and 75th, ending up in 63rd position after tie-breaks (Singapore was seeded 58th). Both IM Goh and Ben Foo were unsuccessful in their respective GM and IM norm attempts, unfortunately, although both made rating points. GM Zhang Zhong consistently played well throughout, losing only to the higher rated GM Radoslaw Wojtaszek (FIDE 2736) of Poland.


Screen capture from chess-results.com, showing the individual performances of the Singapore men’s and women’s teams.

The women’s team, however, performed brilliantly, defeating the higher ranked England team in the final round to finish 38th on tiebreak (we were seeded 55th of 140 teams). The lower boards Emmanuelle Hng and Siew Kai Xin performed well above their current ratings and made astonishing rating gains of 67 and 31 points respectively.

Singapore at the 42nd Chess Olympiad – Round 8

The chess Olympiad at Baku is approximately two-thirds through now and the Singapore teams are doing extremely well. The women’s team – seeded 55th of 140 teams – is currently playing on table 14 and is placed 34th after 7 rounds. The men’s team – seeded 59th of 180 teams – is playing on table 12 today and is placed 24th.

In the men’s team, GM Zhang Zhong has been a tower of strength on Board 1, scoring 5 points from 6 games – no losses – with a performance rating of 2802 (the current world champion, Magnus Carlsen, has a rating of 2857 but has performed only at 2753 so far). IM Goh Wei Ming had an unfortunate loss in Round 6, but has so far put in a solid performance. He will need to start winning in order to have a shot at his final GM norm. 

A remarkable position that arose during the game between IM Goh and the Greek GM. Wei Ming had to find the rather inhuman Kd8 to reach a better position. He captured the bishop instead, and the game ended in perpetual check.

IM Tin Jingyao has had a spotty tournament, and appears somewhat off-form. IM Shanmugam Ravindran has only played three games so far, losing two against GMs. Ben Foo is playing the tournament of his life, beating players rated far higher than himself to reach a score of 4.5/5 and a performance rating of 2552.

The Olympiad is held over 11 rounds and if the Singapore teams continue playing with their current form, the men’s team will certainly improve over the previous best of 33rd in 1986 (albeit during a period where Soviet Union only had a single team, rather than the dozen or more strong ex-Soviet republics and Russia that are currently playing). Singapore has participated in 22 chess Olympiads to date, since 1968.