Endemic infectious diseases: the next 15 years

Aug 24, 2016 | Blog, Emerging Diseases, Endemic Diseases, Latest news

Endemic infectious diseases: the next 15 years

I have recently returned from the International AIDS Conference in Durban, South Africa. It was, as many have noted, a landmark event: a chance to celebrate the remarkable success of the HIV response over the past 15 years.

But it was also a stark wake-up call. Despite the tangible results – which include millions of lives saved – it is increasingly clear that to achieve the goal of ending the AIDS epidemic as a public health threat by 2030, the world needs to take the fight several steps further.

Accelerating progress across all infectious diseases

Dr Ren Minghui, Assistant Director-General for HIV/AIDS, Tuberculosis, Malaria and Neglected Tropical Diseases
WHO

The Sustainable Development Goals (SDGs), agreed last September at the United Nations in New York, offer an ample opportunity to accelerate progress across all infectious diseases. The focus on equity, health systems strengthening, universal health coverage, and multi-sectoral action will transform the way we tackle these diseases.

The SDGs build on the momentum generated during the Millennium Development Goals era, and on lessons learned during the first 15 years of this century. And they recognize that while the global response has significantly reduced the infectious disease burden and saved over 50 million lives, much more needs to be done.

In 2000, who would have thought that by 2015 the world could get 17 million people in low- and middle-income countries on antiretroviral treatment, reduce malaria mortality rates by 60% and cut tuberculosis (TB) deaths by 47%? Who would have predicted that, within the space of 15 years, it could bring down the number of guinea worm infections from over 75 000 to just 22? But it did.

What we have to do now is maintain our resolve and further intensify our efforts.

“More than anything, the next 5 years should be about creating solid foundations for ending the infectious disease epidemics everywhere. This is not a moment to lift our foot off the accelerator. These diseases are known for returning with a vengeance, if we ever slow down.”

Dr Ren Minghui, WHO Assistant Director-General for HIV/AIDS, Tuberculosis, Malaria and Neglected Tropical Diseases

Infectious diseases continue to have far-reaching impacts on people’s lives. In some of the poorest countries of the world, they continue to devastate economies and cripple health systems. Progress remains uneven and millions are not being reached with prevention measures and treatment.

From the outset, the fight against infectious diseases has been dogged by social, legal and economic barriers, and funding gaps have been significant. These are a major reason why HIV, TB, malaria, viral hepatitis and neglected tropical diseases (NTDs) still kill more than 4 million people every year.

Globally, 480 000 people develop multi-drug resistant TB each year, and drug resistance is starting to complicate the fight against HIV and malaria, as well. A coordinated effort to tackle this challenge – under the umbrella of the WHO global action plan on antimicrobial resistance – will be critical to success.

Global strategies on infectious diseases

To help countries deliver on their pledge to ‘end the epidemics’ by 2030, the World Health Assembly has adopted global strategies on HIV, TB, and malaria. This year, it passed the world’s first-ever global hepatitis strategy and set the first global hepatitis targets. Since 2012, a WHO roadmap has been available to guide global efforts on NTDs which affect over a billion people.

The strategies are backed up by a set of evidence-based guidance documents to help countries design and implement their own plans. They emphasize opportunities to maximize the impact of prevention, treatment and care services, and to mitigate the impact of biological challenges, such as drug and insecticide resistance, and climate change.

At the same time, WHO is working to help countries move closer to universal health coverage, by ensuring that all people have access to the health services they need, without being thrown into poverty as a result.

As well as establishing robust health financing systems, this means building up a qualified workforce and investing in efforts to improve the quality of treatments, diagnostics and prevention tools. It means assuring adequate supplies of affordable, safe and effective health products and putting an end to stock-outs. And it means joining up the dots: a greater integration of services, as we are already seeing in many places.

More than anything, the next 5 years should be about creating solid foundations for ending the infectious disease epidemics everywhere. This is not a moment to lift our foot off the accelerator. These diseases are known for returning with a vengeance, if we ever slow down.

This post was authored by Dr. Ren Mingui (WHO Assistant Director-General for HIV/AIDS, Tuberculosis, Malaria and Neglected Tropical Diseases) originally appeared as a commentary on the World Health Organisation website on 17th August 2016. Available at: http://www.who.int/mediacentre/commentaries/2016/Endemic-infectious-diseases-next-15-years/en/

Sampling Kibera chickens-a look at urban farming in its most innovative form

Jun 15, 2016 | Blog, Food Safety, Latest news, Poultry, Urban Zoo Project

Sampling Kibera chickens-a look at urban farming in its most innovative form

IMG_20160525_122708896 Under the Urban Zoo umbrella, we have been sampling chicken farms as well as chicken meat retailers in Kibera, Nairobi, in order to investigate the prevalence of a food-borne pathogen, Campylobacter. Kibera, said to be the largest urban slum in Africa, is a surprising, challenging and rewarding environment to work in. The constantly evolving environment illustrates urban farming in its most inventive form. Densely populated and very low-income, the urban landscape goes from shiny newly-built roads, public toilets and other community spaces, often sponsored by donors, to muddy alleyways with open sewers and precarious living spaces.

Livestock is part of everyday life. Goats roam everywhere – some even took a nap under our car – as well as chickens, ducks, and sometimes even camels. People are keen to discuss their farming arrangements and projects, or laugh at our interest for the local chickens (kienyeji kukus), which seem so uneventful to them. As sampling is ongoing, results for Campylobacter presence are not yet available. This bacteria, common in chickens, yet not harmful to them, can lead to severe diarrhoea in humans, especially children. Poultry in Kibera often sleep in houses; kids and chickens run alike in courtyards; we have found chicken-raising pens on a shelf, behind doors, above some roofs and in other unexpected places. With such a diverse interface between humans and chickens, it will be valuable to determine the presence of Campylobacter and better understand related public health risks.

Maud Carron

Article by Maud Carron

This blog entry is an article on our quarterly Urban Zoo Newsletter Volume 3 Issue 3 which can be accessed by clicking here.

Human, Food and Environmental data collection

Jun 15, 2016 | Blog, Emerging Diseases, Latest news, Research, Urban Zoo Project

Human, Food and Environmental data collection

Human, food and environmental data are among the wide range of data collected within the 99 households. The data are often collected by Clinical Officers. Human sampling involves among others, individual consenting to participate, questionnaire interviews administration, general physical examination and anthropometric measurements, biological data collection and offering feedback and health education on the outcome of the laboratory based investigations. Two sets of structured questionnaires are administered; a general household and individual participant questionnaires. Biological data that is collected includes fecal samples and nasal swabs. Fecal samples are assessed for E. coli and campylobacter bacteria while nasal swabs are assessed for antimicrobial resistance. Collection and transportation of human samples from the field to laboratories involves sterile techniques.

Like human sampling, sterile steps are also observed during food and environmental data collection. Only livestock sourced foods are collected in the study. A sample of meat, milk and a wipe of egg shells if available, are collected. Sterile wipes of kitchen working surfaces such as chopping boards as well as kitchen door knobs are also collected. Environmental samples are collected using sterile boot socks. Normal saline-wet boot socks are worn and environmental samples collected by walking around the area surrounding the household as well as surfaces within livestock pens if available. Whirl pack bags are used in transportation of environmental samples. Water samples from water puddles, boreholes or storage water tanks are also collected as environmental samples. Subsamples of food and environmental samples are marked with a red dot to identify those going for whole genome sequencing and a blue dot on those being analyzed for campylobacter. All collected data are de-identified using barcode numbers to enhance participant and sample anonymity.

On completion of data collection, participants in the household are either given Albendazole or Mebendazole anthelminthic depending on age. Anyone found to be clinically ill is offered a prescription. If they are seriously ill a written referral letter to the nearest and most preferred health facility for further management is offered. Laboratory outcomes are communicated back to individual participants within two to three weeks of data collection. This is accompanied by health education with emphasis on how to maintain proper hygiene as well as interaction with livestock. Like many other community studies, our study is not devoid of challenges. Some of the challenges encountered involve heavy traffic. As investigators, we have to sometimes anticipate early morning starts. Participants which means rescheduling the day to collect data. Others include withdrawal from participation and inability to access household heads especially in high income settings.

Laureen Alumasa Fredrick Amanya

Article by Lorren Alumasa & Amanya Fredrick

This blog entry is an article on our quarterly Urban Zoo Newsletter Volume 3 Issue 3 which can be accessed by clicking here.

Update: 99 Households study: wildlife component

Jun 15, 2016 | Blog, Latest news, Research, Urban Zoo Project, Zoonotic Diseases

Update: 99 Households study: wildlife component

Wildlife 2 As we approach the final quarter of the 99 household study, it is a pleasure to be asked to reflect on the wildlife sampling component of this study. The wildlife sampling team has come a long way since its inception in September 2015, when we were all relative novices in trapping Nairobi’s diverse array of wildlife species. We have had some long days and sleepless nights, but to their credit, the enthusiasm of those involved has never waivered.

A typical day for the wildlife team starts at 5am, when we embark on bird sampling. To ensure we follow best practice for all of our trapping we collaborate with experts at the National Museums of Kenya, and in the mornings Titus Imboma (an ornithologist from the museums) helps us set up an array of mist nets, aimed at trapping birds as they fly in proximity to the household and livestock-keeping areas of each compound. Once caught, each bird is placed in a paper bag to collect a faecal sample, before a number of other body measurements and biological samples are collected. Such opportunistic sampling is a common philosophy among wildlife Table 1-Taxa disease ecologists, and additional samples provide an important resource for future epidemiological work. We next check the rodent traps – we use live-capture Sherman traps which are set throughout the house, livestock-keeping facilities and the household compound. Any rodents that we catch are transported back to the lab at ILRI, where they are humanely euthanized and subjected to a post-mortem examination (PME). This procedure is used to permit the collection of fresh faeces and organ samples which are stored frozen and in formalin. The latter ensures that tissues from these animals are preserved for histopathological interpretation, should the need arise in the future. As dusk settles over Nairobi, the sampling team heads back to the house to trap bats.

The techniques used to trap bats are vey similar to those for birds; very fine mist nets are suspended between fly-ways where bats seek their food (either insects or fruit depending on the species of bat). Due to their propensity to bite, bats present a challenge to remove from the nets and restrain during sampling, but with the appropriate techniques and equipment (i.e. tough gloves!) they can be safely held to collect measurements and samples. We sacrifice a maximum of two bats each night, which are taken back to the lab at ILRI for PME. The rest are sampled live, and released Wildlife 4 unharmed. When we encounter a bird or bat roost, we use tarpaulins spread underneath the roost in order to collect pooled faecal samples representative of the individual animals using the roost.

Something that has become evident as we move from house-to-house, navigating Nairobi’s maze of leafy suburbs, high-rise apartments and river-side slums, is the shear diversity of wildlife habitat present in this city. This is reflected in the number of species (birds, rodents, bats, primates and carnivores) we have sampled to date (see table 1). All of these species inhabit different ecological niches which likely govern their levels of interaction with humans and livestock; as an example one would expect very different levels of interaction between house rats that scavenge on animal feed and sunbirds that rely on nectar. How this translates to the risk of disease transmission is something we hope to shed light on by studying the genetic diversity of E. coli in these wildlife, and comparing it to those from humans, livestock and the
environment.

James Hassell

Article By James Hassell

This blog entry is an article on our quarterly Urban Zoo Newsletter Volume 3 Issue 3 which can be accessed by clicking here.

Update: 99 Household study update

Jun 15, 2016 | Blog, Emerging Diseases, Latest news, Research, Urban Zoo Project

Update: 99 Household study update

Well, time has flown since we sampled the first household in the 99 households study. On 7th June we visited our 66^th household, meaning that after 8 months we are now two thirds of the way through. The project is taking us to all parts of Nairobi, as the maps illustrate. The field teams normally spend Monday to Wednesday collecting data, then use Thursdays and Fridays to recruit new households to the study, meet with local chiefs and county officials, give feedback to participants and keep on top of all the other jobs, such as vehicle maintenance, stock-keeping, accounting and paperwork. The wildlife team regularly go out on evenings and weekends to set and check traps for rodents and bats (who inconveniently refuse to venture out during normal working hours!) In some areas it has occasionally been necessary to conduct the study interviews in the evening, when participants return from work. Having to be flexible to fit around our human and animal participants’ needs, plus the perennial problem of Nairobi traffic, means early starts and long days.

The laboratory teams also come in for their share of hard work. Even with motorbike couriers, samples normally do not arrive at the labs until the afternoon, especially when large households are sampled. To process all these samples takes time. Each sample is first incubated in an enrichment broth, then undergoes two rounds of purification on a special type of agar which selects for E. coli, before being cultured on a more general agar prior to freezing the bacteria for storage. As you may imagine, this is several days’ work – each step takes at least 24 hours – and of course the bacteria don’t stop growing at weekends! Timing of steps is crucial, to ensure that pure colonies can be selected for storage. Later on, batches of isolates are revived and a number of biochemical tests are performed, to check that the bacteria we send to the UK for sequencing really are the E. coli that we are interested in. Once we are reasonably sure that what we have is an E. coli, they have to be regrown once more so that they can be sent to ILRI, where the DNA is extracted to send to the sequencing facility at Oxford.

So as you might imagine, it is extremely gratifying to finally start to see some of the results of all this hard work. Dr. Melissa Ward recently visited the teams in Nairobi and brought with her some of the first outputs of the sequencing to show us. In return, we took her along to see the sampling in action, in one of the slum sites. Melissa said, “It really brings the project to life, to see exactly how all the data and the samples are collected. Now, when I sit at my computer, I can really understand where it’s all coming from.” For us, it was equally exciting to get some tantalising glimpses of what the final dataset might look like and what kind of patterns we may be able to identify from the phylogenetic structure and genomic data. We’re not giving anything away at this stage – but we can tell you that we definitely have E. coli – and lots of it!

Article by Judy Bettridge