Category Archives: epidemiology

Plasmodium knowlesi: A New Ancient Malaria Parasite

There are over a hundred different species of the malaria-causing Plasmodium parasites in reptiles, birds and mammals. Being so widespread among terrestrial vertebrates, zoonotic transfer of Plasmodium has come at humans from multiple different sources. Plasmodium knowlesi had been known for some time as a parasite of long-tailed macaques but was not considered a significant human parasite until 2004 when a large number of human infections were identified in Borneo. Molecular analysis implies that Plasmodium knowlesi is as old as Plasmodium vivax and Plasmodium falciparum.

Cover image the phases of Plasmodium knowlesi from the April 2013 issue of Clinical Microbiology Reviews.

Diagnosis is complicated by the histological similarity between Plasmodium knowlesi and Plasmodium malariae. They can’t be distinguished in blood smears like those shown here, so infections were most often misdiagnosed as P. malariae even though they cause a quotidian (daily) fever. The WHO recommends that microscopic detection in areas where P. knowlesi is found report positive results as “P. malariae/P. knowlesi”.  It can only be securely diagnosed by molecular methods  that can distinguish all five human malarial species. PCR based detection methods have shown promise but no one method has been clinically tested with a large enough number of cases to become the standard of care. Antibody-based Rapid Diagnostic Tests (RDT dipstick tests) for malaria do not reliably detect knowlesi malaria which was discovered in humans after the RDT tests were developed. For now in resource poor areas, microscopic analysis followed by molecular testing where available is the only way to detect knowlesi malaria. Clinical research continues for a RDT test that can be employed areas with poor laboratory resources.

Infections have now been confirmed in all of the countries of southeast Asia. Between 2000 and 2011, 881 cases of local P. knowlesi local transmission have been identified in Borneo, with only 8 cases of P. malariae.  It is now suspected that past diagnoses of P. malariae in the region were actually P. knowlesi. Unlike other forms of malaria, P. knowlesi infects more adults than children, although actual infection rates are still not known.

Long-tailed and pig-tailed macaques are the reservoirs for P. knowlesi. In some areas of Malaysia the macaques are around 90% seropositive for malaria, in one study 87% were P. knowlesi. The malaria vector for P. knowlesi and other malarial parasites is Anopheles leucosphyrus group which is also concentrated in southeastern Asia.  Anopheles balabacensis is the most efficient vector, capable of transmitting P. knowlesi from monkey-to-human, human-to-human and human-to-monkey. A. latens, on the other hand, has been most commonly indicated as the vector to humans in Borneo, where it feeds in the high elevation canopy.  As the map below shows, the macacque reservoir and the mosquito vectors are limited to  the islands and peninsulas south-east Asia. It has been hypothesized, based on genetic diversity, that P. knowlesi has caused human malaria as long as  humans, macaques and the Anopheles vectors have all been on the islands of south-east Asia.

Source: Singh, B., & Daneshvar, C. (2013). Human Infections and Detection of Plasmodium knowlesi. Clinical Microbiology Reviews, 26(2), 165–184. doi:10.1128/CMR.00079-12

Difficulty in diagnosis has made it made it challenging to study the full spectrum of knowlesi malaria across the population. What studies have been done show that it produces a full spectrum of malarial disease from mild to fatal. Most cases reported to-date are in adult males, making an occupational exposure a significant possibility.

Symptoms are representative of other malarial infections: fever, chills and rigor, headache, along with a cough, abdominal pain and diarrhea. Gastrointestinal symptoms correlate with high levels of the parasite in the blood. Thrombocytopenia (low platelet counts) is the most common clinical finding and more severe than in either vivax or falciparum malaria, while anemia appears to be mild in knowlesi malaria. In the few pediatric cases that have been observed, they all responded to anti-malarial therapy. In the few cases of severe disease reported, abdominal symptoms have been so severe in some that malaria was not initially suspected. Acute Respiratory Distress Syndrome (ARDS) has been reported in about 50% of severe cases and acute renal failure in approximately 40%. There have not yet been enough confirmed cases of knowlesi malaria to accurately determine the case fatality rate. Although it appears to respond to a wide range of anti-malarial drugs, an optimized treatment based on a sufficient number of cases was not yet available in 2013.

The discovery of Plasmodium knowlesi in humans comes in the context of increasingly successful control of vivax and falciparum malaria in southeastern Asia. Some of the latest epidemiology from Malaysia suggest that 50-60% of the cases of malaria are now knowlesi. There are fears that knowlesi will jeopardize regional malaria elimination efforts. Is the rate really increasing or is it only apparent as levels of falciparum and vivax decrease? Does a real increase represent an opening niche for knowlesi as vivax and falciparum decrease? Only time and more data will answer our questions.

Primary Reference:

Singh, B., & Daneshvar, C. (2013). Human Infections and Detection of Plasmodium knowlesi. Clinical Microbiology Reviews, 26(2), 165–184. doi:10.1128/CMR.00079-12

For additional epidemiology from Malaysia:

Yusof, R., Lau, Y. L., Mahmud, R., Fong, M. Y., Jelip, J., Ngian, H. U., et al. (2014). High proportion of knowlesi malaria in recent malaria cases in Malaysia, Malaria Journal 13(1), 1–9. doi:10.1186/1475-2875-13-168

William, T., Jelip, J., Menon, J., Anderios, F., Mohammad, R., Mohammad, T. A. A., et al. (2014). Changing epidemiology of malaria in Sabah, Malaysia: increasing incidence of Plasmodium knowlesi, Malaria Journal 13(1), 1–11. doi:10.1186/1475-2875-13-390

Syndemics and Historic Diseases

I’ve been looking for a model or framework to bring together interdisciplinary evidence on diseases of the past. There are a variety of disciplinary approaches but few that can readily incorporate very different types of evidence well.

Apart from past discussions of discrete co-morbidities, the most common framework for understanding historic disease ecology has been pathocoenosis or ‘disease pools’ originated by M. D. Grmek in 1969 and popularized as ‘disease pools’ through McNeill’s Plagues and Peoples (1976). While this concept has proven popular among historians of medicine in high level overviews of human history, the concept begins to break down when practically applied to specific problems, as outlined by Robert Sallares (2004). It is hard enough to identify all of disease-causing microbes in a modern environment, much less a historic environment or population. It is often the minor or chronic disease-causing agents that make the most difference during a co-infection; malaria being a prime contender for the most important.  Pathocoenosis doesn’t adequately take into account the dynamic complexity of microbes in any population (however defined) and the idea that epidemics are disruptions in the equilibrium of pathogens in the population caused by new entrants to the population often doesn’t hold up.

Syndemics is a related concept emerging among biologists and medical anthropologists as a way to understand the diverse complex outcomes of diseases in populations. Syndemic comes from the terms synergistic and epidemic; it is a synergistic epidemic. A synergism exists when two conditions together produce a much greater effect than either individually added together ( ex. 1 +1 = 5 not 2).

A syndemic, in short, involves a set of enmeshed and mutually enhancing health problems that, working together in a context of deleterious social and physical conditions that increase vulnerability, significantly affect the overall disease status of a population (Singer, 2014).

The theory of syndemics is still evolving. The CDC’s definition refers specifically to two epidemics in the same population that produce a synergistic adverse outcome in human health. Consequently biology and medicine focus primarily on coinfections with an occasional look at nutrition. So far they are beginning to find some fascinating insights into how the immune system copes with two or more disease-causing microbes at once. We have to really take in that we are all coinfected all of the time. It comes down to if there is a significant interaction between multiple microbial species and the immune system. (It should be also said that coinfection can occasionally be protective as well.) Not surprisingly medical anthropologists insist on there always being a social component like malnutrition causing events, human behaviors like drug abuse and sexual practices,  or social disorder and inequality. So far from what I’ve read, these different focuses are complementing each other pretty well.

Some of the well-recognized syndemics include:

  • malaria + malnutrition
  • influenza + bacterial pneumonia
  • HIV + TB
  • HIV + HCV
  • HIV + HCV + IV drug use
  • Lyme disease + other Tick Borne Diseases
  • malnutrition + war (social disruption) + infectious disease (mostly diarrhea)

HIV has had a critical role in recognizing syndemics. Not unexpectedly, HIV coinfection with multiple organisms causes recognized synergetically worse outcomes. In many parts of the world, liver disease is a leading cause of HIV+ patient deaths due to Hepatitis C (HCV). It has also highlighted social conditions and behaviors that increase risk and vulnerability. The massive size, duration and amount of research done on AIDS is what has really allowed syndemic theory to become established.

Syndemics is just beginning to look at zoonotic disease but the future is already promising. As has already been suggested by work on pathocoenosis, malaria is a leading candidate to understand the syndemics of zoonoses. Syndemic effects have been suggested for malaria plus malnutrition, HIV and influenza.  Patients with long-term and serious health outcomes from Lyme disease are often coinfected with other less common tick born infectious diseases that are often undiagnosed (Singer & Bulled, 2014).

From what I have read so far, syndemics appears to take the best parts of the pathocoenosis paradigm, while jettisoning the unsupportable, over-reaching baggage. As we can already see for HIV and malaria, the syndemics approach has the potential to build up a foundation to understand the multifaceted outcomes of disease causing agents in different environments and provide insights into how the human microbiome and immune system interact. While its not perfect and doesn’t incorporate all of the disciplines needed to understand historic disease, it may provide a basis to build upon.

References and further reading:

Sallares, R. (2005). Pathocoenoses ancient and modern. History and Philosophy of the Life Sciences, 27 (2): 201–220. [Malaria]

Singer, M. (2014). Pathogen-pathogen interaction.Virulence, 1(1), 10–18. doi:10.4161/viru.1.1.9933

Singer, M., & Clair, S. (2003). Syndemics and public health: reconceptualizing disease in bio-social context. Medical Anthropology Quarterly, 17(4), 423–441.

Rock, M., Buntain, B. J.,Hatfield, J. M., & HallgrImsson, B. (2009). Animal–human connections, “‘one health,’” and the syndemic approach to prevention. Social Science & Medicine (1982), 68(6), 991–995. doi:10.1016/j.socscimed.2008.12.047

Singer, M. C. (2009). Doorways in nature: Syndemics, zoonotics, and public health. A commentary on Rock, Buntain, Hatfield & Hallgrı ́msson. Social Science & Medicine (1982), 68(6), 996–999. doi:10.1016/j.socscimed.2008.12.041

Ostrach, B., & Singer, M. (2013). Syndemics of War: Malnutrition-Infectious Disease Interactions and the Unintended Health Consequences of International War Policies.  Annals of Anthropological Practice, 36(2), 257–273. doi:10.1111/napa.12003

Morano, J. P., Gibson, B. A., & Altice, F. L. (2013). The Burgeoning HIV/HCV Syndemic in the Urban Northeast: HCV, HIV, and HIV/HCV Coinfection in an Urban Setting. PLoS ONE, 8(5), e64321. doi:10.1371/journal.pone.0064321.t003

Kwan, C. K., & Ernst, J. D. (2011). HIV and Tuberculosis: a Deadly Human Syndemic. Clinical Microbiology Reviews, 24(2), 351–376. doi:10.1128/CMR.00042-10

Conant, K. L., Marinelli, A., & Kaleeba, J. A. R. (2013). Dangerous liaisons: molecular basis for a syndemic relationship between Kaposi’s sarcoma and P. falciparum malaria. Frontiers in Microbiology, 4(article 35), 1–14. doi:10.3389/fmicb.2013.00035/abstract

Faure, E. (2014). Malarial pathocoenosis: beneficial and deleterious interactions between malaria and other human diseases. Frontiers in Physiology, 5. doi:10.3389/fphys.2014.00441/abstract

Herring, D. Ann, & Sattenspiel, L. (2007). Social contexts, syndemics, and infectious disease in northern Aboriginal populations. American Journal of Human Biology, 19(2), 190–202. doi:10.1002/ajhb.20618   [1918 influenza]

Singer, M., & Bulled, N. (2014). Ectoparasitic Syndemics: Polymicrobial Tick-borne Disease Interactions in a Changing Anthropogenic Landscape.Medical Anthropology Quarterly, n/a–n/a. doi:10.1111/maq.12163

A Synopsis of an Unusual Pneumonic Plague Outbreak in Madagascar, 2011

Plague appears in Madagascar every year, but it can still come as a surprise. It did in the January of 2011 when it appeared in an area of northern Madagascar that had never had an outbreak before. Not only was it a new area, but all of the cases were pneumonic. Not one case of bubonic plague. Eleven people were dead before antibiotics were given to the first patients on January 28. Vincent Richard and colleagues describe the outbreak in the forthcoming January issue of Emerging Infectious Diseases.

The index case was a thirteen year old boy who worked in a copper mine and developed a headache, fever and chills on a trip to his home village on January 6. He progressed to a fever, headache, a cough, severe chest pain and bloody sputum before dying at home on January 14. By January 22, his mother, her husband, daughter and granddaughter had died. Three other family members were showing symptoms of pneumonic plague when a neighboring family began to care for them beginning the second round of infections in twelve other people.  Visitors to the second household transmitted it to three more households. The last two fatal cases (19 & 20) were the brother who carried his sister to a traditional healer who was the last fatal case dying on February 9.

Plague transmission (Richard et al, 2015)
Plague transmission (Richard et al, 2015)

The epidemiological investigation identified 41 contacts: 17 from infected households and 25 who had more fleeting contact with a fatal case. None of these contacts had plague specific symptoms. All contacts were serum tested for plague with the Rapid Diagnostic Test (RDT, ‘the dipstick’) and all, but two who refused, were given prophylactic antibiotics. Details of how the contacts are connected are shown in the graphic above and narrated in the report by Richards et al in Emerging Infectious Diseases. Only two of these carriers were seropositive; one had a cough and refused antibiotics (c25) but did not progress. He is not considered a symptomatic case in the report. Three other contacts had mild pulmonary symptoms but were seronegative. They are not considered plague cases.  The wife of a fatal case cared for her husband and shared his bed until his death; she never turned seropositive.

Public health response followed the WHO protocols but was hampered by the outbreak being spread over seven villages 30 km from the index household in an area where plague had not been previously reported. This slowed the identification of contacts and dispensing antibiotics. Unfortunately postmortem specimens were not collected so there were only five specimens from symptomatic cases  to analyze. Initial sputum samples for three cases were positive for the Yersinia pestis F1 antigen by the RDT dipstick and all five specimens were transported about 900 km to the Institut Pasteur de Madagascar in Antananarivo to be analyzed. All attempts to culture Yersinia pestis from the specimens in bacterial media and mice failed.  Diagnoses were confirmed and titers quantitated by an ELISA based immunological detection for three cases. Cases were classified as suspected (17), presumptive (2) and confirmed (3) based on the WHO diagnostic criteria. The two presumptive cases were the seropositive non-symptomatic contacts. This highlights a problem with the WHO criteria since one seropositive case refused antibiotics and never developed plague specific symptoms. Presumptive should be a higher standard than suspected, which is based on clinical symptoms alone.

All cases that developed symptomatic pneumonic plague had the same symptoms: fever, chest pain, a cough, and bloody sputum. They were infectious for 48-72 hours after a 4-6 day latency period. This relatively long latency period allowed antibiotics to prevent the development of symptomatic plague in contacts. The effect of antibiotics on symptomatic patients was stark; five treated patients survived while all fifteen untreated patients died. With such a drastic difference between treated and untreated, the overall 75% case fatality rate is not really reflective of the virulence of the pathogen. Antibiotics alone determined the survival of symptomatic cases. Of the 36 people living in infected households, 20 developed symptomatic plague for an attack rate of 55% within the households; non-household contacts are excluded from the attack rate calculation.

Investigation of the presumptive focus is not begin until two months after the beginning of the plague response. Trapping of rodents in the area around the initial two villages,  Ambakirano and Ankatakata, produced 64 rodents and five dogs were sampled. Only one greater hedgehog (1 of 6) and two dogs were seropositive for Yersinia pestis by ELISA.  As wide ranging carnivores who are fairly resistant to plague, seroconversion in dogs is considered to be a good sentinel indicator. No fleas were collected; no dead rats were observed. All 51 black rats collected were seronegative, but Yersinia pestis DNA was isolated from the spleens of five rats. All strains fit the Malagasy specific 1.ORI3-k SNP pattern. There was enough minor variation in CRISPRs (a type of genetic fingerprinting information) to suggest a pre-existing enzootic focus is present. With such benign animal evidence, there is no reason to think that there was an epizootic that spilled over to humans. This is not surprising considering there were no bubonic cases. All of the human cases appear to be connected to the index case and to have passed human to human. Unfortunately, there is no mention of investigating a potential plague focus near the copper mine where the index case was working before symptoms appeared on his way to his home village.

While the survivors of the 2011 outbreak responded well to streptomycin, resistant strains were reported in the 2011 outbreak to Richards et al (2015) as personal communication. It is unclear if this means in an animal isolate from the region or another outbreak in 2011. Resistant strains have been reported in Madagascar since 1995 and are now apparently persistent.

This outbreak highlights how difficult it is to initially identify a pneumonic only outbreak. Spread by droplets, transmission can be broken by simple masks or, the Malagasy team suggests, even hygiene like turning away from others while coughing or covering the mouth and nose. People were able to care for and bury their dead without contracting disease.  On the other hand, antibiotics alone stopped the outbreak. Whether or not it would have ended on its own, we will never know. Although only two contacts were seropositive, prophylactic antibiotics likely prevented more infections.


Richard V, Riehm JM, Herindrainy P, Soanandrasana R, Ratsitoharina M, Rakotomanana F, et al. Pneumonic plague outbreak, northern Madagascar, 2011. Emerg Infect Dis [Internet]. 2015 Jan [ahead of print publication 5 Dec 2014].

See my previous post for more information on antibiotic resistant Yersinia pestis in Madagascar.