Salmonella/My Soul Mate


I started doing microbiology so that I could avoid people. I did not think of myself as a people person. I was a bacteria person. I loved to stay in the laboratory as far away from people as possible…..bacteria are so much calmer and more peaceful!! However, I slowly found out that the laboratory is not the only place we find these tiny calm. Though I did not like interacting with people a lot, I am interested in health; what makes people sick? What makes them well? And, What makes our bodies react the way they do to foreign particles? The calm creatures (bacteria), being one such foreign particle.

In order to answer some of these questions, continue getting my work funded (so that I could survive within the laboratory!!) I decided to do a PhD!! After many applications, meeting of supervisors, mentors and numerous professors, I decided to do the degree from Oxford University (me having been lucky enough to be accepted by this most respectable institution). The study would look at epidemiology of enteric fever, i.e. how much of the disease there is in the community, how it is spread and how it can be controlled. Enteric fever includes both typhoid and paratyphoid fever, and for the four years of my life while doing the PhD, Salmonella Typhi and Salmonella Paratyphi A became my soul-mates.


As part of the study I had to go out into ‘the field’ (researchers call everything outside the hospital, lab or university the field). I was not too happy about this fact but my soul-mates apparently loved to live in water and could even survive in food if it had high water content!! So, for four years, wherever I could find my soul-mates, I looked…….blood, water and food……….in the hospital, in the community, I even went to households asking for water so that I could find more of them. I did such a thorough job of looking for these soul-mates of mine that I even mapped the houses where they came from (Tracking them using Global Positioning Satellites (GPS) This way, I would know where they were from when I saw them and their relatives again in the laboratory. I was obsessed with this relationship I guess! However, at the end of the day, the obsession and using these new research methods paid off. There were some pretty big findings! We saw:

  • A lot of the enteric fever (fever with stomach problem) cases coming to Patan hospital over four years.

  • We saw that this was caused by two kinds of Salmonella bacteria called S. Typhi and S. Paratyphi.

  • More people got sick during rainy season.

  • We thought that this would be worse in places where there was the highest density of people but we did not find this. Most infected people were coming from Lalitpur Sub Metropolitan City (LSMC).

Younger people (school age) seemed to be affected with S. Typhi whereas it wsa adolescent males who seemed to be affected by S. Paratyphi A.


This left us with two big questions. Why was disease incidence not linked to population density within LSMC? The findings were weird….. in nearly all other studies we see that the more the people within a limited space…the more the disease with people passing it directly from person to person.

And also, why were so many young men getting sick? …I had a few ideas,. Maybe young people go out more for work or college and eat out more! Maybe young people eat or drink something in particular that was making them sick... But, then why males more than females?

What do you think? What is different in the lifestyle and behaviour of young men to young women that might make them more susceptible to falling ill from disease in water?


My favorite hypothesis (which still needs to be tested) is: That there are more young males coming to the Kathmandu valley from remote areas for work and higher education. This population has a ‘naïve’ immune system, one which has not build but resistance to the things people in Kathmandu are exposed to from a young age, and it is this that makes them more prone to getting enteric fever compared to the local people. .

Our findings only provide a snapshot in time into the patterns of enteric fever in Kathmandu. The uneven distribution of enteric fever patients within the population suggests that certain things cause a bigger risk of catching disease such as drinking water contaminated by the bacteria.

This was the first study….

We still needed to understand how typhoid is transmitted through Patan itself and through the people of Patan. I took a novel research approach for Nepal called, a ‘longitudinal spatial case control study’ This means that we collected and looked at lots of different water sources across different sited over one whole year. I needed to know exactly how different bacteria were related to each other at each site and could understand this by looking at their genes. Close relatives have a similar kinds of patterns in their genetic code just like you do with your relatives. If I looked at this information and used their satellite positioning, I could see how and where bacteria multiplied and moved to (I mapped and tagged them obsessively)….and found out that:

  • Big clusters of typhoid occur whether or not there is a big population people living close to one another.

  • Lots of different genotypes (or families) of typhoid can be living together in clusters. Even within one human household. This means that some of the bacteria came from lots of different sources not just one type multiplying in the same place.

  • This was the first study to every show this and was completely unexpected. Enteric fever, was thought to happen through direct transmission (from one human to another). Polite, calm things we thought they were I assumed they would introduce themselves only once they were introduced to the household and then stay in that one household….(I imagined they were very polite like the British)………however, our study suggests that they are more like Nepalese…….running helter skelter all over the neighbourhood, entering whichever household they fancied!)

  • Furthermore, the study detected S. Typhi and S. Paratyphi A in water supplies and found that typhoid especially prevalent at public water sources (the ancient stone spouts we see around old Patan) and low elevation.

This was a useful finding……..both my bacteria friends, Typhi and Paratyphi A love water, but it was people who lived closed to stone spouts at lower elevations seemed to get more sick with enteric fever compared to those who lived next to spouts at higher elevation.


Why do you think that there might be more bacteria in the stone spout water at lower elevations than higher elevations?


It used to be the opposite way around! The lower the water the cleaner it was because it was filtered more through the soils and sand the further it flowed.


Figure 1: Samples of water from the 10 locations investigated in the research study

The water in the first vial is the first water from a spout after the monsoon has started. Its black because of human excrement. People say that the water runs this colour for three weeks from the start of the monsoon. Still some say that they will leave it to settle and will drink it.


Our hypothesis has not been proven links us to politics and recent history. The recent breakdown in infrastructure Kathmandu faced during the civil unrest of the 90s and mid 2000s means that water and sewerage pipes laid close to each other have not been maintained. As water flows down get intermingled with the sewage pipes and /or other contamination sources thereby making water at lower elevations more contaminated than that at higher elevations. And you can guess what it is contaminated with! Yes, human excrement…Poo!

These findings have implications for typhoid-control strategies as well as other diseases that live in water.

Next….We wanted to further test our theory that transmission was not just from one human to another but through something else...like water. We also wanted to understand what was happening in the municipal piped drinking water (rather than the public stone spouts) and so water samples were collected from 10 water sources weekly for one year. That’s every week for 56 weeks. We then analyzed the water…never before has water been so closely examined. We looked at whether certain chemicals were in the water, we looked at which bacteria lived in it and we looked at the DNA of the bacteria so that we could see family lines.

We found that:

  • Kathmandu municipal drinking water (in the government pipe systems) was found to have faecal contamination (contamination by human excrement…or…poo!) and this is WAY above what the international WHO guidelines for acceptable levels!

  • What is more, this got worse when it rained. When it rained we saw more faecal contamination and along with it more Typhi and Paratyphi A so we think that rain is a key driver of the problem.

  • The chemical composition of water was different at all the sites, which suggested that it was something happening locally that was causing the contamination…


It seems that sewerage is getting into the water pipes locally, being washed in more easily when there is more rain. So we have a bit more of an idea about what might be happening with a relationship between rainfall and sewerage pollution and typhoid bacteria in the water system.


But the mysteries do not end there!:

One more weird thing we found was that we knew that there was bacteria in the water we sampled because we were able to identify their DNA in the water samples throughout the year but despite this, we were not able to grow the Typhi and Paratyphi from the water that we collected. It should have been easy!

Also, if the bacteria is present throughout the year, why do we see a spike in the number of cases only during the monsoons? One of our early theories was that maybe there is just more bacteria in the water during monsoon, but this was not the case, we were able to count the number of bacteria by looking at the amount of Typhoid DNA in water samples and it was high whether or not it was monsoon.

So what was it about monsoon that is causing more sick people? Its not that there is more bacteria in the water. Something else is contributing…

From the data we have we know that the municipal water in Kathmandu is a predominant vehicle for the transmission of S. Typhi and S. Paratyphi A. This study represents the first extensive investigation of water pollution in a place where typhoid fever is found and implicates locally dumped human waste as the major contributor to poor water quality in the Patan and probably the rest of the Kathmandu Valley.

Basically our research at the end left us with some major questions. Here is a recap of what they are. If you live in the area you probably have some ideas. What do you think?

  • Why can’t Salmonella be grown from the water though they are definitely there?

  • If Salmonella are always there in the water, why do we see a rise of illness only during monsoons?

  • Why do some people get sick but not others within the same household/neighbourhood/community?

  • Why are adolescent males are disproportionately affected?

  • If we clean up the available drinking water will it affect the incidence of diarrhea in the community? How can this be done? Perhaps through filters?



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