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U.S. Department of Health and Human Services

Animal & Veterinary

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Challenges of Surveillance of Antimicrobial Resistance in Kenya by Samuel Kariuki, M.Sc., Ph.D.

DR. KARIUKI: Thank you very much particularly to the organizers for the opportunity to present some of the overviews about what we are doing in our efforts to try and initiate some effort to surveillance. That is our main concern in Nairobi, at the Medical Microbology Institute.


And what I plan to do is take you through an overview of some of the challenges we have in developing countries, trying to initiate meaningful surveillance for both usage and resistance. And particularly in Kenya where I’m based infrastructure and sanitation come under heavy challenges particularly do to increasing population pressure and obviously foodborne pathogens become an issue of major public health importance.

Some of the challenges include Staphylococci food poisoning, Salmonella, Bacillus cereus, infections --- infections. Also plant poisoning, particularly when we have heavy rains and it’s time for harvesting, cassava poisoning, aflatoxicosis are major issues.


There are a few infectious diseases are officially under some surveillance by the Ministry of Public Health and Sanitation. And -- initially we have public health officers stationed at district hospitals. And what they do is to have syndromic diagnosis for either typhoid or dysentery or cholera outbreaks. And then they report these to the central government, the Central Ministry of Health.


And most of the cases are either through syndromic diagnosis or through self-reporting. And those are institutional reporting for example from boarding schools outbreaks, refugee camps, or prisons or so forth.

Sometimes through the National Public Health Laboratories we are able to obtain some of the samples from the outbreak areas and then we analyze these and feedback the information and data to the National Public Health laboratories and the disease surveillance unit within the Ministry of Health.

However, the majority of the cases particularly in very remote sites in the country obviously do not report for either medical treatment or go unrecognized. So some of these really fall out of the way and we cannot document them.


What I want to do is take you through some retrospective data, just to highlight some of the main issues that we face in developing country, kind of a ---. And as I say food poisoning, the cases, most of which are being done most either through patients coming in and through syndromic analysis of cases. And in this particular recent data that I got from the Ministries of Public Health and Sanitation, can see that setphococci food poisoning particularly around informal setting, informal --- is a quite a major issue. But we do also have other issues of chemical poisoning, botulism and so forth.


This is another instance of again cases of food poisoning due to S. aureus, Salmonella. We had very recently a large outbreak of anthrax in the northern part of Kenya. Where a whole village ate meat that was uninspected. So these are just the highlights of cases that may go to the Ministry of Health and obtain in times of surveillance that is available.


I will go through a few slides to show you some of our efforts, particularly at the Kenya Medical Research Institute to try and augment the efforts by the Ministry of Public Health and Sanitation to add -- trying to understand the -- trying to understand particularly the effects of antimicrobial resistance in various sentinel sites that we do our studies.


And these are studies that we carried out mainly at DSS site in the coast region of Kenya in Kilifi where the local trend has been dream work -- both in malaria and other infectious diseases particularly Blackbone infections for the last 15 years or so. And also in Nairobi, where we base our work mainly at the National Referral Hospital.

And as you can see this data between 1998 and 2006 shows -- this is particularly S. typhimurium where they raise specific serotype and very specific sequence type, 3-1-3 that is highly invasive and causing epidemics both in Kenya in Minoui, and extremely high levels of resistance are commonly available antimicrobials.


But the case has not always been really --- in some instances, for example this is data from Kilifi, which is a rural DSS site down at the coast where we followed antimicrobial resistance over a 10 year period. And due to interventions, particularly the provision of adequate health for all the children who report with bacteria in the hospital, we have found that over the last 10 years when we observed these cases, the resistance was actually decreasing for quite a number of antibiotics that are commonly available. Again emphasizing that interventions do work. And can revise the trends of antibiotic resistance.


And during the course of our sentinel surveillance we have also looked a the data from animals. And while I do not want to put some blame on who is -- who are the source of resistance, again we see here that Salmonella, non-typhi Salmonella here, from animals, particularly from cattle and pigs, very low levels of resistance to commonly used antibiotics.

And this is data again over the same period when we studied isolates from humans. And suffice it to say that these isolates are most species were either --- or Campylobacter and a few Typhimurium. And we did --- and this is not published we were observed that they are fairly unique serotypes and fairly unique genotypes within the animal population.


We have also been able to follow up cases typhoid outbreaks. As you know typhoid is endemic in most countries in --- Africa. And in this four, four and a half year period of surveillance we were able to show that very small percent of isolates were fully sensitive to all drugs that were commonly available.

And of importance here is the extremely high levels of multi-drug resistance, S. typhi. And this is again one of the clones that is in circulation particularly in that east African region, --- 58 that is commonly also isolated in Southeast Asia. And as you can see again, extremely high levels of resistance to commonly available antibiotics.


And just to reemphasis again, the high levels of MICs for commonly used antibiotics, just to show you the trends over time.


And again a special note here is the --- resistance to the quinolones, this non-MBR strains, if you see the MICs for --- and you compare with MBR typhi they are four times higher and almost 20 times higher for the ciproxin. Of course which is the drug of choice for the treatment of multi-drug resistance, S. typhi.


And we have also through our central sentinel sites been able to look at trends in E. coli from children in the area. Again, very similar trends in resistance to commonly used antibiotics. And when we compare these with similar isolates from homes of children where we obtained the isolates, we find that the chicken isolates had very low levels of resistance but you can see these notable high level therefore on ampicillin, and tetracycline here. And it does not surprise me because most farmers use tetracycline in watering their chickens.

So, as a whole I think what we have shown here is the fact that we are observing quite a lot of resistance to commonly used antibiotics for quite a number of isolates from both area and --- but apart from that the Minister of Health and the Ministry of Public Health and Sanitation has put an effort particularly through non-government organizations to try and drive particularly issues of usage and present usage through, particularly through pharmaceuticals and also through universities.

We are locating through universities particularly continue the curriculum for medical students to understand the -- what preventive use of antibiotics is and the Department of Pharmacy particularly is very, very keen that the curriculum be developed to integrate usage antimicrobial resistance surveillance be in the curriculum for medical students.

So, with that I will really welcome any suggestions, any efforts to be able to improve surveillance in Kenya. And I would like also to mention that through the Global Food Network we have pilot studies that are beginning fairly soon, we’re looking at integrated surveillance of -- integrated surveillance of resistance to foodborne --- from meat samples from slaughter houses and tracking these down to retail centers, the retail outlets, and then again to homes of people who consume these meats and being able to track down the resistance.

So, we have made some efforts and we hope that these efforts will bear some fruits in persuading the government to realize the importance of -- including surveillance as part of the Ministry of Health agenda for the whole country. Thank you very much.


DR. CARATTOLI: Thank you very much for this interesting presentation. Any question from the audience.

I have one, during the last meeting on antimicrobial resistance and pathogens as organized in Canada and last month how have different use from animals from Africa for --- for instance, I know you have a -- data on chickens in of 2000 or so. This light, and maybe this --- is much more difficult, especially for ciprofloxacin and --- so that of really impressive prevalence. So maybe entire Africa situation is really far to be know I guess on this respect and should be updated, because maybe it changed a lot.

DR. KARIUKI: I agree with you. There is still a lot of be done because most of this data is from sentinel surveillance and what we need is to probably have more coordinated surveillance system that can be either national and also regional, so that we gather more data that actually shows clear trends in both animals and human medicine.

So, there is still -- this is a very modest efforts. And persuading particularly governments in developing countries, to apportion budgets, to be able to do surveillance work is extremely difficult. So that’s why I’m so grateful to Debby Cho and the Welcome Trust for funding this kind of sentinel surveillance to ascertain at least some data to show us some trends.

So, as situations change, I’m sure, probably a few years down the line, we may find that there is a change in usage patterns, for animals, but this needs to be monitored over time.

DR. CARATTOLI: And also from your data I was impressed for the 28 percent of resistance to augmentin in your Salmonella from humans, from five percent to ceftazidime, so -- this could be considered relevant for Salmonella isolates from your own cases. It should be increased and sustained also, this kind of surveillance.

DR. KARIUKI: Thank you.

DR. CHILLER: And Sam, I have one question. I think one of the most interesting things that I found working with you and others in Africa, Karen Ketty, is that there seems to be this phenomena of these very invasive Salmonella, like the outbreak or the sort of epidemic in South Africa, the Songi, they are highly resistant, that seem to be more hospital associated, in those in commingle in nature.

And so there’s clearly the -- and then there is also going to be the foodborne pathogens as well, but there seems almost to be two phenomena.

And I’m wondering are you, because I don’t know in Kenya if -- but I know that it seems like these are ---, these are bloodstream isolates, for the most part, right, these weren’t stool isolates, so these are sick, invasive -- do you also feel that maybe some of the isolates you’re showing us are more part of this sort of nosocomial MDR type Salmonella that we’re seeing in humans in Africa and maybe not so much food associated, per se. I’m just interested in your thoughts on that.

DR. KARIUKI: Thank you, Tom, for that excellent question. And clearly what we’ve seen and documented is that the sequence type 3-1-3, S. typhimurium after full gene sequencing, when we are fully sequenced now that the five strains through help from the --- Institute in Cambridge, U.K., is that this particular strain hasn’t shed a lot of its genes and some of the genes are actually metabolic genes. And it’s tending towards becoming more host adopted. And actually almost becoming like typhi, S. typhimurium. This is the new phenomena we are observing with S. typhimurium.

And it’s becoming --- but becoming less adopted to animals resistance but more to human resistance. It is multi-drug resistant, highly invasive. And predominantly causing extremely invasive infectious, viral infections in children less than five years of age, who are particularly immune suppressed either malnutrition, sickle-cell anemia, or HIV.

And this is something that we have shown in both Kenya studies, also in --- studies that this very, very specific strain type, sequence 3-1-3, is likely in the coming years to become more and more like S. typhi.

And that -- the findings should be interesting is the fact that this -- the strain itself past other non-typhi Salmonella serotypes, have dramatically reduced and this is work that has already been published in the last two months, in the ---, with the reduction in the free --- malaria, particularly the endemic areas of the coastal Kenya. Malaria has declined drastically in the last 15 years. And with that we see very, very few cases on this --- non-typhi Salmonella particularly in the coastal regions that are watched closely with incidents, high incidents of malaria.

But this is not the case when you go to the highlands, which tells us of course there is close relationship between malaria incidents and the occurrence of invasive non-typhi Salmonella.

So, as a whole I think in -- the epidemiology of MTS seems slightly different from what we know as a purely foodborne pathogen in this situation.

DR. CARATTOLI: Thank you so much. Danilo Lo Fo Wong now again. Thank you. And the WHO activities to build laboratory surveillance around the world. That we need so much it seems.