1. Soil borne pathogens have significantly impacted human health over centuries by causing infections that contributed to population declines and societal changes. 2. These pathogens reside in soil communities and include bacteria, viruses, parasites, and protozoa that are important to public and animal health. Many are potential bioterrorism agents. 3. Real-time PCR is an effective technique for detecting soil borne pathogens due to its ability to quantify pathogens during each reaction cycle without needing gel electrophoresis. This allows for safer and earlier detection compared to culturing and conventional PCR.

1. DIAGNOSTIC STRATEGIES FOR THE DETECTION OF SOIL BORNE
PATHOGENS
Haroon Rashid Chaudhry, Tariq Jamil, Umair Ahsan and Shehzad Ashraf Khan Baloch
haroon.rashid@iub.edu.pk
College of Veterinary & Animal Sciences, The Islamia University of Bahawalpur
Department of Microbiology, UVAS Lahore
Across the realm of time in units of centuries soil borne pathogens have had an incredible impact on human
health. Sometimes scientists believe that the advent of Europe and America was based on the infections
caused by these soil borne pathogens which paved the way for the development caused by wiping out
half the population of these countries leading to the survival of the fittest theory to input its design.
These pathogens inhabit the soil mostly in minority with respect to other soil community, which is
found in abundance in a biological commune. These include a number of viral, bacterial, parasitic
and/or protozoan agents in nature. Many of them are of zoonotic and of public health importance and
are placed for Category A bioterrorism diseases due to their severity and peracute nature of the disease
they cause. A few of the biological threat diseases are e.g. Anthrax, Botulism, Plague, Tularemia,
Glanders to name a few. In animals, these soil borne bacteria gain entry through the contaminated feed,
water and inhalation which may be through grazing or through the ingestion of contaminated, and or
soiled hay, whereas, in humans, it is through ingestion of dust polluted food and contaminated water
sources. As they reside in soil in a commune, soil may act as a possible reservoir for transmission of
such pathogens. In most of the developed countries we have not experienced an outbreak by the causal
agents but with the problem caused by Anthrax letters in America and the potential socioeconomic
losses incurred to USA to control these diseases it has been established that the organisms survive in
unique niches in the third world countries where they may be procured and be used as a biological agent
or may cause a spontaneous outbreak in the area leading to devastation in the world. Thus it has been
considered by considerate countries to study and make screening of these public health significant
organisms from soil. As there is only a small quantity of the agent in the soil commune its detection is
difficult and has become crucially important in order to determine local threat and prevent any future
occurrences.
ELISA
Antigen capture ELISA has some potential. This is an area where conventional ELISA has proved of little
significance due to poor results. Another problem is the cost of the kits which can capture the antigen
and give fruitful results. Due to fact the number of antigen is very low in soil to elute the bacteria in
question from soil can be very troublesome and not very sensitive. Another threat is the use of live
agents which can be a threat to the technician.
Routine Culturing
Routine culturing and identification practices may be of use but since these are category ‘A’ bioterrorism
agents growing them may be dangerous not only to the community but may become an international
threat. To grow them the legislations are strict and require very expensive techniques and require
expensive equipment.
PCR
PCR is a molecular technique used to amplify DNA sequences. This technique enables us to early
diagnose genetic disorders and to detect non-cultureable, slow growing and infectious microorganisms. This
technique is also used to differentiate between pathogenic and non-pathogenic strains of microorganisms.

2. Sometimes inhibitors in the reaction mixture block PCR due to self annealing of the products that make the
band results unreliable.
Real Time PCR
Real-Time PCR is a technique that solves this problem. This technique allows detection and
quantification of the PCR products during each cycle of the reaction. It is possible by introducing sequence
specific DNA probes attached with a dye (FAM or TAMRA) that binds to template DNA and gives
florescence when cleaved by the polymerase enzyme by its 5’-nuclease activity. Thus Real-Time PCR saves
time by eliminating the need of Gel Electrophoresis by the end. This makes Real-Time PCR technique to be
used for quantification and screening of the samples on the basis of nucleic acids of diagnostic importance
(infectious diseases) both.
Screening of samples by using Real-Time PCR is helpful in early diagnosis of the disease and also
for prophylactic measures where positive samples are found. This technique also does not require
sophisticated laboratory facilities that are required to culture such pathogens hence minimizing the potential
laboratory hazards. The positive areas may be mapped further to observe spatial ecology and epidemiology
using GIS/GPS techniques. Information on natural prevalence of these public health significant pathogens
can help understanding of potential source of the disease in future and design policies and prevention plans.