Article published on 12 January 2024
last modification on 8 May 2024

The XIX century was the century of the industrial revolution, but also that of the scientific revolution with microbiology being one of the foremost scientific advances of the time. While complementing each other’s scientific works and discoveries, Louis Pasteur (1822-1895) and his German counterpart Robert Koch (1843-1910) are the founding fathers of microbiology. Once they had been drawn into the sphere of influence of Pasteur’s doctrine, scientists from different countries started to "track down micro-organisms". Whenever they heard of the breakout of an epidemic in a country, they would rush to it. Most of the time it was in an insalubrious and inhospitable tropical country, but this poor reputation had much more to do with the infectious peril than with the characteristics of the climate. It is nevertheless a fact that several scientific researchers who were either physicians or pharmacists ruined their health or lost their life, linking their fate through disease and death with that of native populations.

At this particular point in time France had an advantage over other countries : it had its Colonial Army Medical Corps which was ready to take part in this competition. This Corps was used to implementing military rules of obedience, it was financially supported by the French government which provided a budget allocation. Its medical personnel were scattered across this new colonial domain in the very places where these epidemics were raging. This medical corps together with the Pasteurian Institute schools where young personnel were taught an up-to-date training and a cutting edge technology, can claim the discovery of micro-organisms and thereafter the development of serological tests, of therapeutic sera and of vaccines against the diseases which are caused by them.

Within a few decades the gigantic scientific international to-ings and fro-ings which followed, resulted in making possible the identification of pathogens responsible for nearly all infectious diseases which were then known, and also in figuring out how they were transmitted, and how they could possibly be prevented or treated.



At first the identification of a disease is made through its typical clinical symptoms. Discovering its causative agent and its routes of transmission to healthy individuals is usually a long term job. In the ancient times, infectious diseases were thought to be due to mystical reasons : either Heaven inflicted castigation or evil spells. Later on came the time of mythical causes : miasmas and humours. It was not before the dawn of Pasteur’s era that they could be scientifically explained. Advantage was then taken of the renovated scientific way of thinking and of the methods of scientific research which had been initiated by Claude Bernard (1813-1878), undisputed founder of experimental medical science.

During the 17th century A. Van Leewenhoek invented the microscope and in 1878 Sedillot created the word "microbe" for the designation of all living creatures which could not be seen without the help of this device. The word received the approval of Littré, a French language expert and also of Pasteur. With a microscope "infinitely small" creatures could be seen but circumstances which made them appear, and also their role, remained unknown. Over two hundred years the "spontaneous generation theory" had been supported by official coteries and these micro-organisms were not thought to be harmful.

After studying fermentations Louis Pasteur (1822-1895) became convinced that these transformations were due to specific micro-organisms which originated from pre-existing ones. This became known as "the theory of germs".

With the discovery and demonstration of the deleterious role of microbes, of how they proliferate and what were the body’s defence reactions, Pasteur triggered in medical science such a sudden and profound upheaval that the resulting breakthrough is well worth the name of revolution which warrants his being designated as "Mankind’s benefactor". These successful achievements were followed in 1888 by the foundation in Paris of an Institute which at first was dedicated to the preventive treatment of rabies. Pasteur remained at the head of this institution until his death.

Robert Koch (1843-1910) is another founding father of medical micro-biology. Unlike his elder French counterpart, this German scientist was a well travelled MD. After having discontinued his medical practice, he became interested in the new scientific field of micro-biology. As the advisor of his country’s government he was commissioned to go to Egypt, Cameroon, India, Java, New Guinea and so on. Among the bacteria he discovered, two are of a worldwide interest : the tuberculosis bacillus (1882) and the cholera vibrio (1883). He also studied numerous diseases such as Anthrax, Malaria and Amoebiasis.

Koch was a remarkable leader for his followers. In 1891 he was appointed Director of Berlin Institute of Infectious Diseases which is now named after him. He was awarded the Nobel Prize in 1905.


Once they were back home after a long journey to some remote places, European travellers expressed the feeling they had of having come across miserable and unhealthy populations. Upon returning from tropical Africa in 1846, a French explorer named A. Raffenel put the following in writing : "Once I started to hit the trail I could not go through a village without being shown patients afflicted with desperate conditions such as lepers, patients with total ophthalmias, with chronic elephantiasis or with dropsy...".

Highly respected medical authorities upheld the scare and emphasized the dangers of undertaking an adventurous tropical expedition. In 1875 back from Congo where everyone had been impressed by the extensive range of his knowledge, Mahé, Professor of Medicine at the Naval Medical Academy in Brest told his students : "On the stinking shores of the Atlantic Ocean you will meet the sphinx of malaria which should inspire awe and which constitutes a pernicious protean condition, ghost of typhus, the ashen and frosty specter of cholera, and the icteric mask of vomito negro. Watch out ! there is there a poisonous breeze which rises there from earth and water".

Commemorative plate at the Pharo

Still, in 1931 one could read in a magazine named "L’Echo de Paris" : "The very fact that someone was going to the outback in Africa or in Indochina after leaving the homeland, conveyed the idea that there was something he could be remorseful for. No one could understand why a smart and active young man could be foolish enough to show his contempt for good and quiet positions in the civil service and why he would rather live in the tropics where some pernicious fevers could possibly be caught and where he would certainly also get in cahoots with coloured persons".

Mentioning the detrimental effects of hot climates which were found there, or the threat of miasmas and of deleterious principles was absolutely not a deterrent for some strong minded individuals and in fact it was the other way around ! Many were willing to work in these countries with the prospect of helping native populations to achieve better health and living standards. Tribute should be paid among those who were ready to engage in a colonial adventure, to French Naval Officers and to Medical Officers of the Colonial Army Medical Corps dubbed "La Coloniale" who went overseas. As far as Pasteur’s Institute colonial trainees were concerned they could not help dreaming of epidemics to confront.

Still, good health and even life remained in danger overseas. Up to 1960, it was quite impossible to keep working there without having some day an attack of malaria or dysentery. During the 19th century, by the very dramatic times of large epidemics, French colonization was accompanied by the death of a large number of colonists with among them a lot of physicians and pharmacists of the military. The names of those who died in the line of duty are engraved on a commemorative plaque which is displayed on a wall of the Pharo Institute in Marseilles. The largest loss of lives happened during a yellow fever epidemic which occurred in Senegal in 1878. With thirty physicians and pharmacists on duty there, twenty one of them were victims of this epidemic and passed away in Gorée and St Louis. Other pestilential diseases are responsible for other fatalities such as cholera for Guichoux*, plague for Mesny* in 1911, and Bourret* in 1917 and trypanosomiasis for Le Hir* in 1932. Once they had already returned to France a number of them died in the aftermath of a disease which they had caught overseas, but there is no possible assessment of this figure as sometimes their death happened years after they were back and Jamot* is an illustrious example for that. Wives and children also paid a heavy toll to these climates.

Preparation of the virus vaccine (Tannanarive Pasteur Institute 1900)

The British contended that to carry on the ruling of these countries three governors were needed : one in a coffin on board a ship bound back for the UK before being laid to rest, the second one effectively in charge and the third one on his way to take over as the second one was likely to get sick very shortly.

The mortality rate of Europeans living there, provides a good evidence of the risk which was taken : during a three year period of time from 1907 to 1910 among the five hundred of them who were on active duty, thirty two physicians and pharmacists of the Colonial Medical Corps died. In a cohort of men aged 25 to 55, these numbers speak for themselves.

Today millions take advantage of the advances of modern science over ignorance and these accomplishments make a change for the quality of life in these countries, where many tourists can go now without putting their lives at unacceptable risk.


France was the only country with an organized formation, the Colonial Medical Corps, ready to fight these epidemics, which had been set up, organized, headed, fostered and counselled by the founders of Microbiology, namely Pasteur and those who succeeded him. Pasteur was not a physician and his ideas were not unanimously accepted by the medical establishment. In 1864, it was the Academy of Science and not the National Academy of Medicine, which was the one to acknowledge officially that he was right and to substitute the "theory of germs" to the one of "spontaneous generation".

A new impetus was given to microbiology but there were also some backlashes well until 1870. Right away physicians of the Military Medical Corps, who did not belong to any medical coterie, joined Pasteur and they cooperated with him. Among them Calmette*, P.L. Simond*, Marchoux*, trained with him and signed up for the Colonial Medical Corps upon its inception in 1890.

Some other students of Pasteur such as Yersin* joined them. The scope of research was then widened and included the whole range of infectious diseases and with Pasteur’s former trainees scattered across the world, Overseas Pasteur Institutes were founded. Working together with the Main Institute in Paris they were assigned to discover new microbes so that the whole of mankind could take advantage of the advances of the new microbiological science.

Daily testing of rats caught in town (Pasteur Institute, Antananarivo 1900)
Émile ROUX

They were all servicemen of the Colonial Army Medical Corps which was financed and supported by the budget from France. Moreover inside this Corps, these men had the opportunity of renewing former ties of friendship when they happened to come across their former buddies of the "Ecole de Santé Navale" or of the "Pharo Institute" who had been their fellow students in medical school or for some of them, their fellow trainees in the Pasteur Institute. As a result, there was a feeling of solidarity between them which helped when it came to carrying out as a team a fantastic and fruitful work. Exchanges between physicians who were posted in the outback (bush doctors) and biologists in Pasteur Institutes were going both ways with one giving and the other receiving and vice versa. This, most of the time was done while having the feeling of belonging to a friendly confraternity.

Most servicemen of the Colonial Medical Corps who trained at the Pasteur’s Institute had started their career with one or two tours of duty in medical posts in the outback before having the opportunity of specializing in the field of biology. In 1903 there was an agreement between the Colonial Army Medical Corps and the Pasteur Institute which provided that "micro-biologists" of the corps were accepted as trainees at the Pasteur Institute where they attended Dr Roux’s Complete Course of Bacteriology.

Later on some of them, happened to be the founders of fifteen Overseas Pasteur Institutes. Several of them came back to the Main Institute and were assigned to important positions at the head of scientific departments or at the Institute Management Department.

No other country had such an instrument of scientific research. After the death of Pasteur, the collecting of a considerable amount of data was carried on which included : The discovery of microbes and parasites and the identification of epidemiological chains, some laboratory tests were developed which ascertained the diagnosis of some conditions or led to a presumable diagnosis for some others, the development of vaccines, of therapeutic sera, of specific medications, as well as the discovery and the working out of methods of prevention of infectious diseases for individuals or communities.

The work which was done about plague is a good example of an exclusively French achievement as a few physicians of the Colonial Army Medical Corps are responsible for finding the links between the bacterium which Yersin* had found and the animal reservoir. P.L. Simond* gave evidence of the fact that after biting an infected rat the flea can transmit the disease through a bite to a healthy human being. Girard* and Robic* were the developers of the plague vaccine.

Breeding rats


By the end of the 19th century the United Kingdom was the other big colonial power of the time and commissioned teams of scientists to go to colonies it was ruling. Some other competitors showed up : Germany, the United States, Russia, Italy, Belgium etc…, and Japan as well.

The competition which followed was a tough one. Then, diseases which now are encountered in the tropics only, struck well beyond those latitudes and occurred at the time in much colder places. The Leprosy Bacillus was discovered in Norway and the parasite responsible for amoebiasis in St Petersburg. We can talk of an "international mobilisation". As soon as they would hear of an epidemic outbreak in some place, scientists and their expeditions would rush there, even if they had to go to the antipodes… but of course at the transportation pace of the time. One can easily find numerous examples of that.

In 1882 cholera was raging in Egypt : Koch, who was German was competing with Thuillier, a French scientist who died after he had caught the disease. Koch attended his funeral and the following year discovered Vibrio Cholerae in Alexandria.

In 1894 plague was present in Hong Kong. Kitasano, a former Japanese student of Koch’s, was at odds with his challenger the French Yersin* as both wanted to be the only one to get buboes which had been taken from corpses of patients who had deceased from bubonic plague. Kitasano thought he was the winner with the discovery of a micro-organism which was not in fact the one involved in the disease but his challenger later found the real plague bacillus.

In 1881 yellow Fever was present in tropical America and Carlos Finlay, a Cuban, took into consideration a previous hypothesis, which made a domestic mosquito (Stegomya) responsible for its transmission. As the epidemic outburst kept spreading , this hypothesis was checked and confirmed in several countries and among those who were involved in this study the names of Marchoux*, Simond*, and Salimbeni, members of an expedition of the Pasteur Institute should be remembered.

In 1926 another outbreak of the disease occurred in Western Africa. And two expeditions worked on it : one of them, from the Pasteur Institute in Dakar and the other, from the Rockefeller Institute. Four members of the latter lost their lives there. Both expeditions succeeded in identifying - for the first time - the virus which is responsible for the disease (Mathis* and Laigret* for the French).


The opportunity of studying tropical diseases widened the range of medical knowledge as it gave evidence of the role which either animals designated as "virus reservoirs" or insects or molluscs or "intermediary hosts or vectors" can have in the transmission of human diseases.

The first ones are domestic or wild animals which are very often natural hosts to the microbe or to the virus such as rodents for plague, or forest monkeys for yellow fever.

The latter ones carry the disease from a sick animal to a healthy person after one or two consecutive steps.

These are captivating investigations but also long term endeavours as once the identification of these steps by researchers has been made, they have a hard time identifying the other links, or causative agents.

Raising monkeys (Dakar)

And it is exactly what happened with Malaria ! The "hematozoaire" was identified in 1880, but nobody knew how it could be transmitted to humans. Clarac* who was a renowned tropical medicine specialist wrote the following in 1887 : "This pathogen lives in the ground and the cause of this endemic disease is related to the nature of the soil". It is only later between 1895 and 1897 that a mosquito bite (Anopheles), was first suspected and then identified as the way of transmission of this pathogen.

As far as Yellow Fever is concerned it was the other way around. In 1881 Finlay showed that transmission of this disease occurred through the bite of a mosquito, named Stegomya but the pathogen remained unknown over the next forty five years and this very fact was a matter of controversy. In 1897 Auvray* asserted : "I am convinced that the annual seasonal flare ups of the disease have a telluric origin. The pathogen keeps proliferating on corpses and contaminates the soil so that the deceased have to be buried between two layers of quicklime in order to prevent the pathogen from proliferating in the surrounding soil". This pathogen is now known to be a virus and not a microbe which does not survive on corpses in the earth.

Now when all is said and done, it can be said that Colonial Army Medical Officers, the "toubibs", heralded French medicine across the world and in so doing provided an important contribution to the spreading of the influence of France across the world. So, after all, the concept of "the French doctors" is not a new one...