Sexually Transmitted Infections: Laboratory Investigations and Diagnosis

Sexually Transmitted Infections (STIs) (Also referred as Sexually Transmitted Diseases (STDs) are a group of infections that are primarily spread through sexual contact. They can affect both men and women and may lead to serious health consequences if left untreated. 

Early diagnosis and prompt treatment are crucial in managing these infections effectively. Prevention is an important component as well. This article aims to provide comprehensive information on laboratory investigations and diagnosis of STDs

STIs: Summary

Definition: An infectious disease transmitted primarily through unprotected sexual contact
Symptoms : Urethral discharge, foul smell, genital ulceration, swelling. Occasionally no symptoms at all
Causes: Viral, bacterial , fungal, protozoal
Commonest examples: HIV/AIDS, Gonorrhea, Syphilis, chlamydia, trichomoniasis
Diagnosis: History, physical examination, laboratory tests, imaging

What exactly are STIs/STDs

Sexually Transmitted Infections (STIs), also known as Sexually Transmitted Diseases (STDs), are infections that are transmitted through sexual activity. They can be caused by bacteria, viruses, parasites, and other microorganisms. Common examples of STIs include chlamydia, gonorrhea, syphilis, human papillomavirus (HPV), herpes, and HIV.

So, its 2023, why are we talking about STIs.
Well, because these diseases are still with us and wrecking havoc among communities in pretty much every corner of the world. From ancient times, STIs have been part of the human story. Even at present time, STIs are a clear and present danger. They contribute significant disease burden as well as  deaths not just to adults, but also unborn and newborn babies. HIV is the most lethal STI at the moment and has no cure.


Do STI and STD mean the same thing?

Under normal usage, yes. However, technically the meaning is slightly different. STI means colonization and multiplication of organisms on the persons body – genital organs in this case. Sexually transmitted disease, on the other hand, refers to development of symptoms as a result of the infection. In this article we use the terms interchangeably.

Once in a while these pathogens acquire more lethal properties, transforming overnight into public health emergencies. In late 2022, a superbug causing gonorrhea was circulating in Nairobi in 2023/2023 , causing panic in residents and medical fraternity alike.

How STDs are Transmitted

The mode of transmission of STIs is pretty much in the name, sexual contact.  However, its important to keep in mind these microbes  can be transmitted through other  modes as well.

  1. Sexual Transmission: Unprotected sexual intercourse with a person already infected, including vaginal, anal, and oral sex, is the most common mode of transmission for most STIs. It does not matter the sexual orientation, as long as there is genital contact, there is risk of transmitting an STD
  2. Mother-to-Child Transmission: Pregnant women infected with certain STIs can pass the infection to their unborn or newborn child  while in the uterus or during childbirth. 
  3. Blood Transfusion: Some Although rare due to strict screening measures, some STIs can be transmitted through infected blood or blood products. 
  4. Organ Transplant. Microbes causing STIs can  potentially be transmitted via organ transplant, though in practice its extremely rare. This includes syphilis

The overwhelming majority are through sexual contact, and for the rest of this article we will reference this mode of transmission.

How are STIs *NOT* Transmitted?

There are many misconceptions about STI transmission online. One, can you get STI form toilet seat? NO. Can you get it form sharing personal effects like towels. NO

Types of STIs

There are quite a number of STIs, come more common and dangerous than others. There are 2 ways we look at STIs.

The first classification  depends on the  primary symptoms they cause, this is known as syndromic classification. So if the STI cause discharge of pus its called a urethral(male) or Vaginal (discharge) in females. This is primarily used in low resource settings as they lack the diagnostic facilities to identify the actual microbe causing the infection. 

The second classification  looks at the actual pathogen either virus, bacteria fungi or even protozoa.

Lets look at each broad classification

Syndromic Classification of STIs

  1. Vaginal Discharge Syndrome
  2. Urethral Discharge
  3. Genital Ulcer Syndrome
  4. Lower abdominal Pain / Pelvic inflammatory disease
  5. Oral -Pharyngeal syndrome
  6. Anorectal syndrome

Note: to read more information on each of the syndrome, head over to our detailed article on syndromic classification of STIs

Etiological Classification 

This simply a fancy way of saying the STI is caused by specific microbe, be it bacteria, fungi, virus or even protozoa. In brief these are the most commonly encountered  causative agents of STIs


  1.  Chlamydia: Caused by the bacterium Chlamydia trachomatis, it is one of the most prevalent STIs worldwide. To learn more about Chlamydia, see this article: Chlamydia
  2. Gonorrhea: Caused by the bacterium Neisseria gonorrhoeae, it can affect the genitals, rectum, and throat.
  3. Syphilis: Caused by the bacterium Treponema pallidum, syphilis progresses through stages if left untreated.
  4. Chancroid:  caused by Hemophilus ducryei 
  5. Mycoplasma genitalium (Mgen)


  1. Human Papillomavirus (HPV): A viral infection causing genital warts and linked to cervical cancer.
  2.  Herpes Simplex Virus (HSV): Causing genital herpes, it is caused by two types of HSV,  HSV-2 is the more common one.
  3.  Human Immunodeficiency Virus (HIV): Attacks the immune system and can lead to acquired Acquired Immunodeficiency Syndrome (AIDS).


  1. Candidiasis


  1. Trichomonas vaginalis

Uncommon/ Emerging STI

Of late, uncommon organisms not routinely associated with STIs have been isolated from genital lesions. The more common are listed below, the list is by no means exhaustive.

List of emerging pathogens causing STI/STDs

1️⃣M-Pox (previously called Monkey Pox)

2️⃣Shigella sonnei,

3️⃣hepatitis A, 

4️⃣Neisseria meningitidis, 



In 2022, The WHO has recognised the threat of the new, emerging and re-emerging pathogens and has called for concerted effort to tackle the threat

Head up: We will cover each separately in our upcoming posts, so register to get a notification when published

Common Signs and Symptoms of Sexually Transmitted Infections

Symptoms of STIs can vary depending on the specific infection and the individual. Some common signs and symptoms include:

  1. Unusual genital discharge
  2. Pain or burning during urination
  3. Genital sores or ulcers
  4. Itching or irritation in the genital area
  5. Pain during sexual intercourse
  6. Abdominal pain or pelvic inflammatory disease (PID) in females
  7. Swollen lymph nodes
  8. Rash or flu-like symptoms in the early stages of HIV infection
  9. Skin rash, fever, arthritis, septic shock – in deseminated disease especially gonorrhea

We will look into each of these specific diseases in detail, be sure to check the links.

STIs: Laboratory Methods for Diagnosis

Accurate and timely diagnosis of STIs is vital for appropriate treatment.  At the present, most STIs in Kenya are not subjected to laboratory confirmation

Various laboratory methods are used for the diagnosis of STIs, including:

1.Molecular Techniques

DNA based techniques have revolutionized STI testing. These include tests like PCR, Nucleic Acid Amplification Tests (NAATs). They are  highly sensitive and specific tests that detect the genetic material of pathogens, such as chlamydia and gonorrhea as well as  viruses. However, they are quite expensive and not readily available. They are the most accurate and 

2. Immunoassay / Serological Tests

Serological tests are based on the concept of immune reaction where antigen and antibodies interact. These tests detect either components of the pathogen (Antigens) or evidence of body’s reaction to the infection( Antibodies) There are many variations of serologic tests. Examples include ELISA, IFA, chromatographic assays (used primarily in RDTS). Immunoassays are the most commonly used diagnostic tests for STIs in Kenya.

3. Microscopic Studies

These are used to visualize causative agents under a microscope. Based on how the organism appear, the experienced microscopist is able to identify the organism.  In addition, the pattern of cellular damage may give a clue as to the responsible pathogen eg in pap smears

4. Cultures

Though not routinely used due to long turn around time and costs, culture remains important in research settings as well as in situations of drug resistance. Bacteria, fungi as well as viruses can be subjected to culture

Home Testing for STDs

In recent years, home testing kits for certain STIs have become available. These kits allow individuals to collect samples in the privacy of their homes and mail them to a laboratory for testing. While home testing offers convenience, it is essential to follow instructions carefully and ensure the reliability of the testing service.

Home testing kits tend not to be as accurate or reliable as laboratory based methods. They are best treated as screening tests and confirmatory testing is often necessary.

Where are STI/STDs Tested in Kenya

Access to screening, testing as well as treatment for STIs remain a big challenge in Kenya. Only a few major public hospitals like KNH and select county hospitals have the capacity to test for specific pathogens. Private hospitals charge an arm and a leg, as such treatment of STIs is largely syndromic.

Sexually Transmitted Infections (STIs) are an ever present danger. Understanding the modes of transmission, common symptoms, and the importance of early diagnosis through laboratory investigations is crucial in controlling the spread of these infections. Regular STI testing, practicing safe sex, and seeking timely medical care are essential steps in managing and preventing the complications associated with STIs. Remember, knowledge and awareness are powerful tools in the fight against sexually transmitted diseases.

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