The national Escherichia coli reference laboratory was established in 2008 by obtaining authority from the health reference laboratory of the Ministry of Health, Treatment and Medical Education, and since then, it has been affiliated with the health reference laboratory, the Department of Combating Diseases Transmitted Through Food and Water, and the Management Center for Infectious diseases, of the Ministry of Health has had close and continuous cooperation. This laboratory provides services, such as culture of sent samples on specific and differential media to isolate Escherichia coli bacteria, determine biochemical identity, perform serological and molecular tests to determine Escherichia coli serotypes and pathotypes, perform cell culture tests to check pathogenicity, perform gel electrophoresis tests in the field of pulsation to monitor the circulation of pathogenic strains (Pulsed-Field Gel Electrophoresis) (PFGE) for the aforementioned managements and providing DNA of standard strains of Escherichia coli to the academic community of the country.

For more information about the services of this laboratory, an interview with Dr. Nader Shahrokhi, the head of this laboratory, is presented below:

Dr. Nader Shahrokhi, born in 1965 in Tehran, is married and has a daughter and a son. He is a member of the Faculty of Molecular Biology and the head of the national reference laboratory of Escherichia coli (AMCA). He has a Bachelor's degree in microbiology from Isfahan University, a Master's degree in microbiology from Tehran University, and a specialized doctorate in medical biotechnology from Pasteur Institute of Iran.

The molecular biology department was established in the early 90’s with the efforts of Dr. Anis Jafari, Dr. Saeid Bouzari, and Mr. Ali Farhoudi. The beginning of Dr. Shahrokhi's activity in this department was to complete his specialized doctorate dissertation and now, after years of gaining experience in the presence of valuable professors of the department, he has assumed the presidency of this department.

  One of the important achievements of the molecular biology department in the field of providing specialized services is the establishment of the Escherichia coli reference laboratory, performed with the efforts of Dr. Saied Bouzari and his colleagues. National reference laboratories are very important in the diagnosis, prevention, and monitoring of target diseases. In recent years, with the emergence of the COVID-19 disease, it has become clear that infectious diseases can turn from a minor epidemic at the regional and national level into a global and pandemic challenge, and therefore their monitoring should still be the focus of the decision makers of the countries.

Escherichia coli bacteria of the intestinal flora that can become invasive

Escherichia coli (with the scientific name Escherichia coli or E.coli for short) is a type of facultative anaerobic Gram-negative bacillus from the Escherichia family and the Enterobacteriaceae family, which is commonly found in the intestines of warm-blooded animals. Most strains of Escherichia coli are harmless, but some serotypes cause food poisoning, diarrhoea, urinary tract infection, wound infection, and disseminated infections. The harmless strains of this category are part of the normal intestinal flora of healthy people, which play a role in the production of vitamin K2. And they prevent the establishment of pathogenic bacteria in the intestine. This bacterium is one of the most abundant bacteria in the intestinal flora, whose infectious form is transmitted from one person to another through the fecal-oral route. Escherichia coli has many pathogenic strains and can cause all kinds of diseases. Diseases caused by E. coli are mainly transmitted through contaminated food and water, which can cause widespread epidemics. This organism can cause diseases that involve the digestive system or the urinary system and bother the patient for years. They do not respond well to treatment and cause many problems for people, especially children under five years old, people over 65 years old and women. Escherichia coli is considered one of the causes of hospital infections, which can cause death. Therefore, this organism can cause a wide range of diseases. After entering the body, bacteria such as Escherichia coli can cause disease both by themselves and by the toxins they produce.

The National Escherichia coli National Reference Laboratory is working on the definitive diagnosis of Escherichia coli pathogens. In this laboratory, we mainly work on Escherichia coli, which causes digestive diseases, but it is also possible to examine other strains and substrains of E. coli.

Determination of bacterial serotype and pathotype

E. coli reference laboratory can use classical methods along with biochemical fingerprinting methods, serotyping and modern molecular typing tests to detect bacterial strains. The mission of the E. coli reference laboratory is to monitor and determine the pathotype and serotype of E. coli strains that cause diarrheal epidemics in the country. In addition to the diagnosis process, the E. coli reference laboratory is also responsible for investigating other characteristics of isolated E. coli strains, such as microbial resistance, preparation of a microbial bank of isolated strains, and targeted regional and national research. In this regard, more than a thousand strains of E. coli pathogens are available in the microbial bank of the reference laboratory. The national plan for determining E. coli pathotypes is also available in the history of research activities of the laboratory.

In cases of diarrheal epidemics, the health reference laboratory and the Department of Combating Diseases Transmitted by Water and Food of the Communicable Disease Management Center of the Ministry of Health are responsible for dealing with and controlling the epidemic in direct interaction with the E. coli reference laboratory and determining the cause of the epidemic. In this regard, suspicious samples are sent to us from all parts of Iran according to the criteria of the E. coli reference laboratory, and we report the results of the tests to one of these two authorities, who, according to their control policy, will determine the procedure for dealing with that epidemic. Define.

Before the COVID-19 pandemic, there were more samples sent to this laboratory, but during the COVID-19 era, more people's health care and at the same time the attention of the health care system was more focused on the COVID-19 disease, and as a result, as expected, the samples referred to us It also decreased that again with the return to normal state and the passing of the covid 19 pandemic, the necessity of dealing with diarrheal diseases and determining their cause has become very important.

Before the establishment of this laboratory, it was unknown what strains of E. coli, in what season, in which gender, at what age, in which regions, etc. are circulating in Iran, and with the establishment of this laboratory, for the first time We published the load of common strains circulating in the country according to pathotype, season, gender, age, geographical region, etc. in one of the prestigious scientific journals. Before 2011 and the widespread E. coli epidemic in Germany, developed societies thought that diarrheal diseases are related to developing countries and do not appear in developed countries; But after the 2011 epidemic in Germany due to the new strain of E. coli, following the widespread fear created in this country and other advanced societies, an alarm was sounded for the country's health authorities and they decided to get a clear picture of the situation before this epidemic entered the country. have an environment in the country to adopt targeted care and preventive protocols. In this regard, this important mission was assigned to Marjae E. coli Laboratory, and this comprehensive study came to fruition, for the first time, a clear picture of this organism was presented in the country. Fortunately, the new strain did not enter Iran and was controlled in Europe.

Monitoring of native strains/identification of dangerous strains

The reference laboratory of E. coli is responsible for monitoring the native strains of Iran, and the results of their investigations in terms of circulating strains, their prevalence and the state of microbial resistance in them, are directly reported to the health system of the country and through They are reported to doctors and health centres. According to the information of the country's health professionals and active scientists in this field, the continuous monitoring of circulating strains requires funding, which despite many efforts has not been provided to this laboratory, and the coordination of obtaining it requires a lot of time and energy from the personnel. And the managers of this laboratory waste.

One of the pathotypes of E. coli is the enterohemorrhagic pathotype, which is generally a subset of Shigatoxin-producing E. coli and is highly lethal; Because the hemolytic uremia syndrome causes kidney failure and then death. A person infected with this dangerous strain, after being treated with antibiotics, due to the death of the bacteria, shigatoxin poison in the person's body. The patient is released and the complications mentioned above are caused by the effects of this poison in the body. So far, we have several reports of shigatoxin-producing E. coli strains causing death in children. In such cases, before prescribing antibiotics, the strain should be identified quickly antibiotic treatment should not be carried out, and only supportive treatments should be used. In cases of diarrhoea caused by E. coli, people's deaths should be prevented.

  Drug resistance, a new and important challenge

Regarding the monitored strains whose pathotyping has been determined and we are trying to determine serotyping, we have also checked the antibiotic resistance of the strains, and the results of this check have been published in the form of several scientific articles. Unfortunately, the state of microbial resistance identified in the monitoring of the circulating strains in Iran shows that we do not have a favourable situation compared to other countries and proper planning should be done for this challenge. To be able to monitor the issue of microbial resistance regularly and based on official and international frameworks in E. coli strains isolated in Iran, we need to provide sufficient financial resources, which unfortunately has not been achieved so far.

Continuous training of university experts

One of the items on the agenda of the E. coli reference laboratory is continuous training in the form of training workshops for disease-fighting experts at medical sciences universities across the country. In addition, this laboratory participates in the development of national guidelines for fighting diarrheal diseases. In training programs, necessary training is given on sampling methods, conditions of receiving samples, and methods of definitive detection of bacteria and determination of serotypes and pathotypes.

Most of the employees of the molecular biology department of the Pasteur Institute of Iran, including five faculty members and two experts, are involved in the processes of this laboratory and each of them is engaged in activities according to their specific duties.

Membership in the Global Network of Foodborne Diseases

E. coli Reference Laboratory has the honor of being a member of the Global Foodborne Infections Network (GFN) which is affiliated to the World Health Organization.