Envis Centre, Ministry of Environment & Forest, Govt. of India

Printed Date: Saturday, July 13, 2024

Pathogens in Human Excreta

Human excreta and the lack of adequate personal and domestic hygiene have been implicated in the transmission of many infectious diseases including cholera, typhoid, hepatitis, polio, cryptosporidiosis, ascariasis, and schistosomiasis. The World Health Organization (WHO) estimates that 2.2 million people die annually from diarrhoeal diseases and that 10% of the population of the developing world are severely infected with intestinal worms related to improper waste and excreta management (Murray and Lopez 1996; WHO 2000a). Human excreta-transmitted diseases predominantly affect children and the poor. Most of the deaths due to diarrhoea occur in children and in developing countries (WHO 1999). 

Proper excreta disposal and minimum levels of personal and domestic hygiene are essential for protecting public health. Safe excreta disposal and handling act as the primary barrier for preventing excreted pathogens from entering the environment. Once pathogens have been introduced into the environment they can be transmitted via either the mouth (e.g. through drinking contaminated water or eating contaminated vegetables/food) or the skin (as in the case of the hookworms and schistosomes), although in many cases adequate personal and domestic hygiene can reduce such transmission. Excreta and wastewater generally contain high concentrations of excreted pathogens, especially in countries where diarrhoeal diseases and intestinal parasites are particularly prevalent. Therefore for maximum health protection, it is important to treat and contain human excreta as close to the source as possible before it gets introduced into the environment.

The current situation as regards various diseases due to pathogens in human excreta urgently demands that people be made aware of microbes and the role they play in causing diseases so that the right measures to control infectious diseases are taken. One has then to devise strategies to limit the breeding grounds of microbes, take steps to avoid their spread, instill good hygienic habits in the masses and also provide facilities such as those, which are part of the Sulabh Movement. Sensitizing the masses about the close connection between microbes and diseases by providing proper information and understanding is another important task in this fight against infectious diseases.

The scientific basis of the connection between lack of sanitation and infectious diseases was provided by Louis Pasteur, Robert Koch, Elie Metchnikoff and other ‘microbe hunters’ who established that these diseases are caused by micro-organisms, viz bacteria, fungi and viruses. Antoni van Leeuvenhoek was the first person to work on microbes by peering through microscopes of his own making. The work of these and several other scientists resulted in mankind’s biggest advance in fighting diseases. Ronald Ross’s work on malaria carried out at Calcutta and that of Valdemaar Haffkine on plague at Bombay is some other exciting episodes in the same pursuit of tracking deadly microbes. 

The work of these and several other scientists led to the development of three concepts, which play an important role in the control of infectious diseases.


These are:


  •   Infectious diseases are caused when we come in contact with pathogens;
  •   These pathogens are present in several environmental reservoirs, which include drinking water, food, garbage heaps, sewage and human excreta;
  •   One can protect oneself from these diseases by avoiding contact with the pathogenic micro-organisms. The most effective way to do this is the eliminate the environmental reservoirs of these microbes; the second best alternative is to keep ourselves away from these reservoirs.


As the links between microbes and diseases became clear, people understood the reasons why simple measures, especially involving personal and public hygiene, protected them from infectious diseases. Advances in immunology (vaccination) and antibiotics soon followed, and the global health situation improved still further. 

India has an unenviable record of high incidence of several infectious (and non-infectious) diseases. The 1993 World Development Report, Investing in Health, ranks India next only to Sub-Saharan African countries (all countries in the Middle East, in the number of people afflicted with infectious diseases has achieved a marked improvement in health and sanitation status of its people during the past 15 years, especially with reference to infectious diseases. In any given year, an average Indian loses at least four times more healthy days due to infectious diseases than does an average Chinese. This is not due to lower expenditure on health care but lack of concern for health and sanitation. Indeed, India spends more funds per person ($ 21/annum) on healthcare than China ($11/annum) only to be behind it in the race. (Source: Microbes and Disease by M.S. Mahajan).

However, the significant difference lies in the fact that China has spent a considerable amount in the public sector on specific public health measures, rather than on setting up hospitals and other facilities for treatment of diseases as is done in India. Public health programmes, which have a direct bearing on promoting a healthy environment, include provision of clean and adequate quantities of water and sanitation, sewerage and solid-waste collection and disposal. Direct investment in the development of these programmes leads to removal of reservoirs of pathogens and, in turn, to reduction in the incidence of infectious diseases, a healthy and growing society.

Amongst people living in the developing countries, almost three-fifths have no basic sanitation facilities, one-third without safe drinking water, a quarter lack adequate housing, one-fifth have no health care facilities, and one-fifth of children drop out of schools. Although the global consumption of goods and services has expanded at an unprecedented pace in the twentieth century, (with the public and private consumption expenditures reaching $24 trillion in 1998, six times the figure for 1995), civic facilities have declined relative to population. This was revealed in the Human Development Report, 1998.

The report focuses on consumption of goods and services and looks at how the global consumption boom has resulted in historic gains in human development. India, which was ranked 138th in 1998, has slipped one rank to 139, just behind Pakistan, in 174 countries. However, India has a more equitable distribution of resources as the country has adopted “fairly pro-poor policies”. 

About the Microbes:

Of the estimated 3.5 million children who die from diarrhoeal diseases each year in developing countries, almost 600,000 die from the sanitation-related ailments alone. This disease is endemic throughout the world. Refugee population and children suffering from malnutrition are among the badly affected. During 1994, dysentery was the leading cause of death in the Rwandan refugee camps in Burundi, Tanzania and Zaire. Elsewhere in Africa, 11 countries were hit by water-related epidemics in 1994 in Asia.
There are four clinically important species of Shigellae (dysentery) but most life-threatening diseases are caused by just two species-S. dysenteriae and S. Flexneri-and by 5 serotypes. S.Sonnei is the leading cause of endemic disease in industrialized countries. In 1993, it was responsible for over 90 per cent of cases of dysentery reported in the USA. And, all of them are caused in unclean areas.

Vibrio cholerae-one of the oldest scourges known to men-causes about 5.5 million cases of cholera every year and about 120,000 deaths, i.e. over a fifth of those deaths occur among children under five and a quarter in children aged 5 to 14. Most cholera deaths occur in Africa and Asia. Without treatment (rehydration therapy and antibiotics) it is one of the most dangerous infectious diseases-leading to fatality rates as high as 40 per cent. The disease is associated with poverty, poor sanitation, lack of hygiene and unsafe drinking water. It is spread by contaminated water or food and by person-to-person contact.

In 1991, there were more cases of cholera and more countries were affected by the disease than in any other year on record. Both Latin America and Africa were hit by explosive epidemics. The first outbreak occurred in Peru and spread rapidly throughout South and Central America sparing only seven countries. More than 4,000 people died. In the same year, a major epidemic swept across Africa killing 14,000 people in over 20 countries. In India and Bangladesh the emergence of a new strain of V. Cholerae was reported in the 1992 following an initial outbreak in Chennai and followed by another among fishermen on remote islands in the Bay of Bengal. The new strain spread rapidly to China, Malaysia, Myanmar, Nepal and Pakistan involving thousands of deaths – mainly among adults. This is the report of the World Health Organisation, 1996.

The faeces of babies and young children are not considered to be dirty in many societies. However, the faeces of babies and young children are often the most dangerous because they may have a higher concentration of pathogens. It is the faeces of these two groups that are most frequently found in the environment (WHO, 1993). Several studies have shown associations between the incidence of diarrhoea in a household and children defecating in living areas (Han and Moe, 1990; Clemens and Stanton, 1987).

Baltazar and Solon (1989) found that the unsanitary disposal of children's faeces was associated with a 34% increase in clinical diarrhoea and a 64% increase in pathogen positive diarrhoea in children from families that did not adequately dispose of their faeces compared to a control group. Sanitation interventions that facilitate the safe disposal of faeces from babies and young children will reduce diarrhoeal disease at the household and community levels. 

Interventions to promote personal and domestic hygiene are also effective in reducing disease. In particular, handwashing with soap; after defecation; after handling babies' faeces; before feeding and eating; and before preparing food have significant impacts on diarrhoeal morbidity (WHO, 1993). 

One gram of faeces contains:


  •   10,000,000 Viruses
  •   1,000,000 Bacteria
  •   1,000 Parasite cysts
  •   100 parasitic eggs.

These pathogens cause infections which lead to over 1.3 million deaths world-wide annually. Children and the immuno-depressed are the most vulnerable to these organisms which contributes to this burden, specifically bacteria, viruses and parasites.

In the following tables a comprehensive list of the various microbes generally found in human excreta and the diseases caused due to each have been mentioned. 


Viruses Diseases


Human Carrier States Reservoir
Polioviruses Poliomyelitis Paralysis and other conditions Yes Human
Hepatitis A Virus Infectious hepatitis


Yes Human
Rotaviruses Diarrhoea


Numerious conditions Yes Human
Coxsackie viruses


Numerious conditions Yes Human


Numerious conditions Yes




Numerious conditions Yes Human
Astrovirus         (many types) Gastroenteritis                  




Calicivirus    (several types) Gastroenteritis




Corona virus Gastroenteritis




Entero viruses (many types) Gastroenteritis various



Hepatitis E virus Infectious hepatitis     




Norwalk virus Gastroenteritis




Norwalk-like viruses Gastroenteritis




Parvovirus     (several types) Fifth disease






Bacteria Diseases Bacteria also excreted in urine Symptom Human carrier
States Reservoir


Salmonella typhi

Typhoid fever


Yes Human
Para typhi Paratyphoid Yes


Yes Human
Other salmonella Food poisoning etc. No


Yes Human & Animal
Shigella Bacillary dysentery No


Yes  Human
V. Cholera Cholera No


Yes Human
Pathogenic E. Coli Diarrhoea or gastroenteritis No    


Yes Human & Animal
Yersini Yersiniosis Yes


Yes Animal & Man (b)
Campylobacter Diarrhoea No


Yes Animal&Man(?)
Leptospira (spp.) Leptospirosis





Helicobacter pylori



Abdominal pain, peptic ulcers, gastric cancer



Chlamydia trachomatis  Trachoma





1. Each serotype is more or less specific to a particular animal host. 
2. Some 30 or more serotypes appear to be associated with particular animal species. Any specific distinct serotypes, specific to prionates, is still under investigation. 


Viruses Diseases Symptom Human Carrier  States Reservoir 
Entamoeba histolytica Colonic ulceration Amoebic dysentery and liver abscess Yes Man
Giardia lambia Diarrhoea Malabsorption Yes Man
Balantidium coli Mild diarrhea Colonic ulceration Yes Man
Cryptosporidium parvum Cryptosporidiosis Diarrhea Fever



Cyclospora cayetanensis Persistent diarrhoea    






Diseases Common Name Pathogens Transmission Distribution
Ascariasis Roundworm Ascaris lumbricoides Man-soil-man World wide
Clonorchiasis Chinese liver fluke Clonorchis sinensis Animal or man-aquatic snail-fish-man S.E. Asia
Opisthorchiasis Cat liver fluke Opisthorchis felineus Animal-aquatic snail fish-man USSR Thailand
Diphyloboth-riasis Fish tape worm O.Viverrini Man or animal-copepod-fish-man wide distributed mainly in temperate areas
Enterobiasis Pinworm Enterobius vermicularis Man-man Worldwide
Fascioliasis Sheep liver fluke Fasciola hepatica Sheep-aquatic snail-aquatic vegetation-man S.E. Asia mainly China
Fastrodiscoidiaisis Gastrodiscoides Hominis Pig-aquatic snail-aquatic vegetation-man India, Bangladesh, Vietnam
Hymenolepiasis Dwarftape worm Hymenolepis spp Man/rodent-man Worldwide
Trichurias Whipworm Trichuris trichiura Man-soil-man Worldwide









Likely effect of

Likely effect of

Major control of infections





Sanitation hardware alone

Hygiene promotion alone


Faecal-oral (non-bacterial)
Hepatitis A, Amoebic dysentery Rotavirus giadiasis
Person to person contact and domestic contamination
Domestic water supply, health education, improved housing and provision of Toilets.
Faecal oral (bacterial)
Cholera, Salmonellosis, Shigellosis
Person to person contact, domestic contamination, water contamination, and crop contamination
Slight to moderate
Domestic water supply, health education , improved housing, provision of toilets, treatment of excreta prior to discharge or reuse
Soil Transmitted Helminths
Hookworm, Roundworm, Whipworm
Path/ Compound contamination, Communal defecation areas Crop contamination
Provision of toilets, Treatment of excreta prior of discharge or reuse
 Beef Tapeworm, Pork tapeworm
Path/ Compound contamination Fodder contamination Field contamination
Provision of toilets, treatment of excreta prior to discharge or reuse
Water based helminths
Water Contamination
Provision of toilets, treatment of excreta prior to discharge or reuse
Excreta Related insect vectors
Filariasis, some faecal-oral diseases
Insects breed in sites of poor sanitation
Slight to moderate
Provision of toilet, treatment of excreta prior to discharge or reuse


E Histolytica 1%-28% 
A Lumbricoides 41%
A Duodenale 05-600%
N Americana
S Stecoralis 5%
T Trichuria 
E Vermicularis 6%
Giardiasis 19%

The Environmental Transmission of pathogens occurs through several different routes. These may be:


  •   Directly, by contact with human excreta;
  •   Directly through contaminated drinking water;
  •   Directly through vegetables, shellfish or other food products exposed to contaminated water or soil;
  •   By accidental ingestion of contaminated water during swimming or recreational activities;
  •   By inhalation of aerosols or dust due to irrigation with wastewater, from scums, from showers or by other means;
  •   Vector-borne transmission where the vector or the intermediate host breeds in water;
  •   By contact with animals and birds, both domestic and wild acting as a host for pathogenic bacteria and parasites;
  •   By direct contact with the organisms occurring in water bodies (for example Leptospira (spp.); and
  •   By secondary spread through contact with infected individuals.

The main organisms that pose a threat to health are pathogenic bacteria, viruses, parasitic protozoa and helminths that are excreted in large numbers (up to 1011/g faeces for some viruses) from infected individuals. Many of these organisms have low infectious doses (e.g., helminths, protozoa and viruses) i.e., only small quantities of infectious agents are needed to infect a new host (the infective dose varies between organisms and with respect to the susceptibility of the exposed individual). 
Shifts in the nitrogen and phosphorous composition may promote the growth of toxin producing cyanobacteria (blue-green algae) (Chorus and Bartram, 1999); Certain species may produce different toxins, affecting people that come into contact with the water (e.g., through bathing/occupational exposure) or through drinking water. Algal toxins may also enter the food chain. For example, filter-feeding molluscan shellfish (e.g., oysters, mussels, clams), filter large amount of water and can accumulate toxic chemicals and human pathogens in their tissues. Humans are exposed to the toxins and/or pathogens when they eat the shellfish (cooking has no effect on many algal toxins and may not destroy all of the pathogens). Eutrophication and organic load may also enhance the occurrence of opportunistic bacterial pathogens. 

The sources of pollution affecting the occurrence and abundance of pathogens in a watershed and receiving coastal regions are primarily due to the direct or indirect load of excreta. The impact is due to:


  •   the direct load of human faeces and urine:
  •   the quantities of wastewater from large-scale wastewater plants and on-site sanitation units;
  •   greywater;
  •   stormwater;
  •   impact from sludge and manure through land run-off;
  •   impact from wild animals and birds; and
  •   other watershed activities affecting the leakage from surrounding lands.

The load of pathogens varies from time to time and reflects their abundance in the human and animal population. The contamination load and the linked degree of risk are a result of the sum contribution of different environmental transmission pathways.

Disease transmission is determined by several pathogen-related factors:


  •   An organism's ability to survive or multiply in the environment (some pathogens require the presence of specific intermediate hosts to complete their lifecycles).
  •   Latent periods (many pathogens are immediately infectious, others may require a period of time before they become infective).
  •   An organism's ability to infect the host (some pathogens can cause infections when present in small numbers e.g. Ascaris, others may require a million or more organisms to cause infection); (Feachem et al., 1983).
  • Disease transmission is also affected by host characteristics and behaviour: :
  •   Immunity (natural or as a result of prior infection or vaccination);
  •   Nutritional status;
  •   Health status;
  •   Age;
  •   Sex;
  •   Personal hygiene;
  •   Food hygiene.