Drug Resistant Bacteria: How Superbugs Impact Mom And Baby



As soon as a baby is born, their gut is colonized by bacteria that come from mom or the environment. And these first bacteria have an important relationship to baby gut health.

It may come as a surprise, but even if a baby was not exposed to antibiotics, it’s not uncommon for their gut to be colonized by at least some drug-resistant bacteria in their first days of life. Babies born by hospital C-section birth, for example, are often more colonized by these bugs than vaginally born babies.

But how exactly does antibiotic resistance develop and spread? Let’s see first how antibiotics work.

What are antibiotics?

Antibiotics have existed in nature long before humans. They are produced by bacteria and fungi that live in soil and water to protect themselves from other bacteria. In fact, most antibiotics used in human medicine were derived from environmental bacteria known as actinomycetes [1].

Antibiotics work in different ways [2]. Amoxicillin, for example, works by preventing bacteria from building their cell walls. Ciprofloxacin prevents bacteria from copying their DNA, which is how bacteria multiply.

Do antibiotics only attack unfriendly bugs? Unfortunately not.

Both unfriendly and beneficial bacteria have cell walls. And both need to copy their DNA in order to grow in numbers. So although we take antibiotics to fight a bacterial infection, these drugs also inevitably attack beneficial bacteria. That’s why antibiotic treatments alter the gut microbiome community [3].

What are drug resistant bacteria?

The overuse of antibiotics in medicine and animal agriculture has put a lot of pressure on bacteria and contributed to antibiotic resistance.

In order to survive, these bugs have developed sophisticated ways of protecting themselves from an antibiotic attack.

When bacteria multiply, they create an identical copy of their DNA. But sometimes there are errors in this process, and genetic mutations occur. Some bacteria will be lucky enough to suffer mutations in a gene that will allow them to survive or ‘resist’ an antibiotic giving rise to antibiotic resistance genes (ARGs) [4].

Also, bacteria are generous folk. Those that are resistant to an antibiotic can share their ARGs with those that aren’t, through a process scientists call horizontal gene transfer (HGT).

Since our gut is home to many different bacterial species and is often exposed to antibiotics, it’s not surprising that this generous exchange occurs within the gut [5], [6].

Superbugs, explained

In fact, antibiotic resistant genes can be shared from unfriendly bacteria to beneficial gut allies [5], [6].

While this may not pose any direct danger for us because these species won’t cause us an infection, the genes can be re-shared to other unfriendly bacteria [6]. This leads to the appearance of the so-called superbugs.

Superbugs are greedy bacteria that start collecting ARGs.

This gives them protection against many different antibiotics. They are also known as multidrug-resistant bacteria and are a global health concern [7].

Some of the top drug resistant bacteria [7] include:

  • Escherichia
  • Klebsiella
  • Staphylococcus

This is why our Tiny Health gut test measures the levels of these species. We ideally expect to find them at low levels in both adults and little ones.

How drug resistant bacteria impact pregnant moms and babies

When you take an antibiotic, your gut microbiome suffers a drop in numbers. That’s when drug resistant bacteria may take the lead and grow, by taking advantage of those that died that cannot  keep them in check any longer [3].

Luckily, soon after you finish the antibiotic treatment, beneficial bacteria start to repopulate your gut.

But the process of getting back to normal can take weeks. Also, even if the gut microbiome composition goes back to normal for most people, the amount of ARGs may remain elevated long after you took the antibiotic [3], [8], [9].

What’s more, studies have shown that ARGs present in mom’s gut can be inherited to baby through vaginal birth or breastfeeding [10]–[12]. But not all ARGs found in babies come from mom.

As it turns out, babies born by C-section and babies fed with formula tend to have more ARGs than vaginally-born babies and breastfed babies [13], [14]. That’s because these babies were more exposed to unfriendly bacteria - the ones that are usually antibiotic resistant - and less exposed to beneficial ones.

High numbers of antibiotic resistant bacteria in the gut may lead to treatment failure and increase the risk of antibiotics side effects, like diarrhea [15].

How does Tiny Health gut test help?

The Tiny Health gut test tracks the different stages of gut recovery after an antibiotic treatment. Testing the gut microbiome can let you know if you or your little one have returned to baseline. Or if extra help is needed.

The sequencing technology we use is called deep-shotgun metagenomics.

This type of sequencing allows us to calculate your “antibiotic signature.” This is a metric that considers:

  • Your gut microbial diversity
  • The amount of bacteria in your gut that are associated with antibiotic resistance
  • The number of antibiotic resistant genes in your gut microbiome

With this in hand, we can give you personalized advice to help you and your baby's gut recover faster.


[1] M. I. Hutchings, A. W. Truman, and B. Wilkinson, “Antibiotics: past, present and future,” Curr. Opin. Microbiol., vol. 51, pp. 72–80, Oct. 2019, doi: 10.1016/j.mib.2019.10.008.

[2] G. Kapoor, S. Saigal, and A. Elongavan, “Action and resistance mechanisms of antibiotics: A guide for clinicians,” J. Anaesthesiol. Clin. Pharmacol., vol. 33, no. 3, pp. 300–305, Sep. 2017, doi: 10.4103/joacp.JOACP_349_15.

[3] W. E. Anthony et al., “Acute and persistent effects of commonly used antibiotics on the gut microbiome and resistome in healthy adults,” Cell Rep., vol. 39, no. 2, p. 110649, Apr. 2022, doi: 10.1016/j.celrep.2022.110649.

[4] J. M. A. Blair, M. A. Webber, A. J. Baylay, D. O. Ogbolu, and L. J. V. Piddock, “Molecular mechanisms of antibiotic resistance,” Nat. Rev. Microbiol., vol. 13, no. 1, pp. 42–51, Jan. 2015, doi: 10.1038/nrmicro3380.

[5] S. C. Forster et al., “Strain-level characterization of broad host range mobile genetic elements transferring antibiotic resistance from the human microbiome,” Nat. Commun., vol. 13, no. 1, p. 1445, Mar. 2022, doi: 10.1038/s41467-022-29096-9.

[6] A. G. Kent, A. C. Vill, Q. Shi, M. J. Satlin, and I. L. Brito, “Widespread transfer of mobile antibiotic resistance genes within individual gut microbiomes revealed through bacterial Hi-C,” Nat. Commun., vol. 11, no. 1, p. 4379, Sep. 2020, doi: 10.1038/s41467-020-18164-7.

[7] Antimicrobial Resistance Collaborators, “Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis,” Lancet Lond. Engl., vol. 399, no. 10325, pp. 629–655, Feb. 2022, doi: 10.1016/S0140-6736(21)02724-0.

[8] A. Palleja et al., “Recovery of gut microbiota of healthy adults following antibiotic exposure,” Nat. Microbiol., vol. 3, no. 11, pp. 1255–1265, Nov. 2018, doi: 10.1038/s41564-018-0257-9.

[9] A. W. D’Souza et al., “Cotrimoxazole Prophylaxis Increases Resistance Gene Prevalence and α-Diversity but Decreases β-Diversity in the Gut Microbiome of Human Immunodeficiency Virus-Exposed, Uninfected Infants,” Clin. Infect. Dis. Off. Publ. Infect. Dis. Soc. Am., vol. 71, no. 11, pp. 2858–2868, Dec. 2020, doi: 10.1093/cid/ciz1186.

[10] M. Yassour et al., “Strain-Level Analysis of Mother-to-Child Bacterial Transmission during the First Few Months of Life,” Cell Host Microbe, vol. 24, no. 1, pp. 146-154.e4, Jul. 2018, doi: 10.1016/j.chom.2018.06.007.

[11] M. J. Gosalbes et al., “High frequencies of antibiotic resistance genes in infants’ meconium and early fecal samples,” J. Dev. Orig. Health Dis., vol. 7, no. 1, pp. 35–44, Feb. 2016, doi: 10.1017/S2040174415001506.

[12] K. Zhang et al., “Antibiotic resistance genes in gut of breast-fed neonates born by caesarean section originate from breast milk and hospital ward air,” BMC Microbiol., vol. 22, no. 1, p. 36, Jan. 2022, doi: 10.1186/s12866-022-02447-8.

[13] F. Bäckhed et al., “Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life,” Cell Host Microbe, vol. 17, no. 5, pp. 690–703, May 2015, doi: 10.1016/j.chom.2015.04.004.

[14] R. M. Lebeaux et al., “The infant gut resistome is associated with E. coli and early-life exposures,” BMC Microbiol., vol. 21, no. 1, p. 201, Jul. 2021, doi: 10.1186/s12866-021-02129-x.

[15] “Antibiotic-associated diarrhea - Symptoms and causes,” Mayo Clinic. https://www.mayoclinic.org/diseases-conditions/antibiotic-associated-diarrhea/symptoms-causes/syc-20352231 (accessed Jun. 10, 2022).