Do you Need an Antibiotic? What are they, What do they do, and How do they do it?


I love getting messages from readers, and G.L asks some very good questions about how modern medicine works. So good in fact, that I have decided to share them with you and to devote this month’s post to antibiotics. 

“Dear Dr. Davis,

I read your blog and I have a question you might be able to answer for me. Recently I went to my doctor for a cold that was not getting any better. When I left, I asked about getting an antibiotic. He said taking an antibiotic would not help. I remember always getting one in years past. Has the cold bug changed or does he just not want to bother?

Thank you,


Dear G.,

The cold bug has not changed, well not very much anyway. But the way doctors treat infectious disease has. If he diagnosed you with a cold, which is caused by any number of viruses, he knows that prescribing you an antibiotic will do more harm than good. For one thing, it will not affect the virus, and may, in fact, destroy many of the good bacteria that are helping you combat the cold. Your physician will tell you that a large part of our immune system is comprised of what is termed commensal or “good bacteria” that are not only beneficial but also critical for boosting our immune system. This is why your physician will not prescribe antibiotics for a viral infection. Aside from this, the bacteria in your digestive system, called the microbiome, which allows you to process food, can be destroyed, causing any number of unpleasant conditions. Thank you for your great question. Your doctor is providing you the safest and best treatment currently available.

This was a great question, and has prompted me to write a brief post on exactly what antibiotics do, and more importantly, how they do it. There are now hundreds of antibiotics of various types and actions, but the average person will encounter only a handful that can be broadly classified into several groups. This is a brief listing and not meant to be exhaustive. Any discussion on antibiotics must start at the beginning.

As the story goes, biologist Alexander Fleming returned to his office one September in 1928 to find he had left a petri dish of bacteria uncovered. The dish contained staphylococcus bacteria, and Fleming noticed the bottom of the dish was covered with blue-green mold. Being a man of science and highly observant, he noted that a clear ring surrounded the mold, where the bacteria had been inhibited. The mold, Penicillin Notatum had somehow prevented the bacteria from growing near it. This original and entirely accidental discovery would set in motion the creation of one of the most used drugs in medical history.

Before the 1900’s physicians treating infections caused by bacteria, including many forms of pneumonia, gonorrhea, tuberculosis, rheumatic fever, urinary tract and kidney infections, among numerous others had no real effective response. By 1929, Flemings discovery of penicillin changed the way medicine, in particular, infectious disease, was treated. Since that time, researchers have identified several antibiotic classes that combat bacteria (and some parasites) through a number of actions. These include Penicillins, Aminoglycosides, Cephalosporins, Macrolides, Fluoroquinolones, Sulfonamides, Tetracyclines, and Lincosamides.

Current Antibiotics- A Brief Overview (sort of brief)

Penicillins are the oldest group of antibiotics. As β-lactams (meaning they contain a beta-lactam ring in their molecular structures) they work by inhibiting the cell wall of the bacteria, blocking the synthesis of a molecule called peptidoglycan. Bacteria that have cell walls (some do not) contain a layer of peptidoglycan in a crystal lattice structure formed from linear chains of two alternating amino-sugars (N-acetylglucosamine and N-acetylmuramic acid), along with inner plasma membrane and its cellular contents. When this membrane is weakened, the cell wall is prone to failure.

Aminoglycosides include Vancomycin, Amikacin, Gentamicin, and Tobramycin. Another group ofβ-lactam antibiotics, they have a similar action to Penicillin, attacking the assembly of peptidoglycan in a slightly different way. Used to treat acute infections caused by bacteria that either multiply very quickly or that have become resistant. Because aminoglycosides are typically used to treat serious infections, they are usually administered by injection (Gentamicin, Amikacin, Tobramycin, Kanamycin, Neomycin, and Streptomycin), orally (Neo-Fradin), or as ear or eye drops (Gentak, and Genoptic). These drugs are often used to treat highly serious illnesses such as resistant forms of Septicemia, and they can sometimes cause serious side effects.

The Cephalosporins, another β-lactam group, originally derived from the fungus Cephalosporum acremonium, and together with Cephamycin, are used to treat a wide range of infections including more serious infections such as Septicemia and Bacterial meningitis. Cephalosporins can be broken down by generation: the first generation includes Cefadroxil, Cefazolin, Cephalexin, and Cephradine, for use against many gram-positive infections including Staphylococcus aureus. The second generation, Cefaclor, Cefoxitin, Cefprozil, Cefonicid, and Cefuroxime, these have a much broader antibacterial application and are effective against Citrobacter, Enterobacter, Haemophilus influenzae, Neisseria and Serratia genus. The third generation, Cefdinir, Cefditoren, Cefixime, Cefoperazone, Cefotaxime, Cefpodoxime, Ceftazidime, Ceftibuten, Ceftizoxime, and Ceftriaxone, are targeted toward gram-negative organisms. The fourth generation includes Cefepime, effective against a wide range of both gram-positive and gram-negative organisms. Finally, the advanced generation includes Ceftaroline and Ceftolozane/tazobactam, used to treat highly resistant organisms including Methicillin-resistant Staphylococcus aureus, of MRSA.

The Macrolides includes Erythromycin, Clarithromycin, Azithromycin, Fidaxomicin, and Telithromycin. These act by inhibiting protein synthesis, are often used to treat bacterial lung and chest infections, and are a choice for patients with a penicillin allergy, or when dealing with a bacterium that has become penicillin-resistant. Erythromycin was initially isolated in 1952 from Streptomyces erythreus, while the other macrolide antibiotics are semisynthetic derivatives (a type of chemical synthesis that uses chemical compounds isolated from natural sources like microbial cell cultures or plant material as the starting materials to produce novel compounds with distinct properties). These compounds have proven highly effective (thus far) against Streptococci, Staphylococci, Clostridia, Corynebacteria, Listeria, Haemophilus sp., Moxicella, and Neisseria meningitidis. Clarithromycin and Azithromycin are useful in treating Mycoplasma pneumonia, and Helicobacter pylori, and are prescribed to treat obligate intracellular parasites (protists) including Toxoplasma gondii and Cryptosporidia.

The Fluoroquinolones, a group that includes Ciprofloxacin, Gemifloxacin, Levofloxacin, Moxifloxacin, Norfloxacin, and Ofloxacin, are another broad-spectrum group of antibiotics, can be used to treat a wide range of infections by selectively targeting the DNA of the bacteria through interfering with the enzyme topoisomerase necessary in the winding and unwinding of strands of DNA for cellular replication. These “unwinding” enzymes are a necessary aspect of the replication process.

The Sulfonamides were introduced in the 1930’s and are considered bacteriostatic in that they inhibit the bacterial biosynthesis of folic acid necessary for bacterial cell growth. Over the years, many bacteria have become resistant to sulfonamides, and as a result usage has decreased significantly although they are still used to treat urinary tract infections (frequently in combination with trimethoprim), or in treatment of parasitic infections including Toxoplasmosis, Pneumocystosis jiroveci, and (in conjunction with Pyrimethamine), chloroquine resistant strains of malaria. Another sulfonamide, Dapsone, is still used to treat leprosy.

The Tetracyclines include Doxycycline and Streptomycin, inhibit protein synthesis in the bacterial cell by obstructing the binding of aminoacyl-tRNA to the mRNA-ribosome complex. Because protein synthesis is a complicated, multi-stepped process necessary for the replication of the bacteria, any significant disruption in the operation disrupts biosynthesis. Rifamycin has a similar effect.

Lincosamides are made from the yeast Streptomyces Lincolnensis and include Lincomycin and Clindamycin. Used as “narrow spectrum” antibiotics, this group has proven to be effective against cell wall-less bacteria, including several pathogenic species of Streptococcus, Staphylococcus, and Mycoplasma. Lincomycin is often used to treat severe bacterial infections in patients who cannot use Penicillins. Other forms of these drugs include Hygromycin B, and Kanamycin, which cause polypeptide-chain termination by creating a false error (STOP) translation codon (UAA, UAG, UGA) on the bacteria ribosome.

As you can see, no antibiotic is effective against a virus, and expecting or demanding such a treatment for a virus is not only ineffective but also detrimental to your health and socially irresponsible. Consider that the over- prescribing of antibiotics in the last few decades, along with the significant use of antibiotics in factory farming, has created significant resistant strains of bacteria, a few of which there is no currently active treatment.

If you are prescribed an antibiotic, you should always take it exactly as your care provider directed, and finish the medication regardless of if you feel better. Failing to take all of your prescription allows some bacteria to remain, and they will become resistant to the drug. Do not share medicines with others, and never save them for future use. Your doctor knows what infection you have, and has prescribed a certain type, strength, and number of antibiotics.

Should you have further questions on antibiotics, antibiotic resistance, or antibiotic use, consult your physician or care provider, or by consulting reputable information sources such as MedLine Plus: (

or the Centers for Disease Control and Prevention: (




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